Twice Mixed? Testing hypotheses of Neanderthal Introgression

Human migration in, and out of Africa was wrought with complex patterns of admixture (see my previous post summarizing the story so far). Of note were some recent findings on the disparity in amounts of Neanderthal introgression/ancestry between East Asians and Europeans (eg. see Vernot and Akey 2014). In yet another duel of sorts, two recent studies by Vernot and Akey (2015), and Kim and Lohmueller (2015) use separate approaches to test the hypothesis proposing the efficacy of purifying selection in bottlenecked East Asian populations to retain more Neanderthal ancestry (Sankararaman et al. 2014).

Infographic describing Neanderthal admixture into humans. Image courtesy:

Vernot and Akey (2015) partitioned East Asian and European genomes into windows based on B-values (degrees to which neutral variation has been reduced as a result of linked selected sites), and also computed proportions of observed Neanderthal ancestry in the same windows.  If indeed greater Neanderthal ancestry in East Asians is due to purifying selection, then these proportions should vary significantly by B-values. Vernot and Akey report that this isn’t true, and yet East Asians have ~17.5% more introgressed sequence. Subsequent explorations of demographic models using ABC indicate only 2 pulse models as acceptable, strongly rejecting the model of a single pulse.

Kim and Lohmueller (2015) test the same hypothesis using forward Wright-Fisher simulations of a million independent informative genomic sites, under the model of a single pulse of Neanderthal admixture, 1900 generations back. Starting proportions of Neanderthal ancestry were varied (although one wouldn’t expect these to vary between East Asian and European genomes under a single pulse model). Remnant Neanderthal ancestry in each population was then measured. Alternate simulations also explored loci with various selection coefficients, dominance effects, and bottlenecks.

In all cases of evolved loci that matched empirical expectations, however, the proportion of Neanderthal ancestry in East Asians to Europeans was equivalent, also unchanging with altering the length or severity of population bottleneck. The proportion does however change with varying the amount of starting ancestry – indicative of a 2 or more pulse model of Neanderthal introgression.

Two studies with similar conclusions, and indicative of so much more that’s left to learn about the complex anthropological and genomic history of modern humans.


Vernot and Akey, Complex History of Admixture between Modern Humans and Neandertals, The American Journal of Human Genetics (2015),

Kim and Lohmueller, Selection and Reduced Population Size Cannot Explain Higher Amounts of Neandertal Ancestry in…, The American Journal of Human Genetics (2015),



About Arun Sethuraman

I am a computational biologist, and I build statistical models and tools for population genetics. I am particularly interested in studying the dynamics of structured populations, genetic admixture, and ancestral demography.
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