A global catalog of whole-genome diversity from 233 primate species

Abstract

The rich diversity of morphology and behavior displayed across primate species provides an informative context in which to study the impact of genomic diversity on fundamental biological processes. Analysis of that diversity provides insight into long-standing questions in evolutionary and conservation biology, and is urgent given severe threats these species are facing. Here, we present high coverage whole-genome data from 233 primate species representing 86% of genera and all 16 families. This dataset was used, together with fossil calibration, to create a nuclear DNA phylogeny and to reassess evolutionary divergence times among primate clades. We found within-species genetic diversity across families and geographic regions to be associated with climate and sociality, but not with extinction risk. Furthermore, mutation rates differ across species, potentially influenced by effective population sizes. Lastly, we identified extensive recurrence of missense mutations previously thought to be human-specific. This study will open a wide range of research avenues for future primate genomic research.

Assessing the recovery of Y chromosome microsatellites with population genomic data using Papio and Theropithecus genomes

“…The successful identification of informative markers, even when using evolutionary distant reference Y chromosome sequences, suggests that this approach could be applied more extensively. This is particularly of relevance considering that a total of 30 Y chromosome references and WGS from 86% of primate genera became available following recent publications 39 , 42 . Targeting species in key primate groups to assemble Y chromosome references would make possible a more extensive application of the approach presented here.…”

The impact of Quaternary Amazonian river dynamics on patterns and process of diversification in uakari monkeys (genusCacajao)

“…These shifts were responsible for the limited geographic distribution of the populations, et al, 2019) led to episodes of population contractions in the last 70 Kya, as we found in our demographic analysis (Table 1). These events also explain the relatively low genetic diversity found in Cacajao (Kuderna et al, 2023).…”

“…The demographic parameters of the best-fit model, as well as the confidence intervals, were calculated from 100 parametric bootstrap replications, using jSFS obtained from the simulation run with the best composite likelihood value. For time estimates, we applied a mutation rate of 8.48 x 10 -9 substitutions per site per generation (Kuderna et al, 2023).…”

Illuminating the Function of the Orphan Transporter, SLC22A10 in Humans and Other Primates

“…Despite the long SLC22A10 isoform not being annotated in RefSeq for bonobo and orangutan, we included these two species in the alignment considering the plausibility of the protein model in the context of their genomes and the high genomic conservation in comparison to chimpanzee and gorilla. Allele frequencies from non-human great apes were obtained from available whole-genome sequencing data including 59 chimpanzees, 10 bonobos, 49 gorillas and 16 orangutans [48][49][50][51] . All samples were mapped to Hg19.…”