Patterns of coding variation in the complete exomes of three Neandertals
Open accessAbstract
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.
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Limited genetic data suggest the opposite, i.e. the Neanderthal lineage might be the more derived.
“However, limited genetic data seem to suggest the opposite, i.e. the Neanderthal lineage might be the more derived [23].”
From The origin and evolution of <i>Homo sapiens</i> (2016) · cites this paper as [23]
The paper’s Significance section reports a larger fraction of derived amino acid-changing alleles in the three Neandertals studied than in the present-day humans studied. Its conclusion says that morphology-related genes may have changed more on the Neandertal and Denisovan lineages, but behavior-related genes may have changed more on the modern human lineage. These findings do not establish that the Neandertal lineage was more derived overall. (LLM, conf=0.82)
Experimental — accuracy not yet measuredCastellano et al. highlight genes involved in skeletal development and associated with aggressive phenotypes in their comparison of archaic Homo and AMH.
“It is striking that Castellano et al. [115] highlight genes involved in skeletal development and associated with aggressive phenotypes in their comparison of archaic Homo and AMH.”
From Self-domestication in Homo sapiens: Insights from comparative genomics (2017) · cites this paper as [115]
No genes in S1 Table display reported archaic-derived alleles.
“We examined the genes associated with archaic-derived alleles [115] and found that no genes in S1 Table display reported archaic-derived alleles.”
From Self-domestication in Homo sapiens: Insights from comparative genomics (2017) · cites this paper as [115]
ADSL has been pointed out before as under positive selection.
“which has been pointed out before as under positive selection31,33,34,122.”
From A catalog of single nucleotide changes distinguishing modern humans from archaic hominins (2019) · cites this paper as [31]
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A high-coverage Neandertal genome from Vindija Cave in Croatia
Prüfer, K., de Filippo, C., Grote, S., Mafessoni, F., Korlević, P., Hajdinjak, M., Vernot, B., Skov, L., Hsieh, P., Peyrégne, S., et al. (2017) · Science · doi:10.1126/science.aao1887 · Cited by 719 · see citing works
Self-citationAncient gene flow from early modern humans into Eastern Neanderthals
Kuhlwilm, M., Gronau, I., Hubisz, M. J., de Filippo, C., Prado-Martinez, J., Kircher, M., Fu, Q., Burbano, H. A., Lalueza-Fox, C., de la Rasilla, M., et al. (2016) · Nature · doi:10.1038/nature16544 · Cited by 577 · see citing works
Self-citationEvidence for archaic adaptive introgression in humans
Racimo, F., Sankararaman, S., Nielsen, R., & Huerta-Sánchez, E. (2015) · Nature Reviews Genetics · doi:10.1038/nrg3936 · Cited by 521 · see citing works
Self-citationThe Genetic Cost of Neanderthal Introgression
Harris, K., & Nielsen, R. (2016) · Genetics · doi:10.1534/genetics.116.186890 · Cited by 419 · see citing works
The origin and evolution of <i>Homo sapiens</i>
Stringer, C. (2016) · Philosophical Transactions of the Royal Society B: Biological Sciences · doi:10.1098/rstb.2015.0237 · Cited by 395 · see citing works
The evolution of modern human brain shape
Neubauer, S., Hublin, J.-J., & Gunz, P. (2018) · Science Advances · doi:10.1126/sciadv.aao5961 · Cited by 389 · see citing works
The Strength of Selection against Neanderthal Introgression
Juric, I., Aeschbacher, S., & Coop, G. (2016) · PLOS Genetics · doi:10.1371/journal.pgen.1006340 · Cited by 309 · see citing works
Deschamps, M., Laval, G., Fagny, M., Itan, Y., Abel, L., Casanova, J.-L., Patin, E., & Quintana-Murci, L. (2016) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2015.11.014 · Cited by 257 · see citing works
Self-domestication in Homo sapiens: Insights from comparative genomics
Theofanopoulou, C., Gastaldon, S., O’Rourke, T., Samuels, B. D., Messner, A., Martins, P. T., Delogu, F., Alamri, S., & Boeckx, C. (2017) · PLOS ONE · doi:10.1371/journal.pone.0185306 · Cited by 174 · see citing works
Brain ontogeny and life history in Pleistocene hominins
Hublin, J.-J., Neubauer, S., & Gunz, P. (2015) · Philosophical Transactions of the Royal Society B Biological Sciences · doi:10.1098/rstb.2014.0062 · Cited by 173 · see citing works
The nature of Neanderthal introgression revealed by 27,566 Icelandic genomes
Skov, L., Coll Macià, M., Sveinbjörnsson, G., Mafessoni, F., Lucotte, E. A., Einarsdóttir, M. S., Jonsson, H., Halldorsson, B., Gudbjartsson, D. F., Helgason, A., et al. (2020) · Nature · doi:10.1038/s41586-020-2225-9 · Cited by 145 · see citing works
A catalog of single nucleotide changes distinguishing modern humans from archaic hominins
Kuhlwilm, M., & Boeckx, C. (2019) · Scientific Reports · doi:10.1038/s41598-019-44877-x · Cited by 108 · see citing works
Self-citationHuman evolution: a tale from ancient genomes
Llamas, B., Willerslev, E., & Orlando, L. (2017) · Philosophical Transactions of the Royal Society B Biological Sciences · doi:10.1098/rstb.2015.0484 · Cited by 100 · see citing works
Testing for ancient selection using cross-population allele frequency differentiation
Racimo, F. (2016) · Genetics · doi:10.1534/genetics.115.178095 · Cited by 96 · see citing works
Self-citationNuclear DNA from two early Neandertals reveals 80,000 years of genetic continuity in Europe
Peyrégne, S., Slon, V., Mafessoni, F., de Filippo, C., Hajdinjak, M., Nagel, S., Nickel, B., Essel, E., Le Cabec, A., Wehrberger, K., et al. (2019) · Science Advances · doi:10.1126/sciadv.aaw5873 · Cited by 82 · see citing works
Self-citationNeanderthal-Derived Genetic Variation Shapes Modern Human Cranium and Brain
Gregory, M. D., Kippenhan, J. S., Eisenberg, D. P., Kohn, P. D., Dickinson, D., Mattay, V. S., Chen, Q., Weinberger, D. R., Saad, Z. S., & Berman, K. F. (2017) · Scientific Reports · doi:10.1038/s41598-017-06587-0 · Cited by 69 · see citing works
Inferred divergent gene regulation in archaic hominins reveals potential phenotypic differences
Colbran, L. L., Gamazon, E. R., Zhou, D., Evans, P., Cox, N. J., & Capra, J. A. (2019) · Nature Ecology & Evolution · doi:10.1038/s41559-019-0996-x · Cited by 50 · see citing works
The evolution of FOXP2 in the light of admixture
Kuhlwilm, M. (2018) · Current Opinion in Behavioral Sciences · doi:10.1016/j.cobeha.2018.04.006 · Cited by 56 · see citing works
Self-citationKramer, K. L., Schacht, R., & Bell, A. (2017) · Philosophical Transactions of the Royal Society B Biological Sciences · doi:10.1098/rstb.2016.0316 · Cited by 54 · see citing works
Selection against archaic hominin genetic variation in regulatory regions
Telis, N., Aguilar, R., & Harris, K. (2020) · Nature Ecology & Evolution · doi:10.1038/s41559-020-01284-0 · Cited by 51 · see citing works
Evolutionary History, Selective Sweeps, and Deleterious Variation in the Dog
Freedman, A. H., Lohmueller, K. E., & Wayne, R. K. (2016) · Annual Review of Ecology, Evolution, and Systematics · doi:10.1146/annurev-ecolsys-121415-032155 · Cited by 50 · see citing works
Neanderthal introgression reintroduced functional ancestral alleles lost in Eurasian populations
Rinker, D. C., Simonti, C. N., McArthur, E., Shaw, D., Hodges, E., & Capra, J. A. (2020) · Nature Ecology & Evolution · doi:10.1038/s41559-020-1261-z · Cited by 44 · see citing works
Globularization and domestication.
Benítez-Burraco, A., Theofanopoulou, C., & Boeckx, C. (2018) · Topoi · doi:10.1007/s11245-016-9399-7 · Cited by 42 · see citing works
The Muskox Lost a Substantial Part of Its Genetic Diversity on Its Long Road to Greenland
Hansen, C. C. R., Hvilsom, C., Schmidt, N. M., Aastrup, P., Van Coeverden de Groot, P. J., Siegismund, H. R., & Heller, R. (2018) · Current Biology · doi:10.1016/j.cub.2018.10.054 · Cited by 42 · see citing works
A test for ancient selective sweeps and an application to candidate sites in modern humans
Racimo, F., Kuhlwilm, M., & Slatkin, M. (2014) · Molecular Biology and Evolution · doi:10.1093/molbev/msu255 · Cited by 30 · see citing works
Self-citation
- Authors
- Castellano, S., Parra, G., Sánchez-Quinto, F. A., Racimo, F., Kuhlwilm, M., Kircher, M., Sawyer, S., Fu, Q., Heinze, A., Nickel, B., Dabney, J., Siebauer, M., White, L., Burbano, H. A., Renaud, G., Stenzel, U., Lalueza-Fox, C., de la Rasilla, M., Rosas, A., Rudan, P., Brajković, D., Kucan, Ž., Gušic, I., Shunkov, M. V., Derevianko, A. P., Viola, B., Meyer, M., Kelso, J., Andrés, A. M., & Pääbo, S.
- Affiliations
- Max Planck Society (DE)
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany;
- Institute of Evolutionary Biology, Consejo Superior de Investigaciones Científicas, Universitat Pompeu Fabra, 08003 Barcelona, Spain;
- Max Planck Institute for Evolutionary Anthropology (DE)
- Chinese Academy of Sciences (CN)
- Max Planck Institute for Developmental Biology (DE)
- Área de Prehistoria, Departamento de Historia, Universidad de Oviedo, 33011 Oviedo, Spain;
- Consejo Superior de Investigaciones Científicas (ES)
- Croatian Academy of Sciences and Arts (HR)
- Anthropology Center of the Croatian Academy of Sciences and Arts, HR-10000 Zagreb, Croatia;
- Russian Academy of Sciences (RU)
- Paleolithic Department, Institute of Archeology and Ethnography, Russian Academy of Sciences, Siberian Branch, Novosibirsk 630090, Russia; and
- ORCID
- Venue
- Proceedings of the National Academy of Sciences
- Publisher
- National Academy of Sciences
- Published
- 2014-04-21
- Volume
- 111
- Issue
- 18
- Pages
- 6666-6671
- ISSN
- 0027-8424 (ISSN-L)
- 1091-6490
- PMC
- PMC4020111
- OpenAlex
- W2131870855
- Cited by
- 247
- References
- 82
- Citations by year
- 2026: 6 · 2025: 14 · 2024: 9 · 2023: 16 · 2022: 18 · 2021: 17 · 2020: 21 · 2019: 23 · 2018: 27 · 2017: 28 · 2016: 33 · 2015: 26 · 2014: 9
- FWCI
- 153.35
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Locations
- Proceedings of the National Academy of Sciences (publishedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- Consultation of the Doctoral Thesis Database (TESEO) (Ministerio de Educación, Cultura y Deporte) (submittedVersion, cc-by-nc-nd)
- DIGITAL.CSIC (Spanish National Research Council (CSIC)) (submittedVersion)
- Max Planck Digital Library (submittedVersion)
- MPG.PuRe (Max Planck Society) (submittedVersion)
- Funders
- Ministerio de Economía y Competitividad
- Max-Planck-Gesellschaft
- Topics
- Social Sciences › Anthropology › Pleistocene-Era Hominins and Archaeology
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Forensic and Genetic Research
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Keywords
- Neanderthals, non-synonymous mutations, protein-coding genes, genetic diversity, effective population size, amino acid substitutions, skeletal morphology, pigmentation genes
- MeSH terms
- Animals, DNA, Gene Frequency, Humans, Paleontology, Phylogeny, Siberia, Spain, Genetic Variation, Croatia, Amino Acid Substitution, Polymorphism, Single Nucleotide, Neanderthals, Exome
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Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
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