Poise n Pen
10-01-2016, 10:54 AM
http://biorxiv.org/content/early/2016/09/30/078360
The basic idea of this paper is to try and show evidence of steppe migration through looking at differences in X chromosome homogeneity. Since males donate just one X chromosome then in theory we can infer some details about male and female mixing ratios when populations mix.
Dramatic events in human prehistory, such as the spread of agriculture to Europe from Anatolia and the Late Neolithic/Bronze Age (LNBA) migration from the Pontic-Caspian steppe, can be investigated using patterns of genetic variation among the people that lived in those times. In particular, studies of differing female and male demographic histories on the basis of ancient genomes can provide information about complexities of social structures and cultural interactions in prehistoric populations. We use a mechanistic admixture model to compare the sex-specifically-inherited X chromosome to the autosomes in 20 early Neolithic and 16 LNBA human remains. Contrary to previous hypotheses suggested by the patrilocality of many agricultural populations, we find no evidence of sex-biased admixture during the migration that spread farming across Europe during the early Neolithic. For later migrations from the Pontic steppe during the LNBA, however, we estimate a dramatic male bias, with ~5-14 migrating males for every migrating female. We find evidence of ongoing, primarily male, migration from the steppe to central Europe over a period of multiple generations, with a level of sex bias that excludes a pulse migration during a single generation.
Not off to a great start talking about Anatolian immigration since this route has been all but obliterated by archaeology at this point, but whatever. It doesn't really matter to anything because there is no apparent mixing anyway. The neolithics (here at least) simply are what they are.
The other part is more interesting. Before I get into that though, I should talk about some of the big reasons steppe theory can be hard to swallow. Ultimately, if the early Yamnaya samples are truly the ancestors of modern NW Europe, it would seem that the y-dna came along with them but little of anything else. How can that even happen? You go from 100% wrong mtdna, 100% brown eyes, 0% of a now ubiquitous Eauropean pigment gene to populations that are 80-90% light eyes, 100% proper pigmentation genes and very low levels of Yamnaya mtdna. And that's ignoring the idea that there virtually has to be certain mtdna in the original r1b population which don't show up at Yamnaya, such as mtdna V which is found even in African r1b populations!
Well, it's possible, just highly unlikely. First you would have to have a nearly all male invasion, but even that won't be nearly enough. If you conquered a 100% light-eyed, light pigmented population you could never get more than 25% light eyes from an originally brown eyed population. But say you conquered one population, then you could do it for another, and another. By then the numbers would be more or less correct for modern NW European groups like Irish, Scottish etc.. Multiple waves of 100% replacement seems unlikely but that is what this paper tries to show actually happened, or at least they say something along those lines though their explanation as stated could not actually produce these results.
https://4.bp.blogspot.com/-HoCbDtzW10k/V--IEajyVeI/AAAAAAAAAEc/wrlPGmcz9fQzb_1Xf4M0zmnXSZ1Cuoa6gCLcB/s1600/paper.jpg
They admit off the bat that this ratio of X to Steppe dna shows too much mixture for a single event. Their explanation is constant influx of steppe dna. This would not produce this result though because there is still autosomal mixing on the X chromosome so if it were continuous mixture then the mixture would very quickly wash away. That does not really matter though I guess. The exact way it got that way only matters if it contradicts the basic idea of steppe migration which I don't think is the case. It's unlikely to have waves of conquest like that where a tiny minority basically washes itself out except for the y-dna but that's always been a necessity for this idea to work.
The main problem is you can explain it in other ways. X chromosome is extremely well-preserved compared to other parts of the genome. The X chromosome actually matters, unlike most autosomal dna. Your IQ largely comes from the X chromosome and hence is passed on by the mother. Since all males have just one copy of X, any slight defect or advantage has a very telling effect on the male population. I don't think it's really true most dna is "junk dna: as has become a popular theory, but some dna segments are definitely WAY more important than others.
So when you talk about X chromosome changes compared to autosomal dna OVER THOUSANDS OF YEARS...I simply have to call bullshit. Now mixing is probably almost never an overnight event, but for this kind of idea to work and be reliable then we would have to be able to do these samples immediately after the mixing occurred.
Otherwise, how do we know what happened? Was there a mixing event, after which the X chromosome steppe dna was weeded out? Was there a very unlikely complete male replacement MULTIPLE TIMES as would have to occur to get this mixing result? Or is there little to no mixing occurring at all? In this time frame it could just as easily be that X chromosome has rapidly changed over completely, which is possible because selection on it is WAY stronger than on random autosomal segments. And features like eye and hair color should be completely neutral.
The other issue is...how do you get here from there? That is the ultimate question, and one that seems to get completely ignored. Now the whole sequence I went through can work, but it requires the population that the r1b people are mixing to actually have all the attributes in modern people today. But we know they don't. For this to work and get to the modern NW European populations then we have to start off with some population that has 100% both the European pigment genes that are ubiquitous, instead of 100% of one and 0% of the other. And has basically 100% light eyes. And has V mtdna and other modern mtdnas. And then discard basically everything but the y-dna and some autosomal clutter here and there...through multiple waves of complete replacement.
WHERE IS THAT POPULATION? Here's the ultimate question that constantly gets ignored. Of course people care about THEIR ACTUAL ANCESTORS and especially the ones who give them the actual attributes that matter. If all you get from Yamnaya is the r1b then how much does Yamnaya actually even matter?
We have Yamnaya and Corded Ware and then suddenly we have Bell Beaker that is basically 100% like fully white Northern European populations today with very high levels of light skin, hair and eye genes that Yamnaya does not seem to have at all.
Now there's two possibilities. One, we will find this population and it will have r1b already. then all this is pure bullshit. That is what I suspect will ultimately happen...some day. The other is that we will find this population and they will have every feature we are looking for except the y-dna. In that case, steppe theory is basically proven. But that is what we ultimately need to find, without it everything else is masturbation.
But it's a little unfair to push that much responsibility onto the paper I guess. They don't seem to be really trying to explain the whole ethnogenesis of central Europe in detail, just making some observations between a few populations. Populations that may have only limited continuity with modern populations.
Since the whole paper relies on X chromosome though, it would have been nice to talk about X chromosome haplotypes (and yes they do exist for autosomals). From there it would be a lot easier to tell how these populations compare to modern ones and to each other, and try to figure out how they have interacted.
The basic idea of this paper is to try and show evidence of steppe migration through looking at differences in X chromosome homogeneity. Since males donate just one X chromosome then in theory we can infer some details about male and female mixing ratios when populations mix.
Dramatic events in human prehistory, such as the spread of agriculture to Europe from Anatolia and the Late Neolithic/Bronze Age (LNBA) migration from the Pontic-Caspian steppe, can be investigated using patterns of genetic variation among the people that lived in those times. In particular, studies of differing female and male demographic histories on the basis of ancient genomes can provide information about complexities of social structures and cultural interactions in prehistoric populations. We use a mechanistic admixture model to compare the sex-specifically-inherited X chromosome to the autosomes in 20 early Neolithic and 16 LNBA human remains. Contrary to previous hypotheses suggested by the patrilocality of many agricultural populations, we find no evidence of sex-biased admixture during the migration that spread farming across Europe during the early Neolithic. For later migrations from the Pontic steppe during the LNBA, however, we estimate a dramatic male bias, with ~5-14 migrating males for every migrating female. We find evidence of ongoing, primarily male, migration from the steppe to central Europe over a period of multiple generations, with a level of sex bias that excludes a pulse migration during a single generation.
Not off to a great start talking about Anatolian immigration since this route has been all but obliterated by archaeology at this point, but whatever. It doesn't really matter to anything because there is no apparent mixing anyway. The neolithics (here at least) simply are what they are.
The other part is more interesting. Before I get into that though, I should talk about some of the big reasons steppe theory can be hard to swallow. Ultimately, if the early Yamnaya samples are truly the ancestors of modern NW Europe, it would seem that the y-dna came along with them but little of anything else. How can that even happen? You go from 100% wrong mtdna, 100% brown eyes, 0% of a now ubiquitous Eauropean pigment gene to populations that are 80-90% light eyes, 100% proper pigmentation genes and very low levels of Yamnaya mtdna. And that's ignoring the idea that there virtually has to be certain mtdna in the original r1b population which don't show up at Yamnaya, such as mtdna V which is found even in African r1b populations!
Well, it's possible, just highly unlikely. First you would have to have a nearly all male invasion, but even that won't be nearly enough. If you conquered a 100% light-eyed, light pigmented population you could never get more than 25% light eyes from an originally brown eyed population. But say you conquered one population, then you could do it for another, and another. By then the numbers would be more or less correct for modern NW European groups like Irish, Scottish etc.. Multiple waves of 100% replacement seems unlikely but that is what this paper tries to show actually happened, or at least they say something along those lines though their explanation as stated could not actually produce these results.
https://4.bp.blogspot.com/-HoCbDtzW10k/V--IEajyVeI/AAAAAAAAAEc/wrlPGmcz9fQzb_1Xf4M0zmnXSZ1Cuoa6gCLcB/s1600/paper.jpg
They admit off the bat that this ratio of X to Steppe dna shows too much mixture for a single event. Their explanation is constant influx of steppe dna. This would not produce this result though because there is still autosomal mixing on the X chromosome so if it were continuous mixture then the mixture would very quickly wash away. That does not really matter though I guess. The exact way it got that way only matters if it contradicts the basic idea of steppe migration which I don't think is the case. It's unlikely to have waves of conquest like that where a tiny minority basically washes itself out except for the y-dna but that's always been a necessity for this idea to work.
The main problem is you can explain it in other ways. X chromosome is extremely well-preserved compared to other parts of the genome. The X chromosome actually matters, unlike most autosomal dna. Your IQ largely comes from the X chromosome and hence is passed on by the mother. Since all males have just one copy of X, any slight defect or advantage has a very telling effect on the male population. I don't think it's really true most dna is "junk dna: as has become a popular theory, but some dna segments are definitely WAY more important than others.
So when you talk about X chromosome changes compared to autosomal dna OVER THOUSANDS OF YEARS...I simply have to call bullshit. Now mixing is probably almost never an overnight event, but for this kind of idea to work and be reliable then we would have to be able to do these samples immediately after the mixing occurred.
Otherwise, how do we know what happened? Was there a mixing event, after which the X chromosome steppe dna was weeded out? Was there a very unlikely complete male replacement MULTIPLE TIMES as would have to occur to get this mixing result? Or is there little to no mixing occurring at all? In this time frame it could just as easily be that X chromosome has rapidly changed over completely, which is possible because selection on it is WAY stronger than on random autosomal segments. And features like eye and hair color should be completely neutral.
The other issue is...how do you get here from there? That is the ultimate question, and one that seems to get completely ignored. Now the whole sequence I went through can work, but it requires the population that the r1b people are mixing to actually have all the attributes in modern people today. But we know they don't. For this to work and get to the modern NW European populations then we have to start off with some population that has 100% both the European pigment genes that are ubiquitous, instead of 100% of one and 0% of the other. And has basically 100% light eyes. And has V mtdna and other modern mtdnas. And then discard basically everything but the y-dna and some autosomal clutter here and there...through multiple waves of complete replacement.
WHERE IS THAT POPULATION? Here's the ultimate question that constantly gets ignored. Of course people care about THEIR ACTUAL ANCESTORS and especially the ones who give them the actual attributes that matter. If all you get from Yamnaya is the r1b then how much does Yamnaya actually even matter?
We have Yamnaya and Corded Ware and then suddenly we have Bell Beaker that is basically 100% like fully white Northern European populations today with very high levels of light skin, hair and eye genes that Yamnaya does not seem to have at all.
Now there's two possibilities. One, we will find this population and it will have r1b already. then all this is pure bullshit. That is what I suspect will ultimately happen...some day. The other is that we will find this population and they will have every feature we are looking for except the y-dna. In that case, steppe theory is basically proven. But that is what we ultimately need to find, without it everything else is masturbation.
But it's a little unfair to push that much responsibility onto the paper I guess. They don't seem to be really trying to explain the whole ethnogenesis of central Europe in detail, just making some observations between a few populations. Populations that may have only limited continuity with modern populations.
Since the whole paper relies on X chromosome though, it would have been nice to talk about X chromosome haplotypes (and yes they do exist for autosomals). From there it would be a lot easier to tell how these populations compare to modern ones and to each other, and try to figure out how they have interacted.