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  • Review Article
  • Published:

Comparative primate genomics: emerging patterns of genome content and dynamics

Key Points

  • Whole-genome assemblies are now available for all the great apes and several other non-human primate species. The published analyses document inter-species differences in gene content, segmental duplications, retrotransposon insertions and other genomic features.

  • Next-generation sequencing has made whole-genome sequencing and draft assembly more practical; consequently, additional non-human primate genome assemblies with detailed annotation and other associated analyses are in progress.

  • The available data on non-human primate population genomics indicate that these species show as much intra-species genetic variation as, or more such variation than, that found among humans, and some species have substantially higher rates of polymorphism.

  • Differences between species in patterns of gene expression are common; such differences have been influenced by natural selection and are likely to contribute to phenotypic differences among species.

  • The evolutionary radiation (that is, the speciation events) that produced the extant human, chimpanzee and gorilla lineages resulted from a complex process that is characterized by incomplete lineage sorting and/or gene flow among partially differentiated lineages.

  • Whole-genome analyses and more targeted sequencing have been carried out in non-human primate species that are used in disease-related research. This has identified specific variants relevant to human disease risk and found differences among primate model species that are directly relevant to disease mechanisms and to other biomedically important phenotypes (for example, drug metabolism).

Abstract

Advances in genome sequencing technologies have created new opportunities for comparative primate genomics. Genome assemblies have been published for various primate species, and analyses of several others are underway. Whole-genome assemblies for the great apes provide remarkable new information about the evolutionary origins of the human genome and the processes involved. Genomic data for macaques and other non-human primates offer valuable insights into genetic similarities and differences among species that are used as models for disease-related research. This Review summarizes current knowledge regarding primate genome content and dynamics, and proposes a series of goals for the near future.

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Figure 1: Primate phylogenetic tree.
Figure 2: Geographical distribution and genetic variation in selected primates.
Figure 3: Incomplete lineage sorting and gene flow.

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Acknowledgements

The authors thank K. Worley, S. Richards, M. Raveendran, G. Fawcett, D. Rio Deiros and F. Yu for discussion, and three anonymous reviewers for their comments. This work was supported by the US National Institutes of Health grants U54-HG006484 and R24-OD011173.

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Glossary

Hominins

Members of the evolutionary lineage leading to humans after divergence from the ancestors of chimpanzees. Hominins include species that are directly ancestral to modern humans and related species such as Neanderthals or older branches such as australopithecines.

Old World monkeys

Members of the branch of primates that includes extant anthropoid primates (monkeys) native to Asia and Africa; they belong to the superfamily Cercopithecoidea.

New World monkeys

Members of the branch of primates that includes extant anthropoid primates (monkeys) native to South and Central America; they belong to the parvorder Platyrrhini.

Positive selection

Natural selection acting on phenotypes and the relevant DNA sequences that results in directional change towards a new sequence and phenotype. It is in contrast with negative selection, which eliminates deleterious traits and therefore acts against any new mutations that generate them.

Effective population sizes

A basic concept from population genetics that describes the number of individuals required in an ideal breeding population (that is, equal numbers of breeding males and females, with equal reproductive success among them) of constant size to sustain a given amount of intra-population genetic variation. As genetic variation in a given population is affected by current and past demographic factors, estimation of effective population size allows researchers to infer aspects of population history.

Coalescent models

Used in population genetics to investigate various aspects of population history and dynamics, these models are based on the genealogy or relationships within a gene tree among alleles of a specific DNA sequence. All alleles found in a population or a set of related populations can be traced back to a common ancestral sequence, and the statistical properties of those allelic relationships are exploited to investigate questions of population genetics and history.

Incomplete lineage sorting

(ILS). The process by which, as a result of segregation of an ancestral polymorphism, the evolutionary relationships among a series of homologous DNA sequences in a set of distinct populations do not match the phylogenetic relationships among the overall populations; that is, the gene trees do not match the population trees.

Allopatric

Pertaining to separate, non-overlapping geographical distributions.

Strepsirrhine primates

Members of the branch of primates that includes lemurs, lorises, galagos and cheirogaleids, and that belongs to the suborder Strepsirrhini.

Hybrid zones

Geographical areas that are often, but not always, elongated and narrow in shape, where two distinct species occur together, mate and produce hybrid offspring that are fertile.

Parapatric

Pertaining to geographical distributions that are adjoining but that do not overlap extensively.

Introgression

The transfer of alleles or genes by hybridization and gene flow from one species to another.

Catarrhine primates

Members of the primate evolutionary lineage that includes Old World monkeys (superfamily Cercopithecoidea) or hominoids (superfamily Hominoidea). The catarrhines include all extant apes, anthropoid monkeys native to Asia and Africa, and humans.

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Rogers, J., Gibbs, R. Comparative primate genomics: emerging patterns of genome content and dynamics. Nat Rev Genet 15, 347–359 (2014). https://doi.org/10.1038/nrg3707

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