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Multiple episodes of interbreeding between Neanderthal and modern humans


Neanderthals and anatomically modern humans overlapped geographically for a period of over 30,000 years following human migration out of Africa. During this period, Neanderthals and humans interbred, as evidenced by Neanderthal portions of the genome carried by non-African individuals today. A key observation is that the proportion of Neanderthal ancestry is ~12–20% higher in East Asian individuals relative to European individuals. Here, we explore various demographic models that could explain this observation. These include distinguishing between a single admixture event and multiple Neanderthal contributions to either population, and the hypothesis that reduced Neanderthal ancestry in modern Europeans resulted from more recent admixture with a ghost population that lacked a Neanderthal ancestry component (the ‘dilution’ hypothesis). To summarize the asymmetric pattern of Neanderthal allele frequencies, we compiled the joint fragment frequency spectrum of European and East Asian Neanderthal fragments and compared it with both analytical theory and data simulated under various models of admixture. Using maximum-likelihood and machine learning, we found that a simple model of a single admixture did not fit the empirical data, and instead favour a model of multiple episodes of gene flow into both European and East Asian populations. These findings indicate a longer-term, more complex interaction between humans and Neanderthals than was previously appreciated.

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Fig. 1: Graphic representation of the process to make an FFS.
Fig. 2: Individual and joint fragment frequency spectra.
Fig. 3: Representation of the five different demographic models simulated in msprime.
Fig. 4: Results from the FCNN classifier.

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No novel datasets were generated or analysed during the current study.


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We are grateful to S. Mathieson and J. Spence for several useful discussions about neural network architecture and appropriate methods for training neural networks. We also thank J. Spence and M. Steinrücken for extensive discussions on errors in fragment calling. I. Mathieson, S. Mathieson and J. Spence provided invaluable feedback on an early draft of this manuscript that helped improve its clarity. K. Harris provided invaluable discussions during the conception and work of this manuscript. We are grateful to M. Petr and B. Vernot for sharing processed simulation data with us, and for discussions about the impact of selection on Neanderthal ancestry. J.G.S. and F.A.V. were supported by NIH grant R35 GM124745. This research was supported in part by the National Science Foundation through major research instrumentation grant number 1625061 for the Owl’s Nest high-performance cluster at Temple University.

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F.A.V. and J.G.S. designed the study, analysed the data, performed the simulations and wrote the manuscript.

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Correspondence to Joshua G. Schraiber.

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Supplementary information

Supplementary Information

Supplementary Methods and Supplementary Figures

Reporting Summary

Supplementary Table 1

Parameter estimates from the Asian data

Supplementary Table 2

Parameter estimates from the European data

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Villanea, F.A., Schraiber, J.G. Multiple episodes of interbreeding between Neanderthal and modern humans. Nat Ecol Evol 3, 39–44 (2019).

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