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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 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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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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Citation: European Journal of Human Genetics advance online publication, 4 June 2014; doi:10.1038/ejhg.2014.106

Since I am now the father of a son my Y chromosomal haplogroup, R1a1a, has replicated itself one more time. That’s not a big deal seeing as it is probably the most widespread Eurasian paternal lineage. But why this particular lineage has the distribution it does is interesting and complex. In the early 2000s Spencer Wells published The Eurasian Heartland: A continental perspective on Y-chromosome diversity, which seemed to suggest that its expansion was due to that of the Indo-Europeans. Others have argued for an earlier diversification, due to divergences between European and Asian branches of R1a1a. A new paper puts these debates into deeper historical perspective, and nicely sums up where we are with uniparental lineages. Improved phylogenetic resolution and rapid diversification of Y-chromosome haplogroup K-M526 in Southeast Asia, with relevant bits:

These haploid systems are subject to stronger genetic drift and large evolutionary variance, and may not render accurate signals of population processes by themselves. Yet, the considerable geographic structure at these loci suggests that current patterns of variation may be informative of past population processes. With the implicit assumption that groups dispersing in the Pleistocene were small and experienced strong and long-lasting bottlenecks, patterns of mtDNA and NRY variation have been deemed useful as starting points to formulate hypotheses about human demographic history.

Note the caution. Also, I would take a slight issue with the last quoted sentence: the reason that haploid lineages were useful starting points had less to do with their utility in reconstructing the history of populations and more to do with technical constraints. Mitochondrial DNA is famously copious in comparison to nuclear DNA, while the nonrecombining nature of uniparental lineages makes them very amenable to transparent tree building. Rather than starting points, mtDNA and Y chromosomal lineages should be seen as informative supplements. With the rise of dense SNP chip technologies, and now whole genome sequencing, that’s they’re becoming.

This particular paper is interesting insofar as it traces back the emergence of the ancestor of R1a1a, and more generally R, among the panoply of non-African haplogroups. You can see on the map above that the light blue is basically absent from eastern Eurasian. Those are the R and Q lineages.The diversity of lineages in southeast Asia is very suggestive. Usually where lineages diversify they’ve been around for a while. Areas with lower diversity have often been settled later, and gone through diversity decreasing bottlenecks and such. The authors conclude:

In sum, our results support the hypothesis of a Southeast Asian/Oceanian center for the diversification of Oceanian K-haplogroup lineages and underscore the potential importance of Southeast Asia as a source of genetic variation for Eurasian populations.

The K group in question being the broader linage of which R is just a subset. I’m not sure that I buy the specific model here, but do note that it seems that the ~20,000 year old Siberian remain seems to have been of haplogroup R. And in the above paper they state “Interestingly, ancient DNA evidence suggests that haplogroup R1b – the current dominant lineage in western Europe –
did not reach high frequencies until after the European Neolithic period as given in Lacan et al 26,27 and Pinhasi et al. 28” In other words the results above would have seemed really strange a few years ago, as one would have previously though R was an ancient western Eurasian lineage just by its distribution. And it is today clearly a western Eurasian lineage, but did it always have to be so?

Recall that Y lineages are subject to “stronger genetic drift and large evolutionary variance.” The people today who tend to be carriers of the R lineages don’t exhibit any strong connection to the peoples of southeast Asia. But this one lineage may have risen in frequency among elite males at some point in a particular Eurasian population which came to be dominant. Rapid spread of males and constant intermarriage would dilute the whole genome signal quite rapidly, but the Y chromosomal lineage can maintain itself in the face of this because it does not mix. It replaces or is replaced. Chance may have increased the frequency of the eastern R lineage, but eventually it hitchhiked with destiny.

• Category: Science • Tags: R1a1a 
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As many of you know around the year 2000 the analyses of Y chromosomal human lineages became a pretty big deal. The reason these lineages are important and useful is that they record the uninterrupted ancestry of males, from father to son, along the Y chromosome. Instead of the complexities of the whole genome, as with mtDNA you have a simple and elegant phylogenetic tree to interpret. The clusters along this tree are defined as broad haplogroups, united by derived states from a common ancestor. One of the largest haplogroups is R1a1a. It happens to be my paternal lineage, as well as Dr. Daniel MacArthur’s and Dr. Zack Ajmal’s.

The map above illustrates the peculiarity of R1a1a: it is geographically enormously expansive. How to explain this distribution? A naive response might be that this distribution is surprising similar to that of the Indo-European languages. Unfortunately this runs up against the conundrum that low caste South Indian groups, relatively untouched by Indo-Aryan culture (at least until the past few hundred years), also manifest high frequencies of R1a1a.

To make a long story short it seems that R1a1a is an old haplogroup with a lot of structure across Eurasia. Maju points me to a paper in American Journal of Physical Anthropology which simply & elegantly brings home to us some obvious insights, New Y-chromosome binary markers improve phylogenetic resolution within haplogroup R1a1:

Haplogroup R1a1-M198 is a major clade of Y chromosomal haplogroups which is distributed all across Eurasia. To this date, many efforts have been made to identify large SNP-based subgroups and migration patterns of this haplogroup. The origin and spread of R1a1 chromosomes in Eurasia has, however, remained unknown due to the lack of downstream SNPs within the R1a1 haplogroup. Since the discovery of R1a1-M458, this is the first scientific attempt to divide haplogroup R1a1-M198 into multiple SNP-based sub-haplogroups. We have genotyped 217 R1a1-M198 samples from seven different population groups at M458, as well as the Z280 and Z93 SNPs recently identified from the “1000 Genomes Project”.

The two additional binary markers present an effective tool because now more than 98% of the samples analyzed assign to one of the three sub-haplogroups. R1a1-M458 and R1a1-Z280 were typical for the Hungarian population groups, whereas R1a1-Z93 was typical for Malaysian Indians and the Hungarian Roma. Inner and Central Asia is an overlap zone for the R1a1-Z280 and R1a1-Z93 lineages. This pattern implies that an early differentiation zone of R1a1-M198 conceivably occurred somewhere within the Eurasian Steppes or the Middle East and Caucasus region as they lie between South Asia and Eastern Europe. The detection of the Z93 paternal genetic imprint in the Hungarian Roma gene pool is consistent with South Asian ancestry and amends the view that H1a-M82 is their only discernible paternal lineage of Indian heritage.

The table to the left shows you an Indian population from Malaysia. Malaysian Indians tend to be Tamils, from the south of the subcontinent. If they were finding individuals who were carriers of R1a1a, the data set is probably somewhat enriched for Tamil Brahmins and people of North Indian ancestry, though this does not alter the basic story. What you see is that all the Indians carry this one distinctive mutation. I find it unlikely that all these Malaysian Indians are Brahmins or North Indians, especially given that there is a non-trivial proportion of R1a1a in Tamil lower castes. So here you have a population with is probably representative of Indian Y chromosomal phylogeography before the Indo-Aryans arrived. Second, you see that M458 is well represented among Hungarians. This makes sense, insofar as this is a very common variant in Eastern Europe. Z280 also seems to be found in northern Eurasia. An interesting aspect is that in the Uzbek sample z93 has a high frequency. The Uzbeks are an admixed population. A Turkic component overlain atop an Iranian substrate. The frequency of Z93 suggests to me that the Eastern Iranians share common ancestry with South Asians. This is not a revolutionary finding, but it does imply that Z93 may have come, in part, with the Indo-Aryans (i.e., there were two or more waves of Z93).

The authors note that Z458 and Z93 carrying individuals exhibit “star like” phylogenies when STRs were analyzed. They are the top two panels. The Genghis Khan haplotype exhibits a star like phylogeny. In other words, it’s indicative of rapid expansion from a small founder group. In contrast, they argue that Z280 carrying Y chromosomes do not exhibit a star like phylogeny. The implication being that it did not undergo the same expansion. Dates of expansion (looking at the most recent common ancestor) for Z458 and Z93 are pegged to 7 and 10 thousand years before the present. I don’t put much stock in these dates personally, but I thought I’d relay them.

What can we say from this? If these results hold what they tell us is that R1a1a is a very lucky haplogroup, and its current range is a function of multiple expansions from a common and diverse R1a1a pool, probably in Central Eurasia. The presence of Z93 in Uzbeks, and Mongols, suggests to me that this variant was and is present in Iranians. Therefore, I don’t think that Z93 is indigenous to South Asia, but is intrusive. I believe it arrived with the “Ancestral North Indians.”

• Category: Science • Tags: Anthropology, R1a1a 
Razib Khan
About Razib Khan

"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"