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Neanderthal introgression reintroduced functional alleles lost in the human out of Africa bottleneck

View ORCID ProfileDavid C. Rinker, View ORCID ProfileCorinne N. Simonti, Evonne McArthur, Douglas Shaw, Emily Hodges, View ORCID ProfileJohn A. Capra
doi: https://doi.org/10.1101/533257
David C. Rinker
1Department of Biological Sciences, Vanderbilt University, Nashville, TN, 37235, USA
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Corinne N. Simonti
2Department of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, 30332, USA
3Vanderbilt Genetics Institute, Vanderbilt University, Nashville, TN 37235, USA
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Evonne McArthur
3Vanderbilt Genetics Institute, Vanderbilt University, Nashville, TN 37235, USA
4Medical Scientist Training Program, Vanderbilt University, Nashville, TN 37235, USA
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Douglas Shaw
3Vanderbilt Genetics Institute, Vanderbilt University, Nashville, TN 37235, USA
5Department of Biochemistry, Vanderbilt University, Nashville, TN, 37235, USA
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Emily Hodges
3Vanderbilt Genetics Institute, Vanderbilt University, Nashville, TN 37235, USA
5Department of Biochemistry, Vanderbilt University, Nashville, TN, 37235, USA
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John A. Capra
1Department of Biological Sciences, Vanderbilt University, Nashville, TN, 37235, USA
3Vanderbilt Genetics Institute, Vanderbilt University, Nashville, TN 37235, USA
6Departments of Biomedical Informatics and Computer Science, Vanderbilt University, Nashville, TN, 37235, USA
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  • For correspondence: tony.capra@vanderbilt.edu
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ABSTRACT

Neanderthal ancestry remains across modern Eurasian genomes, and introgressed sequences influence diverse phenotypes, including immune, skin, and neuropsychiatric diseases. Interpretation of introgressed sequences has focused on alleles derived in the Neanderthal lineage. Here, we demonstrate that Neanderthal introgression also reintroduced thousands of ancestral hominin alleles lost in the Eurasian out of Africa bottleneck. Combining evolutionary simulations, expression quantitative trait loci (eQTL), massively parallel reporter assay (MPRA) data, and in vitro validation, we show that reintroduced alleles (RAs) have different fitness effects than Neanderthal-derived alleles (NDAs) and that some RAs regulate gene expression independent of NDAs. Illustrating the broad potential influence of RAs, we find that over 70% of known phenotype associations with NDAs are equally associated with RAs. Finally, we discover enrichment for RA eQTL activity in several tissues, with strongest enrichment in the brain. In summary, our study reveals that Neanderthal introgression supplied Eurasians with many lost functional variants and demonstrates that RAs must be considered when evaluating the effects of introgression.

ONE SENTENCE SUMMARY Neanderthal interbreeding with modern humans restored to Eurasians, hundreds of thousands of ancient alleles that were lost in the out of Africa bottleneck.

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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. All rights reserved. No reuse allowed without permission.
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Posted January 29, 2019.
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Neanderthal introgression reintroduced functional alleles lost in the human out of Africa bottleneck
David C. Rinker, Corinne N. Simonti, Evonne McArthur, Douglas Shaw, Emily Hodges, John A. Capra
bioRxiv 533257; doi: https://doi.org/10.1101/533257
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Neanderthal introgression reintroduced functional alleles lost in the human out of Africa bottleneck
David C. Rinker, Corinne N. Simonti, Evonne McArthur, Douglas Shaw, Emily Hodges, John A. Capra
bioRxiv 533257; doi: https://doi.org/10.1101/533257

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