The DNA of the mesolithic hunter. Absent or present in northern European population?

[LeBrok]

No, what I was saying was that models will always be prone to error and that they cannot be validated. There may be periods that have rapid mutation, aka Ghould's punctuated equilibrium, and mutaion rates in the future will most certainly be in the hands of genetic engineers.

Certain random events are impossible to model.

The model works in realm of statistical probabilities. It means that it will predict most of mutations timing right. It doesn't mean that it will predict all of them correctly. It is not a perfect tool but it is the best we have, and it will be in use till someone invents more precise one, yet always based on probabilities.

 

[james stock]

The idea that Y-line mutation rates aren't too random to model is an assumption that we'd be validating, though. That's the point. If the model consistently predicts the age of ancient samples across time and place, then tada, we've validated. If it gets some groups wrong and others right, or systematically gets all groups wrong but in different ways, then that assumption is incorrect, and we'll need to adjust or train our model somehow to be able to cope with the apparent randomness. If it still doesn't work for other groups coming in, then we can assume that it is too random to model. But not before then.

You cannot validate a model. I tried to explain that to you with logic, but you don't seem to understand. Models work until they don't, and when they stop working (think economic models) the results can be devastating.

The model works in realm of statistical probabilities. It means that it will predict most of mutations timing right. It doesn't mean that it will predict all of them correctly. It is not a perfect tool but it is the best we have, and it will be in use till someone invents more precise one, yet always based on probabilities.

The most precise method is to sequence and date skeletons.

 

[LeBrok]

You cannot validate a model. I tried to explain that to you with logic, but you don't seem to understand. Models work until they don't, and when they stop working (think economic models) the results can be devastating.

What do you mean by stopped working? Do you mean recent economic hiccup?

The most precise method is to sequence and date skeletons.

If we can find all the skeletons with new haplogroup mutations at the time they occur it would be the best thing for dating. Do you know what are the odds of finding them?

 

[sparkey]

You cannot validate a model. I tried to explain that to you with logic, but you don't seem to understand. Models work until they don't, and when they stop working (think economic models) the results can be devastating.

I understand exactly what you're saying, you're just wrong. We're not talking about proving that models always work and always will work no matter how circumstances change. We're talking about normal model validation, where we compare predicted results to actual results, and chart the differences across different data sets.

 

[MOESAN]

But Otzi was far less related to north Europe. Even the farmers at Gokhem showed more relation to local hunter-gatherers.

Otzi was from the beginning of the metals era; and surely it was a "mix" of pre-neolithic and neolithic people and perhaps other ones! - all the way the relation between autosomals (approximative poolings) and mt DNA or Y-DNA IN AN UNIQUE INDIVIDUAL is of a very low confidence - as time was passing an history running on the populations got more and more mixed, even if not with the same average speed and so the previous statistical links between these three kinds of genes got looser and looser -

 

[MOESAN]

I don't know. Would it make a difference?

I'm trying to assimilate this new thread so I do just some remarks concerning my understanding of some points before doing more -
the female-male difference at some periods of possible new contacts between populations of different origins can have some importance: in history some rate of exchange of females between (new?) neighbouring populations seem checked - even after some generations of bipolar mixings some differences can remaind between two populations and the keeping on exchanges can yet send some differences between males and females "mean" autosomals...

 

[MOESAN]

Hi forum,

Recently genetic information from two mesolithic hunter-gatherer burials from La Brana in northern Spain has been published. I have read a number of articles about it and I am confused by the results. The main reason for my confusion lies in the fact that the la Brana skeleton seem related to northern Europe rather than the current day local Iberian population. The two carried mtDNA U5b2c1 which is not very abundant in current day Iberia - neither is any U5 - and the full sequence show relation to northern European population rather than local. The results are presented as evidence for a large population overhaul during the Neolithic transition in Iberia.

http://dienekes.blogspot.nl/2012/06/mesolithic-iberians-la-brana-arintero.html
http://eurogenes.blogspot.com.au/2013/12/brana-1-had-blue-eyes.html

Mesolithic and upper paleolithic mtDNA recovered until recently is mostly U4 and U5, and we do have quite a number of finds.

http://www.eupedia.com/europe/ancient_european_dna.shtml
http://www.ancestraljourneys.org/ancientdna.shtml


The autosomal genetic relation with northern Europe is all good and well were it that northern European population, which the la Brana autosomal DNA is clearly related to, would have carried lots U5. That is true for Finland, the Saami and the Baltic region - although in the latter U, U4 + U5 does not exceed the 21% - but it isn't true for most of the northwestern European culture, including Sweden, Denmark and Norway. There have been Farmers from the neolithic have been sequenced as well as hunter-gatherers from the Pitted Ware culture, found on Gotland. Mitochondrial DNA showed greet difference between the mainland Swedes and the hunter-gatherers, presented as evidence for.. you guessed it: a population overhaul in Sweden after the arrival of the neolithic.

http://ac.els-cdn.com/S096098220901...t=1387632483_de9e8b5f85e80f8936c82a48bacac689

However, autosomal DNA between the northerners with and those without a strong U5 presence hardly differs. Also, phenotypes are remarkably similar. And the autosomal admixture is mostly north European in both Finnish and Swedish samples. Even both the la Brana and the Gotland Pitted Ware samples show autosomical relation to Swedish and Saami rather than Saami.

"northern Europe" autosomals pooling is very rough and I think N-W differ from N-E - and we have few and scarce samples <> what kind of Finns? (Finland population is less homogenous (I don't say "pure", but homogenous- on its territory than roughly the all Scandinavian even if in Norway - Saami have chances to be a severely drifted population

 

[Idun]

I'm trying to assimilate this new thread so I do just some remarks concerning my understanding of some points before doing more -
the female-male difference at some periods of possible new contacts between populations of different origins can have some importance: in history some rate of exchange of females between (new?) neighbouring populations seem checked - even after some generations of bipolar mixings some differences can remaind between two populations and the keeping on exchanges can yet send some differences between males and females "mean" autosomals...

The exchange of females is found with Uralics, part of not marrying in the same clan and used also sealing an alliance and peace, I believe it dates back to the mammoth steppe.

U5 > East
H < West

Get the idea?

 

[MOESAN]

There are finds of Pitted Ware burials, that lived alongside farmers. They show the same amount of U as mesolithic hunter-gatherers.

thanks; but: what sample size? where and when? i'm interested -
we have a lot of parameters to take in account - some neolithicized population of W and N Europe showed phenotypically they were accultured ancient mesolithic populations poorly penetrated by true first farmers genes: it complicates the problem of classification

 

[Idun]

I will give you an interesting snippet, Finnish word for mother, Äiti, comes from Gothic Aithe.
Traditional Finnic word would be Emo.

 

[adamo]

I hope Elmo isn't traditionally Finnish as well or that would be pretty catastrophic if combined with emo.

 

[Angela]

Otzi was from the beginning of the metals era; and surely it was a "mix" of pre-neolithic and neolithic people and perhaps other ones! - all the way the relation between autosomals (approximative poolings) and mt DNA or Y-DNA IN AN UNIQUE INDIVIDUAL is of a very low confidence - as time was passing an history running on the populations got more and more mixed, even if not with the same average speed and so the previous statistical links between these three kinds of genes got looser and looser -

Your point about the relationship between autosomal DNA and uniparental markers in an un unique individual is often lost sight of, but it is extremely important in my view.

However, even when looking at populations, or breeding groups, I think it's becoming more and more clear that uniparental markers are volatile and we can see big changes without changes of a proportionate size in the autosomal composition, and I think differential mating patterns, especially in terms of yDNA, founder effect and subsequent drift, selection for different mtDNA and yDNA subclades in the face of a changed climatic or personal environment, and also, (which is not often explored) sheer random chance, can affect the frequency of these uniparental markers. To the last point, a study was done of Icelandic mtDNA covering 300 years. No new geneflow, and yet because of the differential pattern of "daughtering out", certain sub-clades became rare, and others dominant. If anyone is interested, I'll try to find the site, but I'm not making it up!

 

[Idun]

Your point about the relationship between autosomal DNA and uniparental markers in an un unique individual is often lost sight of, but it is extremely important in my view.

However, even when looking at populations, or breeding groups, I think it's becoming more and more clear that uniparental markers are volatile and we can see big changes without changes of a proportionate size in the autosomal composition, and I think differential mating patterns, especially in terms of yDNA, founder effect and subsequent drift, selection for different mtDNA and yDNA subclades in the face of a changed climatic or personal environment, and also, (which is not often explored) sheer random chance, can affect the frequency of these uniparental markers. To the last point, a study was done of Icelandic mtDNA covering 300 years. No new geneflow, and yet because of the differential pattern of "daughtering out", certain sub-clades became rare, and others dominant. If anyone is interested, I'll try to find the site, but I'm not making it up!

Im interested, please try. =)

 

[epoch]

The exchange of females is found with Uralics, part of not marrying in the same clan and used also sealing an alliance and peace, I believe it dates back to the mammoth steppe.

U5 > East
H < West

Get the idea?

I figured that too. Suppose France and the Benelux (the latter having a culture of which archeological evidence shows continuity from hunter-gathering to some form of farming, the Swifterband cuklture) were the home of a different mesolithic hunter-gatherer population, whose later lineages then provided H1 and H3 to Western Europa. The area was hardly tested. However, the first result from Luxembourg is, you guessed it, U5.

For H1 and H3 to be derived from hunter-gatherers we need a number of supporting results.

 

[epoch]

However, even when looking at populations, or breeding groups, I think it's becoming more and more clear that uniparental markers are volatile and we can see big changes without changes of a proportionate size in the autosomal composition, and I think differential mating patterns, especially in terms of yDNA, founder effect and subsequent drift, selection for different mtDNA and yDNA subclades in the face of a changed climatic or personal environment, and also, (which is not often explored) sheer random chance, can affect the frequency of these uniparental markers. To the last point, a study was done of Icelandic mtDNA covering 300 years. No new geneflow, and yet because of the differential pattern of "daughtering out", certain sub-clades became rare, and others dominant. If anyone is interested, I'll try to find the site, but I'm not making it up!

I thinks this answers my initial question. However, U5 and U4 declined *everywhere* - apart from the fringes - in the area where the latest study shows large Western Hunter Gatherer admixture. It gets stranger and stranger.

http://eurogenes.blogspot.nl/2013/12/ancient-human-genomes-suggest-three.html

 

[epoch]

thanks; but: what sample size? where and when? i'm interested -
we have a lot of parameters to take in account - some neolithicized population of W and N Europe showed phenotypically they were accultured ancient mesolithic populations poorly penetrated by true first farmers genes: it complicates the problem of classification

It's this study:

http://ac.els-cdn.com/S096098220901...t=1387632483_de9e8b5f85e80f8936c82a48bacac689

Pitted Ware Culture living in Gotland, compared to Gokhem Bell Beaker farmers.

 

[epoch]

I'm trying to assimilate this new thread so I do just some remarks concerning my understanding of some points before doing more -
the female-male difference at some periods of possible new contacts between populations of different origins can have some importance: in history some rate of exchange of females between (new?) neighbouring populations seem checked - even after some generations of bipolar mixings some differences can remaind between two populations and the keeping on exchanges can yet send some differences between males and females "mean" autosomals...

Yeah. There always is the possibility that men brought the autosomal part in. Say, hired as warrior and rewarded with local women?

 

[MOESAN]

Your point about the relationship between autosomal DNA and uniparental markers in an un unique individual is often lost sight of, but it is extremely important in my view.

However, even when looking at populations, or breeding groups, I think it's becoming more and more clear that uniparental markers are volatile and we can see big changes without changes of a proportionate size in the autosomal composition, and I think differential mating patterns, especially in terms of yDNA, founder effect and subsequent drift, selection for different mtDNA and yDNA subclades in the face of a changed climatic or personal environment, and also, (which is not often explored) sheer random chance, can affect the frequency of these uniparental markers. To the last point, a study was done of Icelandic mtDNA covering 300 years. No new geneflow, and yet because of the differential pattern of "daughtering out", certain sub-clades became rare, and others dominant. If anyone is interested, I'll try to find the site, but I'm not making it up!

I agree totally for the question of mt, Y and autosomals DNA respective rapports
concerning Iceland, i red this survey (or an abstract, rather) and yes, some precise subclades of mt-DNA HGs disappeaaed (very often the rarest ones) but the "big" HGs distribution was not too affected if I remember well - maybe on a largest range OF TIME or a smallest sample it could be more drastic?

 

[Angela]

I agree totally for the question of mt, Y and autosomals DNA respective rapports
concerning Iceland, i red this survey (or an abstract, rather) and yes, some precise subclades of mt-DNA HGs disappeaaed (very often the rarest ones) but the "big" HGs distribution was not too affected if I remember well - maybe on a largest range OF TIME or a smallest sample it could be more drastic?

This is the Helgason 2009 paper on drift in Icelandic mtDNAm and how as a result, the mtDNA of the ancient samples was closer to that of the source populations than to that of modern Icelandic people. Unfortunately it's not the one to which I was referring, which I still can't find, but it's interesting none the less.
http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1000343

The study to which I had referred had to do with statistical patterns over a smaller period. (I still haven't found it, Epoch.)

Generally, I think that selection is extremely important, particularly as it relates to mtDNA. I think the huge expansion of the "H" clades since the Neolithic is a big factor in the changed mtDNA map of Europe. Clearly, that has something to do with the expanding populations made possible by the agricultural revolution, but I think it's also partly a reflection of certain selective advantages in terms perhaps of climate adaptability, but also as regards disease protection and fertility, both in women who are mtDNA "H", and men who carry it.

I think I remember a study that found that mtDNA "H" provides an advantage in terms of resistance to infection...perhaps someone has a citation handy. At any rate, with all of the benefits of farming in terms of expanding populations (I think hunter-gatherers have spent most of history on the verge of extinction) raising domestic animals for food is a filthy business even today with our increased knowledge of the importance of sanitary conditions. MtDNA "H" as well as other mtDNA clades involved with the early development of animal husbandry might have increased resistance to diseases carried or spread by the animals. (Hasn't even tuberculosis been linked to transmission from animals? ) I've also wondered what effect that might have had in times of plague, not only Justinian's, but also the Black Death.

This is John Hawks' take on all of this:
http://johnhawks.net/weblog/reviews/genetics/mtdna_migrations/selection-mtdna-iceland-2009.html

In terms of the "Y", the other issue is fertility rates. I know I read something about reduced sperm motility in men carrying certain mtDNA clades.

 

[MOESAN]

This is the Helgason 2009 paper on drift in Icelandic mtDNAm and how as a result, the mtDNA of the ancient samples was closer to that of the source populations than to that of modern Icelandic people. Unfortunately it's not the one to which I was referring, which I still can't find, but it's interesting none the less.
http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1000343

The study to which I had referred had to do with statistical patterns over a smaller period. (I still haven't found it, Epoch.)

Generally, I think that selection is extremely important, particularly as it relates to mtDNA. I think the huge expansion of the "H" clades since the Neolithic is a big factor in the changed mtDNA map of Europe. Clearly, that has something to do with the expanding populations made possible by the agricultural revolution, but I think it's also partly a reflection of certain selective advantages in terms perhaps of climate adaptability, but also as regards disease protection and fertility, both in women who are mtDNA "H", and men who carry it.

I think I remember a study that found that mtDNA "H" provides an advantage in terms of resistance to infection...perhaps someone has a citation handy. At any rate, with all of the benefits of farming in terms of expanding populations (I think hunter-gatherers have spent most of history on the verge of extinction) raising domestic animals for food is a filthy business even today with our increased knowledge of the importance of sanitary conditions. MtDNA "H" as well as other mtDNA clades involved with the early development of animal husbandry might have increased resistance to diseases carried or spread by the animals. (Hasn't even tuberculosis been linked to transmission from animals? ) I've also wondered what effect that might have had in times of plague, not only Justinian's, but also the Black Death.

This is John Hawks' take on all of this:
http://johnhawks.net/weblog/reviews/genetics/mtdna_migrations/selection-mtdna-iceland-2009.html

In terms of the "Y", the other issue is fertility rates. I know I read something about reduced sperm motility in men carrying certain mtDNA clades.

Thanks
I red this survey but did not conserve it - I have to read it again, maybe was I wrong?
all the way, the sperm mobility is according to me of very light impact I explaoined that two times before answering to Maciamo - the mt DNA and the metabolic skills linked to it could very well undergo more severe selection, I agree - the very level distribution of mt DNA HGs in Europe even if subclades -differ, could be linked to a climatic/environmental pressure -
that said, when two populations living side by side and having had females or males exchanges between them are not completely evenly mixed and crossed it is of some interest to precise the sex of people studied even for mt DNA - have an happy and intellectually rich new year