Razib Khan One-stop-shopping for all of my content

May 26, 2018

Y chromosomal star-phylogenies as inter-group competition between paternal lineages

Filed under: Human Population Genetics,Star phylogenies,Y chromosomal lineages — Razib Khan @ 11:37 pm

The figure to the left should be familiar to readers of this weblog. It is taken from A recent bottleneck of Y chromosome diversity coincides with a global change in culture (Kamin et al.). Over the past few years a peculiar fact long suspected or inferred has come into sharp focus: some of the Y chromosome haplogroups very common today were not so common in the past, and their frequency changed very rapidly over a short time period.

What Kamin et al. did was look at sequence data across the Y chromosome to make deeper inferences. The issue is that the Y chromosome is not genetically very diverse. Earlier generations of researchers focused on highly mutable microsatellite regions for identification. While microsatellites are good for identification and classification because of their genetic diversity, they are not as good when it comes to making evolutionary inferences about parameters such as time since last common ancestor. They have very high and variable mutation rates.

Single nucleotide polymorphisms (SNPs) are probably better for a lot of evolutionary inference, but the Y chromosome doesn’t have too many of these. SNP-chip era technology which focuses on a select subset of polymorphisms at specific locations didn’t have much to choose from and likely missed rare variants.

This is where whole-genome sequence of the Y comes in. It retrieves maximal information, and with that, the authors of Kamin et al. could definitely confirm that some Y chromosomal lineages under explosive expansion ~4,000 years ago after a bottleneck.

By and large ancient DNA take a different angle, focusing on genome-wide autosomal ancestry, and lacking in high-coverage whole-genome sequences. But they have confirmed the inferences from whole-genomes that some of these lineages exhibit explosive growth in the last ~4,000 years. One moment they were rare, and the next moment ubiquitous.

But geneticists are geneticists. They’re interested in genetical questions, methods, and dynamics. To be frank cultural models for how those genetic patterns might have come about are either exceedingly simple and probably true (e.g., gene-culture coevolution with lactase persistence), or vague and handwavy. With the surfeit of genomic data to analyze it isn’t surprising that this happens.

This is why researchers in the field of cultural evolution need to get involved. They’re model-builders and should see which models predict the copious empirical results we have now when it comes to genetic change over time.

For several years now I have been asserting that inter-group competition of paternal lineages best explains the pattern of Y chromosome expansions ~4,000 years ago. A new paper brings forth a formal model which explores this hypothesis, Cultural hitchhiking and competition between patrilineal kin groups explain the post-Neolithic Y-chromosome bottleneck:

In human populations, changes in genetic variation are driven not only by genetic processes, but can also arise from cultural or social changes. An abrupt population bottleneck specific to human males has been inferred across several Old World (Africa, Europe, Asia) populations 5000–7000 BP. Here, bringing together anthropological theory, recent population genomic studies and mathematical models, we propose a sociocultural hypothesis, involving the formation of patrilineal kin groups and intergroup competition among these groups. Our analysis shows that this sociocultural hypothesis can explain the inference of a population bottleneck. We also show that our hypothesis is consistent with current findings from the archaeogenetics of Old World Eurasia, and is important for conceptions of cultural and social evolution in prehistory.

Their model is interesting because inter-group competition between paternal lineages can result in a loss of haplogroup diversity without huge reproductive skew. That is, instead of a highly polygynous society, one can simply posit that group dynamics of expansion and extinction produce expansions of Y chromosomal lineages.

A formal model synthesized with genomic results is a major step forward, though I haven’t dug into the methods (computational or analytic). Presumably, this is a first step.

But the discussion does review a lot of anthropological literature about the nature of human conflict and social interaction. Basically, it seems that between nomadic hunter-gatherers and before chiefdoms, biologically defined paternal clans were often the organizing principle of society. To some extent this makes total sense since the meta-ethnic religious and social identities explicitly appeal to fictive relationships of blood even after blood was no longer paramount. Ancient Near Eastern kings addressed each other in familial terms (e.g., “brother” and “son”), while universal religions deploy the construct of brotherhood.

In Empires of the Silk Road the author makes the case that these bands of brothers were more influential in shaping history than we realize today. Not surprisingly, the authors of the above paper suggest that the Inner Asian nomad zone is where star-phylogenies have been most pervasive and persist down to historical time. As in Steven Pinker’s The Better Angels of Our Nature it seems that the rise of the state suppressed the viciousness of the paternal kin group. How do we know this? Because the period of the maximal explosion of star-phylogenies seem to be a transient between the early Neolithic and the historical age.

The Y chromosomal literature is just the low hanging fruit. I suspect in the next decade cultural evolutionary models will be brought to bear on the huge mountain of genomic data….

Citation: Cultural hitchhiking and competition between patrilineal kin groups explain the post-Neolithic Y-chromosome bottleneck Tian Chen Zeng, Alan J. Aw & Marcus W. Feldman.

April 2, 2017

Why are so many of us “star-men”

Filed under: Anthroplogy,Culture,R1a,R1b,Star phylogenies — Razib Khan @ 11:32 pm

Seven years ago I wrote 1 in 200 men direct descendants of Genghis Khan. It’s the most popular post I’ve ever written. As of now there have been 630,000 “sesssions” (basically visits) on that page alone. I suspect that many more have read my summary of The Genetic Legacy of the Mongols, the original paper on which it was based, than that paper (though it’s a good paper, you should read it).

At the time I wrote that people often asked me if I was a descendent of Genghis Khan. That seems unlikely on the paternal lineage. My Y chromosome is R1a1ab2-Z93. This is typically found in South Asia, and among Iranian peoples, as well as in the Altai region of western Mongolia. It is not common among Mongols though, even if it is found amongst them, likely due to gene flow from the west. The particular branch of R1a1a that I carry has been found in ancient remains from the Srubna culture of the eastern Pontic steppe. As a friend of mine might say, I am the scion of marauders from the steppe, even though not Genghiside ones. The fact that I have the last name Khan is simply a legacy of the custom whereby South Asian Muslim lineages of a particular status accrued the surname to denote their position within Islamicate civilization.

But though I am no direct descendent of Genghis, it turns out that my Y chromosome shares a similar history. The figure to the left is focused on European Y chromosomes, and at the top you see various “R” lineages. It turns out that R1b and R1a are both basically subject to the same explosive dynamics as the Genghis Khan haplotype: both exploded into star phylogenies relatively recently in time. Trees of the R1 lineages always show them to exhibit a rake-like pattern. This is due to the fact that starting from a small base they expanded so rapidly that they did not develop the intricate node-structure you see in lineages which accrued mutations at a more normal pace.

What could have caused such explosive growth? We know why Genghis Khan and his sons left so many descendents: conquest yielded social status. For many generations having a male Genghiside bloodline was highly effective as a means to gain bonus points when attempting to scale the summits of power and wealth. This was even true in the Muslim regions of Central Asia, despite Genghis Khan’s negative impact on Islamic civilization (Transoxiana arguably never recovered from this period).

We don’t have anything like the “Secret History of the Indo-Aryans” to explain the emergence of these older star phylogenies. In The Horse, the Wheel, and Language, David Anthony argues that mobile populations domesticated the horse, and used that as a killer cultural advantage to spread their Indo-European language. In his book from the 2000s Anthony argues for elite transmission of language by the Kurgan people. But more recently he has been persuaded by genetic work which suggests massive population displacements and migrations into Europe during the late Neolithic and early Bronze Age.

Unfortunately the timing doesn’t work from what I can tell. The expansion of groups like the Corded Ware seem to pre-date the emergence of the steppe chariot toolkit by many centuries. It does so happen that the chariot was invented in the region where R1a1a2b-Z93 was also found to exist. So I suspect this “Scythian” R1a lineage did sweep across much of Central-South Eurasia thanks to the horse and the wheel. But a technological explanation is more difficult for the rest.

I will posit another speculative answer, stealing the idea from Snorri Sturluson. He believed that the gods that were remembered by his pagan Norse ancestors were at one point men of great renown and fame. Kings of yore. Over time they had been deified, and legends had grown up around them. Sturluson may have been right. Perhaps the Indo-European gods recollect the forefathres of R1a and R1b. What was there advantage? Perhaps it was a hierarchical stratified social structure which brooked no individualism against the interests of the lineage unit? It may be that asabiyya is worth more than a chariot?

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