The Diversity of Primates: From Biomedicine to Conservation Genomics

Abstract

Until now, the field of primate genomics has focused on two major themes: understanding human evolution and advancing biomedical research. We propose that it is now time for a third theme to receive attention: conservation genomics. As a result of anthropogenic effects, the majority of primate species have become threatened with extinction. A more robust primate conservation genomics will allow for genetically informed population management. Thanks to a steady decline in the cost of sequencing, it has now become feasible to sequence whole primate genomes at the population level. Furthermore, technological advances in noninvasive genomic methods have made it possible to acquire genome-scale data from noninvasive biomaterials. Here, we review recent advances in the analysis of primate diversity, with a focus on genomic data sets across the radiation. Expected final online publication date for the Annual Review of Animal Biosciences, Volume 9 is February 16, 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

Rocks and clocks revised: New promises and challenges in dating the primate tree of life

“…Anthropologists can now obtain large-scale genomic data in relatively easy and affordable ways, even for non-model organisms. [17][18][19][20] While the number of primate species for which we have high-quality annotated genomes is still relatively low (Figure 3), various types of genomic data are now available for many taxa. 17,19,20,98 These data range from hundreds or thousands of loci obtained using sequence capture techniques (e.g., exome, ultra-conserved regions) 21 to thousands of single nucleotide polymorphisms obtained using reduced representation libraries (e.g., dRAD or ddRAD) [99][100][101] or whole-genome sequencing.…”

“…[17][18][19][20] While the number of primate species for which we have high-quality annotated genomes is still relatively low (Figure 3), various types of genomic data are now available for many taxa. 17,19,20,98 These data range from hundreds or thousands of loci obtained using sequence capture techniques (e.g., exome, ultra-conserved regions) 21 to thousands of single nucleotide polymorphisms obtained using reduced representation libraries (e.g., dRAD or ddRAD) [99][100][101] or whole-genome sequencing. 22,23,102,103 Although these datasets do not necessarily include the whole genome, they represent a dramatic increase in the amount of data available to reconstruct phylogenetic relationships among primates.…”

“…[12][13][14][15][16] Second, the promises of more efficient and affordable sequencing technologies have contributed to the rapid accumulation of a vast amount of genetic data for a growing number of primate species. [17][18][19][20] Now, evidence from hundreds or even thousands of loci across the genome, not only from one or a few genes, can be combined with morphological and fossil data to simultaneously estimate tree topology and divergence times. [21][22][23] These recent developments generated great excitement in the field of molecular anthropology, phylogenetics, and paleontology.…”

A high-quality, long-read genome assembly of the endangered ring-tailed lemur (Lemur catta)

“…The vast majority of strepsirrhines (103 species) are members of the Lemuroidea, colloquially known as “lemurs,” and endemic to Madagascar. Despite their geographic isolation, the lemur radiation is exceptionally diverse, including both the smallest living primate ( Microcebus berthae ) and one of the largest (the recently extinct subfossil lemur, Archaeoindris fontoynontyii ) [ 2 , 3 ]. Although lemurs are highly diverse, they are comparatively understudied relative to other primates, and ∼87% of species are threatened with extinction, raising major conservation challenges [ 1 ].…”

Initiation of the Primate Genome Project

“…This will allow us to investigate the genetic basis of speciation and characterize the history and genomic outcomes of hybridization, as observed in major primate lineages ( Ayoola et al, 2021 ; de Manuel et al, 2016 ; Svardal et al, 2017 ). Conservation genomic analyses of population data will be highly informative regarding genomic diversity and recent demographic history, which are crucial parameters for evaluating the conservation status of species ( Orkin et al, 2021 ).…”