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.

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.

Background: The Neacomys genus is predominantly found in the Amazon region, and belongs to the most diverse tribe of the Sigmodontinae subfamily (Rodentia, Cricetidae, Oryzomyini). The systematics of this genus and questions about its diversity and range have been investigated by morphological, molecular (Cytb and COI sequences) and karyotype analysis (classic cytogenetics and chromosome painting), which have revealed candidate species and new distribution areas. Here we analyzed four species of Neacomys by chromosome painting with Hylaeamys megacephalus (HME) whole-chromosome probes, and compared the results with two previously studied Neacomys species and with other taxa from Oryzomyini and Akodontini tribes that have been hybridized with HME probes. Maximum Parsimony (MP) analyses were performed with the PAUP and T.N.T. software packages, using a non-additive (unordered) multi-state character matrix, based on chromosomal morphology, number and syntenic blocks. We also compared the chromosomal phylogeny obtained in this study with molecular topologies (Cytb and COI) that included eastern Amazonian species of Neacomys, to define the phylogenetic relationships of these taxa. Results: The comparative chromosome painting analysis of the seven karyotypes of the six species of Neacomys shows that their diversity is due to 17 fusion/fission events and one translocation, pericentric inversions in four syntenic blocks, and constitutive heterochromatin (CH) amplification/deletion of six syntenic autosomal blocks plus the X chromosome. The chromosomal phylogeny is consistent with the molecular relationships of species of Neacomys. We describe new karyotypes and expand the distribution area for species from eastern Amazonia and detect complex rearrangements by chromosome painting among the karyotypes. Conclusions: Our phylogeny reflects the molecular relationships of the Akodontini and Oryzomyini taxa and supports the monophyly of Neacomys. This work presents new insights about the chromosomal evolution of this group, and we conclude that the karyotypic divergence is in accord with phylogenetic relationships.

Proechimys is the most diverse genus in family Echimyidae, comprising 25 species (two of which are polytypic) and 39 taxa. Despite the numerous forms of this rodent and their abundance in nature, there are many taxonomic problems due to phenotypic similarities within the genus and high intraspecific variation. Extensive karyotypic variation has been noted, however, with diploid numbers (2n) ranging from 14 to 62 chromosomes. Some heteromorphism can be found, and 57 different karyotypes have been described to date.

A ordem Didelphimorphia é composta somente pela família Didelphidae, exclusiva do continente americano. Esta família é amplamente distribuída na região Neotropical, ocupando grande variedade de hábitats. A literatura registra 68 espécies de didelfídeos no Brasil, das quais 24 delas têm ocorrência confirmada para a Bacia do Alto Paraguai (BAP). As espécies presentes nessa região pertencem a três subfamílias – Glironiinae (1 gênero, 1 espécie), Caluromyinae (1, 2) e Didelphinae (11, 21) – e, dentre elas, inclui-se Monodelphis saci, espécie há pouco descrita, bem como outras três, recentemente validadas em nível de espécie, Gracilinanus peruanus, Philander canus e Marmosa rapposa, e duas espécies ameaçadas de extinção, Thylamys karimii e T. macrurus. A proposta deste artigo foi fazer um levantamento de todas as espécies de marsupiais registradas na BAP até o presente momento, trazendo, na medida da disponibilidade de dados, uma breve descrição morfológica de cada uma das 24 espécies, bem como a comparação com espécies congêneres ou assemelhadas, a revisão dos dados de ecologia e de história natural e informações específicas de suas populações e de seus graus de ameaça. Por fim, este estudo traz informações inéditas que podem ser utilizadas para a tomada de decisões em políticas públicas e para o norteamento de pesquisas básicas para esse grupo zoológico nessa região tão pouco conhecida e fortemente ameaçada.