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On the Apportionment of Archaic Human Diversity

View ORCID ProfileKelsey E. Witt, View ORCID ProfileFernando Villanea, Elle Loughran, View ORCID ProfileEmilia Huerta-Sanchez
doi: https://doi.org/10.1101/2021.07.15.452563
Kelsey E. Witt
1Ecology, Evolution, and Organismal Biology, Brown University
2Center for Computational Molecular Biology, Brown University
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Fernando Villanea
3Department of Anthropology, University of Colorado Boulder
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Elle Loughran
4Smurfit Institute of Genetics, Trinity College Dublin, Dublin, Republic of Ireland
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Emilia Huerta-Sanchez
1Ecology, Evolution, and Organismal Biology, Brown University
2Center for Computational Molecular Biology, Brown University
4Smurfit Institute of Genetics, Trinity College Dublin, Dublin, Republic of Ireland
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  • For correspondence: emilia_huerta-sanchez@brown.edu
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Abstract

The apportionment of human genetic diversity within and between populations has been measured to understand human relatedness and demographic history. Likewise, the distribution of archaic ancestry in modern populations can be leveraged to better understand the interaction between our species and its archaic relatives, and the impact of natural selection on archaic segments of the human genome. Resolving these interactions can be difficult, as archaic variants in modern populations have also been shaped by genetic drift, bottlenecks, and gene flow. Here, we investigate the apportionment of archaic variation in Eurasian populations. We find that archaic genome coverage at the individual- and population-level present unique patterns in modern human population: South Asians have an elevated count of population-unique archaic SNPs, and Europeans and East Asians have a higher degree of archaic SNP sharing, indicating that population demography and archaic admixture events had distinct effects in these populations. We confirm previous observations that East Asians have more Neanderthal ancestry than Europeans at an individual level, but surprisingly Europeans have more Neandertal ancestry at a population level. In comparing these results to our simulated models, we conclude that these patterns likely reflect a complex series of interactions between modern humans and archaic populations.

Competing Interest Statement

The authors have declared no competing interest.

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
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Posted July 16, 2021.
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On the Apportionment of Archaic Human Diversity
Kelsey E. Witt, Fernando Villanea, Elle Loughran, Emilia Huerta-Sanchez
bioRxiv 2021.07.15.452563; doi: https://doi.org/10.1101/2021.07.15.452563
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On the Apportionment of Archaic Human Diversity
Kelsey E. Witt, Fernando Villanea, Elle Loughran, Emilia Huerta-Sanchez
bioRxiv 2021.07.15.452563; doi: https://doi.org/10.1101/2021.07.15.452563

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