Gene Expression

Tocharians within the last 6,000 years?

From Different Matrilineal Contributions to Genetic Structure of Ethnic Groups in the Silk Road Region in China:

Although our samples were from the same geographic location, a decreasing tendency of the western Eurasian-specific haplogroup frequency was observed, with the highest frequency present in Uygur (42.6%) and Uzbek (41.4%) samples, followed by Kazak (30.2%), Mongolian (14.3%), and Hui (6.7%).

The paper supports the idea that Uyghurs are an admixed population from Western and Eastern sources. But is this just an ancient cline of allele frequencies? In other words, are Uyghur lineage frequencies simply a function of their geographical position between East and West?


These are Y lineage frequencies. The Uyghurs look to be more than 50% “Western” here. This figure is from The Eurasian Heartland: A continental perspective on Y-chromosome diversity.

Something else….


This is from Genetic Evidence for the Convergent Evolution of Light Skin in Europeans and East Asians. I’ve indicated which pie chart are the Uyghers, #30. These are the allele frequencies based on an SNP on SLC24A5 which confers light skin in Europeans. It is ancestral in both Africans & East Asians.



This is from Population differences of two coding SNPs in pigmentation-related genes SLC24A5 and SLC45A2. The Uyghurs are where you would expect for an admixed population.

The data from the skin color genes suggest to me that the Uyghurs weren’t always there, and that they aren’t a transitional population. The Uyghurs are a Turkic speaking people who settled within the Tarim Basin in the last few thousand years. Around 2,000 years ago the people who spoke the Uyghur dialect and identified as Uyghurs (or whatever proto-type tribe there existed as Uyghurs) were resident in Mongolia. Eventually these groups settled along the oases of the Silk Road, Kashgar, Turfan, Khotan and so on. But these cities were not uninhabited. Within them lived people who we know as Tocharians, of Indo-European speech and often exhibiting a phenotype associated with northern Europeans, fair of skin, eye and hair. The famous Tarim Mummies, which seem to be ancestral to the later Tocharians (i.e., many “look” European), can be dated as early as 1800 BCE. About 4,000 years before the present.

If you read this weblog you know I’ve been obsessing with the timing of selective sweeps on skin color genes. That is, at some point in the past all Europeans were fixed for the ancestral variant of SLC24A5, while today they are fixed for the derived. Preliminary work suggests that this new allele might have started rising in frequency very recently, perhaps just 6,000 years ago (though the range could push it up to 12,000 years before the present). Some scholars argue that the Tocharians are derived from the Afanasevo culture, which flourished between 5,500 and 4,500 years before the present in southern Siberia. Taking the extreme dates the selective sweep for SLC24A5 coincides with the migration south of the proto-Tocharians from their Siberian homeland. Could the derived allele have swept that fast across populations from the west? Did it sweep from Siberia to the west? Perhaps it was extant at low minor allele frequencies across central to western Eurasia and a mysterious simultaneous ecological pressure (a plague?) triggered a sweep across many populations.

So perhaps I am wishing to push back the sweep of SLC24A5 based on these rather tenuous archaeological conjectures. I bet the proto-Tocharians were fixed for SLC24A5 when they arrived on the scene, the earliest mummies are rather fair. Where are the alleles of the prior residents? I bet Inner Asia was barely populated, new agricultural techniques and domesticated animals were probably opening up huge swaths of land previously inhabited by very sparse groups of hunter-gathers. The Tocharians came with a culture which could support dense populations, ergo, the Turks who settled among them amalgamated, they did not supersede (at least genetically, the Turkish language of the Uyghurs is apparently intelligible with Turkish in Turkey).

Back to SLC24A5. Look at it barging across mountains all across Western Eurasia and into North Africa. And yet the derived form doesn’t exist at very high frequencies in China. Why? Remember those hunter-gatherers before the Tocharians? I bet that their gene flow was very low. By the time the derived SLC24A5 SNP showed up on the North China plain it could be that another allele which did the same thing, or was good enough, was on the scene. The fitness of a new mutant is contingent upon the genetic landscape in which it resides. I’ve already referred to Genetic Evidence for the Convergent Evolution of Light Skin in Europeans and East Asians. I don’t think that could happen today. I also don’t think it could have happened 2,000 years ago. Gene flow wasn’t anything to shout about, but it was enough that I suspect a super-mutant like SLC24A5 (derived) would have shown up on the scene before something else bubbled out of the genetic background to upstage it.

After the end of the last Ice Age, but before the rise of “civilization,” there was a period when isolated groups of humans took up farming. These populations expanded and launched a demic tidal wave in the local area, they simply swallowed up neighboring populations. They underwent lots of adaptive change because of new selective pressures, and perhaps because of magnification of instrinsic population genetic parameters. In short, during this formative period they were exploring their own adaptive landscapes, coming up with their own solutions to the problems that nature posed. By 2000 BCE this age of independent evolution was coming to an end. “Red haired folk” were on China’s horizon to the west. 2,000 years later the eastward thrust would be countered, as the first of a long series of nomadic peoples from the east would swoop out of the Altai and ravage the plains of Europe and the Middle East.

In this post I mixed phylogenetics, models of adaptive evolution, results from genomics and the historical & archaeological record. Many of the pieces are very rickety, and I don’t have great faith in the narrative that I’m presenting above. But, it’s all proof of principle, the genomic era will usher in a new world of data and novel tools, and the reality that many of the questions asked are historical means that findings from more traditional fields can be brought to bear. It’s a good time to be alive.

Note: There are 1,000 ways to spell “Uyghur.” Do not persecute me for my choice.


  1. #1 AG
    December 24, 2007

    This article will help Uyghur to understand their relationship with those Caucasian mummies.

  2. #2 Porfiriy
    December 30, 2007

    I, for one, support your spelling of Uyghur. It makes the most sense given the phonetic depiction of the word in the Arabic script and the most recent and widely accepted Latin transliterations of Uyghur. :)

    Interesting article! Most if it was beyond me, but I still liked it.