Limits of long-term selection against Neandertal introgression

Several studies have suggested that introgressed Neandertal DNA was subjected to negative selection in modern humans. A striking observation in support of this is an apparent monotonic decline in Neandertal ancestry observed in modern humans in Europe over the past 45,000 years. Here, we show that t...

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Bibliographic Details
Published in:Proceedings of the National Academy of Sciences - PNAS 2019-01, Vol.116 (5), p.1639-1644
Main Authors: Petr, Martin, Pääbo, Svante, Kelso, Janet, Vernot, Benjamin
Format: Article
Language:English
Subjects:
Alleles
Animals
Biological Sciences
Computer simulation
Conserved Sequence - genetics
Demography
Deoxyribonucleic acid
Depletion
DNA
DNA - genetics
Europe
Evolution, Molecular
Gene flow
Gene Flow - genetics
Genomes
Hominids
Homo neanderthalensis
Human populations
Humans
Neanderthals - genetics
Negative selection
Proteins
RNA, Untranslated - genetics
Selection, Genetic - genetics
White People - genetics
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Summary:Several studies have suggested that introgressed Neandertal DNA was subjected to negative selection in modern humans. A striking observation in support of this is an apparent monotonic decline in Neandertal ancestry observed in modern humans in Europe over the past 45,000 years. Here, we show that this decline is an artifact likely caused by gene flow between modern human populations, which is not taken into account by statistics previously used to estimate Neandertal ancestry. When we apply a statistic that avoids assumptions about modern human demography by taking advantage of two high-coverage Neandertal genomes, we find no evidence for a change in Neandertal ancestry in Europe over the past 45,000 years. We use whole-genome simulations of selection and introgression to investigate a wide range of model parameters and find that negative selection is not expected to cause a significant long-term decline in genome-wide Neandertal ancestry. Nevertheless, these models recapitulate previously observed signals of selection against Neandertal alleles, in particular the depletion of Neandertal ancestry in conserved genomic regions. Surprisingly, we find that this depletion is strongest in regulatory and conserved noncoding regions and in the most conserved portion of protein-coding sequences.
ISSN:0027-8424
1091-6490
1091-6490
DOI:10.1073/pnas.1814338116