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Thread: DNA testing companies under attack

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    DNA testing companies under attack

    On GPS origins, see:
    http://cruwys.blogspot.co.uk/2016/11...test-four.html

    On BritainsDna, see:
    https://www.buzzfeed.com/tomchivers/...q5#.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!


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    2 members found this post helpful.
    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

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    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 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.
    Last edited by Maciamo; 06-12-16 at 00:14.
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    2 members found this post helpful.
    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.

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    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".

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    1 members found this post helpful.
    Quote Originally Posted by Tomenable View Post
    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. 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), 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.

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    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.

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    Quote Originally Posted by Angela View Post
    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.

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    Quote Originally Posted by DebbieK View Post
    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, 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.

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    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.

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    2 members found this post helpful.
    Quote Originally Posted by DebbieK View Post
    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. 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 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 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, 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.

    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, 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). 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.
    Last edited by Maciamo; 07-12-16 at 20:04.

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    Over confidence

    Quote Originally Posted by Maciamo View Post
    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.



    Quote Originally Posted by Maciamo View Post
    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.

    Quote Originally Posted by Maciamo View Post
    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).

    Quote Originally Posted by Maciamo View Post
    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?

    Quote Originally Posted by Maciamo View Post
    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.



    Quote Originally Posted by Maciamo View Post
    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.

    Quote Originally Posted by Maciamo View Post
    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.

    Quote Originally Posted by Maciamo View Post
    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?

    Quote Originally Posted by Maciamo View Post
    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.


    Quote Originally Posted by Maciamo View Post
    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?

    Quote Originally Posted by Maciamo View Post
    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).

    Quote Originally Posted by Maciamo View Post
    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?

    Quote Originally Posted by Maciamo View Post
    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.


    Quote Originally Posted by Maciamo View Post
    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?

    Quote Originally Posted by Maciamo View Post
    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.

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    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.

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    1 members found this post helpful.
    Thanks for your reply, Mark Thomas (I presume, from the content of your reply).

    Quote Originally Posted by Empty_Genes View Post
    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. 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, 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, 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, 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 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). 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.
    Last edited by Maciamo; 08-12-16 at 17:28.

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    1 members found this post helpful.
    Thanks again for your input, Debbie.

    Quote Originally Posted by DebbieK View Post
    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) 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). 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.

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    Mark and Debbie, I had a look at your Debunking Genetic Astrology on the UCL website, including the news stories. 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, 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, 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 and that Guardian article, 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).

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    @ 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?
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    Quote Originally Posted by Sile View Post
    @ 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.

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    Quote Originally Posted by Maciamo View Post
    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

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    Quote Originally Posted by Empty_Genes View Post
    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.

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    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.
    Last edited by DebbieK; 10-12-16 at 13:37. Reason: typo

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    Thanks for your reply, Debbie.

    Quote Originally Posted by DebbieK View Post
    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.



    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.

    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 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? 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, 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.
    Last edited by Maciamo; 11-12-16 at 01:10.

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    likelood

    Quote Originally Posted by Maciamo View Post
    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?

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    Quote Originally Posted by Empty_Genes View Post
    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.

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    Quote Originally Posted by Maciamo View Post
    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'?

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