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Angela
05-12-16, 17:58
On GPS origins, see:
http://cruwys.blogspot.co.uk/2016/11/a-review-of-gps-origins-test-four.html

On BritainsDna, see:
https://www.buzzfeed.com/tomchivers/this-dna-ancestry-company-is-telling-its-customers-mostly-to?utm_term=.xcLrP64Yq5#.cjXm9Pa4nJ

The above is Buzz Feed, so take note.

Personally, if I have to see that ridiculous Ancestry ad about the Italian ancestor who's really eastern European one more time, I may barf. I've not tested with them, partly because of the ads they've run, like the guy trading in his lederhosen for a Scottish kilt. Oy veh!

Tomenable
05-12-16, 19:38
From the first link:

"If you go back 3,000 years, your ancestors are almost everybody’s ancestors."

This is utter nonsense.

The number of ancestors does not grow exponentially with generations due to a thing called "pedigree collapse":

https://en.wikipedia.org/wiki/Pedigree_collapse

Maciamo
05-12-16, 22:16
The article criticising BritainsDNA was written after an interview with Adam Rutherford, the author of A Brief History of Everyone Who Ever Lived. It looks like he is going on a personal crusade against that company. Quoting the article, he told BuzzFeed News that the descriptions of ancestors accompanying BritainsDNA’s genetic test reports are “eloquent, but mostly total bollocks” because the results only seem to take the origin of the haplogroups to determine distant ancestry. In short, Rutherford criticises BritainsDNA for telling its customers that their ancestors were Germanic if they belong to Y-haplogroup I1, for instance. It is of course a gross oversimplification, but either those customers are clever enough to research and understand what a Y-DNA haplogroup is and what is really represents in terms of ancestry (just one chromosome), or they aren't and it doesn't really matter what you tell them as they won't understand anything complicated anyway.

Talking about 'total bollocks', Adam Rutherford made quite a few blunders of his own.


On average, a human generation takes about 28 years. At that rate, by the time you’ve gone back 1,100 years, you would have about 600 billion ancestors, says Rutherford. “By that point there are more people in your family tree than have ever existed,” he says. Of course, that’s not possible; instead, there’s lots of overlap, so your great-great-[etc]-grandfather is also your great-great-[etc]-uncle and your 10th cousin twice removed, and so on.

What that means is that it’s meaningless to talk in terms of what “your ancestors” did over 1,000 years ago, according to Rutherford: Everyone who was alive at that time in, say, Europe is either the ancestor of every European currently alive, or of no one at all – because their line died out.

This is also a gross oversimplification and is very misleading indeed. Europe is not a single fluid gene pool where all its inhabitants freely intermix with all others. It has physical, political and linguistic boundaries, which constrain most people to find mates within their country or region and linguistic group. These barriers have become much less of a problem since the late 20th century thanks to the removal of borders between EU countries, faster transportation (aeroplanes, trains), and university exchange programmes, and the fact that most educated Europeans have learned several foreign languages. But that wasn't the case throughout most of history. Actually the vast majority of people were farmers who married people from their local community, usually within 20 km from the place where they were born. A few people migrated, especially among the merchant class. Nobles and royalties sought spouses much further away. But they always were a minority, and did not intermingle much with the rest of society. At best they left bastards behind that were raised by peasants and got to mix with the rest of society.

The bottom line is that genetic differences exist between regions of Europe because of this historic lack of mobility between regions. That is how the Basques, Sardinians, Tyroleans, and others managed to preserved their genetic identity throughout the millennia, practically since the Neolithic. That is why modern Scandinavians or Poles haven't changed much since the Bronze Age. It is simply wrong to say that a Pole descend from all Portuguese, Greek and Irish people who lived 1000 years ago (and who had descendants to this day).

Another example of "bollocks" was given by Debbie Kennett, a volunteer project administrator at Family Tree DNA also interviewed apparently with the only purpose to bash BritainsDNA.


For instance, she says, haplogroup M – which in modern humans is only found in India – has been found in the preserved corpses of ancient people in France and Belgium. When you look at ancient DNA like this, she says, “you end up with all sorts of different haplogroups in unexpected places”.

MtDNA haplogroup M is not found only in India. It is a pan-Asian haplogroup and is indeed quite well represented in East Asia (M7, M8, M9, M10, etc) and even in North Africa (M1).

So the whole article seems to be financed by FTDNA to hurt the competition. No wonder then that there is no mention of FTDNA's European subsidiary iGenea, who has made some of the wildest and most absurd claims on its website over the years.


I am surprised that even a UCL professor would say this:


Mark Thomas, a UCL professor of evolutionary genetics, has previously written that it is “extremely difficult to demonstrate scientifically” claims about the detailed history of your mtDNA or Y-chromosome haplogroup, although it is “reasonable to use large samples of these DNA types to say something about the histories of populations”. Kennett agrees: “[People] have made all sorts of fanciful claims about haplogroups originating in this or that place, but there’s no scientific evidence.”

That just goes to show that even professors of evolutionary genetics at top universities don't necessarily know much about haplogroups. In this case, he doesn't seem to be aware of the role of ancient DNA tests in tracing back the prehistoric migration of haplogroups. It is true that until a few years ago, people could just emit any fanciful theory about where this or that haplogroup originated, and with what historical migration it propagated. Top academics, even those researching specifically haplogroups, were not immune from such fancies, and were often the first culprits in spreading them. Everyone remembers how until 2008 the academic establishment would tell the world that haplogroup R1b descended from Cro-Magnons, because its modern geographic distribution looked like it expanded from the Franco-Cantabrian refugium after the LGM. I had just started to get interested in population genetics at the time, but even then I felt something wasn't right considering the extremely wide distribution of R1b until Siberia and central Africa. In 2009, Balaresque et al. theorised that R1b spread to Europe with Neolithic farmers almost exactly when I wrote my article on R1b arguing that it came with the Proto-Indo-European from the Pontic Steppe during the Bronze Age. Lazaridis/Dienekes was among the most ardent defenders of that Neolithic Anatolian R1b theory (he also didn't believe that modern humans carried any Neanderthal DNA until the test results proved him wrong). In fact, the majority of academics only accepted that R1b really did come from the Steppe when the first Yamna Y-DNA results came in in 2015. Even the, Haak, Krause and other members are still sticking to this Neolithic Anatolian diffusion of R1b and PIE languages, arguing now that only R1b-Z2103 was part of Yamna, but ignoring the fact that no R1b-L51 was found among Neolithic farmers either.

So, allow me to be sceptical about the value of the opinion of a UCL evolutionary geneticist who isn't specialised in haplogroups or ancient DNA. Most of these scientists have practically no knowledge of prehistory/archaeology, anthropology or linguistics.

I am not trying to defend BritainsDNA here, but I find it mildly disgusting that articles like this should target one specific company when they are all guilty of oversimplification for the sake of marketing their products to the wider part of society who doesn't have any clue about prehistory or genetics. I know from experience (either on forums or with people I have tried to convince to take ancestry DNA tests) that the majority of people isn't well-versed in history and even less in archaeology or phylogenetics, and that they respond better when things are dumbed down for them. Marketing is the same as politics in a democracy. People aim to reach as many people as possible, as in order to do so have to lower the intellectual bar. At least here at Eupedia I am trying to explain things as clearly as possible, using colours for haplogroups, making maps, using clear statistic tables, and avoiding too much jargon, while keeping all the facts in check. After all, I have nothing to sell, unlike DNA testing companies. All that matters for me is to educate people. I have noticed over the years that a big part of the job is to correct the erroneous and oversimplified information that many DNA test customers got from their testing company's website. And no testing company is immune to it.

Personally, I only recommend testing companies (http://www.eupedia.com/europe/dna_project_faq.shtml#Company) based on the quality of their raw DNA tests. This means essentially the number of SNP's tested for autosomal, Y-DNA and mtDNA, and whether the autosomal included useful medical info should one wish to check for specific conditions. And I am saying that after having tried several of them. FTDNA's FamilyFinder thinks that I am half British and half "Alpine" and doesn't mention any Belgian ancestry even though I am 100% Belgian genetically over the last 7 generations. 23andMe correctly places me in French/German category (which includes Belgian) but fails to do so for my parents who haven't replied to the ancestry survey. So it looks like the results are essentially based on what one declares about one's ancestry. That's why I don't care about their interpretations because I know that most of it is unreliable and I prefer my own interpretation. What matters is the price to value ratio for the test. I have long recommended 23andMe over other companies, especially when their Ancestry + Health test was at $99. But at present, I think that the two best values on the market are LivingDNA and Geno 2.0.

That being said, a company like GPS Origins, which only interprets data from other companies, is just a waste of money, as it isn't more accurate than the others. In fact, it is much more useful to use tools like the Dodecad and Eurogenes admixtures than to bother with such companies.

Angela
05-12-16, 23:28
I agree with you, Maciamo. The biggest problem with dna testing is that most of the people doing the testing don't know how to interpret the results. That said, these companies all use rather deceptive advertising and perhaps should make some effort to explain the results a little more clearly.

Tomenable
06-12-16, 00:23
Maciamo,

Family Finder test on FTDNA now has a new feature called "Ancient Origins" (apart from "My Origins" report), and descriptions from this new report acknowledge that R1b most likely expanded to Western Europe from the Steppe.

Here is what descriptions of some ancestries in "Ancient Origins" report say:


METAL AGE INVADER

Following the Neolithic Era (New Stone Age), the Bronze Age (3,000–1,000 BCE) is defined by a further iteration in tool making technology. Improving on the stone tools from the Paleolithic and Neolithic Eras, tool makers of the early Bronze Age relied heavily on the use of copper tools, incorporating other metals such as bronze and tin later in the era. The third major wave of migration into the European continent is comprised of peoples from this Bronze Age; specifically, Nomadic herding cultures from the Eurasian steppes found north of the Black Sea. These migrants were closely related to the people of the Black Sea region known as the Yamnaya.
This migration of Asian Steppe nomads into the temperate regions further west changed culture and life on the European continent in a multitude of ways. Not only did the people of the Yamnaya culture bring their domesticated horses, wheeled vehicles, and metal tools; they are also credited for delivering changes to the social and genetic makeup of the region. By 2,800 BCE, evidence of new Bronze Age cultures, such as the Bell Beaker and Corded Ware, were emerging throughout much of Western and Central Europe. In the East around the Urals, a group referred to as the Sintashta emerged, expanding east of the Caspian Sea bringing with them chariots and trained horses around 4,000 years ago.
These new cultures formed through admixture between the local European farming cultures and the newly arrived Yamnaya peoples. Research into the influence the Yamnaya culture had on the European continent has also challenged previously held linguistic theories of the origins of Indo-European language. Previous paradigms argued that the Indo-European languages originated from populations from Anatolia; however, present research into the Yamnaya cultures has caused a paradigm shift and linguists now claim the Indo-European languages are rooted with the Yamnaya peoples.
By the Bronze Age, the Y-chromosome haplogroup R1b was quickly gaining dominance in Western Europe (as we see today) with high frequencies of individuals belonging to the M269 subclade. Ancient DNA evidence supports the hypothesis that the R1b was introduced into mainland Europe by the Asian Steppe invaders coming from the Black Sea region. Further DNA evidence suggests that a lactose tolerance originated from the Yamnaya or another closely tied steppe group. Current day populations in Northern Europe typically show a higher frequency of relatedness to Yamnaya populations, as well as earlier populations of Western European Hunter-Gatherer societies.

And this "Metal Age Invader" includes two categories:


YAMNAYA
Eurasian Steppe (~5,800 years ago)

At roughly 3,800 BCE, the people of the Yamnaya culture emerged in the Eurasian Steppe. The Yamnaya relied on a subsistence strategy of pastoralism, and displayed an advanced understanding of metals (primarily copper) and animal domestication. They mined the metals they used to construct daggers, axes, and jewelry; and used domesticated horses to guide the movement of their herds. Large swaths of land are necessary for herds to graze; and as little evidence of Eastern Yamnaya settlements have been found, experts suggest that the Yamnaya peoples were partially nomadic. It is likely the Yamnaya peoples spent much of their time in wagons moving their herds in response to seasonal changes. Archaeological digs on land used for ancient Yamnaya burials have discovered that burials were ritualized, as scientists have unearthed material goods and wheeled carts buried with high ranking individuals. Finally, DNA evidence shows that a common Y-chromosome haplogroup of the Yamnaya pastoralists is R1a and R1b, which is still prevalent in Western Europe today.

CORDED WARE
Central Europe (~4,000 years ago)

The Neolithic Early Farming culture of Central Europe was culturally and physically replaced by 2,800 BCE. The new inhabitants of this region, the Yamnaya, brought culture and Early Bronze age technology originating from the Eurasian Steppe. Later cultures inhabiting Central Europe, most notably the Corded Ware culture of the late Neolithic, could identify an average of 75% ancestry from the Yamnaya culture. The remaining 25% show ancestry from Early Neolithic Farming Cultures like the Linearbandkeramik. Changes in subsistence strategy and culture can be identified through DNA analysis, as well as changes in cultural practices such as burial rituals and practices. Cultural evolution in this area is displayed in the arrival of pit burial practices and agro-pastoral subsistence strategies.

But it seems, that they are counting only CHG (or Gedrosia-Caucasus) admixture as part of "Metal Age Invader". On the other hand, it seems that EHG admixture is being counted - together with WHG and SHG - as "Hunter-Gatherer".

Maciamo
06-12-16, 10:05
Maciamo,

Family Finder test on FTDNA now has a new feature called "Ancient Origins" (apart from "My Origins" report), and descriptions from this new report acknowledge that R1b most likely expanded to Western Europe from the Steppe.

Here is what descriptions of some ancestries in "Ancient Origins" report say:



And this "Metal Age Invader" includes two categories:



But it seems, that they are counting only CHG (or Gedrosia-Caucasus) admixture as part of "Metal Age Invader". On the other hand, it seems that EHG admixture is being counted - together with WHG and SHG - as "Hunter-Gatherer".

I know about that new feature. I criticised it in this thread (http://www.eupedia.com/forum/threads/33091-FTDNA-ancientOrigins). It's another good example of useless and misleading interpretation offered by commercial companies in the hope to lure new customers. They are indeed equating CHG (Caucasus-Gedrosia) with Metal-age Invaders, which is utter nonsense since Yamna and Corded Ware people had only about 30% of that admixture, and it was quickly lost by the time of Unetice. In fact I am now doubting that the western R1b-L51 branch of PIE ever had 20 to 30% of Gedrosia to start with. The Gedrosian ancestry may have been inherited from the J2b farmers (mtDNA H2a1, I, T1a1a, T2 and W?) who settled in the Volga-Ural region during the Neolithic. If R1b-L51 tribes were the western Yamna in Ukraine, there is a good chance that they carried less of that Caucasian admixture, but may have had more Balkanic Neolithic farmers admixture (Mediterranean in K12, Atlantic_Med in K12b) from Cucuteni-Trypillian neighbours. That would explain why German Bell Beaker R1b and Unetice samples had only 8-9% of Gedrosia (see analysis here (http://www.eupedia.com/forum/threads/33090-Dodecad-Eurogenes-admixture-of-Late-Copper-Early-Bronze-Age-genomes)), like modern NW Europeans. When R1b tribes arrived in Central Europe c. 2500 BCE, they had only a few percent of Caucasian admixture. And when they invaded Western Europe from 2200 BCE, they had less than 10% of Gedrosia. So FTDNA's claim that they were 100% Gedrosia-Caucasus is utterly ludicrous.

DebbieK
07-12-16, 03:34
There seem to be a lot of misunderstandings here so I wanted to take this opportunity to set the record straight.

The bad science from BritainsDNA has attracted a huge amount of coverage in mainstream national newspapers (The Times, The Guardian, the Telegraph, the Mail, etc) and on TV and on the radio in the UK. Their former managing director was a journalist not a scientist but he had very good media contacts so he got a free ride for many years. The coverage was very unbalanced and no scientists were ever given the opportunity to counter the claims. The Buzzfeed article was written to highlight the problem of the pseudoscience. It had nothing to do with Family Tree DNA. I agree with you about the claims on the iGENEA website but they are not selling their tests in the UK and have not been featured in the media in the UK. All companies by necessity have to over-simplify when they are marketing their DNA tests. However, the other companies do not try to generate free publicity by writing pseudoscientific stories that are picked up by gullible reporters on national newspapers. They are also not in the habit of sending out threatening legal letters to their critics.

Adam Rutherford’s claims about the recent shared ancestry of Europeans are well supported in the scientific literature. Carl Zimmer summarises some of the research in an article for National Geographic. I can't post links here but Google for "Charlemagne's DNA and our universal royalty".

Empirical evidence was provided in a genetic study by Ralph and Coop (2013) on "The geography of recent ancestry across Europe".

I had a telephone conversation with the reporter and I can’t recall the exact words I used but I’m well aware that mtDNA haplogroup M is not just found in India so I think I must have been misheard or misquoted. However, it is prevalent in India today and if people of British ancestry find they belong to haplogroup M it is usually an Indian connection. The ancient DNA paper I was referring to is "Pleistocene mitochondrial genomes suggest a single major dispersal of non-Africans and a late glacial population turnover in Europe" by Posth et al (2016). However, the paper is incorrect because we do have a few European samples of haplogroup M. There are some sequences from Italy and France published on GenBank.

Mark Thomas is a respected scientist who has been involved in ancient DNA research from the very early days. His name appears on most of the big ancient DNA papers of the last few years as you can see from his list of publications. You can find this by doing a Google search for "Mace Lab UCL". As you will also see, much of his early research was on the Y-chromosome. Indeed, his group was one of the first to coin the term haplogroup back in the mid 1990s. A lot of his research has been done in collaboration with archaeologists and anthropologists. The Buzzfeed reporter made the right choice in this case by asking an expert.

There have been some poor papers making unsubstantiated claims about haplogroups but fortunately these are now on the decline, and not all population geneticists agreed with them at the time anyway. While ancient DNA provides direct evidence of the presence of haplogroups in specific locations at particular time points there are still only a small number of samples available so only very limited inferences can be made. There are also many regions of the world where the conditions are not right and we will probably never be able to get much in the way of ancient DNA.

By the way, GPS Origins do not just re-analyse results from other testing companies. They have their own chip which tests 800,000 markers. I’ve not found anyone who has tested on this chip. If anyone does have results I would be interested to have access to the raw data.

Twilight
07-12-16, 05:50
I agree with you, Maciamo. The biggest problem with dna testing is that most of the people doing the testing don't know how to interpret the results. That said, these companies all use rather deceptive advertising and perhaps should make some effort to explain the results a little more clearly.

You can always question and Critique AncestryDNA via email or help edit for the site. I'm sure you'd make a wonderful explainer of the genetic components. :)

Another option is that Eupedia can start their own genetic testing company that they can either transfer from other genetic sites or sample some DNA at the lab. And explain every component from every era sampled.

Maciamo
07-12-16, 12:39
There seem to be a lot of misunderstandings here so I wanted to take this opportunity to set the record straight.

Thanks for your feedback, Debbie. I appreciate it.


The bad science from BritainsDNA has attracted a huge amount of coverage in mainstream national newspapers (The Times, The Guardian, the Telegraph, the Mail, etc) and on TV and on the radio in the UK. Their former managing director was a journalist not a scientist but he had very good media contacts so he got a free ride for many years. The coverage was very unbalanced and no scientists were ever given the opportunity to counter the claims. The Buzzfeed article was written to highlight the problem of the pseudoscience. It had nothing to do with Family Tree DNA. I agree with you about the claims on the iGENEA website but they are not selling their tests in the UK and have not been featured in the media in the UK. All companies by necessity have to over-simplify when they are marketing their DNA tests. However, the other companies do not try to generate free publicity by writing pseudoscientific stories that are picked up by gullible reporters on national newspapers. They are also not in the habit of sending out threatening legal letters to their critics.

If I understand well, the issue has more to do with the way BritainsDNA advertised its products in a pseudoscientific manner in British media. But then why post this article on BuzzFeed, which is American?

Regarding iGenea, they do sell their product to the UK. It is the European branch of FamilyTreeDNA and their website has rates in EUR, CHF and GBP. But even companies like FTDNA, AncestryDNA and 23andMe are in my opinion misleading potential customers with their advertising by claiming that they can find relatives through their database. I personally don't care about finding relatives, as I know all my (large) extended family. But I was shocked that such companies would suggest matches as close as 3rd or 4th cousin for people who were completely unrelated to me. We did compare family trees, and many didn't even have ancestors in my country by going back 7 generations, so it's impossible that we would anything less than 7th cousin, which is completely meaningless in terms of shared DNA. Actually even 4th or 5th cousin is meaningless genetically, especially for Europeans who have all their ancestors in one small geographic region, and could be closer genetically to anyone from that region than from a 5th cousin, simply by common shared ancestry in the last 1000 years. I think it is far more vicious of DNA testing companies to make gullible customers believe that there is any interest in finding 3rd, 4th or 5th cousins than in oversimplifying the "history" of their haplogroup. People can choose to identify with any of their ancestors, even if that means forgetting other ancestors. That's human nature. People need to create identities, even if they are oversimplifications. I am not saying I agree or would do it myself. But if the majority of people didn't think like that, there would be no countries, flags and other national symbols.




Adam Rutherford’s claims about the recent shared ancestry of Europeans are well supported in the scientific literature. Carl Zimmer summarises some of the research in an article for National Geographic. I can't post links here but Google for "Charlemagne's DNA and our universal royalty".

I have read it but it's wrong. It's based on a mathematical model and completely ignores physical, political and linguistic boundaries between human groups. It also fails to take into account pedigree collapse and the fact that DNA is not inherited in a mathematical manner. OUt of 4 grand-parents a mathematician will say we inherited 25% of DNA from each, but in fact it may be something like 23%, 27%, 24.5% and 25.5%. After 15 or 20 generations, many genealogical ancestors end up contributing nothing, while other contribute two, three or four times their mathematical share, simply because of the way genetic recombination works.

Furthermore, Charlemagne lived 1250 years ago, which represents about 45 to 50 generations. At the 50th generation, we have theoretically 1,125,899,900,000,000 ancestors (over 1 quadrillion), which is 375,000 times the size of the human genome (in base pairs), and 37.5 million times more than the human exome (coding DNA). In other words, to inherit just one coding base pair from an ancestor who lived 50 generations ago, at the age of Charlemagne, one must descend in average 37.5 million times from that ancestor. That is why even if someone can prove through paper trail that they descend from Charlemagne through nobility, only one line doesn't guarantee at all that they inherited even the slightest bit of DNA from Charlemagne. But a mathematician will claim that this is a proof that all people descend from Charlemagne as there weren't one quadrillion people alive around 800 CE (or ever) and we must therefore be descended from all people who left descended. Such reasoning is utterly wrong because it is not the way DNA is inherited. You can't cut a nucleobases in two, let alone in millions of fragments.




I had a telephone conversation with the reporter and I can’t recall the exact words I used but I’m well aware that mtDNA haplogroup M is not just found in India so I think I must have been misheard or misquoted. However, it is prevalent in India today and if people of British ancestry find they belong to haplogroup M it is usually an Indian connection. The ancient DNA paper I was referring to is "Pleistocene mitochondrial genomes suggest a single major dispersal of non-Africans and a late glacial population turnover in Europe" by Posth et al (2016). However, the paper is incorrect because we do have a few European samples of haplogroup M. There are some sequences from Italy and France published on GenBank.

Actually, if you check the FTDNA mtDNA M Project (https://www.familytreedna.com/public/M%20mtDNA%20Haplogroup/default.aspx?section=mtmap), you will see that there are dozens of European members from almost every country. The subclades are varied too. The most common is the North African M1, but there is also M3, M5, M18, M33, etc. M33 is found in eastern Europe, Siberia, China, Central Asia and South Asia. It cannot eb excluded that it descended from Palaeolithic Europeans that survived in Northeast Europe and passed that lineage to the Proto-Indo-Europeans of the R1a-Z93 branch.



Mark Thomas is a respected scientist who has been involved in ancient DNA research from the very early days. His name appears on most of the big ancient DNA papers of the last few years as you can see from his list of publications. You can find this by doing a Google search for "Mace Lab UCL". As you will also see, much of his early research was on the Y-chromosome. Indeed, his group was one of the first to coin the term haplogroup back in the mid 1990s. A lot of his research has been done in collaboration with archaeologists and anthropologists. The Buzzfeed reporter made the right choice in this case by asking an expert.

There have been some poor papers making unsubstantiated claims about haplogroups but fortunately these are now on the decline, and not all population geneticists agreed with them at the time anyway. While ancient DNA provides direct evidence of the presence of haplogroups in specific locations at particular time points there are still only a small number of samples available so only very limited inferences can be made. There are also many regions of the world where the conditions are not right and we will probably never be able to get much in the way of ancient DNA.


It is not necessary to test ancient samples from every country to be able to tell with high confidence that Y-haplogroup G2a came to Europe with Anatolian Neolithic farmers, or that R1a1a and R1b-M269 came from eastern Europe to central and western Europe during the Bronze Age. If Mark Thomas has worked in the field of historical population genetics for many years, I find it very odd that he should claim otherwise.



By the way, GPS Origins do not just re-analyse results from other testing companies. They have their own chip which tests 800,000 markers. I’ve not found anyone who has tested on this chip. If anyone does have results I would be interested to have access to the raw data.

You are right. Sorry about that. I didn't realise it since nobody seems to choose them to test.

DebbieK
07-12-16, 15:59
Maciamo

Buzzfeed have a UK website and they tailor the content for a UK audience. Tom Chivers is their UK science reporter so I presume this article is aimed at the UK readership. iGENEA do have a website in English so in theory they could sell their tests in the UK but most people in the UK buy their kits direct from Family Tree DNA. I have not seen a single newspaper article in the UK that mentions iGENEA. The concern with BritainsDNA was not so much the marketing but the fact that their pseudoscience made its way into the editorial content of newspapers and was presented as scientific research as part of a "project". That is why there was so much concern. Their fake project also got featured on TV and on the radio.

Autosomal DNA testing is still in its infancy, and predicting relationships is complicated at the best of times. The predictions are generally only accurate up to about the second cousin level. The 3rd and more distant predictions are often much further back than indicated and in general it's impossible to find a genealogical connection with these distant cousins. Everyone has a different reason for testing but it is autosomal DNA that is driving the market growth and not Y-DNA testing which by its very nature also excludes half the population. AncestryDNA have already sold nearly three million kits, and there are now well over five million people who have tested. Y-DNA testing is only a small part of this market. There are a lot of people out there who are interested in using autosomal DNA to connect with their cousins.

As stated previously the concept of universal shared European ancestry is also demonstrated by genetic evidence in the paper by Ralph and Coop. Do you know of any studies that contradict this paper?

More recent mathematical simulations have taken into account the effects of pedigree collapse. Have a look at the 2015 paper by Speed and Balding on "Relatedness in the post-genomic era". Check out Supplementary Information S2 on DNA and pedigree ancestors. As you say, we only inherit DNA from a small percentage of our billions and billions of ancestors but that does not invalidate the fact that we have genealogical relationships with all those ancestors. Of course there were geographical and linguistic barriers which will have an effect on migration but they don't stop migration completely. Humans have always moved around and this is now evidenced in the ancient DNA data.

I'm aware of the haplogroup M project. I only mentioned haplogroup M to the reporter as an example of a haplogroup whose past distribution and frequency is markedly different from its present-day distribution.

I'm not aware that Mark has made any claims about G2a and R1b. Please can you point me to this reference? It is possible to hypothesise that a haplogroup came to Europe with Anatolian Neolithic farmers or that it moved from western Europe to central Europe in the Bronze Age but scientists have to find a way to test these hypotheses using the scientific method. We can't be confident that a haplogroup originated in a region where it is very common today or in the past. You might want to have a read of the ISOGG Wiki page on phylogeography which explains some of these concepts and describes the sort of testing that has to be done. You might also find it useful to read some of the papers cited there.

Maciamo
07-12-16, 16:59
Maciamo

Buzzfeed have a UK website and they tailor the content for a UK audience. Tom Chivers is their UK science reporter so I presume this article is aimed at the UK readership. iGENEA do have a website in English so in theory they could sell their tests in the UK but most people in the UK buy their kits direct from Family Tree DNA. I have not seen a single newspaper article in the UK that mentions iGENEA. The concern with BritainsDNA was not so much the marketing but the fact that their pseudoscience made its way into the editorial content of newspapers and was presented as scientific research as part of a "project". That is why there was so much concern. Their fake project also got featured on TV and on the radio.

That is odd. I read The Guardian, New Scientist, The Economist and BBC News practically everyday, as well as The Telegraph and other British publications occasionally, but I have never seen any article about BritainsDNA. If these are published in tabloids, then I don't see why there should be any concern about their scientific credibility considering that almost anything published in tabloids in rubbish anyway.



Autosomal DNA testing is still in its infancy, and predicting relationships is complicated at the best of times. The predictions are generally only accurate up to about the second cousin level. The 3rd and more distant predictions are often much further back than indicated and in general it's impossible to find a genealogical connection with these distant cousins. Everyone has a different reason for testing but it is autosomal DNA that is driving the market growth and not Y-DNA testing which by its very nature also excludes half the population. AncestryDNA have already sold nearly three million kits, and there are now well over five million people who have tested. Y-DNA testing is only a small part of this market. There are a lot of people out there who are interested in using autosomal DNA to connect with their cousins.

I think that this kind of behaviour of the majority of customers tells you exactly why DNA companies are resorting to pseudoscience. As I said, there is no validity in getting an autosomal DNA test to try to find 4th or 5th cousins. This is a complete waste of money. Companies like 23andMe and LivingDNA have their marketing more in line with what people should look for in a DNA test, which is distant ancestry and, in 23andMe's case, health reports (especially carrier risks). I would never recommend any ancestry test that exclude Y-DNA and mtDNA as these are the main tools in historical population genetics and are far more accurate to trace historical population movements than autosomal admixture. Of course Y-DNA and mtDNA only show a very small part of the total ancestry, but they are useful when pooled into regional projects like those of FTDNA, or combined to make regional statistics like those I have compiled on this site (http://www.eupedia.com/europe/european_y-dna_haplogroups.shtml). Autosomal DNA is interesting for ancestry when using tools like Dodecad and Eurogenes to compare with ancient and modern populations. Mitochondrial DNA is also associated with numerous health conditions (http://www.eupedia.com/forum/threads/24801-Medical-conditions-and-risk-factors-associated-with-mtDNA-haplogroups) and affects an individual's overall fitness. Personally I think that the most important reason to take a DNA test for anyone is to know more about their health. Ancestry DNA tests are especially useful for history buffs. I have absolutely no idea why at the moment the majority of people ordering DNA tests are looking for distant cousins. When we see the millions of people who have ordered tests like FamilyFinder and AncestryDNA for that reason, I think it may be one of the biggest commercial fraud done in the name of science. I don't think BritainsDNA caused half as much harm.



As stated previously the concept of universal shared European ancestry is also demonstrated by genetic evidence in the paper by Ralph and Coop. Do you know of any studies that contradict this paper?

More recent mathematical simulations have taken into account the effects of pedigree collapse. Have a look at the 2015 paper by Speed and Balding on "Relatedness in the post-genomic era". Check out Supplementary Information S2 on DNA and pedigree ancestors. As you say, we only inherit DNA from a small percentage of our billions and billions of ancestors but that does not invalidate the fact that we have genealogical relationships with all those ancestors. Of course there were geographical and linguistic barriers which will have an effect on migration but they don't stop migration completely. Humans have always moved around and this is now evidenced in the ancient DNA data.

Many scientific paper have been wrong. That's one of the main reason why I started the Genetics section (http://www.eupedia.com/genetics/) on this website, and so far the vast majority of my predictions have been confirmed by ancient DNA tests.


I'm aware of the haplogroup M project. I only mentioned haplogroup M to the reporter as an example of a haplogroup whose past distribution and frequency is markedly different from its present-day distribution.

You are assuming ancient distribution based on only two samples from the same cave at Goyet. That's not statistically significant. Besides those samples were about 40,000 years old, and most other haplogroups didn't exist at that time. The possibilities for mtDNA haplogroups were pretty much limited to M, N, R, U, U2, U5 and U8. Don't expect to find haplogroup H, the most common in Europe today, when its defining mutations hadn't arisen yet. I agree that haplogroup distributions changed markedly over (pre)historical periods, but your example was not the most judicious. You could just have said that Y-haplogroup R1b-L51, which is the most common in western Europe today, was not found in that region before the Late Chacolithic or Early Bronze Age.



I'm not aware that Mark has made any claims about G2a and R1b. Please can you point me to this reference? It is possible to hypothesise that a haplogroup came to Europe with Anatolian Neolithic farmers or that it moved from western Europe to central Europe in the Bronze Age but scientists have to find a way to test these hypotheses using the scientific method. We can't be confident that a haplogroup originated in a region where it is very common today or in the past. You might want to have a read of the ISOGG Wiki page on phylogeography which explains some of these concepts and describes the sort of testing that has to be done. You might also find it useful to read some of the papers cited there.

I was referring to what he wrotes in the Buzzfeed article, namely:

Mark Thomas, a UCL professor of evolutionary genetics, has previously written that it is “extremely difficult to demonstrate scientifically” claims about the detailed history of your mtDNA or Y-chromosome haplogroup, although it is “reasonable to use large samples of these DNA types to say something about the histories of populations”. Kennett agrees: “[People] have made all sorts of fanciful claims about haplogroups originating in this or that place, but there’s no scientific evidence.”

What is is saying means that it is extremely difficult to demonstrate scientifically where Y-haplogroups G2a and R1b (among others) originated. I could have taken other examples. I could have said that it is easy to confirm with ancient DNA samples that mt-haplogroup N1a1a, K1a, T1a, T2c and X (among others), came to Europe with Near Eastern Neolithic farmers. I can also demonstrate that it is possible to make reliable predictions based on modern distributions (I won't explain the complicated process in detail here). This is exactly what I have done since 2009 for both Y-DNA haplogroups and subclades and mtDNA deep subclades, and I was right in about 90% of the cases. For example I predicted which mtDNA haplogroups would be found among Yamna and Corded Ware people (http://www.eupedia.com/forum/threads/25613-Identifying-the-original-Indo-European-mtDNA-from-isolated-settlements), and which mtDNA and Y-DNA haplogroups were part of the southern wave of Neolithic farmers (http://www.eupedia.com/forum/threads/29400-Correlating-the-mtDNA-haplogroups-of-the-original-Y-haplogroup-J1-and-T1-herders) to North and East Africa. Just look at the articles (https://independent.academia.edu/MaciamoHay) I published on Acamedia.edu over the years, before ancient DNA tests confirmed, for example that R1b was the main haplogroup of the Yamna culture and spread west during the Early Bronze Age to reach Ireland by 2000 BCE. I also predicted that Co-Magnons belonged to haplogroup C1a, F and I, and that I came later during the Gravettian. If I can do it and get it right, it means that my method is scientifically sound. As far as I know, not a single career academic has been able to do the same, so they assume it is not possible.

Of course all kinds of people have made all kinds of predictions on forums and elsewhere. But not many have created a website of this scale dedicated to population genetics and written so many articles about it. I think I have written more on the subject that practically any author of peer-reviewed article. Few academics have also studied both history and biology/genetics as I have. I have no interest to join a university research team because I am a maverick and don't like to follow all the rules and protocols, and to "have to publish" to please one's sponsors and for the sake one's career. I especially don't like to work with others and to be told what to do or how to think, or to have to prove my arguments with 'official methods', which are usually a great waste of time. Then I have too many other interests beyond history and population genetics (e.g. neuroscience, robotics, languages, psychology, medical genetics, microbiology, immunology) to limit my research to these fields. I think that life is a waste of time if you can't satisfy your intellectual pursuits.

I find it a bit condescending that you should ask me to read the ISOGG Wiki page on phylogeography which explains some of the concept of where haplogroups originated. My phylogenetic trees are more accurate than those of ISOGG (as they are based more on Yfull.com but using FTDNA nomenclature as much as possible as more people test their Y-DNA with that company than with any other), and I wrote articles for the history of each haplogroup.

EDIT: I had a look at the page in question and found the video with Mark Thomas's interview, to which you apparently contributed. I noticed that they/you are using one of my maps (Y-haplogroup R1b-S21), even though I don't recall any of you contacting me to ask permission. Perhaps you didn't realise that I was the author, which would explain the tone of your reply.

In that video, around the 16th minute, Mark Thomas explain the difference between 'true v genetic common ancestor'. He claims that 'around 5000 years ago everybody alive was either a common ancestor of everybody alive today, or not an ancestor of anybody alive today'. This may be true at the scale of a country of region, but it just doesn't work at the global scale, because some populations never intermingled with the rest of the world, including many Amazonian and Papuan tribes, Andaman islanders, Australian aborigines (i.e. those who do not have recent European admixture), and so on. Even in sub-Saharan Africa, the back migrations that brought haplogroups R1b-V88, T1a and J1 left the Near East during the Early Neolithic, several millennia before that. By my estimation (http://www.eupedia.com/europe/Haplogroup_R1b_Y-DNA.shtml#Africa), R1b-V88 entered Africa (Egypt) between 8,500 and 9,000 years ago. But they would not have carried any European, North Asian, East Asian or South Asian ancestry. Some African DNA entered the European gene pool during the Neolithic, the Antiquity and the Middle Ages (e.g. Saracens, Moors), but they would have come from North Africa, and would not be representative of the whole continent and all its wide variety of ethnic tribes. Then I don't see how East Asians people could have inherited any African DNA in the last 5000 years. A few ethnic groups like the Uyghurs might have through Middle Eastern ancestry, but not say, the Japanese or specific tribes like the Ainu. So in my opinion this kind of claim is no better than what BritainsDNA is doing and should be dismissed as pseudoscience. I am sorry. I have nothing against Mark Thomas personally, but this kind of narrow-minded thinking is just unacceptable to me.

The dichotomy between systematic and interpretative phylogeography as explained by Mark Thomas in that video is very telling of how blind-sided many scientists have become because of the current education system. My approach is not interpretative, but I would not qualify it as only systematic either, as this would be too restrictive. Using statistical and mathematical models cannot take into account a plethora of factors such as geography, historical mobility and transportation, the propension of people to marry within their social class, linguistic group and within their area (except for a wealthy minority), and so on. There is also the very process of natural selection. This can influence genetic evolution in many ways. It can be the progressive elimination of deleterious alleles and the selection of beneficial ones. But it can also be the fact that powerful men have often had access to many women and left a proportionally much higher number of descendants than ordinary men (leading to the quick expansion of some Y-DNA lineages). You can try to explain how you can take these factors into a single unified mathematical model, but I doubt that this is possible. Just human psychology, e.g. the way people choose their mates, and so on, is practically impossible to put into a mathematical variable. I think that is why most population geneticists fail to see the bigger picture and end up with ridiculous theories of how some haplogroups spread or forget that we cannot descend from population with who not a single of our ancestor ever met, because they lived in the middle of the Amazon forest. From my point of views, anybody who stick to mathematical models simply because it appears more scientific (or so they were told when they were students) are blind-sided, have a simplistic unilateral approach to science, and because of that will never get the history of human populations right.

You mentioned above that a lot of Mark Thomas's research has been done in collaboration with archaeologists and anthropologists. That's part of the problem. To become a medical doctor, you don't just need to know about anatomy, but also biochemistry, pharmacology, molecular biology, microbiology, virology, immunology, genetics, and so on and so on. You don't expect the doctor to just call a virologist to determine what virus is affecting a patient, then call an immunologist to ask how the immune system will respond, then a geneticist to analyse the HLA types in relation to that pathogen, then a pharmacist to ask what medicine might help get rid of the infection. They should already have a global vision of how everything works in relation to everything else, otherwise they are useless and will take bad decisions that will negatively affect the patient. Likewise, to be a decent historical population geneticist, it is absolutely essential to have a solid background in prehistory/archaeology, ethnic history, ethnography, anthropology, evolutionary biology, linguistics, geography, and even historical climatology, in addition to genetics itself. Historical population genetics is a complex, multi-hybrid topic, like medicine. In the same way as you can't expect a biochemist to have the global approach of a medical doctor in treating patients, a mere geneticist with little knowledge of history and ethnography will have a very partial and one-sided vision of things that just isn't sufficient in that field. If I hadn't learned several European languages and analysed them in depth, I would not have understood as clearly how much impact Germanic migrations had in say England as opposed to France or Italy. Without being fluent in Japanese I would have have entertained the idea that the Japanese were not merely the result of a blend between Korean-derived Yayoi and aboriginal Jomon, but that the Jomon themselves were a hybrid of Austronesian and Siberian, while the Yayoi invasion may have been preceded by a wave of Southeast Chinese farmers (see my article The Origins of Japanese people (http://www.wa-pedia.com/history/origins_japanese_people.shtml)). From my point of view, population geneticists whose work consist in making statistical models are just amateurs, regardless of their official title.


Incidentally, I think that most people interested in ancient ancestry care more about knowing how similar their genome is compared to other ancient and modern ethnic groups, rather than knowing if they descend from Vikings, Romans or not. Any learned person would quickly understand that all Europeans have Roman, Celtic, Germanic, Slavic, Greek, North African, and Middle Eastern ancestry. In fact, the vast majority of people have low but detectable traces of East Asian and Sub-Saharan African ancestry too (although not from all East Asian and Sub-Saharan ethnic groups, but a few specific ones that migrated to Europe in ancient times). But none of us (unless recently admixed) have Tupi, Andaman or Papuan ancestry since these tribes live where now.

People on this forum often try to determine what percentage of ancient ancestry they carry from particular periods (e.g. Yamna ancestry, or Nordic Bronze Age ancestry). It's not easy because of the very nature of genetic recombination and admixtures over hundreds of generations. But I don't think any of the regular members here would doubt that they have ancestry from all ancient ethnic groups in European history. The important is to know how much from each, or how similar we are to these ancient peoples. This is meaningful in terms of historical identity. Y-DNA is also meaningful for men because it is a full chromosome inherited in an almost unaltered fashion through the ages, and because patrilineal ancestry has such an important connotation in our society through the link with the surname.

Empty_Genes
07-12-16, 21:13
That is odd. I read The Guardian, New Scientist, The Economist and BBC News practically everyday, as well as The Telegraph and other British publications occasionally, but I have never seen any article about BritainsDNA. If these are published in tabloids, then I don't see why there should be any concern about their scientific credibility considering that almost anything published in tabloids in rubbish anyway.

I believe that Private Eye covered BritainsDNA's misdemeanors on 5 occasions (Issue numbers 1345, 1348, 1361, 1387 and 1394), and the Sunday Times on 23/12/12, to name but a few.




I think that this kind of behaviour of the majority of customers tells you exactly why DNA companies are resorting to pseudoscience. As I said, there is no validity in getting an autosomal DNA test to try to find 4th or 5th cousins. This is a complete waste of money. Companies like 23andMe and LivingDNA have their marketing more in line with what people should look for in a DNA test, which is distant ancestry and, in 23andMe's case, health reports (especially carrier risks). I would never recommend any ancestry test that exclude Y-DNA and mtDNA as these are the main tools in historical population genetics and are far more accurate to trace historical population movements than autosomal admixture.

This is completely untrue. The autosomal genome contains many orders of magnitude more information on ancestry than the mtDNA or Y chromosome, and is a composite of DNA inherited from many more ancestors. Y-DNA and mtDNA are now considered minor tools in historical population genetics. The reason for this is that because patterns of variation in mtDNA or the Y chromosome are only weakly constrained by population demographic history, they must be only weakly informative on population demographic history. That said, they are very useful for genetic genealogy, and if analysed with appropriate statistical methods, can still be informative on population history.


Many scientific paper have been wrong. That's one of the main reason why I started the Genetics section on this website, and so far the vast majority of my predictions have been confirmed by ancient DNA tests.

Nobody is immune to being wrong. What we need to avoid is conclusions that are "not even wrong" (to quote Wolfgang Pauli).


You are assuming ancient distribution based on only two samples from the same cave at Goyet. That's not statistically significant.

Can you explain what you mean by "not statistically significant"? Not significant in what statistical test?


Besides those samples were about 40,000 years old, and most other haplogroups didn't exist at that time. The possibilities for mtDNA haplogroups were pretty much limited to M, N, R, U, U2, U5 and U8. Don't expect to find haplogroup H, the most common in Europe today, when its defining mutations hadn't arisen yet. I agree that haplogroup distributions changed markedly over (pre)historical periods, but your example was not the most judicious. You could just have said that Y-haplogroup R1b-L51, which is the most common in western Europe today, was not found in that region before the Late Chacolithic or Early Bronze Age.

You do realise that haplogroups are arbitrary categories - right? I suspect the reason DebbieK mentioned the Posth et al (2016) paper is because based on modern distributions, a naive / phylogeographic analysis would predict that it originated in Asia, but as you point out, because "haplogroup distributions changed markedly over" time, their modern distribution is not necessarily a good indicator of their past distribution or origin. Indeed, there are good studies showing that the geographic centre of mass of a genetic variant can be far removed from its location or origin, see:
Edmonds CA, Lillie AS, Cavalli-Sforza LL (2004) Mutations arising in the wave front of an expanding population. Proc Natl Acad Sci U S A 101: 975–979.
Klopfstein S, Currat M, Excoffier L (2006) The fate of mutations surfing on the wave of a range expansion. Mol Biol Evol 23: 482–490.




I was referring to what he wrotes in the Buzzfeed article, namely:

Mark Thomas, a UCL professor of evolutionary genetics, has previously written that it is “extremely difficult to demonstrate scientifically” claims about the detailed history of your mtDNA or Y-chromosome haplogroup, although it is “reasonable to use large samples of these DNA types to say something about the histories of populations”. Kennett agrees: “[People] have made all sorts of fanciful claims about haplogroups originating in this or that place, but there’s no scientific evidence.”

What is is saying means that it is extremely difficult to demonstrate scientifically where Y-haplogroups G2a and R1b (among others) originated.

Yes, that is what I am saying.


I could have taken other examples. I could have said that it is easy to confirm with ancient DNA samples that mt-haplogroup N1a1a, K1a, T1a, T2c and X (among others), came to Europe with Near Eastern Neolithic farmers. I can also demonstrate that it is possible to make reliable predictions based on modern distributions (I won't explain the complicated process in detail here). This is exactly what I have done since 2009 for both Y-DNA haplogroups and subclades and mtDNA deep subclades, and I was right in about 90% of the cases. For example I predicted which mtDNA haplogroups would be found among Yamna and Corded Ware people, and which mtDNA and Y-DNA haplogroups were part of the southern wave of Neolithic farmers to North and East Africa. Just look at the articles I published on Acamedia.edu over the years, before ancient DNA tests confirmed, for example that R1b was the main haplogroup of the Yamna culture and spread west during the Early Bronze Age to reach Ireland by 2000 BCE. I also predicted that Co-Magnons belonged to haplogroup C1a, F and I, and that I came later during the Gravettian. If I can do it and get it right, it means that my method is scientifically sound. As far as I know, not a single career academic has been able to do the same, so they assume it is not possible.

It sounds to me like the main tool you are employing is confirmation bias. Perhaps you would like to take another look at those ancient DNA papers.


Of course all kinds of people have made all kinds of predictions on forums and elsewhere. But not many have created a website of this scale dedicated to population genetics and written so many articles about it. I think I have written more on the subject that practically any author of peer-reviewed article. Few academics have also studied both history and biology/genetics as I have. I have no interest to join a university research team because I am a maverick and don't like to follow all the rules and protocols, and to "have to publish" to please one's sponsors and for the sake one's career. I especially don't like to work with others and to be told what to do or how to think, or to have to prove my arguments with 'official methods', which are usually a great waste of time. Then I have too many other interests beyond history and population genetics (e.g. neuroscience, robotics, languages, psychology, medical genetics, microbiology, immunology) to limit my research to these fields. I think that life is a waste of time if you can't satisfy your intellectual pursuits.

:-) So do you also ignore the findings of university research teams working on neuroscience, robotics, languages, psychology, medical genetics, microbiology and immunology?


I find it a bit condescending that you should ask me to read the ISOGG Wiki page on phylogeography which explains some of the concept of where haplogroups originated.

Condescension is in the eye (or head) of the beholder. I saw no condescension in DebbieK's suggestion.



My phylogenetic trees are more accurate than those of ISOGG (as they are based more on Yfull.com but using FTDNA nomenclature as much as possible as more people test their Y-DNA with that company than with any other), and I wrote articles for the history of each haplogroup.

How do you know that they are more accurate? Have you tested this? Presumably you have examined the literature on phylogenetic inference (which is vast) and settled on a particular method. If so, what method would that be?


EDIT: I had a look at the page in question and found the video with Mark Thomas's interview, to which you apparently contributed. I noticed that they/you are using one of my maps (Y-haplogroup R1b-S21), even though I don't recall any of you contacting me to ask permission. Perhaps you didn't realise that I was the author, which would explain the tone of your reply.

In that video, around the 16th minute, Mark Thomas explain the difference between 'true v genetic common ancestor'. He claims that 'around 5000 years ago everybody alive was either a common ancestor of everybody alive today, or not an ancestor of anybody alive today'. This may be true at the scale of a country of region, but it just doesn't work at the global scale, because some populations never intermingled with the rest of the world, including many Amazonian and Papuan tribes, Andaman islanders, Australian aborigines (i.e. those who do not have recent European admixture), and so on. Even in sub-Saharan Africa, the back migrations that brought haplogroups R1b-V88, T1a and J1 left the Near East during the Early Neolithic, several millennia before that. By my estimation, R1b-V88 entered Africa (Egypt) between 8,500 and 9,000 years ago. But they would not have carried any European, North Asian, East Asian or South Asian ancestry. Some African DNA entered the European gene pool during the Neolithic, the Antiquity and the Middle Ages (e.g. Saracens, Moors), but they would have come from North Africa, and would not be representative of the whole continent and all its wide variety of ethnic tribes. Then I don't see how East Asians people could have inherited any African DNA in the last 5000 years. A few ethnic groups like the Uyghurs might have through Middle Eastern ancestry, but not say, the Japanese or specific tribes like the Ainu. So in my opinion this kind of claim is no better than what BritainsDNA is doing and should be dismissed as pseudoscience. I am sorry. I have nothing against Mark Thomas personally, but this kind of narrow-minded thinking is just unacceptable to me.

The estimate was from Rohde et al (2004) Nature 431, 562-566. Have you read that paper? It is based on very conservative estimates of intercontinental gene flow, and the work of Chang (1999) Adv. Appl. Probab. 31, 1002−1026, who showed that if the population size (n) is large, the number of generations (Tn) back to the most recent common ancestor has a distribution that is concentrated around the base-2 logarithm of n (with low variance). You may be confusing this with the single locus most recent common ancestor (which is relevant for mtDNA or the Y chromosome), where the average time back is 2n (with high variance).


The dichotomy between systematic and interpretative phylogeography as explained by Mark Thomas in that video is very telling of how blind-sided many scientists have become because of the current education system. My approach is not interpretative, but I would not qualify it as only systematic either, as this would be too restrictive. Using statistical and mathematical models cannot take into account a plethora of factors such as geography, historical mobility and transportation, the propension of people to marry within their social class, linguistic group and within their area (except for a wealthy minority), and so on. There is also the very process of natural selection. This can influence genetic evolution in many ways. It can be the progressive elimination of deleterious alleles and the selection of beneficial ones. But it can also be the fact that powerful men have often had access to many women and left a proportionally much higher number of descendants than ordinary men (leading to the quick expansion of some Y-DNA lineages). You can try to explain how you can take these factors into a single unified mathematical model, but I doubt that this is possible.

Well, not impossible, but I agree it would be extremely challenging. But are you suggesting that you do take these factors into account when you infer the origins of some haplogroup or other?


Just human psychology, e.g. the way people choose their mates, and so on, is practically impossible to put into a mathematical variable. I think that is why most population geneticists fail to see the bigger picture and end up with ridiculous theories of how some haplogroups spread or forget that we cannot descend from population with who not a single of our ancestor ever met, because they lived in the middle of the Amazon forest. From my point of views, anybody who stick to mathematical models simply because it appears more scientific (or so they were told when they were students) are blind-sided, have a simplistic unilateral approach to science, and because of that will never get the history of human populations right.

OK, you make some valid points – but don’t suggest an alternative. The processes that generated these genetic patterns are extremely complex and it would not only be very challenging to model them, but more importantly, if we did so then we would be guilty of over-fitting (it is easy to explain complex data with complex models, but the problem is that many different complex models can explain our data equally well; equifinality). That is why scientists prefer simple models; more complex models are just more wrong. To quote the statistician George Box: "Since all models are wrong the scientist cannot obtain a "correct" one by excessive elaboration. On the contrary following William of Occam [s]he should seek an economical description of natural phenomena. Just as the ability to devise simple but evocative models is the signature of the great scientist so overelaboration and overparameterization is often the mark of mediocrity".

But any understanding is a model (whether implicit or explicit). To quote the physicist Neil Gershenfeld: "The most common misunderstanding about science is that scientists seek and find truth. They don’t — they make and test models…. Making sense of anything means making models that can predict outcomes and accommodate observations. Truth is a model".

Its really just a question of information content. One cannot make an inference that contains more information than was in model and data used to make that inference.

But the main point I was making about interpretative phylogeography is that because it is interpretative and not systematic, it is easily steered by subjective biases, and so can and has been used to service any number of theories.



Incidentally, I think that most people interested in ancient ancestry care more about knowing how similar their genome is compared to other ancient and modern ethnic groups, rather than knowing if they descend from Vikings, Romans or not. Any learned person would quickly understand that all Europeans have Roman, Celtic, Germanic, Slavic, Greek, North African, and Middle Eastern ancestry. In fact, the vast majority of people have low but detectable traces of East Asian and Sub-Saharan African ancestry too (although not from all East Asian and Sub-Saharan ethnic groups, but a few specific ones that migrated to Europe in ancient times). But none of us (unless recently admixed) have Tupi, Andaman or Papuan ancestry since these tribes live where now.

I agree with the first part, but suspect that you have severely underestimated the rate at which ancestry spreads geographically as we look back in time. Also, so you say “although not from all East Asian and Sub-Saharan ethnic groups, but a few specific ones that migrated to Europe in ancient times”. Are you suggesting that those “few specific ones” didn’t exchange migrants with other groups in East Asia and sub-Saharan Africa?


People on this forum often try to determine what percentage of ancient ancestry they carry from particular periods (e.g. Yamna ancestry, or Nordic Bronze Age ancestry). It's not easy because of the very nature of genetic recombination and admixtures over hundreds of generations. But I don't think any of the regular members here would doubt that they have ancestry from all ancient ethnic groups in European history. The important is to know how much from each, or how similar we are to these ancient peoples. This is meaningful in terms of historical identity. Y-DNA is also meaningful for men because it is a full chromosome inherited in an almost unaltered fashion through the ages, and because patrilineal ancestry has such an important connotation in our society through the link with the surname.

Without wishing to sound patronizing, you have obviously given a lot of thought to this, but seem to have ignored a vast literature on population genetics. Genetic inheritance is a very stochastic process, and that means high evolutionary variance (identical population histories can give rise to very different patterns in genetic data). Add to that equifinality (very different population histories can give rise to very similar / identical patterns in genetic data), and emergence (population histories can give rise to counter-intuitive patterns in genetic data), and you can see why it is not easy to make population history inferences with high confidence. The trick is to stay within the inferential constraints of what can be said with confidence, while still saying something interesting.

DebbieK
07-12-16, 23:33
Maciamo

I think Mark has dealt very well with most of your comments but I just wanted to add a few extra points.

BritainsDNA was sold at the end of 2015 and the flow of misleading media coverage has now ceased. The pseudoscientific media coverage mostly took place between 2013 and 2014. Have a look at our UCL Debunking Genetic Astrology website and you will find many examples listed. These articles have mostly appeared not in the tabloids like the Mail but in respected broadsheet papers like The Guardian, The Times and the Independent as well as on BBC radio and TV.

DNA testing is best used in combination with genealogical records, and that is my primary area of interest. Autosomal DNA testing, when used carefully, can be very helpful in this regard but because of the random nature of DNA inheritance it is generally not possible to draw conclusions about relationships much beyond four or five generations. People are using AncestryDNA and FTDNA's Family Finder test to confirm genealogies for close cousins up to about the fourth cousin level and not for distant cousins. Indeed, FTDNA market their Family Finder test as only being suitable for finding close relatives. It is the deep ancestry inferences where the pseudoscience creeps in, particularly when companies try and make claims about haplogroup origins. The admixture tools on GedMatch are free and fun to use but from what I've seen they do not produce meaningful results. I am not convinced it is possible to do valid comparisons between modern and ancient DNA using these tools, especially when we are using the results from chip testing rather than whole genome sequencing.

I wasn't making any claims about statistical significance for haplogroup M and was merely commenting that the location where the samples was found was not what one might predict from the present-day distribution.

I think you've misunderstood the terminology. Phylogeny is the use of DNA to form trees. Phylogeography is the process of adding the geography to the phylogeny. We can now produce very detailed phylogenies for the Y-chromosome and for mitochondrial DNA, especially now that we are able to exploit the power of Y-chromosome sequencing and full mtDNA sequencing. We can map the present-day distributions of the haplogroups to the geography but it is much more difficult to make inferences about the past.

I'm not quite sure I understand your analogy about medical doctors. I would not expect my general practitioner to be an expert in every medical field, but I would expect him or her to know which experts to refer me to if I did have a medical problem that needed investigating. If I had a heart problem I would expect to be referred to a consultant cardiologist. If I needed a drug then I would expect my GP to give me a prescription which I would take to the pharmacist. I wouldn't expect the GP to operate on my heart or to dispense drugs. The same applies to population genetics. As a genetic genealogist I do not expect to match the expertise of a population geneticist who has devoted their entire career to the study of the subject and is recognised for their expertise by their peers. I would defer to the expertise of the population geneticist just as I would go to a doctor if I had a medical problem rather than trying to diagnose the problem myself. I would also not expect the population geneticist to go on archaeological digs or write papers about linguistics but he would probably know all the experts in those fields and would collaborate with them. It is impossible for any one individual to be an expert on all subjects. That's why we have seen a welcome growth in multidisciplinary research.

Clearly you have formulated some interesting hypotheses and you have some very strong opinions but these will not have any validity unless you can get articles published in peer-reviewed journals. Methods are proved scientifically sound not because someone is of the opinion that they are right and everyone else is wrong but through the process of publication and replication. This is particularly the case if someone wishes to overturn the scientific consensus and challenge existing methodologies.

Maciamo
08-12-16, 00:54
Thanks for your reply, Mark Thomas (I presume, from the content of your reply).


I believe that Private Eye covered BritainsDNA's misdemeanors on 5 occasions (Issue numbers 1345, 1348, 1361, 1387 and 1394), and the Sunday Times on 23/12/12, to name but a few.

Ok, thank you. I don't read those, so that explains why I missed it.



This is completely untrue. The autosomal genome contains many orders of magnitude more information on ancestry than the mtDNA or Y chromosome, and is a composite of DNA inherited from many more ancestors. Y-DNA and mtDNA are now considered minor tools in historical population genetics. The reason for this is that because patterns of variation in mtDNA or the Y chromosome are only weakly constrained by population demographic history, they must be only weakly informative on population demographic history. That said, they are very useful for genetic genealogy, and if analysed with appropriate statistical methods, can still be informative on population history.

What is completely untrue exactly? All I am saying is that it is a waste of money to buy an autosomal DNA test to find distant cousins. I never said that autosomal tests were useless, on the contrary. I even explain that DNA companies should focus more on the medical aspect, which in my opinion is the most interesting side of a DNA test. As for using autosomal tests for historical population genetics, that is a very useful tool and I have analysed many ancient genomes using autosomal admixture calculators. I have created autosomal admixture maps (http://www.eupedia.com/europe/autosomal_maps_dodecad.shtml). I just don't understand why the majority of customers do not seem to care about autosomal admixtures, or just satisfy themselves with very bad interpretations such as FTDNA's Ancient Origins (see post #6 above).


Nobody is immune to being wrong. What we need to avoid is conclusions that are "not even wrong" (to quote Wolfgang Pauli).

Some researchers just seem to publish because they have to, to make a living, but aren't really trying to understand historical population movements. At least that's how I feel when I read they poor analysis. It's not true for all of them, obviously, but there are quite a few of them.


Can you explain what you mean by "not statistically significant"? Not significant in what statistical test?

I meant that at present only 3 Proto-Aurignacian and 6 Aurignacian mtDNA samples have been tested. 2 samples belonging to haplogroup M out of 6 samples may seem like a high percentage, but the sample size is so small that it is not statistically significant. It could be a sampling bias, especially that they both come from the from the same site (Goyet Cave). Who knows, we may not find any more haplogroup M in the next 100 Aurignacian samples, which would completely change the frequency.



You do realise that haplogroups are arbitrary categories - right?

Not that arbitrary. Many top level Y-DNA haplogroups represent historical bottlenecks and are defined by a long series of SNPs, while deeper subclades are often defined by one or a few SNP's. I have noticed that many top-level haplogroups are actually defined by mutations in the coding sequence of the Y chromosome (http://www.eupedia.com/genetics/Major_Y-DNA_haplogroups_defined_by_gene_altering-polymorphisms.shtml), which would be explained by changes in male fertility that could have given an evolutionary advantage to these lineages. I also found out that mutations in Coenzyme Q gene define most major mtDNA haplogroups (http://www.eupedia.com/genetics/coenzyme_q_mutations_define_major_mtdna_haplogroup s.shtml), which surely played a role in adaptation to the local environment or lifestyle.



I suspect the reason DebbieK mentioned the Posth et al (2016) paper is because based on modern distributions, a naive / phylogeographic analysis would predict that it originated in Asia, but as you point out, because "haplogroup distributions changed markedly over" time, their modern distribution is not necessarily a good indicator of their past distribution or origin. Indeed, there are good studies showing that the geographic centre of mass of a genetic variant can be far removed from its location or origin, see:
Edmonds CA, Lillie AS, Cavalli-Sforza LL (2004) Mutations arising in the wave front of an expanding population. Proc Natl Acad Sci U S A 101: 975–979.
Klopfstein S, Currat M, Excoffier L (2006) The fate of mutations surfing on the wave of a range expansion. Mol Biol Evol 23: 482–490.

I am perfectly aware that the geographic centre of mass of a genetic variant can be far removed from its location or origin. That's why phylogeny is so important. This is how I realised in 2009 that R1b had roots around the Caucasus and not in western Europe, as the subclade diversity was higher there. Actually the very first R1b-M343 probably came from Siberia or Central Asia around the LGM.


Yes, that is what I am saying.

So ancient DNA tests combined with phylogeny (where are older subclades found) and the nodes of genetic diversity (where does a haplogroup have the highest diversity of old subclades) are not a sufficient scientific proofs in your eyes? Then what would be the point of conducting ancient DNA tests?




It sounds to me like the main tool you are employing is confirmation bias. Perhaps you would like to take another look at those ancient DNA papers.


Why would that be confirmation bias? There is a trail of ancient DNA evidence from the Pre-Pottery Neolithic Fertile Crescent that advances hand in hand with archaeological evidence of farming to Anatolia, the Balkans, Central Europe, then Western Europe, and these haplogroups were absent in previous Mesolithic populations. I am not sure how closely you have followed all the papers on ancient DNA, which I have summarised here (http://www.eupedia.com/europe/ancient_european_dna.shtml), but if this is confirmation bias all the authors of these papers suffer from it too. Guessing right and having one's predictions confirmed by hard evidence is not what confirmation bias means. I think you are just coming with phrases like that as a passive-aggressive way to respond to my criticism.


:-) So do you also ignore the findings of university research teams working on neuroscience, robotics, languages, psychology, medical genetics, microbiology and immunology?


I do not ignore hard evidence provided by population genetic researchers, such as the raw test results. The problem I have with many researchers is the same as the one with DNA testing companies: it's their simplistic interpretation of the data due to lack of knowledge of history, ethnography, linguistics, etc.

There are many population geneticists, but very few that are qualified to be historical population geneticists. That's a big difference. That's the difference between a biochemist and a medical doctor. Population geneticists can deal with modern populations, but if to deal with ancient populations, migrations, natural selection based on human nature and local environments, you need more than just manipulating data.


Condescension is in the eye (or head) of the beholder. I saw no condescension in DebbieK's suggestion.

Would it be condescending if I asked you to read the Wikipedia page on evolutionary genetics to familiarise yourself on the subject? I am pretty sure it would, as you are a professor of evolutionary genetics. I don't know many people, even among professors or researchers, who have written as extensively about haplogroup phylogeography as I have, analysing the past and present distribution of hundreds of subclades. Debbie knows it as she befriended me on Facebook and can see my regular updates on the topic there, and apparently follows my posts on this forum too.



How do you know that they are more accurate? Have you tested this? Presumably you have examined the literature on phylogenetic inference (which is vast) and settled on a particular method. If so, what method would that be?

That's not what I meant by accurate. I should have said more extensive and up-to-date. Well, I am aware that I should update the J2 and R1a tree, which I haven't done in 3 years, but the others have more SNP branches than ISOGG as I am using ISOGG + FTDNA + Yfull as references and double-check for inconsistencies between them for all haplogroups. AFAIK, ISOGG trees for each haplogroup are managed by several people and often different people for each haplogroup. I analyse and painstakingly draw all trees myself and memorise most of them in the process.



The estimate was from Rohde et al (2004) Nature 431, 562-566. Have you read that paper? It is based on very conservative estimates of intercontinental gene flow, and the work of Chang (1999) Adv. Appl. Probab. 31, 1002−1026, who showed that if the population size (n) is large, the number of generations (Tn) back to the most recent common ancestor has a distribution that is concentrated around the base-2 logarithm of n (with low variance). You may be confusing this with the single locus most recent common ancestor (which is relevant for mtDNA or the Y chromosome), where the average time back is 2n (with high variance).

I will give you the benefit of the doubt and assume you did not read what I wrote properly, because neither of the articles you mention refute my arguments in the matter.


Well, not impossible, but I agree it would be extremely challenging. But are you suggesting that you do take these factors into account when you infer the origins of some haplogroup or other?
...
OK, you make some valid points – but don’t suggest an alternative. The processes that generated these genetic patterns are extremely complex and it would not only be very challenging to model them, but more importantly, if we did so then we would be guilty of over-fitting (it is easy to explain complex data with complex models, but the problem is that many different complex models can explain our data equally well; equifinality). That is why scientists prefer simple models; more complex models are just more wrong. To quote the statistician George Box: "Since all models are wrong the scientist cannot obtain a "correct" one by excessive elaboration. On the contrary following William of Occam [s]he should seek an economical description of natural phenomena. Just as the ability to devise simple but evocative models is the signature of the great scientist so overelaboration and overparameterization is often the mark of mediocrity".

I am not saying that these factors should been incorporated into a mathematical model, but rather that mathematical models are not the right tool for historical population genetics. Mathematical models are great for physics or engineering. But you cannot deal with people in the same way. That's how you end up omitting that some populations have been secluded from the rest of the world (https://en.wikipedia.org/wiki/Uncontacted_peoples) for over 10,000 years.

George Box's quote is especially valid for mathematical models. Since it is not the appropriate tool to deal with human behaviour, it overelaborates unnecessarily the model. I completely agree with you on that. So why are you still using it?




But any understanding is a model (whether implicit or explicit). To quote the physicist Neil Gershenfeld: "The most common misunderstanding about science is that scientists seek and find truth. They don’t — they make and test models…. Making sense of anything means making models that can predict outcomes and accommodate observations. Truth is a model".

Great, more quotes. Let's place it in a quotation bubble then. It will be nicer.

Models are good for theoretical sciences like physics or to a lesser extent chemistry. Historical population genetics is not about finding the laws of nature or models that have practical application in technology. It's about understanding our roots, and discovering parts of prehistory for which the only evidence that existed before DNA tests were archaeological remains. Now we can tell if an individual who lived in central Germany 7000 years ago had blue or brown eyes, whether he was lactose intolerant, what HLA antibodies he carried, and where his ancestors came from (using haplogroup phylogeny and autosomal admixtures). What is the use of theoretical models in all this? It looks more scientific? Why? Because the modern education system places a higher value on mathematics and abstract models than on analysing the physical and health traits of ancient genomes? I think that has reached a new level of absurdity. That is why I prefer to work as an independent researcher. I don't want to have to please colleagues by working on mathematical models that look academically pleasing when that is not what I am interested to know, what will satisfy my curiosity.



I agree with the first part, but suspect that you have severely underestimated the rate at which ancestry spreads geographically as we look back in time. Also, so you say “although not from all East Asian and Sub-Saharan ethnic groups, but a few specific ones that migrated to Europe in ancient times”. Are you suggesting that those “few specific ones” didn’t exchange migrants with other groups in East Asia and sub-Saharan Africa?

Let's take a concrete example. Some of the East Asian admixture in Europe came from the Proto-Uralic migration from Siberia (Y-haplogroup N1c), which seems to have its roots in the Manchurian Neolithic based on ancient DNA recovered from the West Liao River valley in Manchuria by Yinqiu Cui et al. (2013) (http://www.biomedcentral.com/1471-2148/13/216). The East Asian autosomal DNA became diluted along the way, picking up Siberian (also Mongoloid) DNA, then Northeast European after arriving in the Volga-Ural region then the eastern Baltic. So obviously that long migration gave plenty of opportunities to intermix with other peoples. The Manchurian Neolithic probably has its roots in the Yellow River Neolithic, and would consequently share common genes with the northern Chinese population. However, the original Neolithic Manchurians did not carry any recent ancestry from say Japan (Mesolithic Jomon culture) or Indonesia, which had no contact with Neolithic Manchuria. Therefore I don't see how Jomon Japanese or Indonesian genes from that period (or even a few millennia before) could have come to Europe with that migration. In fact, the other, later migrations from East Asia to Europe always involved people from Mongolia, Siberia or the Altai (Huns, Mongols, Turks), but never from Japan or Southeast Asia. The Chinese and Mongols surely intermingled to some extent as neighbours, and the Chinese in turn might have been in a continuum with the Vietnamese, Thai and Burmese. But insular Japanese, Filipinos and Indonesians would have had no contact with them. Migrations took place from China to Japan, the Philippines and Indonesia, but not the other way round. So we end up with an impossibility for Europeans to have Jomon Japanese or Indonesian ancestry. But the reverse is not necessarily true. Modern Japanese have a barely discernible amount of (Northeast) European DNA, which was in all likelihood brought by the Iron Age Yayoi invaders from Korea to Japan (from 500 BCE), who themselves inherited it from intermarriages with the Mongol neighbours, who were admixed with Proto-Indo-Europeans since the Bronze Age (hence of presence of R1a and R1b and Northeast European and Gedrosian admixture among the Mongols).

This is where knowing a bit of history is essential. It's easy to assume that all populations mixed with all other populations in both directions, but that is just not the case.




Without wishing to sound patronizing, you have obviously given a lot of thought to this, but seem to have ignored a vast literature on population genetics. Genetic inheritance is a very stochastic process, and that means high evolutionary variance (identical population histories can give rise to very different patterns in genetic data). Add to that equifinality (very different population histories can give rise to very similar / identical patterns in genetic data), and emergence (population histories can give rise to counter-intuitive patterns in genetic data), and you can see why it is not easy to make population history inferences with high confidence. The trick is to stay within the inferential constraints of what can be said with confidence, while still saying something interesting.

What did I write to make you think that I didn't know that? Just to be clear, in the paragraph you were quoting here I was explaining what most members on this forum expect from a DNA test (in contrast to the vast majority of regular customers from AncestryDNA and the like who have no real interest in history). I was not referring to me. I don't know how I could have been more clear when I started the paragraph by "People on this forum". I have little interest in comparing my genome to ancient genomes. As I explained recently that is why I have not joined GEDmatch (unlike many forum members). Unlike most people, I have a fairly limited interest in myself (apart from knowing more about my health through my genome, which is why I have recommended 23andMe since 2009). That's also why I don't seek an academic career, or don't even use my real name for my publications. What matters to me is understanding better (pre)history, migrations, and how modern populations and ethnic groups came into existence, what relations exist between them, and how closely culture and language follows genetics. All wide-ranging but impersonal questions.

Maciamo
08-12-16, 01:37
Thanks again for your input, Debbie.



DNA testing is best used in combination with genealogical records, and that is my primary area of interest. Autosomal DNA testing, when used carefully, can be very helpful in this regard but because of the random nature of DNA inheritance it is generally not possible to draw conclusions about relationships much beyond four or five generations. People are using AncestryDNA and FTDNA's Family Finder test to confirm genealogies for close cousins up to about the fourth cousin level and not for distant cousins. Indeed, FTDNA market their Family Finder test as only being suitable for finding close relatives.

I understand that, but I just cannot grasp the interest of confirming the relationship with a 3rd cousin. What good is it to know for sure that someone is a 3rd cousin. That won't make you like them more or vice versa. It won't increase your natural affinities, the compatibility of your personalities, nor the amount of shared interest (beside the fact that you are a bit related). This facet of human nature is completely beyond me. I much prefer to socialise, befriend or discuss with someone with whom I have shared affinities than someone who is related to me. In my experience the two rarely match up.



I think you've misunderstood the terminology. Phylogeny is the use of DNA to form trees. Phylogeography is the process of adding the geography to the phylogeny. We can now produce very detailed phylogenies for the Y-chromosome and for mitochondrial DNA, especially now that we are able to exploit the power of Y-chromosome sequencing and full mtDNA sequencing. We can map the present-day distributions of the haplogroups to the geography but it is much more difficult to make inferences about the past.

I did not misunderstand the terminology. Just look at one of the haplogroup pages I wrote (e.g. this one (http://www.eupedia.com/europe/Haplogroup_I2_Y-DNA.shtml)) and you will see that no only I made a phylogenetic tree (the easy part), but I go on to explain on all the rest of the page where each subclade is found, where it was found in ancient times, and what historical migration propagated this or that subclade. For mtDNA haplogroups I even mention the geographic matches next to each subclade on the tree (e.g. on this page (http://www.eupedia.com/europe/Haplogroup_K_mtDNA.shtml#subclades)). That is phylogeography.



I'm not quite sure I understand your analogy about medical doctors. I would not expect my general practitioner to be an expert in every medical field, but I would expect him or her to know which experts to refer me to if I did have a medical problem that needed investigating. If I had a heart problem I would expect to be referred to a consultant cardiologist. If I needed a drug then I would expect my GP to give me a prescription which I would take to the pharmacist. I wouldn't expect the GP to operate on my heart or to dispense drugs. The same applies to population genetics. As a genetic genealogist I do not expect to match the expertise of a population geneticist who has devoted their entire career to the study of the subject and is recognised for their expertise by their peers. I would defer to the expertise of the population geneticist just as I would go to a doctor if I had a medical problem rather than trying to diagnose the problem myself. I would also not expect the population geneticist to go on archaeological digs or write papers about linguistics but he would probably know all the experts in those fields and would collaborate with them. It is impossible for any one individual to be an expert on all subjects. That's why we have seen a welcome growth in multidisciplinary research.

In my analogy, the specialisation of medical doctors would be the specialisation about specific regions or haplogroups for population geneticists. I admit that I am more specialised in European, and to a lesser extent Asian, population genetics. But a medical doctor must learn many very different subjects to become an MD, whatever the body part they specialise in, because biochemistry, immunology, microbiology, genetics, etc. will always be important in any body part. In the same way, genetics, history, archaeology, ethnography, linguistics, etc. will always be important in historical population genetics, regardless of what part of the world, or what haplogroup you specialise in.



Clearly you have formulated some interesting hypotheses and you have some very strong opinions but these will not have any validity unless you can get articles published in peer-reviewed journals. Methods are proved scientifically sound not because someone is of the opinion that they are right and everyone else is wrong but through the process of publication and replication. This is particularly the case if someone wishes to overturn the scientific consensus and challenge existing methodologies.

Why do you care so much about peer-reviewed journals? This is so 20th century. Nowadays with the Internet researchers can share easily through websites like Academia.edu, ResearchGate, or through one's own website, which in my opinion makes peer-reviewed journals obsolete. What's more these journals often prevent the spread of knowledge by imposing prohibitive access fees. This in my opinion is an outrageous barrier to the propagation of scientific knowledge and that practice should be banned. I think that the only reason most researchers (but not me) insist on publishing through peer-reviewed journals is for the sake of tradition, for the prestige it confers, and for the potential benefits for their career. None of these are valid reasons for me. Anyway 99.9% of researchers will be forgotten after they die. Science shouldn't be a playground for boosting egos. It's about advancing knowledge, understanding the world better. Only that matters. Perhaps scientists should't get paid for their work. This way only people truly motivated by seeking knowledge and understanding will keep researching, leaving people who see science as just a job to pay the bills out of the scene. Anyway, with AI and robots replacing humans in most jobs in a decade or two, and with the inevitable universal income that will have to be implemented to prevent social chaos, that will give the opportunity to practically anybody to become an independent researcher.

Maciamo
08-12-16, 09:33
Mark and Debbie, I had a look at your Debunking Genetic Astrology (http://www.ucl.ac.uk/mace-lab/debunking) on the UCL website, including the news stories (http://www.ucl.ac.uk/mace-lab/genetic-ancestry/news). I now understand better what the fuss is about with BritainsDNA. It is indeed ridiculous to think one is related in a meaningful way to Napoleon or Cleopatra because they share the same haplogroup, and all the more since Cleopatra's DNA has never been tested to the best of my knowledge. Nevertheless it can be interesting (merely interesting) to know that one shares the same deep haplogroup clade as some famous personalities, especially if that clade is less than 500 years old (but that also means that very few people do).

Some claims by BritainsDNA or Moffat really made me cringe, like the ones that a volcanic eruption 70,000 years ago had wiped out all human lineages except those of Adam and Eve, that 97% of men with the last name of Cohen share a single genetic marker, and that one-third of British men are descended from the country’s founding lineages. There may be "some" truth behind, but the facts have been badly distorted and mixed together with other distorted facts. The Toba supereruption 70,000 years ago did happen, and may have wiped out a part of human lineages, but it has nothing to do with the most recent common Y-chromosomal and mitochondrial ancestors of humanity, who are both much older than that. There is a common haplotype within haplogroup J1-Z18271 deep clade, but it is found in less than half of the people with the Cohen surname, not 97%. I have no idea the "one-third of British men are descended from the country’s founding lineages" means. It doesn't even match any haplogroup.

I saw that you criticised a lot the claim that BritainsDNA can tell customers if they have Viking ancestors, but at the same time you (rightly) explain that all Britons have Viking ancestors. I am not sure what the problem is here. If some customers can't understand that DNA recombines at every generation and that they are a mix of Vikings, Anglo-Saxons, Romans, various types of Celtic Britons, and even other ancient ethnic groups, then there is probably little point in trying to explain it too them. Some people will never get it, no matter how long you explain it to them.

In the Y-DNA section of Understanding genetic ancestry testing (http://www.ucl.ac.uk/mace-lab/debunking/understanding-testing), you mention this:


The haplogroup information is often accompanied by a story about the origin of your ancestors, including a map of the world with arrows indicating ancestral migrations. Hundreds of thousands of men from around the world have now had their Y-DNA tested, and we have a very good idea of the distribution of the different haplogroups in the present-day population. It is, however, difficult to be confident about where these haplogroups originated and how they spread; many different histories could explain their current distribution. Sometimes a company will associate a haplogroup with, for example, Viking, Norman or Saxon ancestry, but such associations are at best speculative and should be treated with caution. Just as today most haplogroups are shared among many populations, so would it have been for past populations.

While this is generally true for reports from DNA testing companies, for people more specialised in deep SNP phylogeny and STR haplotypes, fine-scale différentiations within historical times are becoming increasingly accurate, and comparing with large databases it is in some cases possible to ascertain that some deep clades of Y-haplogroup I1 for example, is much more likely of being of Viking than Anglo-Saxon origin, or the other way round. Just knowing that you are I1 or I1-L22 won't do it of course, but being I1-Y18385 (https://www.yfull.com/tree/I-Y18385/), with a TMRCA of 1850 years and an overwhelming presence in Norway, would more confidently indicate Viking ancestry, for example. So qualifying this of genetic astrology, as you did in this BBC article (http://www.bbc.com/news/science-environment-21687013) and that Guardian article (https://www.theguardian.com/science/blog/2013/feb/25/viking-ancestors-astrology), is not just an exaggeration, but can be downright wrong. Of courses those articles were published in 2013, when such claims were harder to substantiate than today. However I have not seen any retraction on your part to explain that phylogeny has now progressed enough to validate such fine-scale ancestry determination. Obviously a Y-haplogroup only represents the patrilineal lineage and a fixed 2% of one's genome (59 million bp out of 3,000), but anybody who orders a DNA test should know that eventually (if they are truly interested, otherwise who cares what they think or believe).

Sile
08-12-16, 19:32
@ Maciamo

What are your thoughts on a company like Yfull that only analyses data .................How accurate is their data once finished, and then to compare it with the source of where they got the data?

Maciamo
08-12-16, 20:04
@ Maciamo

What are your thoughts on a company like Yfull that only analyses data .................How accurate is their data once finished, and then to compare it with the source of where they got the data?

Accessing the Yfull tree is free. I don't really understand the point of paying 49$ for their analysis as normally testing companies are supposed to provide the list of SNPs. I have never found STRs to be very useful compared to SNP's for ancient ancestry, as STRs lack phylogeny.

Empty_Genes
08-12-16, 20:46
Accessing the Yfull tree is free. I don't really understand the point of paying 49$ for their analysis as normally testing companies are supposed to provide the list of SNPs. I have never found STRs to be very useful compared to SNP's for ancient ancestry, as STRs lack phylogeny.

More misunderstanding, this time RE Y STRs. I suspect you are avoiding the complicated stuff

Maciamo
08-12-16, 21:14
More misunderstanding, this time RE Y STRs. I suspect you are avoiding the complicated stuff

I think you see misunderstanding where you want to see them. What I meant is that STRs are only serving as proxies for SNPs. STRs can be used to determine haplogroup and subclades, but they are estimations and usually require a backbone SNP test to confirm deep clades. If I am missing something, please do elaborate on what you meant by misunderstanding.

DebbieK
10-12-16, 03:39
Maciamo

I don’t have time right now to get involved in a lengthy discussion so I’m only responding to a few comments very briefly.

As regards cousin matching, everyone has different reasons for testing. I am more interested in using DNA testing to verify my genealogical research.

I’m somewhat confused about your reference to “historical population geneticists”. Historians specialise in history and population geneticists specialise in population genetics. Ideally we should leave the historians to study history and let the population geneticists analyse the genetic data. There certainly have been problems with papers published by geneticists without any input from historians. Fortunately, research is now very multidisciplinary. Population genetics is a very specialised and highly mathematical discipline. Models are a fundamental part of population genetics. See for example Servedio et al 2015 “Not just a theory—the utility of mathematical models in evolutionary biology”. If you go against the consensus and reject the use of models what methodology are you using to test your hypotheses about the origins of haplogroups?

The peer review process is important because it does at least have the effect of filtering out most of the pseudoscience. It also ensures that published papers conform to acceptable standards in terms of referencing and access to raw data, computer code, etc. The fact that something has gone through the peer review process means that it’s more likely to attract the attention of serious researchers, and also gives the research more credibility. However, the process is not perfect and there are still bad papers that scrape through.

I’m glad you were able to have a look at our website and that you can now appreciate the problems that BritainsDNA caused in the UK with their misleading marketing claims.

I agree that it is possible to produce very fine-scale phylogenies now that we have access advanced Y-DNA testing (eg, the BigY from Family Tree DNA and the Full Genomes YElite test). However, the phylogenies are only telling us about the structure of the tree. The phylogenies do not tell us anything about where these SNPs occurred in the past. There are many different ways of estimating TMRCAs and there are very wide confidence intervals, so even if we can get a reasonably accurate TMRCA for a specific SNP that is still only telling us about the present-day distribution of that SNP and not its past distribution. There is a growing collection of ancient samples that can be used to provide a temporal fix but the number of samples is still very small and comprehensive SNP testing is often not done or is not possible.

As you say, someone could take a Y-DNA test and learn that they are I1-Y1835, and that Y18385 is found today at high prevalence in Norway. With more data the confidence intervals on the TMRCAs are reduced but this still doesn’t tell us where Y18385 originated 1850 years ago plus or minus several hundred years. A lot can happen in 2000 years. Why do you think a male line would have stayed in the same location for all those years? There are always many different stories that will explain the data. That’s why it’s important to do the hypothesis testing to determine the most likely scenario.

Maciamo
10-12-16, 22:38
Thanks for your reply, Debbie.



I agree that it is possible to produce very fine-scale phylogenies now that we have access advanced Y-DNA testing (eg, the BigY from Family Tree DNA and the Full Genomes YElite test). However, the phylogenies are only telling us about the structure of the tree. The phylogenies do not tell us anything about where these SNPs occurred in the past. There are many different ways of estimating TMRCAs and there are very wide confidence intervals, so even if we can get a reasonably accurate TMRCA for a specific SNP that is still only telling us about the present-day distribution of that SNP and not its past distribution. There is a growing collection of ancient samples that can be used to provide a temporal fix but the number of samples is still very small and comprehensive SNP testing is often not done or is not possible.

As you say, someone could take a Y-DNA test and learn that they are I1-Y1835, and that Y18385 is found today at high prevalence in Norway. With more data the confidence intervals on the TMRCAs are reduced but this still doesn’t tell us where Y18385 originated 1850 years ago plus or minus several hundred years. A lot can happen in 2000 years. Why do you think a male line would have stayed in the same location for all those years? There are always many different stories that will explain the data. That’s why it’s important to do the hypothesis testing to determine the most likely scenario.

I don't quite agree. It's part of the job of a population geneticist to investigate where subclades are found and trace back their progressive migration clade after clade. In the case of haplogroup I1, if you notice that a branch is found in Scandinavia and Britain today, you can dig deeper into the phylogeny until you find the split where one subclade is only found in Britain and not in Scandinavia or elsewhere (allowing possibly for minor back migrations, as there are always people who emigrate). At that point, based on the TMRCA and the distribution within Britain, you can determine the likelihood (which will need to be confirmed by ancient DNA tests later) that a subclade is either Anglo-Saxon or Viking. There is nothing extraordinary or magical about that process. That's a well accepted methodology in genetic genealogy.

And that is exactly the methodology I used to determine that R1b originated in Siberia or Central Asia during the late Palaeolithic period, then ended up in various places between the northern Fertile Crescent and Russia during the Mesolithic and Neolithic, and that eventually subclades downstream of R1b-L23 moved westward, reaching central Europe by 2500 BCE, then expanding across western Europe between 2200 and 1200 BCE. I made this migration map in 2013, two years before R1b was found in the Yamna culture.

http://cache.eupedia.com/images/content/R1b-migration-map.jpg

I made another similar map (http://www.eupedia.com/europe/neolithic_europe_map.shtml#R1b_migration) (in Flash format so I can't copy it here) in 2009, three years before any ancient Y-DNA had been tested. Of course those predictions couldn't have been possible, especially regarding the dates, without knowledge of archaeology, comparing morphological types (e.g. skull shape), burial types, and above all following the diffusion of bronze technology from the Steppe to Western Europe. I used the same methodology for haplogroup R1a and others. I never mistook using the combination of phylogeny, TMRCA, and archaeological/anthropological evidence. For R1a and R1b, there was the additional evidence from linguistics, as their diffusion matched quite well the estimated divergence ages of the various branches of Indo-European language.

In science, a methodology works if it leads to verifiable results, and mine were verified by ancient DNA test. I know it can be hard for people who have studied exact sciences to accept some of the methodologies of social sciences, which aren't based on mathematics. But that doesn't mean they are necessarily wrong or can't be verified. My academic background is rather unusual since I studied economics, history, then biomedical sciences (immunology, bacteriology, virology, genetics, neuroscience, and so on). Very few people follow such different paths. People readily cross from one natural science to another, or from a social science to another, but there seems to be some kind of enmity between the two groups. I don't care, because I never studied with the aim of getting a job like most people, for to satisfy my thirst for knowledge and understanding. I always knew I would be self-employed as I am too independent and individualistic. I could study all these subjects, plus learn seven languages (self-taught, including English) because I realised that I learn at least twice faster than an average university student, thanks to a quasi-eidetic memory. There are several exceptionally gifted people in my family, but none really like me. I always joke that the less gifted ones became medical doctors (four in total) as they clearly do not have the same curiosity, thirst for knowledge, and the same aptitude to absorb knowledge and detect patterns that nobody else can see.


Going back to the topic of the BritainsDNA controversy, what your team at UCL said could easily be misconstrued by lay people with no knowledge of population genetics. A title like To claim someone has 'Viking ancestors' is no better than astrology (https://www.theguardian.com/science/blog/2013/feb/25/viking-ancestors-astrology) or Expensive tests claiming to trace person's ancestry are as dubious as astrology, warn scientists (http://www.dailymail.co.uk/news/article-2289400/Expensive-tests-claiming-trace-persons-ancestry-dubious-astrology-warn-scientists.html) will be perceived by the public as if DNA tests cannot determine ancestry at all, which is nonsense. What is the purpose of genetic genealogy and phylogeography if not to be able to tell where our ancestors came from? The only issue was that naive customers could believe that they were 100% Vikings genetically when their test results showed that their patrilineal haplogroup 'probably' came to Britain with the Vikings. That's a problem of human stupidity, not a problem with the DNA test itself, nor with the ability of genetic genealogy to estimate the likelihood of one's Y-DNA haplogroup being of Viking origin. It is far more hazardous to give a reliable percentage of autosomal DNA of Viking origin at present, and it will always be less reliable in terms of probability than the 'simple' Y-DNA line because of recombinations and very similar shared ancestry between Germanic tribes.

As for mtDNA, I have explained for years that it is practically useless for tracing ancestry for at least the last 4000 or 5000 years. At best mtDNA can distinguish between Mesolithic European, Neolithic Near Eastern farmers and Steppe Indo-Europeans, but not anything more since these populations mixed, as mtDNA evolves very slowly and on a 16,569 bases long sequence any mutation can quickly become hazardous for health. I would have understood that you'd qualify of 'genetic astrology' a company that claimed to be able to tell if someone is of Viking descent based solely on mtDNA. But that is absolutely not the case, and as far as I can tell from the result samples you posted on your blog (http://cruwys.blogspot.be/2013/12/a-first-look-at-britainsdna-chromo-2-y.html), they are not really making any outlandish claim. Your criticism was essentially based on the lack of information regarding their sources, or the inability to download the raw mtDNA data. But for most ordinary customers who aren't geneticists and don't care so much about what their test results mean, it's probably not a big issue. I am pretty sure that these were details that could be solved by sending an email to BritainsDNA to request more information. As you said it yourself, this test was heavily marketed in the UK and was therefore intended for ordinary customers, not researchers or professionals. People who are interested enough to want to know more about their test results, including more accurate distribution maps and phylogeography, usually come to this website. ;-)

The bottom line is that when lay people read on the BBCE website or top national newspaper that a professor of genetics from a reputed university is saying that DNA tests can't tell you your ancestry, that is what most people will remember, and that will negatively affect all DNA testing companies, not just BritainsDNA. People will just lose confidence in these tests because of the polemic you created. That's not good for researchers either when we know that there are the very at least 10 times more DNA test results from commercial companies than from research labs. Companies like 23andMe have been very clever to gather all this data for medical research while making a profit from it. But even genetic genealogists can benefit from commercial tests through the numerous regional projects at FTDNA. So I am not sure it's a good idea to give such bad press to ancestry tests, especially when it sounds more like a personal vendetta.

Empty_Genes
11-12-16, 20:57
Thanks for your reply, Debbie.



I don't quite agree. It's part of the job of a population geneticist to investigate where subclades are found and trace back their progressive migration clade after clade. In the case of haplogroup I1, if you notice that a branch is found in Scandinavia and Britain today, you can dig deeper into the phylogeny until you find the split where one subclade is only found in Britain and not in Scandinavia or elsewhere (allowing possibly for minor back migrations, as there are always people who emigrate). At that point, based on the TMRCA and the distribution within Britain, you can determine the likelihood (which will need to be confirmed by ancient DNA tests later) that a subclade is either Anglo-Saxon or Viking. There is nothing extraordinary or magical about that process. That's a well accepted methodology in genetic genealogy.


Are you able to calculate the likelihood of both the tree and the spatial distribution of its branches?

Maciamo
11-12-16, 22:53
Are you able to calculate the likelihood of both the tree and the spatial distribution of its branches?

I am not sure I understand you question. Could you rephrase it and maybe provide an example? Are you still talking about the specific case of Anglo-Saxon vs Viking, or something more general? The methodology and accuracy obviously varies depending on whether we are talking about a well-documented migration in historical times or an undocumented one in prehistoric times.

Empty_Genes
12-12-16, 20:51
I am not sure I understand you question. Could you rephrase it and maybe provide an example? Are you still talking about the specific case of Anglo-Saxon vs Viking, or something more general? The methodology and accuracy obviously varies depending on whether we are talking about a well-documented migration in historical times or an undocumented one in prehistoric times.

You used the term 'likelihood', a concept which is frequently used in phylogenetic inference. Can you explain what you mean by 'likelihood'?

Empty_Genes
12-12-16, 21:30
I don't quite agree. It's part of the job of a population geneticist to investigate where subclades are found and trace back their progressive migration clade after clade.
I am extremely confident that the vast majority of population geneticists would disagree.

In the case of haplogroup I1, if you notice that a branch is found in Scandinavia and Britain today, you can dig deeper into the phylogeny until you find the split where one subclade is only found in Britain and not in Scandinavia or elsewhere (allowing possibly for minor back migrations, as there are always people who emigrate). At that point, based on the TMRCA and the distribution within Britain, you can determine the likelihood (which will need to be confirmed by ancient DNA tests later) that a subclade is either Anglo-Saxon or Viking. There is nothing extraordinary or magical about that process. That's a well accepted methodology in genetic genealogy.
Its not a well-accepted methodology in population genetics. See, for example:
Nielsen & Beaumont (2009) Statistical inferences in phylogeography. Molecular Ecology18, 1034–1047.

Indeed, such a ‘methodology’ is fraught with problems.
In statistics, likelihood is an assessment of the weight of support for a model / model parameter values (θ), given some data. The probability of the data (D) given θ, i.e. P(D|θ), is the likelihood of θ given D, i.e. L(θ|D). This is used widely in science, including population genetics, forensics, etc. It is very useful in phylogenetic tree inference as it provides a means of assessing which is the best of a set of proposed trees. However, to do this you need a likelihood function: a mathematical formulation to calculate P(D|θ). This is possible for trees, but I am not aware of a likelihood function to calculate P(D|θ) where θ is both the tree itself and the spatial / geographic distribution of lineages on that tree through time. If you have such a function, please do let me know.



And that is exactly the methodology I used to determine that R1b originated in Siberia or Central Asia during the late Palaeolithic period, then ended up in various places between the northern Fertile Crescent and Russia during the Mesolithic and Neolithic, and that eventually subclades downstream of R1b-L23 moved westward, reaching central Europe by 2500 BCE, then expanding across western Europe between 2200 and 1200 BCE. I made this migration map in 2013, two years before R1b was found in the Yamna culture.

Have you tested your methodology in cases where you know exactly what the true history is (for example, by applying it to simulated data)?


I made another similar map (in Flash format so I can't copy it here) in 2009, three years before any ancient Y-DNA had been tested. Of course those predictions couldn't have been possible, especially regarding the dates, without knowledge of archaeology, comparing morphological types (e.g. skull shape), burial types, and above all following the diffusion of bronze technology from the Steppe to Western Europe. I used the same methodology for haplogroup R1a and others. I never mistook using the combination of phylogeny, TMRCA, and archaeological/anthropological evidence. For R1a and R1b, there was the additional evidence from linguistics, as their diffusion matched quite well the estimated divergence ages of the various branches of Indo-European language.
So why would you expect the TMRCA of a lineage to correspond to the timing of the demographic processes by which that lineage was spread?


Going back to the topic of the BritainsDNA controversy, what your team at UCL said could easily be misconstrued by lay people with no knowledge of population genetics. A title like To claim someone has 'Viking ancestors' is no better than astrology or Expensive tests claiming to trace person's ancestry are as dubious as astrology, warn scientists will be perceived by the public as if DNA tests cannot determine ancestry at all, which is nonsense. What is the purpose of genetic genealogy and phylogeography if not to be able to tell where our ancestors came from?

Did you not read this bit: “There are some situations where Y chromosome or mitochondrial DNA information can be useful. It is, for example, reasonable to use large samples of these DNA types to say something about the histories of populations, if analyses are performed carefully and at the population level. Also, if genealogical research (parish records, surnames, etc.) suggests that two men share a common male line ancestor in the 16th century, the Y chromosome could be used to support or reject this claim. But individual Y chromosome or mitochondrial DNA types provide no more than the vaguest hint about where their ancestors lived hundreds, or thousands of years ago.”


The only issue was that naive customers could believe that they were 100% Vikings genetically when their test results showed that their patrilineal haplogroup 'probably' came to Britain with the Vikings. That's a problem of human stupidity, not a problem with the DNA test itself, nor with the ability of genetic genealogy to estimate the likelihood of one's Y-DNA haplogroup being of Viking origin. It is far more hazardous to give a reliable percentage of autosomal DNA of Viking origin at present, and it will always be less reliable in terms of probability than the 'simple' Y-DNA line because of recombinations and very similar shared ancestry between Germanic tribes.
I wrote the article because I was concerned that customers were being duped. The company was telling stories that mtDNA and Y chromosome did not, and in most cases, could not support. Is it such a bad thing to point out these legitimate concerns?

DebbieK
13-12-16, 01:57
I don't quite agree. It's part of the job of a population geneticist to investigate where subclades are found and trace back their progressive migration clade after clade. In the case of haplogroup I1, if you notice that a branch is found in Scandinavia and Britain today, you can dig deeper into the phylogeny until you find the split where one subclade is only found in Britain and not in Scandinavia or elsewhere (allowing possibly for minor back migrations, as there are always people who emigrate). At that point, based on the TMRCA and the distribution within Britain, you can determine the likelihood (which will need to be confirmed by ancient DNA tests later) that a subclade is either Anglo-Saxon or Viking. There is nothing extraordinary or magical about that process. That's a well accepted methodology in genetic genealogy.

Genetic genealogy is the combination of genetics with genealogical research. Population genetics requires a different expertise altogether. There is an acquired knowledge base that has been built up over the last 100 years and an extensive literature. To answer questions about historical populations then population genetics techniques must be deployed. An additional problem is the ad hoc nature of the genetic genealogy databases. They are heavily skewed in favour of people of European and British origin. Americans constitute about 70% of the customer database at Family Tree DNA, and the American results are often the subject of founder effects. How are you taking these biases into account? What evidence do you have of Y-chromosome continuity in Europe in the last 1000 years? It is rare to find a male line that has stayed put in the same place. My Cruwys family is a rare example of a surname that has stayed in a single location (Cruwys Morchard in North Devon, England) for over 800 years. However, the surname originates in Normandy or Flanders and not in Britain.


In science, a methodology works if it leads to verifiable results, and mine were verified by ancient DNA test. I know it can be hard for people who have studied exact sciences to accept some of the methodologies of social sciences, which aren't based on mathematics. But that doesn't mean they are necessarily wrong or can't be verified.

Scientists use the scientific method which is a process of formulating hypotheses and testing them. I am still not clear how you have tested your hypotheses. You seem to be doing a post hoc interpretation of the data. It is very easy to detect patterns in data and attribute significance where none exists. This is where the problems of confirmation bias can come into play. Ancient DNA has only provided evidence that a haplotype is in a particular location at a specific point of time. Why do you think this should correlate with the place of origin of the haplogroup?


Going back to the topic of the BritainsDNA controversy, what your team at UCL said could easily be misconstrued by lay people with no knowledge of population genetics. A title like To claim someon has 'Viking ancestors' is no better than astrology or Expensive tests claiming to trace person's ancestry are as dubious astrology will be perceived by the public as if DNA tests cannot determine ancestry at all, which is nonsense. What is the purpose of genetic genealogy and phylogeography if not to be able to tell where our ancestors came from? The only issue was that naive customers could believe that they were 100% Vikings genetically when their test results showed that their patrilineal haplogroup 'probably' came to Britain with the Vikings. That's a problem of human stupidity, not a problem with the DNA test itself, nor with the ability of genetic genealogy to estimate the likelihood of one's Y-DNA haplogroup being of Viking origin. It is far more hazardous to give a reliable percentage of autosomal DNA of Viking origin at present, and it will always be less reliable in terms of probability than the 'simple' Y-DNA line because of recombinations and very similar shared ancestry between Germanic tribes.

A DNA test on its own can't tell us where our ancestors come from. That's why we use genealogical records with the genetic evidence to make inferences within a genealogical time frame. Phylogeography is the process of adding the geographical locations of modern populations to the phylogeny. Phylogeography only tells us about the present-day distribution of populations and not where those populations came from. The problem is that there are often many plausible stories that will fit the data and it is very easy for subjective biases to come into play. The simplest explanation is not necessarily the right one. See: Heber et al 2016. Ancient DNA and the rewriting of human history: be sparing with Occam’s razor. Genome Biol 17: 1. See also the blog post I wrote for Sense About Science on Sense About Genealogical Testing which clarifies the legitimate uses of genetic ancestry for genealogical purposes.


But that is absolutely not the case, and as far as I can tell from the result samples you posted on your blog, they are not really making any outlandish claim. Your criticism was essentially based on the lack of information regarding their sources, or the inability to download the raw mtDNA data. But for most ordinary customers who aren't geneticists and don't care so much about what their test results mean, it's probably not a big issue. I am pretty sure that these were details that could be solved by sending an email to BritainsDNA to request more information. As you said it yourself, this test was heavily marketed in the UK and was therefore intended for ordinary customers, not researchers or professionals. People who are interested enough to want to know more about their test results, including more accurate distribution maps and phylogeography, usually come to this website....

The bottom line is that when lay people read on the BBCE website or top national newspaper that a professor of genetics from a reputed university is saying that DNA tests can't tell you your ancestry, that is what most people will remember, and that will negatively affect all DNA testing companies, not just BritainsDNA. People will just lose confidence in these tests because of the polemic you created. That's not good for researchers either when we know that there are the very at least 10 times more DNA test results from commercial companies than from research labs. Companies like 23andMe have been very clever to gather all this data for medical research while making a profit from it. But even genetic genealogists can benefit from commercial tests through the numerous regional projects at FTDNA. So I am not sure it's a good idea to give such bad press to ancestry tests, especially when it sounds more like a personal vendetta.

The BritainsDNA Chromo2 test was quite a reasonable test. The problems related to their earlier test which was very expensive and only tested around 300 Y-SNPs and 300 mtDNA SNPs. They were also getting the mtDNA haplogroup assignments wrong. This was particularly disappointing for female testers, especially as they could have had their full mtDNA sequenced at FTDNA (16569 bases) for much less than BritainsDNA were charging. However, our criticisms of the company are based not so much on the quality of the tests and the just so reports but the extensive misleading media coverage they have generated. In particular there was concern that the tests were being promoted as part of a "massively subsidised" project with the implication being that the test-takers were contributing to legitimate academic research. If you look at the timeline on the Debunking Genetic Astrology website you'll see that Mark Thomas and David Balding corresponded privately with BritainsDNA but did not get a satisfactory response and instead received a threatening legal letter. The bad science promoted by the company had the effect of bringing population genetics and genetic genealogy into disrepute because the claims made were so outlandish. Some people didn't want to test because they thought it was a scam.

I don't know if you've had any personal contact with customers of BritainsDNA but I've had quite a few of their customers writing to me because they are confused about their results. Some of them have been falsely sold the BritainsDNA test as a genealogy test, and are very disappointed when they discover that the test generally has no application for genealogy. Customers have difficulty locating other sources of information because the company uses its own proprietary SNP naming system (S series SNPs).

sparkey
13-12-16, 20:07
Empty_Genes and DebbieK, I'm curious about your opinion of the work of Stephen Oppenheimer. I bring him up, because when I think of misleading interpretations of Y-DNA data that have dispersed into discussions by laymen, I think of Oppenheimer's work. It got play in Prospect Magazine, The Telegraph, The New York Times, WalesOnline, etc. The amount of people who have read those articles dwarfs the amount of people who have put any serious thought into population genetics, so even though they were published 10 years ago, many still think that Britain is basically full of direct descendants of Stone Age "Basques."


The flaws in Oppenheimer's methodology, I think you'd agree, are obvious. He basically noticed that Basques are R1b dominant, and Britain is R1b dominant, and voila! Of course, the more we've gotten ancient DNA results, the more his hypotheses have been discounted.


The thing is, the same hasn't been true of most of Maciamo's hypotheses. Haplogroups C-V20 and I as Paleolithic/Mesolithic seems to be holding up, as is Haplogroup G2a as Neolithic, and R1b postdating G2a too. What do you think is different about how they developed their interpretations of the data? Something must be better, at least. I've participated in some of this "post hoc interpretation," and although I don't really consider it an exact science, I've been impressed with the predictive power, in particular of predicting what Y-DNA haplogroups ancient samples will belong to. I don't think it's a problem to also give people best-guess stories about the history of their own haplogroups, at least if you add a lot of probably's. Like, "As Haplogroup I, your lineage has probably been in Europe since the Stone Age, and probably predates most other modern European lines in Europe." It gets tougher when trying to distinguish between Celts and Vikings and the like, but there are similar patterns at that scale as well.


Also, whether you think it's a good idea or not, population geneticists have participated in speculative interpretation of data, much like hobbyists do. They've also often gotten it wrong, usually due to drawing conclusions with insufficient data. For example, Rosser 2000 (https://www.ncbi.nlm.nih.gov/pubmed/11078479) gave some possible explanations that turned out to be wrong, in particular putting R1b as Paleolithic, and Balaresque 2010 (http://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.1000285) predicted an early Neolithic entry of R1b, which hasn't been holding up.

Empty_Genes
14-12-16, 19:16
Dear Sparkey

You make some really interesting points; responses below:

Empty_Genes and DebbieK, I'm curious about your opinion of the work of Stephen Oppenheimer. I bring him up, because when I think of misleading interpretations of Y-DNA data that have dispersed into discussions by laymen, I think of Oppenheimer's work. It got play in Prospect Magazine, The Telegraph, The New York Times, WalesOnline, etc. The amount of people who have read those articles dwarfs the amount of people who have put any serious thought into population genetics, so even though they were published 10 years ago, many still think that Britain is basically full of direct descendants of Stone Age "Basques."
I know Stephen Oppenheimer personally, and think he is an extremely decent chap. That said, yes, I agree with you, its nonsense. But the reason I think that is because he is using untested inference methodologies. The speculation of a Paleolithic origin for shared Y chromosomes between Basques and Britain wasn’t even Oppenheimer’s; it was first suggested in Wilson et al (2001: PNAS 98(9):5078-5083).



The flaws in Oppenheimer's methodology, I think you'd agree, are obvious. He basically noticed that Basques are R1b dominant, and Britain is R1b dominant, and voila! Of course, the more we've gotten ancient DNA results, the more his hypotheses have been discounted.
I agree. But as you can probably guess, my concerns about his and other’s using this inference methodology (interpretative phylogeography) are more general. It is of course possible that – based on an interpretative phylogeography – somebody could make predictions that later find support from ancient DNA data. One clear-cut example is that Richards et al (2000: Am. J. Hum. Genet. 67:1251–1276) used this sort of approach to predict that mtDNA U lineages would be predominant in pre-Neolithic Europe, and Bramanti et al (2009: Science 326: 137-140) and others later showed this to be the case.


The thing is, the same hasn't been true of most of Maciamo's hypotheses. Haplogroups C-V20 and I as Paleolithic/Mesolithic seems to be holding up, as is Haplogroup G2a as Neolithic, and R1b postdating G2a too.
It may seem a trivial point, but everybody prior to ~12,000 years ago was Paleolithic/Mesolithic.

What do you think is different about how they developed their interpretations of the data? Something must be better, at least. I've participated in some of this "post hoc interpretation," and although I don't really consider it an exact science, I've been impressed with the predictive power, in particular of predicting what Y-DNA haplogroups ancient samples will belong to. I don't think it's a problem to also give people best-guess stories about the history of their own haplogroups, at least if you add a lot of probably's. Like, "As Haplogroup I, your lineage has probably been in Europe since the Stone Age, and probably predates most other modern European lines in Europe." It gets tougher when trying to distinguish between Celts and Vikings and the like, but there are similar patterns at that scale as well.
Again, I agree that it is OK to “give people best-guess stories about the history of their own haplogroups”. My concerns come with presenting such best-guess stories as science. If you use interpretative phylogeography you can make countless predictions, so obviously some of those will hold up, and those concerning more recent populations are more likely to hold up. But where is the systematic testing of these inference methodologies? There is too much scope for cherry-picking the predictions / confirmation bias, as there is for servicing any of a very large number of mutually exclusive population histories. If I managed to pick some winners in the Epsom races, would you then assume that I have a fool-proof system?
Added to that, just because a particular haplogroup is observed in some ancient DNA sample, that doesn’t mean that is where that haplogroup originated. We recently showed that G2a was present in Aegean early Neolithics (Hofmanova et al (2016: PNAS 113(25): pp6886-6891). We also showed that Aegean early Neolithic individuals were genomically very similar to early farmers from across Europe, in whom G2a is frequently found. So is the presence of G2a in early Aegean framers really that surprising? But that doesn’t mean the Aegean is the G2a homeland.
The main point is that for an inference methodology to be taken seriously as a scientific method, it should systematic (i.e. formulated so that it is free from steering by subjective biases, and can be automated) and then be tested on data where the population histories are fully known. To me, that means tested on data that has been simulated under a known model of population history.


Also, whether you think it's a good idea or not, population geneticists have participated in speculative interpretation of data, much like hobbyists do. They've also often gotten it wrong, usually due to drawing conclusions with insufficient data. For example, Rosser 2000 gave some possible explanations that turned out to be wrong, in particular putting R1b as Paleolithic, and Balaresque 2010 predicted an early Neolithic entry of R1b, which hasn't been holding up.
Indeed, and I could list a whole lot more. But I’d like to make it clear that I do not see hobbyists and professional (i.e. paid) scientists as distinct. I don’t care if you are a professor of some august institution, or working as an assistant examiner in the Swiss Federal Patent Office, or collecting shopping trolleys in a supermarket car park: if you follow the scientific method then you are doing science! In my view there have been many such floored studies – and they are floored primarily because they don’t follow the scientific method, but rather make inferences using ad hoc and untested methodologies.
Interpretative phylogeography isn’t the only untested (and possibly untestable) inference methodology used in the genetic history literature; there are many papers that fall into this category, and most population geneticists consider them problematic at the very least.

Twilight
14-12-16, 19:56
Dear Sparkey

You make some really interesting points; responses below:

I know Stephen Oppenheimer personally, and think he is an extremely decent chap. That said, yes, I agree with you, its nonsense. But the reason I think that is because he is using untested inference methodologies. The speculation of a Paleolithic origin for shared Y chromosomes between Basques and Britain wasn’t even Oppenheimer’s; it was first suggested in Wilson et al (2001: PNAS 98(9):5078-5083 (tel:5078-5083)).



I agree. But as you can probably guess, my concerns about his and other’s using this inference methodology (interpretative phylogeography) are more general. It is of course possible that – based on an interpretative phylogeography – somebody could make predictions that later find support from ancient DNA data. One clear-cut example is that Richards et al (2000: Am. J. Hum. Genet. 67:1251–1276) used this sort of approach to predict that mtDNA U lineages would be predominant in pre-Neolithic Europe, and Bramanti et al (2009: Science 326: 137-140) and others later showed this to be the case.


It may seem a trivial point, but everybody prior to ~12,000 years ago was Paleolithic/Mesolithic.

Again, I agree that it is OK to “give people best-guess stories about the history of their own haplogroups”. My concerns come with presenting such best-guess stories as science. If you use interpretative phylogeography you can make countless predictions, so obviously some of those will hold up, and those concerning more recent populations are more likely to hold up. But where is the systematic testing of these inference methodologies? There is too much scope for cherry-picking the predictions / confirmation bias, as there is for servicing any of a very large number of mutually exclusive population histories. If I managed to pick some winners in the Epsom races, would you then assume that I have a fool-proof system?
Added to that, just because a particular haplogroup is observed in some ancient DNA sample, that doesn’t mean that is where that haplogroup originated. We recently showed that G2a was present in Aegean early Neolithics (Hofmanova et al (2016: PNAS 113(25): pp6886-6891). We also showed that Aegean early Neolithic individuals were genomically very similar to early farmers from across Europe, in whom G2a is frequently found. So is the presence of G2a in early Aegean framers really that surprising? But that doesn’t mean the Aegean is the G2a homeland.
The main point is that for an inference methodology to be taken seriously as a scientific method, it should systematic (i.e. formulated so that it is free from steering by subjective biases, and can be automated) and then be tested on data where the population histories are fully known. To me, that means tested on data that has been simulated under a known model of population history.


Indeed, and I could list a whole lot more. But I’d like to make it clear that I do not see hobbyists and professional (i.e. paid) scientists as distinct. I don’t care if you are a professor of some august institution, or working as an assistant examiner in the Swiss Federal Patent Office, or collecting shopping trolleys in a supermarket car park: if you follow the scientific method then you are doing science! In my view there have been many such floored studies – and they are floored primarily because they don’t follow the scientific method, but rather make inferences using ad hoc and untested methodologies.
Interpretative phylogeography isn’t the only untested (and possibly untestable) inference methodology used in the genetic history literature; there are many papers that fall into this category, and most population geneticists consider them problematic at the very least.

I think what Sparky means by Mesolithic is Mesolilitic Europerans that lived 12,000 ybp. As far as Gedmatch is concerned, I usually check the ancient Dna to see if the test is bias and compare them to what we currently know; if the test is way off keister to our present uptodate knowledge and doesn't guess my countries of origins right then the test is most likely bias, you can see the link below. There is a little disclaimer that Maciamo has made, you can also see the link below. Ultimately if you want to understand your results, I recommend studying the countries your ancestors came from and their history. On a side note, G2a was already spread out during the Neolithic so no of course the Aegean is not the original G2a homeland.


http://www.y-str.org/p/ancient-dna.html



http://www.eupedia.com/europe/origins_haplogroups_europe.shtml




http://www.eupedia.com/europe/neolithic_europe_map.shtml

Rethel
14-12-16, 20:04
From the first link:

"If you go back 3,000 years, your ancestors are almost everybody’s ancestors."

This is utter nonsense.

The number of ancestors does not grow exponentially with generations due to a thing called "pedigree collapse":

https://en.wikipedia.org/wiki/Pedigree_collapse

Yes,
but generally true, at least mathematicly, and
mathematic is the final verification of anything.

It is enaugh to go back 1000 years to have 1,000,000,000,000+ ascendants
when lived 500,000,000 people and in for example everybody country was no
more than 100,000-3,000,000 inhabitants who mostly bred with each other.
It only shows, that any orfanage leftist bubbling about equality of ascendants
is a double Duch speech which is simple a delusion and idiocy.

And ancestor is not the same as ascendant.

Rethel
14-12-16, 20:13
Top academics, even those researching specifically haplogroups, were not immune from such fancies, and were often the first culprits in spreading them. Everyone remembers how until 2008 the academic establishment would tell the world that haplogroup R1b descended from Cro-Magnons, because its modern geographic distribution looked like it expanded from the Franco-Cantabrian refugium after the LGM.

It is a good example, how much idiocy is spreading by "scholars" who based on
wrong assumptions are making wrong conclusions. I started to be interested in
the stuff since the beginning of 2006 and I didn't buy this absurd theory at all
since the beginning, becasue it made no sense. People are still creating other
often even more idiotic theories, which are falling one after another and which
on this forum is plenty. I stick still to the one, and is going more prooved and
true with every year, becasue only the one is obvious from scriptural, historical,
archeological and genetical records, and another is simply impossible.

Twilight
14-12-16, 20:58
It is a good example, how much idiocy is spreading by "scholars" who based on
wrong assumptions are making wrong conclusions. I started to be interested in
the stuff since the beginning of 2006 and I didn't buy this absurd theory at all
since the beginning, becasue it made no sense. People are still creating other
often even more idiotic theories, which are falling one after another and which
on this forum is plenty. I stick still to the one, and is going more prooved and
true with every year, becasue only the one is obvious from scriptural, historical,
archeological and genetical records, and another is simply impossible.

What theories do you have in mind? And what exactly do you mean by "the one" just curious.

bicicleur
14-12-16, 21:05
Yes,
but generally true, at least mathematicly, and
mathematic is the final verification of anything.

It is enaugh to go back 1000 years to have 1,000,000,000,000+ ascendants
when lived 500,000,000 people and in for example everybody country was no
more than 100,000-3,000,000 inhabitants who mostly bred with each other.
It only shows, that any orfanage leftist bubbling about equality of ascendants
is a double Duch speech which is simple a delusion and idiocy.

And ancestor is not the same as ascendant.

that is true

it is impossible to sustain all human life created on earth
human life procreates itself to fast

humans, just like anything else on earth should be subject to natural selection
descendants of 2 humans can easily populate a complete planet earth in about 6-700 years

DebbieK
14-12-16, 23:05
Empty_Genes and DebbieK, I'm curious about your opinion of the work of Stephen Oppenheimer. I bring him up, because when I think of misleading interpretations of Y-DNA data that have dispersed into discussions by laymen, I think of Oppenheimer's work. It got play in Prospect Magazine, The Telegraph, The New York Times, WalesOnline, etc. The amount of people who have read those articles dwarfs the amount of people who have put any serious thought into population genetics, so even though they were published 10 years ago, many still think that Britain is basically full of direct descendants of Stone Age "Basques."

The flaws in Oppenheimer's methodology, I think you'd agree, are obvious. He basically noticed that Basques are R1b dominant, and Britain is R1b dominant, and voila! Of course, the more we've gotten ancient DNA results, the more his hypotheses have been discounted.

I've not read Oppenheimer's book. I did buy it but haven't managed to get beyond the first chapter on the Celts. I agree with Mark's comments. In addition Oppenheimer was wrong to place so much emphasis on the Y-chromosome which only represents half of the human population and only a small percentage of the total genome. Fortunately we now have really good data from the ground-breaking People of the British Isles Project. There should be Y-DNA and mtDNA data published from the POBI Project too, hopefully some time next year. I don't think anyone take's Oppenheimer's Basque hypothesis very seriously these days.

Maciamo
15-12-16, 11:45
I apologise for the delayed reply. I was typing a detailed response yesterday, but my PC restarted following a Windows update when I was on the phone and I lost everything. I don't feel like re-writing everything so I will be more succint.


I am extremely confident that the vast majority of population geneticists would disagree.

Then what are they researching? Where is their work leading them? What questions are they trying to answer?

N.B.: I was of course referring to population geneticists working on human populations, and specialising in haplogroups and other tools relating to human evolution and history - not all population geneticists. I am sure that those specialising on horizontal gene transfers between bacteria couldn't care less. But I think that what I meant was clear from the context of haplogroup subclades.


Its not a well-accepted methodology in population genetics. See, for example:

Perhaps that is why the majority of population geneticists specialising in human (pre)history and migrations either cannot come up with anything useful to say about the data they collect, or when they do try to interpret the data, the result is nonsensical as they ignore many of the factors I mentioned above (geographic barriers, archeological evidence, etc.).

One of the first things I learned at university, as part of a philosophy course, was it was vital to analyse data with the right tools. The scale of things isn't the same in fields like astronomy and molecular biology, and it would be absurd to use laws of astrophysics to try to comprehend, say, the ATP synthesis process within a mitochondrion. It's not just a matter of using scientific tools appropriate to the right scale, but also to look at a problem from every angle, using different tolls appropriate to every appropriate level. That is why it would be wrong, for example, to think one could make sense of human psychology solely on the basis on the underlying biochemical processes between neurons, without taking onto considerations other levels such as neural networks, genetic factors (e.g. variants in genes like COMT, DRD2, SERT, MAOA), nutrition, human language and culture, interpersonal interactions, and the physical environment of the person. One thing that gets on my nerves is scientists that are so focused on their specialised field of expertise that they forget or ignore other relevant fields.

Historical population genetics is by its very nature transdisciplinary (https://en.wikipedia.org/wiki/Transdisciplinarity). The goal is to understand the history of human populations and all the tools available should be combined to achieve that goal. Mathematics have some use, for example to determine TMRCA of Y-haplogroups or calculate autosomal admixtures, but it would be irresponsible to think that one can one can understand human population history using only mathematical models and with complete disregard for variations in human mating behaviours and practices (e.g. exogamy, polygamy, patrilocality, droit du seigneur), causes and motivations for migrations (famine, war, natural disaster, greed, new technological development, new lifestyle, overpopulation, climate change), and without using tools like archaeology or climatology that can shed light on these practices and causes. It is as ridiculous as to try to understand human psychology using only mathematical models. The work of a historical population geneticist like me is more akin to a detective's forensic investigation, gathering all the evidence and using logic and deduction to solve the mysteries of unrecorded human prehistory. No two cases are exactly the same, and we have to work using the evidence and tools that are available to us in each case.

There is no use for theoretical models in this field as there won't be any other application beyond human population history. You can't use the same models for animal population with completely different behaviours, animals that are not organised in societies like us, that do not cultivate plants and domesticate other animals. There is only one human history and once we have reached a satisfying understanding of it, there won't be any use for predictive statistical models any more. Furthermore, a model that works in Bronze Age western Eurasia won't necessarily work in Neolithic Austronesia or Copper Age Mesoamerica because these populations live in completely different environments and have very diverging cultures and lifestyles. Once again, a scientific model based on mathematics cannot take these factors into consideration. It's just not the appropriate tool.

Besides, it's not because a piece of evidence is based on a mathematical model that it is more accurate. TMRCA estimates vary widely between researchers using different methodologies, and none to my knowledge are taking regional historical population densities into consideration. (I have explained (http://www.eupedia.com/forum/threads/25644-Why-it-is-wrong-to-assume-that-a-haplogroup-originated-where-it-is-most-frequent-now) this in a post on this forum nearly seven years ago). It would be very hard to work without TMRCA estimates, but they are only estimates and are often less accurate even than radiocarbon dating (which is only approximate).

Maciamo
15-12-16, 16:02
One methodology I have used to trace back the migration of haplogroups, and that to my knowledge nobody else has used, is to look at isolated populations around the world and see which Y-DNA and mtDNA haplogroups they share. The goal is to estimate which Y-DNA and mtDNA haplogroups spread together, with the help of known prehistoric migrations such as the spread of agriculture or bronze technology. I started doing it in January 2010 with Indo-European migrations (http://www.eupedia.com/forum/threads/25613-Identifying-the-original-Indo-European-mtDNA-from-isolated-settlements), which allowed me to isolate some mtDNA lineages for the R1a branch and the R1b branch. This is one of several methods I used to sort out the separate migrations of each branch many years before ancient Y-DNA tests were available, and it turned out to be correct in every region tested so far. I could even tell if an ancient population was mixed R1a+R1b and which of the two would be dominant.

In 2013, I did the same for the migration of Neolithic farmers to North Africa and Iberia linked to haplogroups J1 and T1a (http://www.eupedia.com/forum/threads/29400-Correlating-the-mtDNA-haplogroups-of-the-original-Y-haplogroup-J1-and-T1-herders). And soon after I analysed the mtDNA lineages of African populations that possessed Y-haplogroup R1b-V88 (http://www.eupedia.com/forum/threads/29401-Retracing-the-mtDNA-haplogroups-of-the-original-R1b-people). It is thanks to this method of linking mtDNA to Y-DNA and predicting the haplogroup make-up of the source population that I was able to predict the presence of Y-DNA haplogroup in ancient samples based on the mtDNA samples that had been tested many years earlier, such as the presence of R1b-V88 in Early Neolithic Spain. I also managed to deduce from the accumulated evidence that Y-haplogroup T1a would originated with Early Neolithic farmers in the eastern Fertile Crescent, and not in East Africa (as modern frequencies suggest), nor among the Natufians or Anatolian farmers, as many people had suggested. So far all the ancient data confirmed this.

No need of mathematical models here. Just data analysis, deduction from evidence and logic. No other population geneticist tried this method because it didn't exist. I had to invent it. The problem with most career academics is that they prefer to use tried and tested methods, and preferably, as you said (Mark), methods that can be quantified and tested with mathematical formulae. I am not afraid to try new methods and I don't care what others think of it as long as I get results. Look at Craig Venter who went against the scientific establishment and managed to sequence the human genome faster and at a fraction of the costs of the official US government-financed Human Genome Project. Why can't there be independent-minded scientists like him? Why are so many people concerned about following the rules, protocols and approved methods?

One of the reasons some scientists still believe in God is that they claim its existence cannot be disproved by the scientific method or by mathematics. That's true, but it can be disproved by logic, as Richard Dawkins brilliantly did in the God Delusion, and as I have done too (e.g. here (http://www.eupedia.com/forum/threads/21223-Has-Maciamo-proved-that-God-doesn-t-exist), although I didn't post much on this subject online). Very often, in complex problem solving logic is more powerful than mathematics because logic is based on our neural networks' ability to process vast amounts of data from different sources that cannot be easily rendered into mathematical data. That's why binary computers, despite their tremendous calculating power and speed, which vastly outrange the human brain for mathematics, cannot easily do things that human do almost without thinking, like reading emotions on someone's face or recognise someone's handwriting. That's why artificial neural networks were developed. But they can't be programmed just with formulae. They need to learn by themselves, just like us. Neural networks gather all available evidence, analyse it, and use logic to process it and find a solution. Most of the scientific method (laws, formulae, algorithms) is binary and linear. It is perfect for things like physics, chemistry and technological applications such as mechanics and electronics. But it sucks at making useful predictions in social sciences, because human behaviour and society are based on neural networks (our brains). When it comes to analysing the history of populations, logic using transdisciplinary evidence is the way to do.

DebbieK
15-12-16, 17:24
I was of course referring to population geneticists working on human populations, and specialising in haplogroups and other tools relating to human evolution and history - not all population geneticists.

Population geneticists do not study haplogroups per se. The Y-chromosome represents only two per cent of our DNA and, because only males have a Y-chromosome, it only represents half of the human population. mtDNA is a tiny molecule of just 16569 base pairs, and provides a very limited view of our ancestry because it only follows the all-female line. While Y-DNA and mtDNA are very useful for genetic genealogy and can be used very effectively within a genealogical timeframe they are less useful for exploring the history of populations. That is why research now focuses on autosomal DNA which is so much more informative.


There is no use for theoretical models in this field as there won't be any other application beyond human population history… There is only one human history and once we have reached a satisfying understanding of it, there won't be any use for predictive statistical models any more. Furthermore, a model that works in Bronze Age western Eurasia won't necessarily work in Neolithic Austronesia or Copper Age Mesoamerica because these populations live in completely different environments and have very diverging cultures and lifestyles. Once again, a scientific model based on mathematics cannot take these factors into consideration. It's just not the appropriate tool... Besides, it's not because a piece of evidence is based on a mathematical model that it is more accurate.

Computer modelling is a basic tool of population genetics that is used by all the best researchers in the field. A good model will take into account different factors. A mathematical model is not a piece of evidence. It provides an unbiased means of testing hypotheses and determining which hypothesis is the most plausible. What methodology do you propose to use for testing hypotheses if you don’t wish to use computer models?


One methodology I have used to trace back the migration of haplogroups, and that to my knowledge nobody else has used, is to look at isolated populations around the world and see which Y-DNA and mtDNA haplogroups they share.

It’s always encouraging to see people coming up with new ideas but any new methods have to be tested to see if they work. You have formulated a hypothesis that Y-DNA and mtDNA haplogroups travel in tandem but how have you tested this hypothesis?

Aaron1981
15-12-16, 17:38
@DebbieK

From a population history stand point I have to disagree. We have seen YDNA patterns from ancient cultures, much less on the female side. While it may not always be exactly black or white, there have been some patterns. ie: R1a showing up in Corded Ware, H2 and G showing up in Anatolian descended farmers, R1b in Yamnaya...etc

DebbieK
15-12-16, 17:53
From a population history stand point I have to disagree. We have seen YDNA patterns from ancient cultures, much less on the female side. While it may not always be exactly black or white, there have been some patterns. ie: R1a showing up in Corded Ware, H2 and G showing up in Anatolian descended farmers, R1b in Yamnaya...etc

Humans are very good at seeing patterns and attributing meaning to those patterns even when the patterns have no significance. That's why we have the scientific method which is a way of testing hypotheses.

Rethel
15-12-16, 18:16
What theories do you have in mind?

For example that R1b was vasconic cro-magnon hg,
or that N1 are blond inhabitans of Scandinavia since
tens of thousands of years... But such insane things
people were claiming as a scientific facts.


And what exactly do you mean by "the one" just curious.

That R1 = IE.
No vasconic R1b.
No uralo-altaic or dravidian R1a.

Goga
15-12-16, 18:21
I do agree with you that genetic science differs from the social science. I studied economics and politcial science and sometimes even (macro) economic models are applicable within political studies. Political science is a social science and even in my field it is necessary to use statistical analyzes to test proposed hypothesis -> thesis, antithesis, synthesis.

Genetic science is much more 'medical' and 'biological'. Without math genetic science is not viable. It is closely related to EXACT science than to social science.

But it is all about patterns if you are using descriptive & inferential statistics and algebra (equations) in general.

Pi (π) is everywehere and where is π there are patterns. It is all about to 'find' those patterns.

Goga
15-12-16, 18:56
Those people who are interested in genetic science but refuse to use statistical methology are not (properly) educated. They simply don't understand what they are talking about. It is how science works, at least since Aristotle. It was the FIRST thing what I learned at the university.

And I read here & there that some folks are against 'peer review'. It is one of the fundamental parts of science. Evaluating others maintain the high quality of researchers & studies and it keeps uneducated laymen and pseudoscience out. That keeps science LESS contaminated from people who are uneducated or who have a hidden agenda and those who try to spread lies, propaganda and try to pollute science.


It is all about finding the truth. Our evolution and development is correlated to science. People who are trying to spread lies/propaganda/racism/politics with all their power/money should be banned from the science forever!

LeBrok
15-12-16, 19:15
Humans are very good at seeing patterns and attributing meaning to those patterns even when the patterns have no significance. That's why we have the scientific method which is a way of testing hypotheses.In this particular discipline of historical population genetics ancient DNA is the final judge, either for scientific models or educated guesses. In a decade or two we should collect so much ancient DNA to figure out all the where how and when they came, went and mixed. Whomever could predict the most, from scientific methods or just from exceptional logic, will be the king. In this field, people with vast knowledge of history and archeology will have huge advantage in connecting the dots.


Humans are very good at seeing patterns and attributing meaning to those patterns even when the patterns have no significance.Generally yes, but there always are these few geniuses who can see how it is. For the rest of us is the daily grind of methodology to figure out something. And even with right methodologies very often there is a lack of good brain power to pull out the right conclusions. Generally speaking of course as I'm not familiar with your work. Just putting things in perspective.

DebbieK
15-12-16, 19:37
In this particular discipline of historical population genetics ancient DNA is the final judge, either for scientific models or educated guesses. In a decade or two we should collect so much ancient DNA to figure out all the where how and when they came, went and mixed. Whomever could predict the most, from scientific methods or just from exceptional logic, will be the king. In this field, people with vast knowledge of history and archeology will have huge advantage in connecting the dots.

Generally yes, but there always are these few geniuses who can see how it is. For the rest of us is the daily grind of methodology to figure out something. And even with right methodologies very often there is a lack of good brain power to pull out the right conclusions. Generally speaking of course as I'm not familiar with your work. Just putting things in perspective.

Ancient DNA is just one type of evidence. As with any evidence it needs to be used in conjunction with other types of evidence to draw conclusions. Hypotheses still need to be tested using the scientific method. Ancient DNA on its own will never provide the answers. Survival of ancient DNA is patchy. There are places in the world where the climate is not amenable to the survival of ancient DNA (eg, much of Africa). Researching past populations is a huge task and no individual can possibly acquire the necessary knowledge. That is why research is multidisciplinary. We need the population geneticists to do the ancient DNA analysis and the bioinformatics, the historians to put the results in context, and the archaeologists to gather the archaeological evidence. Research is generally more effective when experts from multiple disciplines collaborate.

Maciamo
15-12-16, 19:51
Genetic science is much more 'medical' and 'biological'. Without math genetic science is not viable. It is closely related to EXACT science than to social science.


Historical population genetics has practically nothing medical about it. And anyway, I studied biomedical sciences and I can tell you that maths only play a small part in biology and medicine. And when there is maths, it's mostly about calculating risk factors, probabilities and statistical analysis. Nothing very complex.

Goga
15-12-16, 20:38
Historical population genetics has practically nothing medical about it. And anyway, I studied biomedical sciences and I can tell you that maths only play a small part in biology and medicine. And when there is maths, it's mostly about calculating risk factors, probabilities and statistical analysis. Nothing very complex.
What do you mean? DNA is part of our body, it's everywhere. It has to be 'medical'. I don't know anything about this field, but when I think about biomedical science I think immediately about chemistry and chemistry is exact science. To know what your Y-DNA or auDNA is you need chemistry. And chemistry = EXACT science.

Biology is not only what we see, tangtible observation, like human body, bacteria/viruses, flora & founa, but also BEHAVIOR. There is a substream within the economics which we call environmental economy. To understand the behavior of humans we need to study the behavior of animal, fish and birds. Like, about their population balances etc.

In political science behavionarism is also very important. Behavionarism is part of sociologiy and human psychology, but even that field NEEDS statitics for their theories. So, behavionarism can be explained by sociology (history) and economy. And the most scientific way to explain behavionarism is with inferential statistics.

Like I said, I studied also political science. History was part of my edcuation, since we try to study the origin of political theories and paradigms. Most of the times history repeats itself, so you could also use inferential statistics (+economic, environmental and ecological models) if you try to explain history.

So, math (Pi (π) ) is everywhere. Patterns are everywhere, in economy, history, sociology etc. What we need is to find, observe and analyse those patterns. Therefore we need descriptive & inferential statistics.


Every genius in history from Aristotle to Tesla used statistics. Without statistics it is impossible to call yourself a scientist and to be successful..

Maciamo
15-12-16, 20:41
Population geneticists do not study haplogroups per se. The Y-chromosome represents only two per cent of our DNA and, because only males have a Y-chromosome, it only represents half of the human population. mtDNA is a tiny molecule of just 16569 base pairs, and provides a very limited view of our ancestry because it only follows the all-female line. While Y-DNA and mtDNA are very useful for genetic genealogy and can be used very effectively within a genealogical timeframe they are less useful for exploring the history of populations. That is why research now focuses on autosomal DNA which is so much more informative.

I frankly don't understand why you would feel the need to remind me of these things. I did mention in my reply to you above (post #22) that I studied biomedical sciences, including genetics, while you don't seem to have a scientific background (based on your LinkedIn profile). All the things you mention are very, very basic, and I even wrote a page a few years ago with those fundamental concepts of genetics (http://www.eupedia.com/genetics/human_genome_and_genetics.shtml) so that I didn't have to re-explain everything to non-biologists on the forum.

It's the second time in this thread that you tell me that mtDNA has 16569 base pairs, even when after the first time I explained that not only I knew it, but I was one of the few people on this planet who had analysed all the mutations in mitochondrial DNA and that I had identified a pattern of mutations in the Coenzyme Q - cytochrome c reductase gene (MT-CYB) (http://www.eupedia.com/genetics/coenzyme_q_mutations_define_major_mtdna_haplogroup s.shtml) defining successful mtDNA lineages and argued that this was the result of natural selection and environmental adaptations. To the best of my knowledge no other geneticist did such a thorough analysis of gene function alterations in mitochondrial haplogroups.

Still in my reply to you in post #22, which you obviously haven't read properly, I explained how I thought that mtDNA was of little use for tracing ancestry other than distant prehistoric one, justly because of the low resolution that mtDNA offers. Here is what I wrote:

As for mtDNA, I have explained for years that it is practically useless for tracing ancestry for at least the last 4000 or 5000 years. At best mtDNA can distinguish between Mesolithic European, Neolithic Near Eastern farmers and Steppe Indo-Europeans, but not anything more since these populations mixed, as mtDNA evolves very slowly and on a 16,569 bases long sequence any mutation can quickly become hazardous for health.

This is something I have been explaining for at least 7 years on this website (one of the largest for historical population genetics), for longer than you have worked in genetic genealogy. So why are you telling me this in a tone that implies that you know better than me or that I surely need to be reminded of the 101 of historical population genetics? At least I had the decency to check your blog and the UCL pages about the BritainsDNA controversy that you mentioned before replying to you. You apparently did not read anything I posted in link, or anything I wrote in the Genetics section (http://www.eupedia.com/genetics/) of this website (in case you are wondering which articles I wrote, that's all of it). You reply to me as if you had superior knowledge and I was just an amateur, which is ironic considering the extent of your knowledge or your background.



It’s always encouraging to see people coming up with new ideas but any new methods have to be tested to see if they work. You have formulated a hypothesis that Y-DNA and mtDNA haplogroups travel in tandem but how have you tested this hypothesis?

I am yet to see a theoretical or mathematical model in historical population genetics that has achieved any useful prediction. The only way to confirm predictions in this field is to test lots of ancient DNA samples. That's the bottom line. You keep repeating that we won't be able to test samples from every period and every country, but it isn't any more necessary than to test every single individual alive today to know the frequency of haplogroups (or of an allele in a gene, for medical researchers) in a country or region. We will never have perfect knowledge of everything. Even if governments made full genome sequencing compulsory for everyone, with the hundreds of thousands of people who are born and die in the world every day we would need to update frequencies in real time. Not only is that not realistic in our age and time, but it would be quite impractical to manipulate the data, if it keeps changing every millisecond. At the moment, in the field of population genetics, we have to work with the limited amount of samples that is available. Some countries are better sampled and more representative. Others have practically no data. Ancient DNA tests are brand new. The first ancient Y-DNA and autosomal DNA were published only four years ago. But the amount of results is increasing fast and we can expect thousands of ancient samples in the next few years. Eventually we will reach a point when any past theories and predictions about the origins and diffusions of haplogroups and specific prehistoric populations can be verified with a high degree of confidence, one that could very well be higher than the allele frequency databases we have today for modern populations.

If you had read my posts #36 and #37, you'd understand that the scientific method cannot validate any model in a field like historical population genetics, because that field is essentially history (a social science) and genetics is only there to provide data to confirm theories and hypothesis based on archaeological or linguistic evidence. I am a scientist by formation, but I am not going to pretend that there is a way to reduce history to a testable statistical model! That's ludicrous.

Maciamo
15-12-16, 20:59
What do you mean? DNA is part of our body, it's everywhere. It has to be 'medical'. I don't know anything about this field, but if i think about biomedical science I think immediately about chemistryand chemistry is exact science. TO know what your Y-DNA or auDNA is you need chemistry.And chemistry = EXACT science

The DNA itself is exact science. The DNA tests are more or less exact science, because sequencers are not perfect and can misread genetic sequences. That's why good DNA testing companies perform many sequencing (or actually genotyping for most commercial companies) runs, to minimise the number of errors. Sorry to disappoint you, but it's possible that some allele values in your 23andMe test aren't correct. There are surely very few of them, but it's not 100% guaranteed accurate.

Many lay people think that medicine is an exact science, but it is far from being the case. We are only starting to enter (slowly) into the age of precision medicine thanks to DNA tests, not just for our genome, but for the microbiome (bacteria, fungi and viruses) within us and around us. In a near future it should become possible for doctors (and patients) to test almost instantly what kind of pathogen they harbour. That's a huge improvement on how medicine is performed now, which is nothing more than guesswork based on the patient's symptoms. It's recently become possible (and encouraged) to test mutations in cancerous cells so as to be able to determine which treatment could work better. But be it for viruses, bacteria or cancer, treatments are still very random. Not everybody reacts the same way to the same treatment. And microbes can mutate quickly and become resistant today to drugs that worked yesterday. The way new drugs are developed today is also pretty much based on luck, guesswork and a long series of experiments (first on lab animals, then on humans in clinical trials). That's not what I call 'exact science'. In a few decades we will look back in disgust on 20th century and early 21st century medicine as something not much more evolved than witchcraft. Fortunately, that's about to change soon, and it is already changing fast when it comes to cancer treatment thanks to advances in immunotherapy and gene therapy, which is much closer to exact science. But don't ever think that your local GP practices exact science. ;-)

Goga
15-12-16, 21:06
I don't understand what you are talking about. My background is political science. Like I wrote in my previous post, political science is part of the social science. Scientists with the social science background (sociology, politicology, psychology and EVEN history) have to use descriptive & inferential statistics all the time. Otherwise their studies and theories would never be considered 'scientific'/academic. Social science tries to explain the behavior of humans, political actors, interaction of societies on different levels. To explain behavionarism and explain different (historical) paradigms you have to use statistics.

History doesn't mean only field research or just read a historical book or something like that. It is to UNDERSTAND the history and make future 'predictions'. I know people who studied just history and they are using statistics all the time, since history repeats itself and since there are many patterns in human behavior truth history. That's how you can 'predict' the downfall of dictators (political entities/actors), since there is a correlation (patterns) in their behavior. That's why (and how) you can predict the downfall of let say Turkey.


I don't understand what you are trying to prove. You are 'tilting at windmills'...

Maciamo
15-12-16, 23:23
I don't understand what you are talking about. My background is political science. Like I wrote in my previous post, political science is part of the social science. Scientists with the social science background (sociology, politicology, psychology and EVEN history) have to use descriptive & inferential statistics all the time. Otherwise their studies and theories would never be considered 'scientific'/academic. Social science tries to explain the behavior of humans, political actors, interaction of societies on different levels. To explain behavionarism and explain different (historical) paradigms you have to use statistics.

History doesn't mean only field research or just read a historical book or something like that. It is to UNDERSTAND the history and make future 'predictions'. I know people who studied just history and they are using statistics all the time, since history repeats itself and since there are many patterns in human behavior truth history. That's how you can 'predict' the downfall of dictators (political entities/actors), since there is a correlation (patterns) in their behavior. That's why (and how) you can predict the downfall of let say Turkey.


I don't understand what you are trying to prove. You are 'tilting at windmills'...

You must be kidding, right? There is no serious maths in social sciences. Using statistics, making statistics, making predictions, calculating probabilities and stuff like that aren't real maths. That's the kind of things everybody does. I consider that if something is not harder than university entrance level, then it's not worth mentioning it. I have compiled the statistics table for the haplogroups on this sites, which underlie all my research and my articles and were used to make my haplogroup frequency maps. But I would never say that this is mathematics. If I go to the supermarket and add up mentally the price for all the items in the basket, I am not turning into a mathematician. That's something everybody does. When I translate my articles into French or Italian, I don't consider myself a translator, because that's not my job or my field of research or interest. That's just something I have to do. I made all the web design of this site but you never see me call myself a web designer. I can replace a light fixture or fix a leaky pipe under a sink in my house, but that doesn't make of me an electrician or a plumber. The maths used in social sciences is so basic compared to those used in physics or artificial intelligence that it falls into the same 'everyday use' category. And by the way, I also studied economics and I know that theoretical models in social sciences are far from accurate and sometimes dangerously wrong.

My disagreement with Mark and Debbie above comes mainly from the fact that they seem to believe that it is possible to make useful predictions about historical population migrations solely based on theoretical models, completely disregarding all the other fields I have cited in this discussion. You can predict the trajectory of a comet using theoretical models and maths, but you simply can't do it for haplogroup migrations. I have never seen it work, and I can't imagine how it could possibly work. But I remain open to a demonstration. We seem to hold two completely opposite positions:

- I favour a transdisciplinary approach using logic, statistics and analysis of all evidence from every discipline to maximise our understanding of human population history. I favour hard facts over abstract theoretical models. From my point of view, each large migratory event in history (e.g. Neolithic expansion from the near East) is unique and should be used very carefully to extrapolate on other migrations in different ages, cultures and environments (because humans are not just numbers and their behaviour and success is by nature unpredictable).

- They insist that the only valid and recognised methods in population genetics is based on theoretical models that can be mathematically tested. They believe that once we have found a model that works, it can be applied in any population, like the immutable laws of physics. From their standpoint, my methodology is useless because it is case by case and cannot be tested and re-used (which would be understandable if we were working on exact sciences, but we aren't).


I also believe that there are too many unknown factors even for simple mathematical models to be accurate in that field. For example, the age or TMRCA of haplogroups can be calculated from the accumulated mutations, each tempered by the statistical chance of a mutation occurring at that position in the DNA sequence (since mutations are known to happen more frequently in some places than others). But that doesn't take into account the historical population size (http://www.eupedia.com/forum/threads/25644-Why-it-is-wrong-to-assume-that-a-haplogroup-originated-where-it-is-most-frequent-now) at each point in the phylogenetic tree, nor the local radioactivity, which increase the chances of mutation happening. A major difference in population size between two branches of a same haplogroup, for example between Siberian R1a (low population) and Indian R1a (high population) can lead to a number of accumulated mutations hundreds or thousands of times superior in the Indian group over the same period of time. Without knowing exactly where a subclade evolved and what kind of population size it had during this development, calculations are doomed to be mistaken, especially in region with unusually high or low population densities or growth.

In other words, I blame them for having a too simplistic mathematical approach that cannot possibly taken into account all these factors. There has actually been quite a few population geneticists claiming that haplogroup R1a originated in India because genetic diversity was higher there, not realising that this diversity was the result of extremely high historical population size since the Bronze Age. This is what Sharma et al. (2009) (http://www.nature.com/jhg/journal/v54/n1/full/jhg20082a.html) claimed, and their study was not only published in a peer reviewed journal, but the most prestigious of them all, Nature. So much for the peer review system filtering out the pseudoscience. That 'peer' word doesn't mean anything. Having graduated in a scientific subject is not a proof of intelligence, critical sense or discernment. In fact the average IQ of university graduates is quite low; 115 to 130 in the US according to this site (http://www.statisticbrain.com/iq-estimates-by-intended-college-major/). Most wouldn't even make it to Mensa.

LeBrok
16-12-16, 00:05
- I favour a transdisciplinary approach using logic, statistics and analysis of all evidence from every discipline to maximise our understanding of human population history. I favour hard facts over abstract theoretical models. From my point of view, each large migratory event in history (e.g. Neolithic expansion from the near East) is unique and should be used very carefully to extrapolate on other migrations in different ages, cultures and environments (because humans are not just numbers and their behaviour and success is by nature unpredictable).

- They insist that the only valid and recognised methods in population genetics is based on theoretical models that can be mathematically tested. They believe that once we have found a model that works, it can be applied in any population, like the immutable laws of physics. From their standpoint, my methodology is useless because it is case by case and cannot be tested and re-used (which would be understandable if we were working on exact sciences, but we aren't). It is a good description how we all model population history in your brain. We come up with hypothesis, run many models and come up with predictions. Generally not much different than running predictive models in a computer. The difference is that so far good human brain is much better in it, because it analyzes data sets in much broader environment, among others human behavior, religion or climate change.




I also believe that there are too many unknown factors even for simple mathematical models to be accurate in that field. For example, the age or TMRCA of haplogroups can be calculated from the accumulated mutations, each tempered by the statistical chance of a mutation occurring at that position in the DNA sequence (since mutations are known to happen more frequently in some places than others). But that doesn't take into account the historical population size (http://www.eupedia.com/forum/threads/25644-Why-it-is-wrong-to-assume-that-a-haplogroup-originated-where-it-is-most-frequent-now) at each point in the phylogenetic tree, nor the local radioactivity, which increase the chances of mutation happening. A major difference in population size between two branches of a same haplogroup, for example between Siberian R1a (low population) and Indian R1a (high population) can lead to a number of accumulated mutations hundreds or thousands of times superior in the Indian group over the same period of time. Without knowing exactly where a subclade evolved and what kind of population size it had during this development, calculations are doomed to be mistaken, especially in region with unusually high or low population densities or growth.Exactly, and in addition to my previous point. As you mentioned, the complexity of environment is enormes, and it will take a very long time to develop adequate and sophisticated enough computer models to take this huge complexity of human environment under consideration.

Goga
16-12-16, 00:18
You must be kidding, right? There is no serious maths in social sciences. Using statistics, making statistics, making predictions, calculating probabilities and stuff like that aren't real maths. That's the kind of things everybody does. I consider that if something is not harder than university entrance level, then it's not worth mentioning it. I have compiled the statistics table for the haplogroups on this sites, which underlie all my research and my articles and were used to make my haplogroup frequency maps. But I would never say that this is mathematics. If I go to the supermarket and add up mentally the price for all the items in the basket, I am not turning into a mathematician. That's something everybody does. When I translate my articles into French or Italian, I don't consider myself a translator, because that's not my job or my field of research or interest. That's just something I have to do. I made all the web design of this site but you never see me call myself a web designer. I can replace a light fixture or fix a leaky pipe under a sink in my house, but that doesn't make of me an electrician or a plumber. The maths used in social sciences is so basic compared to those used in physics or artificial intelligence that it falls into the same 'everyday use' category. And by the way, I also studied economics and I know that theoretical models in social sciences are far from accurate and sometimes dangerously wrong....

...
In other words, I blame them for having a too simplistic mathematical approach that cannot possibly taken into account all these factors. ...

Social science is to broad. Let's take history. I am making it more difficult for me since history is less mathematical than sociology or psychology that makes use of statistics for their theories. They make use of probilities and empirical studies mostly for predicitions. (like very simple statistical null hypothesis testing)


But now let's talk about history and more heavy models.


If you want to measure some population growth within an area truth history you need some kind of environmental population models.

If you want to know how much money French Revolution costed the French society, you need to use some economical models. If you want to know how much money Dutch goverment earned from it's colonies in SouthEast Asia during the Dutch Golden Age you need some heavy models.

How much money did WW1 cost the Germans? For how many years did the development in Europe stopped due to the The Black Death? For all this questions you need different mathematical models.


Scientists are making mistakes all the time(, it is part of a process). But that's because they are using wrong or too simplistic social research methods. But that doesn't mean that using a method is wrong. In contratry in sciense you have to use the models to support your theories. The ART of science is to find the right methology. And that is very difficult. For every problem there has to be a model. Great scienctists can find this model and use it properly, while weak scientists have hard times to find a propriate model or don't know how to use it efficiently..

Maciamo
16-12-16, 00:20
It is a good description how we all model population history in your brain. We come up with hypothesis, run many models and come up with predictions. Generally not much different than running predictive models in a computer. The difference is that so far good human brain is much better in it, because it analyzes data sets in much broader environment, among others human behavior, religion or climate change.

Not to mention that it would take forever to encode all those variables into a computer.



Exactly, and in addition to my previous point. As you mentioned, the complexity of environment is enormes, and it will take a very long time to develop adequate and sophisticated enough computer models to take this huge complexity of human environment under consideration.

It will be much easier and faster once computers/robots will learn to adapt models, measure, gather and encode the data on their own. But at that point humans won't have anything left to do. That should be some time during the 2040's.

Maciamo
16-12-16, 00:39
Social science is to broad. Let's take history. I ammacking it more difficult for me since history is less mathematical thansociology or psychology that makes use of statistics for their theories. Theymake use of probilities and empirical studies mostly for predicitions. (like very simple statistical null hypothesis testing)

But now let talk about history and heavy models.


If you want to measure some population growth withinan area truth history you need some kind of environmental population models.


If you want to know how much money French Revolutioncosted the French society, you need to use some economical models. If you want to know how much money Dutch govermentearned from it's colonies in SouthEast Asia during the Dutch Golden Age youneed some heavy models.


How much money did WW1 cost the Germans? For how manyyears did the development in Europe stopped due to the The Black Death? For allthis questions you need different mathematical models.


Scientists are making mistakes all the time. But that's because they are using wrong or too simplistic social research methods. But that doesn't mean that using a method is wrong. In contratry in sciense you have to use the models to support your theories. The ART of science is to find the right methology. And that is very difficult. For every problem there has to be a model. Great scienctists can find this model and use it properly, while weak scientists have hard times to find a propriate models or don't know how to use it efficently..

In none of these examples can any mathematical model make any useful estimate. There are so many unknown factors and variables that all you'll get is a very, very rough estimate, and often one that is very far from the truth. It is dangerous because people who don't really understand how these calculations are made (most ordinary people) tend to believe the numbers they are fed because it 'looks scientific', even though it's rubbish.

Goga
16-12-16, 08:26
In none of these examples can any mathematical model make any useful estimate. There are so many unknown factors and variables that all you'll get is a very, very rough estimate, and often one that is very far from the truth. It is dangerous because people who don't really understand how these calculations are made (most ordinary people) tend to believe the numbers they are fed because it 'looks scientific', even though it's rubbish.It was just a quick example. Maybe those questions are to broad and need to be rephrased, but I hope that you do understand where I was heading toward. Sometimes you also have to measure correlation (effect or dependence) between let say two historical events, or between events and actors (subject/object) during a given period. Some statistical coefficients are very simple to determine, but sometimes much more work needs to be done to find correlation coefficients.

No, history is not exactly rocket science and according to some folks history is not even science at all because many times it is subsidiary on personal interpretation. But I do believe that history is part of the social science since there are many patterns in it and since I believe that every 'right' question within this discipline can be approached by a statistical model. Historians research & analyze their sources.

more analitical/statistical approach means more scientific process

If my explanation is wrong and you still don't understand me, maybe this is more helpful:


"4. Historians, local historians and statistical analysis" : http://humanities.uwe.ac.uk/bhr/Main/analysis/4-Statistical%20_analysis.htm
"why historians started counting" : http://historymatters.gmu.edu/mse/numbers/why.html
"Quantitative Methods for Historians (https://www.google.nl/url?sa=t&rct=j&q=&esrc=s&source=web&cd=11&cad=rja&uact=8&ved=0ahUKEwih69i9h_jQAhUH7BQKHUePB7I4ChAWCBowAA&url=https%3A%2F%2Fbooks.google.com%2Fbooks%2Fabout %2FQuantitative_Methods_for_Historians.html%3Fid%3 DJadX1sfwssQC&usg=AFQjCNFccQbM6o2d_A7wtyd2gJZg0yPrDw&sig2=jh5B_wYev4BR_pbKXsyc6w&bvm=bv.141536425,d.d24)" : https://books.google.nl/books/about/Quantitative_Methods_for_Historians.html?id=JadX1s fwssQC&redir_esc=y
"QUANTITATIVE SKILLS FOR HISTORIANS" : https://www.heacademy.ac.uk/system/files/rg_freeman_quantitativeskills_20100131_01.pdf

Dorianfinder
16-12-16, 09:14
Interesting discussion, if I may.

In the humanities or social sciences, research methodology is often viewed as 'soft' (as opposed to hard) science due to a lack of quantifiable data. The majority of papers are qualitative and therefore based on phenomenological and textual analysis.

An important determinant in attempting to acquire 'truth' in a historical context is to determine whether one subscribes to a universal or relativistic truth.

Quantitative analyses as in the field of Mathematics most often provide objective measures for universal 'truth' objectifying and deconstructing constituent variables in meaningful ways. This is the basis of statistical analysis.

However, in qualitative research we are left with subjective meaning units, textual analysis and phenomenological understanding unique to the individual providing the experience/data. In this case one would follow a relativistic 'truth' approach and attempt to extract universal meaning units only if corroborated by quantitative data. This however is contentious as memory has been shown to be neither consistent nor factual.

When we use terms such as 'likelihood' or 'probability' we are using inference to determine a plausible outcome. This is predictive and based on a static contextual environment. Most research questions are based on inference to begin with, the aim being to confirm or deny the hypothesis under review.

bicicleur
16-12-16, 09:43
Interesting discussion, if I may.

In the humanities or social sciences, research methodology is often viewed as 'soft' (as opposed to hard) science due to a lack of quantifiable data. The majority of papers are qualitative and therefore based on phenomenological and textual analysis.

An important determinant in attempting to acquire 'truth' in a historical context is to determine whether one subscribes to a universal or relativistic truth.

Quantitative analyses as in the field of Mathematics most often provide objective measures for universal 'truth' objectifying and deconstructing constituent variables in meaningful ways. This is the basis of statistical analysis.

However, in qualitative research we are left with subjective meaning units, textual analysis and phenomenological understanding unique to the individual providing the experience/data. In this case one would follow a relativistic 'truth' approach and attempt to extract universal meaning units only if corroborated by quantitative data. This however is contentious as memory has been shown to be neither consistent nor factual.

When we use terms such as 'likelihood' or 'probability' we are using inference to determine a plausible outcome. This is predictive and based on a static contextual environment. Most research questions are based on inference to begin with, the aim being to confirm or deny the hypothesis under review.

It is obvious how many times archeologists rewrote prehistory in the last 100 years.

I'm very sceptical about many 'social' studies. I think the science of human psychology will be rewritten many times the next few decades.

Maciamo
16-12-16, 11:37
It was just a quick example. Maybe those questions are to broad and need to be rephrased, but I hope that you do understand where I was heading toward. Sometimes you also have to measure correlation (effect or dependence) between let say two historical events, or between events and actors (subject/object) during a given period. Some statistical coefficients are very simple to determine, but sometimes much more work needs to be done to find correlation coefficients.

No, history is not exactly rocket science and according to some folks history is not even science at all because many times it is subsidiary on personal interpretation. But I do believe that history is part of the social science since there are many patterns in it and since I believe that every 'right' question within this discipline can be approached by a statistical model. Historians research & analyze their sources.

more analitical/statistical approach means more scientific process

If my explanation is wrong and you still don't understand me, maybe this is more helpful:


"4. Historians, local historians and statistical analysis" : http://humanities.uwe.ac.uk/bhr/Main/analysis/4-Statistical%20_analysis.htm
"why historians started counting" : http://historymatters.gmu.edu/mse/numbers/why.html
"Quantitative Methods for Historians (https://www.google.nl/url?sa=t&rct=j&q=&esrc=s&source=web&cd=11&cad=rja&uact=8&ved=0ahUKEwih69i9h_jQAhUH7BQKHUePB7I4ChAWCBowAA&url=https%3A%2F%2Fbooks.google.com%2Fbooks%2Fabout %2FQuantitative_Methods_for_Historians.html%3Fid%3 DJadX1sfwssQC&usg=AFQjCNFccQbM6o2d_A7wtyd2gJZg0yPrDw&sig2=jh5B_wYev4BR_pbKXsyc6w&bvm=bv.141536425,d.d24)" : https://books.google.nl/books/about/Quantitative_Methods_for_Historians.html?id=JadX1s fwssQC&redir_esc=y
"QUANTITATIVE SKILLS FOR HISTORIANS" : https://www.heacademy.ac.uk/system/files/rg_freeman_quantitativeskills_20100131_01.pdf

If I understand well what you are trying to say is that an analytical/statistical approach makes social sciences more scientific? We were talking about the utility of mathematics in social sciences, so I am a bit perplexed by this change of direction since I don't consider data analysis or statistics, nor even statistical analysis to be the prerogative or mathematicians, not any more than the use of language is the prerogative or linguists or philologists. Analytical skills are a prerequisite for all intellectual subjects, and I would go as far as to say that it is indispensable for most aspects of everyday life as well. But then I am surely a far more analytical person than most, and indeed it has happened that people I just met ask me if I am a psychologist or a data analyst because of my tendency to analyse everything around me, including people.

Statistics is just the organisation of data. Analysis is the way the brain process data. Rational thinking wouldn't exist without it. Neither of them is a branch of mathematics in itself, although both are used extensively in mathematics (as in many of subjects). We also use reason, critical thinking, reading and writing in maths, but they aren't branches of mathematics either. That's why I am not really grasping what you are trying to prove. That social sciences are rational endeavours making use of the prefrontal cortex of one's dominant hemisphere? Way to state the obvious.

Nowadays even primary school kids make graphs and pie charts on computers. You can call it 'quantitative skills' if it you prefer the sound of it and it makes it look more professional or important. It's very popular nowadays to try to enhance the image of one's activity using nicer sounding terms, so that a secretary becomes an 'executive assistant' and a cleaner becomes a 'domestic engineer'. That doesn't change their qualifications or job function. It's purely aesthetic (and hypocritical). It's the same with the quantitative skills to describe the use of graphs and statistics in social sciences. That doesn't make it advanced mathematics (i.e. beyond calculus, trigonometry and linear algebra that all secondary schoolers have to learn in order to graduate, at least here in Belgium where there are no elective A-level subjects and everyone must study maths to that minimum level).

Personally I don't care much for linguistic embellissements that make people look and feel more important or intelligent. Many academics who don't have much to say try to hide their incompetence behind flowery jargon. What matters to me is the content, perspicacity and validity of one's arguments, not how many big words one can fill into a sentence. As C.W. Ceran said “Genius is the ability to reduce the complicated to the simple.” This is especially true on a public forum like this one where where one writes for all kinds of people from different backgrounds and with different mother tongues. A good academic or teacher/professor, in my opinion, is someone who can recognise the complexity of one subject, see through that complexity, and re-explain it concisely and clearly for everyone else to understand. As Albert Einstein said (as I am in a quoty mood) “If you can't explain it to a six year old, you don't understand it yourself.” That's why I write my articles about historical population genetics "as simple as possible, but not simpler" (once again getting inspiration from my adolescence idol, Einstein). I think that that approach should be a prerequisite for teaching any subject.

firetown
19-12-16, 11:49
Maciamo

I don’t have time right now to get involved in a lengthy discussion so I’m only responding to a few comments very briefly.

As regards cousin matching, everyone has different reasons for testing. I am more interested in using DNA testing to verify my genealogical research.

I’m somewhat confused about your reference to “historical population geneticists”. Historians specialise in history and population geneticists specialise in population genetics. Ideally we should leave the historians to study history and let the population geneticists analyse the getetic data.
And then what? Wait for a reporter to interpret the two and come up with a silly "conclusion" for the sake of good headlines?
This comment screams indifference.
So I just have to give you the benefit of the doubt that had you had more time on your hands, you would have re-read what you have written and not published that part.

DebbieK
23-12-16, 02:30
And then what? Wait for a reporter to interpret the two and come up with a silly "conclusion" for the sake of good headlines?
This comment screams indifference.
So I just have to give you the benefit of the doubt that had you had more time on your hands, you would have re-read what you have written and not published that part.

I'm afraid I don’t understand your comment. Journalists aren't historians or population geneticists. A reporter’s job is to report on research and not to come up with his or own interpretation of the data. A good science journalist would seek out experts in the field and ask for their comments though sadly this rarely happens.

Coriolan
23-12-16, 08:15
I'm afraid I don’t understand your comment. Journalists aren't historians or population geneticists. A reporter’s job is to report on research and not to come up with his or own interpretation of the data. A good science journalist would seek out experts in the field and ask for their comments though sadly this rarely happens.
If we speak the same English that's exactly what Mike was saying. Journalists have no particular competence to write about history or genetics. If we follow your suggestion that only geneticists should write about genetics and historians about history, who should write about the genetic history of populations? Journalists have a large audience but little expertise in complex fields like this. That's why if no academic has the expertise to combine both history and genetics journalists will interpret the data themselves to write their stories and the result isn't going to be pretty. That causes misinformation on a grand scale for the public. I quite like Maciamo's initiative to combine the two fields into a new field of historical genetics. Perhaps it's time that universities start teaching it. In the mean time I think that Maciamo is doing a fine job in explaining the history of populations using genetic data and you should recognise that.

DebbieK
23-12-16, 20:39
If we speak the same English that's exactly what Mike was saying. Journalists have no particular competence to write about history or genetics. If we follow your suggestion that only geneticists should write about genetics and historians about history, who should write about the genetic history of populations? Journalists have a large audience but little expertise in complex fields like this. That's why if no academic has the expertise to combine both history and genetics journalists will interpret the data themselves to write their stories and the result isn't going to be pretty. That causes misinformation on a grand scale for the public.

We need historians, archaeologists, linguistics, geneticists and academics from other related disciplines to work together to write about these complex topics and this is in fact already happening. Projects are increasingly multidisciplinary. No single individual can possibly be an expert on every subject. Journalists are not academic researchers. The misinformation arises when journalists don't filter out the pseudoscience which was the subject of the Buzzfeed story that started this thread.

DebbieK
26-12-16, 15:25
The Eurogenes blog has alerted us to this excellent new article by Patrick J. Geary and Krishna Veeramah which is very relevant to this discussion. The article summarises the problems of using modern DNA (and especially Y-DNA and mtDNA) to investigate past population histories. The article also stresses the importance of including historians and archaeologists as "integral participants in the planning, collection, and evaluation of data": http://eurogenes.blogspot.co.uk/2016/12/do-it-right-or-dont-do-it-at-all.html

LeBrok
26-12-16, 18:52
The Eurogenes blog has alerted us to this excellent new article by Patrick J. Geary and Krishna Veeramah which is very relevant to this discussion. The article summarises the problems of using modern DNA (and especially Y-DNA and mtDNA) to investigate past population histories. The article also stresses the importance of including historians and archaeologists as "integral participants in the planning, collection, and evaluation of data": http://eurogenes.blogspot.co.uk/2016/12/do-it-right-or-dont-do-it-at-all.html
Thanks Debbie for sharing.