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

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

The landscape of tolerated genetic variation in humans and primates.

Personalized genome sequencing has revealed millions of genetic differences between individuals, but our understanding of their clinical relevance remains largely incomplete. To systematically decipher the effects of human genetic variants, we obtained whole-genome sequencing data for 809 individuals from 233 primate species and identified 4.3 million common protein-altering variants with orthologs in humans. We show that these variants can be inferred to have nondeleterious effects in humans based on their presence at high allele frequencies in other primate populations. We use this resource to classify 6% of all possible human protein-altering variants as likely benign and impute the pathogenicity of the remaining 94% of variants with deep learning, achieving state-of-the-art accuracy for diagnosing pathogenic variants in patients with genetic diseases

Variation in predicted COVID-19 risk among lemurs and lorises

The novel coronavirus SARS-CoV-2, which in humans leads to the disease COVID-19, has caused global disruption and more than 2 million fatalities since it first emerged in late 2019. As we write, infection rates are at their highest point globally and are rising extremely rapidly in some areas due to more infectious variants. The primary target of SARS-CoV-2 is the cellular receptor angiotensin-converting enzyme-2 (ACE2). Recent sequence analyses of the ACE2 gene predict that many nonhuman primates are also likely to be highly susceptible to infection. However, the anticipated risk is not equal across the Order. Furthermore, some taxonomic groups show high ACE2 amino acid conservation, while others exhibit high variability at this locus. As an example of the latter, analyses of strepsirrhine primate ACE2 sequences to date indicate large variation among lemurs and lorises compared to other primate clades despite low sampling effort. Here, we report ACE2 gene and protein sequences for 71 individual strepsirrhines, spanning 51 species and 19 genera. Our study reinforces previous results while finding additional variability in other strepsirrhine species, and suggests several clades of lemurs have high potential susceptibility to SARS-CoV-2 infection. Troublingly, some species, including the rare and endangered aye-aye (Daubentonia madagascariensis), as well as those in the genera Avahi and Propithecus, may be at high risk. Given that lemurs are endemic to Madagascar and among the primates at highest risk of extinction globally, further understanding of the potential threat of COVID-19 to their health should be a conservation priority. All feasible actions should be taken to limit their exposure to SARS-CoV-2.Funding: CERCA Programme del Departament d'Economia i Coneixement de la Generalitat de Catalunya, Grant/Award Number: GRC 2017SGR 880; Secretaria d'Universitats i Recerca; Spanish Ministry of Science and Innovation‐Instituto de Salud Carlos III; Rockefeller University; Centro de Excelencia Severo Ochoa; Natural Sciences and Engineering Research Council of Canada (NSERC DiscoveryGrant); Generalitat de Catalunya (Departament de Salut, Departament d'Empresa i Coneixement); National Institutes of Health, Grant/Award Number:R35GM130333; CERCA,Grant/Award Numbers: BFU2017‐86471‐P(MINECO/FEDER, UE); European Research Council (ERC)‐European Union's Horizon 2020 research and innovation programme,Grant/Award Number: 864203; Smart Growth Operating Program (2014–2020); MINECO/FEDER, UE, Grant/Award Number: CGL2017‐82654‐P; Unidad de Excelencia María de Maeztu, Grant/Award Number: AEI (CEX2018‐000792‐M); Canada Research Chairs Program; European Regional Development Fund, Grant/Award Numbers: MINECO/FEDER, BIO2015‐71792‐P; Howard Hughes Medical Institute; Obra Social "LaCaixa"; Natural Environment Research Council,Grant/Award Number: NERC NE/T000341/