140,000-year divergence time between Eurasians and West Africans

From the paper:

Perhaps our most interesting demographic results are the inferred divergence times. Other studies [11],[12] have estimated divergence times between Europeans and East Asians similar to the ≈23 kya we infer. Interestingly, archeological evidence places humans in Europe much earlier (≈40 kya) [1]. Our inferred divergence time of ≈22 kya between East Asians and Mexican-Americans is somewhat older than the oldest well-accepted New World archeological evidence [2]. The divergence we infer may reflect the settlement of Beringia, rather than the expansion into the New World proper [14]. Finally, the divergence time of ≈140 kya we infer between African and Eurasian populations is consistent with archeological evidence for modern humans in the Middle East ≈100 kya [1], but it is much older than other inferences of ≈50 kya divergence from mitochondrial DNA [1]. This discrepancy may be explained by our inclusion of migration in the model. Migration preserves correlation between population allele frequencies, so an observed correlation across the genome can be explained by either recent divergence without migration or ancient divergence with migration. In fact, the African-Eurasian migration rate we infer of ≈25×10−5 per generation is comparable to the ≈100×10−5 inferred from census records between modern continental Europe and Britain [55].

One difficulty in interpreting our divergence times is that the sampled populations may not best represent those in which historically important divergences occurred. For example, the Yoruba are a West African population, so the divergence time we infer between Yoruba and Eurasian ancestral populations may correspond to divergence within Africa itself. Future studies of more populations [56]–[58] will help alleviate this difficulty.

Some comments:

• The 140ky divergence time between Eurasians and West Africans is consistent with my idea of Africans being divided into Palaeoafricans and Afrasians. The 140ky gap includes both divergence since Eurasians left Africa, as well as divergence between ancestral Eurasians ("Afrasians") and earlier African populations ("Palaeoafricans'). It remains to be seen whether the bulk of the 140ky occurred in Africa itself (in which case conventional Out of Africa c. 40kya is affirmed), or outside Africa (in which case Out of Africa c. 100kya, evidenced by early modern skulls acquires a new significance).
• East Asian - Native American divergence of 22ky predates the known settlement of the Americas. But, this is not a problem, since we must split the 22ky into 15ky (since the settlement), and 8ky, which is reasonable time for divergence between the ancestors of the Chinese and the populations that headed north, and perhaps stayed in Beringia before crossing into the Americas.
• East Asian - European divergence of 23ky suggests, in agreement with recent mtDNA evidence, that Europeans are not primarily descended from the earliest (or even the latest) Upper Paleolithic population of the continent. This seems to also be in agreement with Y-chromosome evidence that suggests interesting East-West connections in Eurasia that are not easily explained by a simple early divergence model with no subsequent link between east and west (e.g., western E vs. eastern D, western R vs. eastern Q, northern N vs. eastern O, etc.). It is also in agreement with the mtDNA picture (West Eurasian N dominance, East Eurasian mixed N/M).

Naturally, both the increased age of divergence of 140ky (compared to other studies), as well as the wide confidence intervals suggest that we must always treat genetic age estimates with the utmost caution.

PLoS Genet 5(10): e1000695. doi:10.1371/journal.pgen.1000695

Inferring the Joint Demographic History of Multiple Populations from Multidimensional SNP Frequency Data

Ryan N. Gutenkunst, Ryan D. Hernandez, Scott H. Williamson, Carlos D. Bustamante

Abstract

Demographic models built from genetic data play important roles in illuminating prehistorical events and serving as null models in genome scans for selection. We introduce an inference method based on the joint frequency spectrum of genetic variants within and between populations. For candidate models we numerically compute the expected spectrum using a diffusion approximation to the one-locus, two-allele Wright-Fisher process, involving up to three simultaneous populations. Our approach is a composite likelihood scheme, since linkage between neutral loci alters the variance but not the expectation of the frequency spectrum. We thus use bootstraps incorporating linkage to estimate uncertainties for parameters and significance values for hypothesis tests. Our method can also incorporate selection on single sites, predicting the joint distribution of selected alleles among populations experiencing a bevy of evolutionary forces, including expansions, contractions, migrations, and admixture. We model human expansion out of Africa and the settlement of the New World, using 5 Mb of noncoding DNA resequenced in 68 individuals from 4 populations (YRI, CHB, CEU, and MXL) by the Environmental Genome Project. We infer divergence between West African and Eurasian populations 140 thousand years ago (95% confidence interval: 40–270 kya). This is earlier than other genetic studies, in part because we incorporate migration. We estimate the European (CEU) and East Asian (CHB) divergence time to be 23 kya (95% c.i.: 17–43 kya), long after archeological evidence places modern humans in Europe. Finally, we estimate divergence between East Asians (CHB) and Mexican-Americans (MXL) of 22 kya (95% c.i.: 16.3–26.9 kya), and our analysis yields no evidence for subsequent migration. Furthermore, combining our demographic model with a previously estimated distribution of selective effects among newly arising amino acid mutations accurately predicts the frequency spectrum of nonsynonymous variants across three continental populations (YRI, CHB, CEU).

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