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Direct estimation of mutations in great apes reconciles phylogenetic dating
Abstract
The human mutation rate per generation estimated from trio sequencing has revealed an almost linear relationship with the age of the father and the age of the mother, with fathers contributing about three times as many mutations per year as mothers. The yearly trio-based mutation rate estimate of around 0.43 × 10-9 is markedly lower than previous indirect estimates of about 1 × 10-9 per year from phylogenetic comparisons of the great apes calibrated by fossil evidence. This suggests either a slowdown in the accumulation of mutations per year in the human lineage over the past 10 million years or an inaccurate interpretation of the fossil record. Here we inferred de novo mutations in chimpanzee, gorilla, and orangutan parent-offspring trios. Extrapolating the relationship between the mutation rate and the age of parents from humans to these other great apes, we estimated that each species has higher mutation rates per year by factors of 1.50 ± 0.10, 1.51 ± 0.23, and 1.42 ± 0.22 for chimpanzee, gorilla, and orangutan, respectively, and by a factor of 1.48 ± 0.08 for the three species combined. These estimates suggest an appreciable slowdown in the yearly mutation rate in the human lineage that is likely to be recent as genome comparisons almost adhere to a molecular clock. If the nonhuman rates rather than the human rate are extrapolated over the phylogeny of the great apes, we estimate divergence and speciation times that are much more in line with the fossil record and the biogeography.
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“The similar mutation rates in Neanderthals and modern humans imply that the apparent slowdown in the human mutation rate 36 is unlikely to have occurred between 500,000 and 55,000 years ago.”
From The nature of Neanderthal introgression revealed by 27,566 Icelandic genomes (2020) · cites this paper as [36]
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“…in the past decade, direct detection of DNMs by sequencing parent-offspring trios has been available for many species, particularly for vertebrates (Besenbacher et al. 2019; Bergeron et al. 2021; Wang et al. 2022, 2025; Zhang et al. 2022, 2023, 2025; Bergeron et al. 2023; Lin et al. 2023;…”
RatesTools: a Nextflow pipeline for detecting de novo germline mutations in pedigree sequence data
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Additional file 4 of A near complete genome for goat genetic and genomic research
Li, R., Yang, P., Dai, X., Nanaei, H. A., Fang, W., Yang, Z., Cai, Y., Zheng, Z., Wang, X., & Jiang, Y. (2021) · Figshare · doi:10.6084/m9.figshare.16606968
Additional file 5 of A near complete genome for goat genetic and genomic research
Li, R., Yang, P., Dai, X., Nanaei, H. A., Fang, W., Yang, Z., Cai, Y., Zheng, Z., Wang, X., & Jiang, Y. (2021) · Figshare · doi:10.6084/m9.figshare.16606971
Additional file 6 of A near complete genome for goat genetic and genomic research
Li, R., Yang, P., Dai, X., Nanaei, H. A., Fang, W., Yang, Z., Cai, Y., Zheng, Z., Wang, X., & Jiang, Y. (2021) · Figshare · doi:10.6084/m9.figshare.16606977
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Additional file 1 of A near complete genome for goat genetic and genomic research
Li, R., Yang, P., Dai, X., Nanaei, H. A., Fang, W., Yang, Z., Cai, Y., Zheng, Z., Wang, X., & Jiang, Y. (2021) · Figshare · doi:10.6084/m9.figshare.16606959
Additional file 2 of A near complete genome for goat genetic and genomic research
Li, R., Yang, P., Dai, X., Nanaei, H. A., Fang, W., Yang, Z., Cai, Y., Zheng, Z., Wang, X., & Jiang, Y. (2021) · Figshare · doi:10.6084/m9.figshare.16606962
Additional file 3 of A near complete genome for goat genetic and genomic research
Li, R., Yang, P., Dai, X., Nanaei, H. A., Fang, W., Yang, Z., Cai, Y., Zheng, Z., Wang, X., & Jiang, Y. (2021) · Figshare · doi:10.6084/m9.figshare.16606965
Additional file 3 of Evolutionary dynamics of pseudoautosomal region 1 in humans and great apes
Bergman, J., & Schierup, M. H. (2022) · Figshare · doi:10.6084/m9.figshare.21351266
Self-citationAdditional file 4 of Evolutionary dynamics of pseudoautosomal region 1 in humans and great apes
Bergman, J., & Schierup, M. H. (2022) · Figshare · doi:10.6084/m9.figshare.21351269
Self-citationAdditional file 5 of Evolutionary dynamics of pseudoautosomal region 1 in humans and great apes
Bergman, J., & Schierup, M. H. (2022) · Figshare · doi:10.6084/m9.figshare.21351272
Self-citationAdditional file 2 of Evolutionary dynamics of pseudoautosomal region 1 in humans and great apes
Bergman, J., & Schierup, M. H. (2022) · Figshare · doi:10.6084/m9.figshare.21351263
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Metadata
- Authors
- Besenbacher, S., Hvilsom, C., Marques-Bonet, T., Mailund, T., & Schierup, M. H.
- Affiliations
- Aarhus University (DK)
- Copenhagen Zoo (DK)
- Corresponding author
- Besenbacher, Søren
- Schierup, Mikkel Heide
- Venue
- Nature Ecology & Evolution
- Published
- 2019-01-21
- Volume
- 3
- Issue
- 2
- Pages
- 286-292
- ISSN
- 2397-334X (ISSN-L)
- OpenAlex
- W2910586282
- Cited by
- 165
- References
- 24
- Citations by year
- 2026: 13 · 2025: 20 · 2024: 19 · 2023: 25 · 2022: 25 · 2021: 30 · 2020: 17 · 2019: 15
- FWCI
- 7.46
- Type
- journal article
- Language
- en
- Update notices
- correction (2019-04-15)
- Open access
- closed
- Licence
- Locations
- Nature Ecology & Evolution (publishedVersion)
- PubMed (publishedVersion)
- DIGITAL.CSIC (Spanish National Research Council (CSIC)) (submittedVersion)
- Scopus (Elsevier) (submittedVersion)
- Funders
- Novo Nordisk Fonden (NNF18OC0031004)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Evolution and Genetic Dynamics
- Social Sciences › Anthropology › Pleistocene-Era Hominins and Archaeology
- Keywords
- mutation rate, de novo mutations, great apes, chimpanzees, gorillas, orangutans, parent-offspring trios, molecular clock, divergence time estimation, speciation time, fossil record, human lineage
- MeSH terms
- Animals, Biological Evolution, Fossils, Mutation, Phylogeny, Genetic Variation, Hominidae, Evolution, Molecular
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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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