Great ape genetic diversity and population history
By Javier Prado-Martinez, Peter Sudmant, J. Kidd, Heng Li, Joanna L. Kelley, B. Lorente-Galdos, K. Veeramah, August E. Woerner, T. O’Connor, G. Santpere and 65 more. Nature, 2013
858 citations recorded by the source corpus.
Most great ape genetic variation remains uncharacterized; however, its study is critical for understanding population history, recombination, selection and susceptibility to disease. Here we sequence to high coverage a total of 79 wild- and captive-born individuals representing all six great ape species and seven subspecies and report 88.8 million single nucleotide polymorphisms. Our analysis provides support for genetically distinct populations within each species, signals of gene flow, and the split of common chimpanzees into two distinct groups: Nigeria–Cameroon/western and central/eastern populations. We find extensive inbreeding in almost all wild populations, with eastern gorillas being the most extreme. Inferred effective population sizes have varied radically over time in different lineages and this appears to have a profound effect on the genetic diversity at, or close to, genes in almost all species. We discover and assign 1,982 loss-of-function variants throughout the human and great ape lineages, determining that the rate of gene loss has not been different in the human branch compared to other internal branches in the great ape phylogeny. This comprehensive catalogue of great ape genome diversity provides a framework for understanding evolution and a resource for more effective management of wild and captive great ape populations.
Subfields: Cell Biology, Ecology, Evolution, Behavior and Systematics, Social Psychology
View Paper: https://www.semanticscholar.org/paper/997aa268f135c565f44cbf29ade131d5efa6bbb4
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In Cell Biology
Citations in the corpus
- Supplementary Information for Predicting the clinical impact of human mutation with deep neural networks (2018, neutral): “Orangutan, Bornean subspecies (5) Prado-Martinez et al., Nature (2013) 21,621 19,793”
- Genome-Wide Inference of Ancestral Recombination Graphs (2013, methodology): “In addition to natural selection, our methods for ARG inference have the potential to shed light on historical demographic processes, an area of particular interest in the recent literature [16,17,51,52,89].”
- The complete genome sequence of a Neandertal from the Altai Mountains (2013, positive): “We first estimated population split times by extending the pairwise sequentially Markovian coalescent model (PSMC) to estimate the distribution of coalescence times between single chromosomes where one comes from one and one from another population 20,21 (SI 12).”