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Large-scale recent expansion of European patrilineages shown by population resequencing:

The proportion of Europeans descending from Neolithic farmers ~10 thousand years ago (KYA) or Palaeolithic hunter-gatherers has been much debated. The male-specific region of the Y chromosome (MSY) has been widely applied to this question, but unbiased estimates of diversity and time depth have been lacking. Here we show that European patrilineages underwent a recent continent-wide expansion. Resequencing of 3.7 Mb of MSY DNA in 334 males, comprising 17 European and Middle Eastern populations, defines a phylogeny containing 5,996 single-nucleotide polymorphisms. Dating indicates that three major lineages (I1, R1a and R1b), accounting for 64% of our sample, have very recent coalescent times, ranging between 3.5 and 7.3 KYA. A continuous swathe of 13/17 populations share similar histories featuring a demographic expansion starting ~2.1–4.2 KYA. Our results are compatible with ancient MSY DNA data, and contrast with data on mitochondrial DNA, indicating a widespread male-specific phenomenon that focuses interest on the social structure of Bronze Age Europe.

Looking at this paper, it basically confirms what we know from ancient DNA, and other large scale sequencing projects. Until recently much Y chromosomal phylogenetic analyses were done utilizing highly mutable regions, microsatellites. This had a major upside, in that variation was copious. But, it wasn’t as precise as more slow mutating regions of the genome would have been. But without next generation sequencing the Y chromosome is just hard to work with due to its paucity of SNP variants. So that’s why we’re seeing some gains here.

The relatively homogeneity in Northern Europe in particular is attributed to a few lineages which have gone through “star-like” expansions. That aligns rather well with the idea that the arrival of populations from the steppe was demographically an earthquake.

 
• Category: Science • Tags: Y Chromosome 
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The_Journey_of_Man_-_A_Genetic_Odyssey Being part of a patrilineage is a big deal today. Ask anyone who is a Cohen, or claims to be a Sayyid, or a descendant of Confucious. Old school cultural anthropologists would assume that these patrilineages are “fictive,” that they exist to bind together disparate elite lineages as a social force. To some extent this is likely true. But not entirely. The complex genetic story of the Cohens highlights that kinship may not always be fictive. In the case of the Sayyids I assume that a lot of this is fictive. When it comes to people in South Asia with the surname Khan there isn’t even a pretense that we descend in any way from a Genghiside lineage. Rather, Khan has gone from being a surname to an honorific.

In my post Patriarchy Came with Cain and Abel I connected a social phenomenon with the drastic crash in Y chromosomal effective population in the mid-Holocene, as reported in the new paper in Genome Research, A recent bottleneck of Y chromosome diversity coincides with a global change in culture. Unfortunately some of the press related to paper seems rather misleading. For example, “8,000 Years Ago, Only One Man Had Children for Every 17 Women” (here’s another take). Aside from the fact that the effective population crash only is true for a subset of lineages, like Greg Cochran I’m skeptical of the image of a winner-take-all reproductive mating market. Specifically, I don’t think there was a given generation where only ~5% of men in a given population had offspring, while the others did not. Rather, I assume that cumulative reproductive skew probably had the impact of socially privileging men from particular patrilineages, so that Y chromosomal haplotypes “swept” through the population over the course of many generations.

k10181 My basic idea dovetails with Greg Clark’s in The Son Also Rises. Clark’s economic historical data sets suggests that over the long term elite lineages are surprisingly insulated from decay in status. Though there is a great deal of inter-generational churn, over the long haul there is a strong trend line of elite lineages remaining elite, and non-elite ones remaining non-elite. This may be due to cultural or genetic forces; Clark is ultimately agnostic on that. But, it suggests that social status is highly heritable. Was it always so? I suspect that these sorts of dynamics only date to the Holocene, with the rise of complex societies, and social status being connected to accumulation of material objects and power which can be passed from father to son. Additionally, with complex societies there emerged group level competitive games which were winner-take-all, as patrilineages faced off against each other with the ultimate outcome being final victory or defeat.

Ultimate this is very different from the image we have of a literal “harem society” that might emerge in small scale societies with such reproductive skew. Rather, it’s a more subtle and gradual rich-get-richer dynamic, where status and privilege compound over the generations in a genetic sense.

Addendum: Both Greg Cochran and the Genome Research paper point out that effective population does not seem to have crashed concomitantly on the autosome, as you’d expect. One minor point I’d add is that admixture can inflate population size inferences, since it elevates diversity. Most of the Holocene populations seem to have been subject to admixture, so autosomal effective population may have been artificially inflated.

 
• Category: Science • Tags: Evolution, Y Chromosome 
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figure2

figure1 I do like to suggest that the genetic and archaeological record support the conjecture of Conan the Barbarian in terms of what our male ancestors thought was “good in life.” Basically, to conquer your enemies and seize their women, which is a distillation of a disputed quote from Genghis Khan. Conan may be fiction, but Genghis Khan is not. As it happens there is a fair amount of circumstantial evidence that the genetic legacy of Genghis Khan is enormous. Not only did Khan father many sons, but so did their sons, and so forth. Tens of millions of men around the world are direct paternal descendants of Genghis Khan and his family.

This is known. But now more is known, thanks to a new paper out of Genome Research, A recent bottleneck of Y chromosome diversity coincides with a global change in culture. The upside of this paper is that it uses whole genome sequence of Y chromosomes to generate phylogenetic inferences. This is important because the Y chromosome has very little genetic variation relative to much of the rest of the genome. The downside is that because techniques were utilized to perform whole genome sequencing of the Y, the sample size, at 299, is not as large as we’ve gotten used to for analyses of uniparental lineages. That will change in the future, as there are many thousands of whole genome sequences of the Y in databases around the world, though perhaps not enough computational power allocated by funding agencies to crunch through them in the fashion on display in the paper (they didn’t use the whole sequence for a lot of the analysis, but ~35,000 SNPs).

So what are the major findings of the paper? Using a Bayesian Skyline Plot (BSP) it is rather clear that 4-8 thousand years ago there was a sharp drop in male effective population sizes across many world populations. It is also clear that the female effective population did not experience the same drastic contraction. The supplements have individual figures, and many of the events of history and archaeology can be easily mapped onto these population size changes. For example, the later reduction of African population sizes probably is due to the later adoption of agriculture in that continent, and timed with the Bantu expansion. In the New World the data seem to show late and persistent reduction in effective population size. The Columbian Exchange and massive population contraction subsequent to that is probably being picked up by this result. figure3Intriguingly there is a detection of a two events in the European data, where the sample size is relatively large. The first major drop seems to coincide with the arrival of the “First Farmers” (e.g., LBK culture) in Northern Europe. In the Middle East (orange) you see collapse, and then a rapid ascent very early. This comports well with the early history of agriculture here. But in the European samples there is a rapid ascent, and then a level off ~3,000 years ago or so. This could be the arrival of Indo-European cultures to Europe. If the sample sizes for other regions were as large and representative as Northern Europe such subtle details might also have emerged there with the BSP method (to be clear, I suspect the crash in effective size in Europe is due to haplogroup I, while the delayed expansion is due to R1a and R1b arriving a few thousand years later).

Also of interest are is the deep structure of the different clades. Those of you stepped in Y chromosomal haplogroups can extract more from the figure to the top left, but it shows relationship of the primary groups as well as their recent expansion. The affinity of the Q and R clades to me indicate that those who argue that these are somehow related to the “Ancestral North Eurasians” are correct. Similarly, the position of I and J in the same clade points to their common descent from ancient West Eurasian Pleistocene groups. The I lineage is most exclusively associated with European hunter-gatherers, while J is traditionally associated with groups of farmers expanding out of the Middle East in all directions (note that one branch of J is found in the Middle East, Central Asia, South Asia, and Europe). I agree with Dienekes that the branch of E that corresponds to the lineages which span Sub-Saharan Africa and Western Eurasia are a indicating a back migration to Africa, probably in the Pleistocene. I do wonder as well whether they have some association with the mysterious “Basal Eurasians.”

An important part of the paper that they emphasize is that ~50,000 years before the present there was a profusion of haplogroups associated with the ones which are today common across Eurasia, and Y chromosomal Ne was ~100. This seems to agree with the rapid expansion of non-Africans in the wake of the “Out of Africa” event, though the authors note they don’t have enough power to reject a model of a separate “Southern Route” migration, which might be detected with autosomal data. This is a good caution on the limitations of Y and mtDNA data; archaic admixture was rejected by these two loci because the non-African hominin lineages went extinct (mtDNA and Y have higher turnover rates than the recombining autosomal regions). figure4Additionally there were some major lacunae in the sampling. For example, among the African populations it doesn’t seem like some of the hunter-gatherer groups, the Khoisan or eastern Pygmy, were included in the data set. The map also shows that Northeast Asia (China, Japan and Korea) and Oceania were not extensively sampled. But these are minor issues in the broader picture of the insights from the population coverage that they did have.

The most important implication of these sorts of results have to do with the nature of the change of human social organization and behavior over the course of the existence of modern humans. The authors of the above paper seem to understand this, as there is extensive focus on the topic within the paper:

An increase in male migration rate might reduce the male Ne but is unlikely to cause a brief drastic reduction in Ne as observed in our empirical data…However, in models with competition among demes, an increased level of variance in expected offspring number among demes can drastically decrease the N e (Whitlock and Barton 1997). The effect may be male-specific, for example, if competition is through a male-driven conquest. A historical example might be the Mongol expansions (Zerjal et al. 2003). Innovations in transportation technology (e.g., the invention of the wheel, horse and camel domestication, and open water sailing) might have contributed to this pattern. Likely, the effect we observe is due to a combination of culturally driven increased male variance in offspring number within demes and an increased male-specific variance among demes, perhaps enhanced by increased sex-biased migration patterns (Destro-Bisol et al. 2004; Skoglund et al. 2014) and male-specific cultural inheritance of fitness.

To restate what’s being said here:

1) During the Holocene we saw the rise of powerful patrilineages which engaged in winner-take-all of inter-group competition.

2) Within the “winning” patrilineages there may have been winner-take-all dynamics, or at least high reproductive variance

When it comes to farmers and nomads against each other I do think a model of inter-demic competition is pretty realistic. But when it comes to farmers and nomads against hunter-gatherers I don’t think one can term it competition. The latter in most circumstances would be quickly overwhelmed by the farmers and nomads; eliminated, excluded, or at least assimilated (there are exceptions in areas where the hunter-gatherer density was high and they were sedentary). And as concerns the complex societies of farmers and nomads, even within them the rise of inequality and stratification mean that subordinate or secondary males and their lineages were marginalized, leaving few descendants.

Men are on average 15-20 percent bigger than women. Men are also stronger than women. But the sexual dimorphism is far less than one can find among gorillas. This suggests that intra-sex competition among males was attenuated, or at least it was not in the physical domain. Though I am not of the camp which believes that war as we understand it must necessarily be a feature of Holocene agricultural societies, it seems likely that the pressure cooker of high population densities resulted in a radical increase in the scale of inter-group atrocity. One way to react to this change would have been to grow larger physically, but there are limitations to how fast biological evolution can resculpt the human physique. Not only that, but larger humans presumably require more nutritional inputs, and the agricultural revolution in Malthusian conditions did not enable that on a mass scale. So humans did what they do best: innovate culturally.

The cultural innovations came as package deals. A central role for patriarchal lineages which tended to apply force to maintain social order, as well as take on the position as the tip of the spear in inter-group competition, eventually resulted in power accruing to those groups almost exclusively. The importance of patrilineages naturally resulted in an increased importance of paternity certainty, and therefore social mores which emphasized female chastity. These powerful lineages fixed upon a solution which gorillas had long ago arrived at: treat females as chattel and defend them as one would property.

The “men in groups” were evoked by particular social-cultural conditions of agricultural society which they themselves did not necessarily trigger in an any way. But once you had a small benefit to the emergence of a caste of men in groups, groups which developed this caste benefited. Within these groups eventually the caste took over the identity of the group, and made its own interests conterminous with the interests of the group. The Athenian polis was democratic, but only for free males who were born of Athenians. In other words, the most radical experiment in radical democracy in the ancient world was also still relatively exclusionary and delimited in the nature of political power and representation (also, recall that the power of freeborn males of lower economic status in Athens has been connected to their importance in the navy as oarsmen).

Speaking as someone with broadly liberal sympathies, economic and social forces over the past few centuries have resulted in an unwinding of the cultural innovations of the past 10,000 years which have put a straight-jacket on the forces of human liberty. This great unwinding to some extent can be understood as the shattering of the great patriarchal monopolies of old, reflected in the great families and lineages which spanned the world, and democratic representation first for all men and then women. In the West the period between 1800 and 1970 saw massive gains in income to unskilled workers, reversing the tendency toward winner-take-all dynamics which arose with the Neolithic.

That being said, the post-Industrial and post-materialist world, in full flower in places like North Europe, is not exactly like the Paleolithic. Some of the innovations of the post-Neolithic world, such as organized religion, are probably here to stay in a world of social complexity and density. The great devolution to power from the elite male lineages is one specific aspect where I believe the modern age more resembles the Paleolithic. More liberal sexual ethics is also another dimension where the modern world is more like that of hunter-gatherers. But the autonomous individual, an island unto himself, is a fiction. Hunter-gatherers were, and are, social creatures. No doubt they were bound by taboos and rules, just as modern hunter-gatherers are. The vision of egalitarianism promoted by many in the modern West is a reaction against the social controls of the post-Neolithic world, but those social controls themselves are rooted in human cognitive impulses. Competition did not come full formed in the world of grain, and the impulse toward violence and domination was present in man long before the scythe was re-purposed toward bloodier ends.

 
• Category: Science • Tags: Phylogenetics, Population Genetics, Y Chromosome 
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Citation: Y-chromosome descent clusters and male differential reproductive success: young lineage expansions dominate Asian pastoral nomadic populations

Citation: Y-chromosome descent clusters and male differential reproductive success: young lineage expansions dominate Asian pastoral nomadic populations

Balaresque_FiguresRevised251114 copy When it comes to human evolutionary genetics there are two broad areas of interest for me. One the one hand there are classic questions of functional biology and population genetics. Variation of traits and how that variation was selected for over time and space. Then there are the issues of demography, phylogeography, and phylogenetics. This is the domain under which “historical population genetics” tends to fall. Between 1995 and 2005 there was a significant period when the focus was on reconstructing phylogenetic trees inferred from uniparental maternal (mtDNA) and paternal (Y chromosomal) lineages. Using a coalescent framework these non-recombining regions generated intuitively appealing and computationally tractable trees, which illustrated relationships across history. These were often superimposed upon geographical maps to reconstruct patterns of the past. The_Journey_of_Man_-_A_Genetic_Odyssey Since 2005 the emergence of dense SNP chips, where individuals could be typed on hundreds of thousands of markers, ushered in a new era and uniparental studies faded somewhat into the backdrop (and today we are moving into whole genome analyses). But sometimes the uniparental research is still useful, in particular since there is already a huge databank of samples and studies which one can leverage. A new paper in The European Journal of Human Genetics does just that, Y-chromosome descent clusters and male differential reproductive success: young lineage expansions dominate Asian pastoral nomadic populations.The figure at the top of this post is a summary of the primary results, which show how extremely common Y chromosomal haplogroups in their data set can be correlated with particular historical events. The authors used a data set of over 5,000 males across a huge range of Eurasian populations. Surveying the genetic variation it is clear that the haplogroup counts exhibited an exponential distribution. Many of the genotypes were found in only a few individuals, but a few were found in many individuals.

510CbnsBGLL._SY344_BO1,204,203,200_ The authors refer to the haplogroups as “Descent Clusters” (DC) rather than haplogroups. You can see what the DCs are in the table at the top. DC2 is the familiar haplogroup R1a1a, of which I am a member. DC1 is the “Genghis Khan” haplogroup. Because they’re using fast mutating microsatellites the coalescence estimates have wide intervals. But, I am nearly 100% sure that R1a1a coalesces to a period more recently than 10,000 years ago in the past. The reason is that I saw some posters using whole genome sequences from the Y chromosome at ASHG. These should be more precise estimates because of the enormous marker set of more slowly mutating SNPs, and they too arrived at a relatively recent period for the last common ancestor of these common male lineages. In fact, if I recall correctly the divergence between R1b and R1a dates to ~10,000 years before the present in these studies, so R1a must have a much more recent coalescence. The TMRCA for the R1a1a expansion is suspiciously close to the most recent paper on the emergence of South Asians from an admixture between an indigenous group and West Eurasians to come out of the Reich lab, Genetic Evidence for Recent Population Mixture in India. But, even in this paper there is evidence of distinct inputs of Y chromosomes from the west into South Asia, so I suspect it too supports the proportion that the admixture between West Eurasian and indigenous groups occurred between separate and diverse West Eurasians, and not just one group (i.e., the Indo-Aryans may have been the last West Eurasians who arrived in rapid succession over the period between 3000 and 1000 BC). These results also seem to support the conjecture that the ancestors of “Austro-Asiatics” ranged far and wide.

R1a1a

R1a1a resplendent

In the ultimate evaluation I am less interested in the specific stories than in the general one. Is this pattern of “super-male” lineages new? The “Altaic” DCs clearly are associated with the Turks and Mongols, and emerged in the light of history. R1a1a and its cousins are older, and live in the shadowy zone of archaeology on the precipice of history. But is this pattern primal to our lineage? My own conjecture is that on the whole this pattern was prefigured in the ancient past whenever founder events occurred. For example, in the expansion into Oceania and the New World. But what is different about the world after the Neolithic is that periodically the tree of patrilineages was “pruned”, as one branch would rise to rule them all for a moment. There would be an elimination of numerous ancient lineages as a new shining star would dominate the firmament. But the echoes of that moment reverberate down the millennia, as one can see in the haplogroups which are prevalent across vast swaths of Eurasia, and at a frequency far out of proportion to the norm. Like a thunderbolt, demographic revolutions explode onto the human cultural landscape, and reshape the future topology of lineages on a regular basis.

 
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Citation: The Y-chromosome tree bursts into leaf: 13,000 high-confidence SNPs covering the majority of known clades

Citation: The Y-chromosome tree bursts into leaf: 13,000 high-confidence SNPs covering the majority of known clades

There’s a new open access paper on human Y chromosome phylogenies, The Y-chromosome tree bursts into leaf: 13,000 high-confidence SNPs covering the majority of known clades, which is just as interesting because of a reference than the paper itself. The paper cited is “Batini, C, P Hallast, D Zadik, et al. submitted. Large-scale recent expansion of European patrilineages shown by population resequencing. Nature Comms.” As I’ve mentioned earlier it was clear from several posters at ASHG that whole genome sequencing of larger sample sizes is making much more clear how recent and rapid the expansion of several of the common lineages across Eurasia was. In particular I’m thinking of R1a and R1b. We know this already from earlier work, but these latest results just confirm it. The truth is visually obviously. Notice in the figure above how R1b fans out in an instant from a single node. This reflects recent rapid population expansion.

The_Journey_of_Man_-_A_Genetic_Odyssey But when The Journey of Man and The Seven Daughters of Eve were being written in the early 2000s it was assumed that Y and mtDNA phylogenies could tell us about human prehistory in totality. In hindsight that was probably asking for too much. But because they are sex specific these two lineages can inform us a great deal about social structures. In particular, rapid expansion of Y chromosomal lineages in the recent past may indicate the rise of patriarchy, as powerful males began to see polygyny as a viable strategy due to their monopolization of the resources of whole societies.

If I had to predict, I believe that female lineages tend to be characterized by isolation by distance dynamics. In contrast, male lineages are pruned periodically by rapid expansions and admixtures by groups which are able to marginalize or exterminate competitors over vast swaths of territory. The Genghis Khan effect is just the most prominent of this sort of phenomenon. It is certain that in prehistory this occurred as well, as new technologies such as agricultural triggered social revolutions, and the rise of specialization and stratification among humans.

 
• Category: Science • Tags: Y Chromosome 
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300px-R1a1a_distribution Over at Greg Cochran’s blog he’s been posting on Indo-Europeans. He’s had many of these ideas for a long time, but after I recounted to him some more information from ASHG 2014 it crystallized a lot in terms of specifical detail. For example, the Kalash of Pakistan share a lot of drift with “Ancestral North Eurasians” (ANE). By “a lot”, I mean in the same range as North Caucasus and Eastern European groups. Other HGDP samples from Pakistan are somewhat lower in their signals, but it still noticeable.* In Iosif Lazaridis’ presentation at ASHG 2014 he outlined the likelihood that the widespread distribution of ANE ancestry in Europe probably had something to do with the migrations of the Yamna culture, from which derived the Battle Axe Culture. The genetic variation you see in eastern and central Europe today is representative of the Yamna people. They know because they have ancient samples from those regions. The Yamna themselves are a mix of an Armenian-like Middle Eastern population, and “Eastern Hunter-Gatherers” (EHG) which resemble those to the west but have a higher fraction of ANE (so the are WHG + ANE, while the Armenian-like population is similar to, but not exactly the same as, the “European First Farmers” (EFF).

But that’s not the point of this post. There were two Y chromosome posters which were of interest. One showed a Bayesian skyline plot which illustrated that many of the Y chromosomal lineages you know and love went through very rapid population expansion on the order of 5 to 10 thousand years ago. A second poster had a phylogeny of Y chromosomes derived from high coverage whole genome sequencing. They had four individuals from the R1 lineages, two of them from R1a1a. One individual was Indian and the other was Russian. The coalescence was ~5,000 years ago. The individual who did this analysis was not aware of the Bayesian skyline plot poster, so she immediately ran off to look at it when I told her. The coalescence with R1b for the R1a individuals was ~10,000 years ago.

I know that there are lots of debates about clocks and calibration when it comes to Y chromosomes. But the archaeology, ancient DNA, autosomal work, and uniparental lineages are all coming together with a coherent picture. The Y chromosomal data strongly suggests that we’re talking about “star phylogenies” in the recent human male past.

* And for what it’s worth the Kalash are not descended from the soldiers of Alexander. Rather, they seem an early example of the admixture which led to modern South Asians. Their drift from other populations is due to them being isolated and endogamous.

 
• Category: Science • Tags: R1a1a, Y Chromosome 
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For various reasons the idea of mitochondrial Eve and Y chromosomal Adam capture the public imagination. This frustrates many people, including me. I’ve gotten into the fatigue stage on this topic, but some sort of counter-attack is necessary against malignant memes. Even geneticists who don’t usually work with populations can get confused by the implications of mtDNA and Y chromosomal phylogenies. Melissa Wilson Sayres, who works on Y chromosomes, has a useful post (promised first of two) at Panda’s Thumb, Y and mtDNA are not Adam and Eve: Part 1. If you have friends/acquaintances who are confused by this issue, it might be a good place to start.


Much of the discussion around this topic was triggered by the recent paper in Science, Sequencing Y Chromosomes Resolves Discrepancy in Time to Common Ancestor of Males Versus Females. As Graham Coop observed on Twitter the idea of a “discrepancy” is not clear, insofar as it would not be that surprising if the last common ancestor of the extant Y chromosomal lineages existed at a different time than the last common ancestor of the mtDNA lineages. Expected coalescence is contingent upon various population genetic parameters such as effective population size, but expectations are also subject to variation in realized outcomes. And, as Sayres observes the references to the Adam & Eve analogy were present within the paper, fueling the fire. Finally, the reference to “dogma” tagged onto the end struck me as a touch too cute.

(Republished from Discover/GNXP by permission of author or representative)
 
• Category: Science • Tags: Adam, Eve, Human Genetics, Human Genomics, MTDNA, Y Chromosome 
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There were two papers in Science which came out on the Y chromosome, Sequencing Y Chromosomes Resolves Discrepancy in Time to Common Ancestor of Males Versus Females and Low-Pass DNA Sequencing of 1200 Sardinians Reconstructs European Y-Chromosome Phylogeny. I can recommend what Dienekes had to say, and I wasn’t going to comment until I saw this egregious piece in The New Scientist: Arabian flights: Early humans diverged in 150 years. Because of the title I did not initially think that this had anything to do with the Y chromosome, but it turns out that the piece uses the finding that three primary non-African haplogroups diverged in rapid succession from each other as the hook for the headline. In fact not only does the Y not offer definitive accounts of human history, it doesn’t even necessarily tell us about the history of men. It’s a marker, not a time machine. To repeat: the history of a specific genetic locus is not the history of a population. It has to be said.

(Republished from Discover/GNXP by permission of author or representative)
 
• Category: Science • Tags: Human Evolutionary Genetics, Y Chromosome 
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Credit: Dan Reeves

The Y chromosome is strange. It’s gene poor and loaded with repeats. That’s one reason mtDNA phylogenetic and phylogeographic analysis preceded the Y chromosome by about 10-15 years (the other major reason in the pre-PCR age is that mtDNA is very copious). While the hypervariable region of mtDNA is an excellent molecular clock because of its high mutation rate (though at a deep enough time depth this causes problems, as bases start to turnover), in the pre-next generation sequencing era hunting around the Y chromosomes for SNPs was tedious (a significant portion of Spencer Wells’ Journey of Man focused on the nitty gritty of extraction and preparation).

Despite all this one of the weirder stories over the past decade in relation to the Y chromosome is the peculiar theory promoted by Oxford geneticist Bryan Sykes, and outlined in his book Adam’s Curse: A Future without Men. As I observed above the Y chromosome has a tendency to be filled up with genetic garbage (since it does not recombine deleterious mutations tend to accumulate). There are a few important functional regions (e.g., SRY), but there’s also a reason that sex-linked diseases occur: in most cases males have to rely on the X chromosome to pick up the slack for the Y. Extrapolating this genetic decay Sykes posited that human males would disappear within ~10 million years due to this process working its inevitable logic. Needless to say most scientists were skeptical. Extrapolating without seeing if the projections pass the sniff test is a fool’s errand. And in any case there’s no Law of Nature that sex determination has to be via the Y chromosome. Birds and reptiles have males despite a somewhat different sex determination system.

Rather than pass judgment on the Y it is more appropriately a proper area of investigation. Because of its copious enrichment with repeats (hard to sequence) and paucity of interesting genes (so why bother) to some extent it has received short shrift outside of its role as a molecular marker via microsatellites (exceptions for those interested in specific genes such as SRY and ZFY)). A new paper in Genome Research attempts to catalog and survey the evolutionary history of Y chromosomes in a select number of mammalian taxa. Comparative analysis of mammalian Y chromosomes illuminates ancestral structure and lineage-specific evolution:

Although more than thirty mammalian genomes have been sequenced to draft quality, very few of these include the Y chromosome. This has limited our understanding of the evolutionary dynamics of gene persistence and loss, our ability to identify conserved regulatory elements, as well our knowledge of the extent to which different types of selection act to maintain genes within this unique genomic environment. Here we present the first MSY (male-specific region of the Y chromosome) sequences from two carnivores, the domestic dog and cat. By combining these with other available MSY data, our multi-ordinal comparison allows for the first accounting of levels of selection constraining the evolution of eutherian Y chromosomes. Despite gene gain and loss across the phylogeny, we show the eutherian ancestor retained a core set of 15 MSY genes, most being constrained by negative selection for nearly 100 million years (My). The X-degenerate and ampliconic gene classes are partitioned into distinct chromosomal domains in most mammals, but were radically restructured on the human lineage. We identified multiple conserved non-coding elements that potentially regulate eutherian MSY genes. The acquisition of novel ampliconic gene families was accompanied by signatures of positive selection, and has differentially impacted the degeneration and expansion of MSY gene repertoires in different species.

It is not surprising that genes related to functions in the testes seem to be constrained or under selection in these organisms. The raison d’être of the Y chromosome in some ways is the testes. Rather what’s not so surprising, but striking, are the radical divergences in the genomic architecture of the Y chromosome across these mammalian lineages. Figure illustrates this well:

Click to enlarge

Looking at these results, rough as they are (I have to wonder if the greater structural complexity upon first blush for the human Y chromosome has to do with the greater resources allocated toward sequencing it in comparison to other organisms), it seems clear that the reason Sykes was wrong is that evolutionary process does not proceed in a linear fashion on the Y chromosome. There have been very different trajectories across these lineages. Some of this may be due to lineage specific selective pressures (e.g., r vs. K selected species and their relation to sperm competition). Others may simply be stochastic. The Y chromosome is subject to greater drift (smaller effective population size) than the broader genome. Whatever the details, there’s a broader story to tell.

(Republished from Discover/GNXP by permission of author or representative)
 
• Category: Science • Tags: Evolution, Evolutionary Genetics, Y Chromosome 
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As recently as 10 years ago one could plausibly talk about mtDNA Eve and Y chromosomal Adam. The “Human Story” might then be stylized into a rapid expansion from a small core East African population which flourished ~100,000 years ago, and engaged in a jailbreak sweep out of Africa and across the rest of the World Island, and beyond, to Oceania and the New World. In the process all other human lineages extirpated, marginalized, and eliminated, their culture and genes consigned to oblivion. No longer, the origin of our species may have been characterized by several admixture events with “other” lineages, both within, and outside of, Africa. Instead of a bifurcating tree, imagine a graph with reticulation. A phylogenetic tree with a light, but noticeable lattice scaffold, tying together disparate branches.

All this must be kept in mind when we see a paper such as An African American Paternal Lineage Adds an Extremely Ancient Root to the Human Y Chromosome Phylogenetic Tree. The authors discovered a Y chromosomal lineage, A00, which diverges on the order of ~338,000 years before the present from other extant paternal lineages (the next oldest divergence is A0, ~200,000 years before the present. The 95% interval is 237 to 581 thousand years. Even taking the lower bound this implies that this Y chromosomal lineage diverged from the others before the emergence of anatomically modern humans in Africa ~200,000 years ago.

This sort of result is not about ingenious method or deep insight, but the reality that thick, dense, and expansive population coverage is going to uncover interesting and insightful detail. Though these basal Y (and mtDNA) lineages tend to be found in African hunter-gatherers, A00 is present among Bantu and West African populations. The simplest explanation is that A00 represents at case of genetic admixture between the dominant root lineage to our own species, as a collateral branch. In light of all that we know about genetics and paleontology now this is not entirely surprising. Rather, my question is simple: why is it that we have not found similar Y and mtDNA lineages in non-African populations?

Cite: Mendez et al., doi:10.1016/j.ajhg.2013.02.002

(Republished from Discover/GNXP by permission of author or representative)
 
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Sydney_opera_house_side_viewSometimes in applied fields artistic license is constrained by the necessity of function to particular creative channels. Architecture comes to mind, at least before innovative technologies produced lighter and stronger materials, freeing up form from its straitjacket (whether this was a positive development is a matter of taste). But there’s only so much you can do with your palette when your palette is limited. This can be a bug, or it can be a feature. Science is not art, but in some ways at its heart it’s a story about the universe. The story can be in words or math, no matter, ultimately it’s the human attempt to map nature and make its subtle patterns comprehensible to us in plainer fashion. Some of the human biases in our quest are transparent. Why is there anthropology? A whole discipline devoted to the study of mankind and his nearest biological kin. We don’t peruse the patters with an objective and uninterested eye. We’re shaped by our presuppositions, as well as the constraints of the methods, and the results we have before us. The emergence of a theoretical evolutionary biology in the decades before the molecular revolution after World War II may have been in part simply a function of the fact that there were only so many results one could squeeze out of classical evolutionary genetic techniques, which relied on tracking only a limited set of phenotypes due to large effect mutations in breeding populations. With the rise of molecular evolution you saw the crystallization of theoretical frameworks, such as the neutral theory, to explain the burst of novel results.

ResearchBlogging.org Around the year 2000 something similar happened in historical population genetics. The analysis of mtDNA lineages, passed from mother to daughter, had matured, and techniques for typing the Y chromosome had started to catch up, so that a symmetry between the sexes could arise. “Mitochondrial Eve” was now paired with “Y chromosomal Adam.” Though mtDNA and Y lineages were only two direct lines of ancestry, because there was no recombination across much of their sequence it was easy to analyze them within the context of coalescent theory. In contrast, the genealogy of autosomal regions of the genome were confounded by recombination, which mixed & matched the variation in a manner which made reconstruction of past history far more difficult. So we had the technology to extract the genetic variation from mtDNA and the Y chromosome, and, we knew how to model their evolution. The two together produced a genetic time machine.

spencer_wells_00aThe result was a swelling of papers utilizing uniparental markers. You can see the chronology to some extent at the frequency of postings at Stanford’s Human Population Genetics Laboratory online repository. Another byproduct was the emergence of public intellectuals who filled the need which arose to interpret and communicate the findings to a lay audience. Four books are emblematic of the era, Bryan Sykes’ The Seven Daughters of Eve: The Science That Reveals Our Genetic Ancestry, Spencer Wells’ The Journey of Man: A Genetic Odyssey, Stephen Oppenheimer’s The Real Eve: Modern Man’s Journey Out of Africa, and Steven Olson’s Mapping Human History: Genes, Race, and Our Common Origins. As a professional journalist Olson’s treatment was the odd one out, as much reportage as a personal interpretation. In contrast, Sykes, Wells, and Oppenheimer were making scholarly cases from their own vantage point. Oppenheimer and Wells also paired their books with television documentaries. Wells continues to remain in the public eye, he’s become a new sort of intellectual entrepreneur with the The Genographic Project. The age of uniparental markers then spawned careers and truisms. For example, the patterns of variation of mtDNA and Y chromosomes resulted in the consensus that ~75% of the ancestors of modern Europeans are descended from Paleolithic hunter-gatherers. The proportion of the ancestry contributed by Neolithic farmers decreased from southeast to northwest, converging upon zero in the far reaches of the British Isles and Norden.

R1bmapThis inference was made in large part based upon the contemporary patterns of genetic variation, by assigning modern haplogroups to putative ancient populations. To the left is a map of the frequency of haplogroup R1b, which is the most common Y chromosomal lineage in western Europe. The frequency is highest among the Basques, who were presumed to be the most pristine reservoir of the genetic substratum of Paleolithic Europe. The conception here was that the Basques were clearly indigenous to Iberia, they were already there before the arrival of outsiders such as the Celts, Phoenicians, and finally Romans (this has influenced modern Basque nationalism to some extent). Their non-Indo-European language was assumed to be a relic of many dialects which once existed before Indo-European swept over them. Using R1b, and other haplogroups at high frequency among the “indigenous peoples” of Europe, historical geneticists pegged the ancestral quanta of hypothetical prehistoric groups using these putative indigenes as modern references. But the inferences rested on assumptions, assumptions which couldn’t be directly tested. Until that is another methodological revolution arrived on the scene: the extraction of ancient DNA! These new waves of results, which came to the fore in the latter 2000s, have unsettled our preconceptions. It now seems that the past was likely more complex than we’d presumed, and the palimpsest of human genetic variation over time may have obscured and clouded our understanding of the map of what once was.

More recently some researches have gone back and looked at the variation within the R1b haplogroup, specifically the subclade which is very common in Western Europe, R1b1b2, and concluded that in fact it was most diverse in the eastern Mediterranean. The most plausible inference to be made from this was that the R1b1b2 originated to the east, and spread to the west, rising in frequency due to genetic drift as populations went through bottlenecks and then rapidly expanded in size. Additionally, the last common ancestor of these lineages was on the order of ~10,000 years ago. This naturally upends the model which geneticists were confidently pushing forward in the early 2000s, shutting the door on debates as to the provenance of modern Europeans and their relationship to Ice Age hunter-gatherers. A follow up paper rebutted this new claim as to the origin and expansion of R1b1b2. What had been a stable and conventional area of historical population genetics has now been thrown into tumult, and researchers are looking more closely at the uniparental lineages which had had their time in the sun. Or so it seemed.

So with that background, a paper in The European Journal of Human Genetics steps into the “R1b controversy,” leaning to the side of those who argue for its origin more recently among Neolithic farmers. A major Y-chromosome haplogroup R1b Holocene era founder effect in Central and Western Europe:

The phylogenetic relationships of numerous branches within the core Y-chromosome haplogroup R-M207 support a West Asian origin of haplogroup R1b, its initial differentiation there followed by a rapid spread of one of its sub-clades carrying the M269 mutation to Europe. Here, we present phylogeographically resolved data for 2043 M269-derived Y-chromosomes from 118 West Asian and European populations assessed for the M412 SNP that largely separates the majority of Central and West European R1b lineages from those observed in Eastern Europe, the Circum-Uralic region, the Near East, the Caucasus and Pakistan. Within the M412 dichotomy, the major S116 sub-clade shows a frequency peak in the upper Danube basin and Paris area with declining frequency toward Italy, Iberia, Southern France and British Isles. Although this frequency pattern closely approximates the spread of the Linearbandkeramik (LBK), Neolithic culture, an advent leading to a number of pre-historic cultural developments during the past 10 thousand years, more complex pre-Neolithic scenarios remain possible for the L23(xM412) components in Southeast Europe and elsewhere.

There’s aren’t incredibly novel techniques of analyses here. Rather, the confusion around R1b1b2 has prompted researchers to expand their population coverage and resequence the markers around the haplogroup. These phylogenetic trees are constructed by genealogies which are separated by mutational steps, with steps of daughter mutations down a particular branch and distinguishing various derived clades. The terminology can kind of get confusing, but R1b1b2 is equivalent to the M269 branch in this study. What they did was analyze the phylogenetic relationships of the branches of R1b1b2 and it sister clades, and plot their frequencies as a function of geography. Below are a set of figures which show the frequencies of various clades across Europe. The last figure has several panels because they’re all subclades, and of somewhat less interest to the big picture. The first figure has the various branches, so you can see how they relate before browsing the maps.

[nggallery id=9]

M269 is really the one to focus on. It and its daughter branches are at the heart of the Paleolithic vs. Neolithic controversy. Compare the phylogenetic tree in the first image, and the distributions of the allele frequencies in the subsequent images. The Western European variants seem to be daughter branches from an ancestral variant which is found in Anatolia or thereabouts. The authors also confirm the coalescence back to the last common ancestor ~10,000 years ago, though the methods have a bias toward inflating the value, so that’s an upper bound. They also used PCA analysis show how the haplogroup variation exhibited cluster patterns. The first panel has the haplogroups, with PC 1 separating the ancestral R1b variant from the daughters, and the second PC separating each daughter branch. The second panel inputs the various fractions of R1b haplogroups in populations. There’s an obvious recapitulation of the geographical map in the distribution of haplogroups.

r1bFinal

What’s the moral of this story? I’m not going to get into the correlations they adduce between various archaeological groups and genetic lineages. That got us into trouble earlier as I implied. I don’t think the fine-grained results are solid enough that we should be taking that sort of interpretation too seriously. Rather, it’s telling us what we don’t know, and what we shouldn’t be clear on. I lean toward the proposition that R1b1b2 was brought by Neolithic farmers at this point, the paper which refuted that finding leaned strong on samples from Sardinia, which I suspect are more than not atypical and not representative (Sardinia tends to be an outlier on genetic plots because of its island isolation). But my confidence is hardly even modest at this point. There’s a lot we don’t know.

Stonehenge_back_wideHistory begins in Sumeria with the written word ~5,000 years ago. But as history dawns agriculture was still new to Norden and the fringes of the Baltic and British Isles. By the time what the ancients called Thule came into some focus, after the fall of the Roman Empire, much had passed beyond our line of sight. The original geneticists and archaeologists who attempted to synthesize their disciplines and construct a plausible model of how Europeans and Europe in its linguistic, genetic, and cultural variation, came to be, followed the principle of parsimony. Cavalli-Sofrza, Ammerman, and Renfrew presented us with a model where Paleolithic Europeans, who hunted & gathered, and spoke non-Indo-European languages, were slowly replaced culturally, linguistically, and partially genetically, by Indo-Europeans who brought farming from the Middle East. This was the “demic diffusion” hypothesis. I don’t think anyone accepts this as likely at this point, at least in its total simplicity of explanatory power. We need to reconsider whether the Basques can even serve as models for Paleolithic European man anymore! It may be that the Basques themselves are culturally and genetically intrusive, bringing their language and folkways along Mediterranean shores with agriculture, eventually marginalizing the thin numbers of hunter-gatherers beyond the limes of their “civilization.” Additionally, we have to remember that there was history before history, that what we term prehistory is rich with many developments which are preserved only vaguely and in the mists of oral tradition (though that tradition rapidly decays in fidelity). The more recent expansion of the Bantu and Austronesian languages do not benefit from copious records, because they spread with preliterate societies. The expansion of Turkic and Indo-Iranian dialects can only be perceived in the outlines because these peoples were on the fringes of societies where writing was part of their culture. Europe’s shift to agriculture occurred over thousands of years, and those thousands of years were all preliterate. Stonehenge and the megaliths were constructed by societies which we can comprehend only through their most robust monuments. The stones speak to a complexity which genetics can not resolve. Sometimes admitting that you don’t know is an answer in and of itself.

Citation: Myres NM, Rootsi S, Lin AA, Järve M, King RJ, Kutuev I, Cabrera VM, Khusnutdinova EK, Pshenichnov A, Yunusbayev B, Balanovsky O, Balanovska E, Rudan P, Baldovic M, Herrera RJ, Chiaroni J, Di Cristofaro J, Villems R, Kivisild T, & Underhill PA (2010). A major Y-chromosome haplogroup R1b Holocene era founder effect in Central and Western Europe. European journal of human genetics : EJHG PMID: 20736979

Image Credit: Frédéric Vincent, Matthew Field, National Geographic, Wikimedia

(Republished from Discover/GNXP by permission of author or representative)
 
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Razib Khan
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"I have degrees in biology and biochemistry, a passion for genetics, history, and philosophy, and shrimp is my favorite food. If you want to know more, see the links at http://www.razib.com"