Patterns of coding variation in the complete exomes of three Neandertals

Sergi Castellano, Genís Parra, Federico A. Sánchez-Quinto, Fernando Racimo, Martin Kuhlwilm, Martin Kircher, Susanna Sawyer, Qiaomei Fu, Anja Heinze, Birgit Nickel, Jesse Dabney, Michael Siebauer, Louise White, Hernán A. Burbano, Gabriel Renaud, Udo Stenzel, Carles Lalueza-Fox, Marco de la Rasilla, Antonio Rosas, Pavao Rudan, Dejana Brajković, Željko Kucan, Ivan Gušic, Michael V. Shunkov, Anatoli P. Derevianko, Bence Viola, Matthias Meyer, Janet Kelso, Aida M. Andrés, and Svante Pääbo
PNAS May 6, 2014 111 (18) 6666-6671; published ahead of print April 21, 2014 https://doi.org/10.1073/pnas.1405138111

  1. Contributed by Svante Pääbo, March 21, 2014 (sent for review January 17, 2014)

Significance

We use a hybridization approach to enrich the DNA from the protein-coding fraction of the genomes of two Neandertal individuals from Spain and Croatia. By analyzing these two exomes together with the genome sequence of a Neandertal from Siberia we show that the genetic diversity of Neandertals was lower than that of present-day humans and that the pattern of coding variation suggests that Neandertal populations were small and isolated from one another. We also show that genes involved in skeletal morphology have changed more than expected on the Neandertal evolutionary lineage whereas genes involved in pigmentation and behavior have changed more on the modern human lineage.

Abstract

We present the DNA sequence of 17,367 protein-coding genes in two Neandertals from Spain and Croatia and analyze them together with the genome sequence recently determined from a Neandertal from southern Siberia. Comparisons with present-day humans from Africa, Europe, and Asia reveal that genetic diversity among Neandertals was remarkably low, and that they carried a higher proportion of amino acid-changing (nonsynonymous) alleles inferred to alter protein structure or function than present-day humans. Thus, Neandertals across Eurasia had a smaller long-term effective population than present-day humans. We also identify amino acid substitutions in Neandertals and present-day humans that may underlie phenotypic differences between the two groups. We find that genes involved in skeletal morphology have changed more in the lineage leading to Neandertals than in the ancestral lineage common to archaic and modern humans, whereas genes involved in behavior and pigmentation have changed more on the modern human lineage.

Footnotes

  • ↵1To whom correspondence may be addressed. E-mail: sergi.castellano{at}eva.mpg.de or paabo{at}eva.mpg.de.

  • ↵2G.P., F.A.S.-Q., F.R., and M. Kuhlwilm contributed equally to this work.

  • Author contributions: S.C., F.R., M.M., J.K., A.M.A., and S.P. designed research; S.C., G.P., F.A.S.-Q., F.R., M. Kuhlwilm, S.S., Q.F., A.H., B.N., J.D., L.W., B.V., M.M., and A.M.A. performed research; S.S., Q.F., A.H., B.N., J.D., H.A.B., C.L.-F., M.d.l.R., A.R., P.R., D.B., Z.K., I.G., M.V.S., A.P.D., and M.M. contributed new reagents/analytic tools; S.C., G.P., F.A.S.-Q., F.R., M. Kuhlwilm, M. Kircher, M.S., G.R., and U.S. analyzed data; and S.C., F.A.S.-Q., F.R., B.V., J.K., A.M.A., and S.P. wrote the paper.

  • The authors declare no conflict of interest.

  • Data deposition: The exome sequence capture data reported in this paper have been deposited in the European Nucleotide Archive (accession no. ERP002457). These data are also available at http://cdna.eva.mpg.de/neandertal/exomes/.

  • This article contains supporting information online at www.pnas.org/lookup/suppl/doi:10.1073/pnas.1405138111/-/DCSupplemental.

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Patterns of coding variation in Neandertal exomes
Sergi Castellano, Genís Parra, Federico A. Sánchez-Quinto, Fernando Racimo, Martin Kuhlwilm, Martin Kircher, Susanna Sawyer, Qiaomei Fu, Anja Heinze, Birgit Nickel, Jesse Dabney, Michael Siebauer, Louise White, Hernán A. Burbano, Gabriel Renaud, Udo Stenzel, Carles Lalueza-Fox, Marco de la Rasilla, Antonio Rosas, Pavao Rudan, Dejana Brajković, Željko Kucan, Ivan Gušic, Michael V. Shunkov, Anatoli P. Derevianko, Bence Viola, Matthias Meyer, Janet Kelso, Aida M. Andrés, Svante Pääbo
Proceedings of the National Academy of Sciences May 2014, 111 (18) 6666-6671; DOI: 10.1073/pnas.1405138111
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