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

May 30, 2018

The cultural conditions of star-shaped phylogenies

Filed under: Population History,Y chromosomal lineages — Razib Khan @ 11:53 pm

In the generality, I think intergroup selection of paternal lineages is the answer to why star-shaped phylogenies are so evident in the phylogenetic record ~4,000 years ago. More precisely, most of the major clades of R1a, R1b, and I1 undergo massive expansion after a sharp reduction in effective population size around this period. The R lineages diversified during the Pleistocene, probably in Central Eurasia (it is a brother clade to Q). The I lineage derives from Western European hunter-gatherers, probably the late Pleistocene expansion which eventually gave rise to the Mesolithic groups that encountered the early farmers.

But what happened here specifically? Let me quote a section of Peter Turchin’s excellet Ultrasociety: How 10,000 Years of War Made Humans the Greatest Cooperators on Earth:

Lanchester’s Square Law yields an enormous return to social scale. If the opposing forces use a mix of ranged and shock weapons, numerical superiority will still be amplified, although not as much as with purely projectile weapons. So there is an intense selection pressure for cultural groups living in flat terrain to scale up, and a very high price to pay by those that fail to do s….

Though human interaction with horses as domesticates is probably older, light chariots emerged on the Pontic steppe ~4,000 years ago. Within a few centuries, this technology was ubiquitous in the Near East. The Indo-Aryan Mitanni arrive with chariots in modern Syria/Northern Iraq by ~3,750 years ago.

In the Near East chariots and bows were closely associated. The evidence from the Eurasian steppe during the Bronze Age seems less definitive (simply, bows may not preserve very well), though by the Iron Age the mounted archer became a ubiquitous feature of the military landscape.

The combination of chariots, likely bows, and the Sintashta/Srubna/Andronovo culture’s known focus on metallurgy, make it hard for me to deny the likelihood that the expansion of R1a1a-Z93 has something to do with intergroup conflict. The reality is that Lanchester’s Square Law means that even small initial advantageousness for a given paternal lineage will probably snowball. One victory will lead to an increase in territory and resources, which will produce later advantage. A sort of Y chromosomal Matthew Effect.

But this doesn’t explain what occurred in Europe, where R1b and I1 also underwent a massive expansion (and R1a as well). Europe’s relatively forested territory beyond the Hungarian plain always blunted the power and reach of mounted archers later in history. We do know that chariots arrived in the Mediterranean around the same time as in the Near East. But the rise to dominance of the Corded Ware and Bell Beaker peoples predates light chariots. Perhaps it is something as simple as the fact that metaethnic institutions and identities that could dampen intergroup conflict hadn’t emerged, but it’s still curious to me that one could have a ~90% population replacement in Britain in a few centuries.

Perhaps we will find out that it has to do with a disease as our understanding of ancient epidemics gets better.

 

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.

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