An Extended Admixture Pulse Model Reveals the Limitations to Human-Neandertal Introgression Dating.

Leonardo N M Iasi,Harald Ringbauer,Benjamin M Peter,Daniel Falush

doi:10.1093/molbev/msab210

Leonardo N M Iasi, Harald Ringbauer + Show 2 more

Open Access

https://doi.org/10.1093/molbev/msab210

Copy DOI

Abstract

Neandertal DNA makes up 2–3% of the genomes of all non-African individuals. The patterns of Neandertal ancestry in modern humans have been used to estimate that this is the result of gene flow that occurred during the expansion of modern humans into Eurasia, but the precise dates of this event remain largely unknown. Here, we introduce an extended admixture pulse model that allows joint estimation of the timing and duration of gene flow. This model leads to simple expressions for both the admixture segment distribution and the decay curve of ancestry linkage disequilibrium, and we show that these two statistics are closely related. In simulations, we find that estimates of the mean time of admixture are largely robust to details in gene flow models, but that the duration of the gene flow can only be recovered if gene flow is very recent and the exact recombination map is known. These results imply that gene flow from Neandertals into modern humans could have happened over hundreds of generations. Ancient genomes from the time around the admixture event are thus likely required to resolve the question when, where, and for how long humans and Neandertals interacted.

Highlights

IntroductionThe sequencing of Neandertal (Green et al 2010; Prufer et al 2013, 2017; Mafessoni et al 2020) and Denisovan genomes (Reich et al 2010; Meyer et al 2012) revealed that modern humans outside of Africa interacted, and received genes from these archaic hominins (Fu et al 2014, 2015; Sankararaman et al 2014, 2016; Vernot and Akey 2014; Malaspinas et al 2016; Vernot et al 2016)
Our model has just two parameters, that can be interpreted as the mean time and duration of gene flow; and has simple closed form solutions for the segment length and ancestry linkage disequilibrium (ALD) distributions
We demonstrate that the segment length distribution and ALD-decay can be directly transformed into each other; in particular, the segment-length distribution is proportional to the second derivative of the ALD-decay curve

Summary

Introduction

The sequencing of Neandertal (Green et al 2010; Prufer et al 2013, 2017; Mafessoni et al 2020) and Denisovan genomes (Reich et al 2010; Meyer et al 2012) revealed that modern humans outside of Africa interacted, and received genes from these archaic hominins (Fu et al 2014, 2015; Sankararaman et al 2014, 2016; Vernot and Akey 2014; Malaspinas et al 2016; Vernot et al 2016). As a second line of evidence, all non-Africans carry genomic segments that are very similar to the sequenced archaic genomes. As these putative admixture segments are up to several hundred kilobases (kb) long, it is unlikely that they were inherited from a common ancestor that predates the split of modern and archaic humans (Sankararaman et al 2014; Vernot and Akey 2014). They entered the modern human populations through later gene flow (Sankararaman et al 2012, 2014, 2016; Vernot and Akey 2014; Vernot et al 2016)

Methods

Results

Conclusion