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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.One-Sentence SummaryThe whole genome sequences of 233 primate species provide insight into the determinants of genetic diversity, phylogenomics, and human uniqueness.

INTRODUCTIONMillions of people have received genome and exome sequencing to date, a collective effort that has illuminated for the first time the vast catalog of small genetic differences that distinguish us as individuals within our species. However, the effects of most of these genetic variants remain unknown, limiting their clinical utility and actionability. New approaches that can accurately discern disease-causing from benign mutations and interpret genetic variants on a genome-wide scale would constitute a meaningful initial step towards realizing the potential of personalized genomic medicine.RATIONALEAs a result of the short evolutionary distance between humans and nonhuman primates, our proteins share near-perfect amino acid sequence identity. Hence, the effects of a protein-altering mutation found in one species are likely to be concordant in the other species. By systematically cataloging common variants of nonhuman primates, we aimed to annotate these variants as being unlikely to cause human disease as they are tolerated by natural selection in a closely related species. Once collected, the resulting resource may be applied to infer the effects of unobserved variants across the genome using machine learning.RESULTSFollowing the strategy outlined above we obtained whole-genome sequencing data for 809 individuals from 233 primate species and cataloged 4.3 million common missense variants. We confirmed that human missense variants seen in at least one nonhuman primate species were annotated as benign in the ClinVar clinical variant database in 99% of cases. By contrast, common variants from mammals and vertebrates outside the primate lineage were substantially less likely to be benign in the ClinVar database (71 to 87% benign), restricting this strategy to nonhuman primates. Overall, we reclassified more than 4 million human missense variants of previously unknown consequence as likely benign, resulting in a greater than 50-fold increase in the number of annotated missense variants compared to existing clinical databases.To infer the pathogenicity of the remaining missense variants in the human genome, we constructed PrimateAI-3D, a semisupervised 3D-convolutional neural network that operates on voxelized protein structures. We trained PrimateAI-3D to separate common primate variants from matched control variants in 3D space as a semisupervised learning task. We evaluated the trained PrimateAI-3D model alongside 15 other published machine learning methods on their ability to distinguish between benign and pathogenic variants in six different clinical benchmarks and demonstrated that PrimateAI-3D outperformed all other classifiers in each of the tasks.CONCLUSIONOur study addresses one of the key challenges in the variant interpretation field, namely, the lack of sufficient labeled data to effectively train large machine learning models. By generating the most comprehensive primate sequencing dataset to date and pairing this resource with a deep learning architecture that leverages 3D protein structures, we were able to achieve meaningful improvements in variant effect prediction across multiple clinical benchmarks. 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.

Versión preprint disponible en: http://hdl.handle.net/10261/229066, 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., ADM is supported bythe Natural Sciences and Engineering Research Council of Canada(NSERC Discovery Grant) and Canada Research Chairs Program.MCJ's postdoctoral appointment is supported by funding from theNatural Environment Research Council (NERC NE/T000341/1). IGand MG acknowledge the support of the Spanish Ministry of Scienceand Innovation through the Instituto de Salud Carlos III and the2014–2020 Smart Growth Operating Program, to the EMBL part-nership and cofinancing with the European Regional DevelopmentFund (MINECO/FEDER, BIO201571792P). We also acknowledgethe support of the Centro de Excelencia Severo Ochoa, and theGeneralitat de Catalunya through the Departament de Salut, De-partament d'Empresa i Coneixement and the CERCA Programme.TMB is supported by funding from the European Research Council(ERC) under the European Union's Horizon 2020 research and in-novation program (grant agreement No. 864203), BFU201786471P (MINECO/FEDER, UE), “Unidad de Excelencia María de Maeztu”,funded by the AEI (CEX2018000792M), Howard Hughes Interna-tional Early Career, Obra Social "La Caixa" and Secretaria d'Uni-versitats i Recerca and CERCA Programme del Departamentd'Economia i Coneixement de la Generalitat de Catalunya (GRC2017 SGR 880). PSA thanks the National Institutes of Health(R35GM130333) for financial support. EL is supported by CGL201782654P (MINECO/FEDER, UE). EDJ and OF's contributions weresupported by funds from Howard Hughes Medical Institute and theRockefeller University. Chris Smith drew the images for Figure 1. Theauthors would like to thank the Veterinary and Zoology staff atWildlife Reserves Singapore for their help in obtaining the tissuesamples, as well as the Lee Kong Chian Natural History Museum forstorage and provision of the tissue samples. Finally, we thank tworeviewers for quick and constructive comments, and Karen Bales forher supportive editorial oversight

The grey gentle lemur Hapalemur griseus is currently divided into three subspecies. Of these, very little is known about the western gentle lemur H. g. occidentalis and survey work to assess its distribution and numbers is urgently needed. The sighting of this species approximately 200 km to the south and 200 km to the north of the previously recorded populations further highlights this need. The Tsiombikibo Forest, where Hapalemur was sighted, may harbour further surprises and should be investigated more extensively in order to assess habitat condition and the species present.

In order to assess the status of lemurs along the lower reaches of the Mahavavy in north-west Madagascar, we carried out transect line sampling at Anjamena between April and August 1995. These data were complemented by additional absence–presence surveys conducted in 1994 and 1995 in many of the remaining forested areas of the region. This is the first study of lemur population density estimates for the faunal subregion between the rivers Mahavavy and Betisboka. Six sympatric lemurs are found at Anjamena: Cheirogaleus medius, Eulemur fulvus rufus, E. mongoz, Lepilemur sp., Microcebus murinus and Propithecus verreauxi coronatus. Data suggest that in some parts of the region large numbers of lemurs may still be found (E. f. rufus 121 individuals per km2, E. mongoz (45), Lepilemur sp. (110), M. murinus (85) and P. v. coronatus (173)). No density data are provided for C. medius. In conclusion, as high lemur population densities may still be found and, in particular, P. v. coronatus is not known to exist in any protected area, Anjamena could serve as an important addition to the protected area system of north-west Madagascar. Resume Dans le but d'evaluer le statut des lemuriens le long du bas Mahavavy dans le nord-ouest de Madagascar, nous avons entrepris un echantillonnage par lignes de transect a Anjamena entre avril et aout 1995. Ces donnees furent completees par des controles additionnels de presence/absence en 1994 et 1995 dans de nombreuses zones forestieres residuelles de la region. C'est la premiere etude sur l'estimation de la densite de population des lemuriens dans la sous-region faunistique situee entre les rivieres Mahavavy et Betisboka. On a trouve six lemuriens sympatriques a Anjamena: Cheirogalus medius, Eulemur fulvus rufus, E. mongoz, Lepilemur sp., Microcebus murinus et Propithecus verreauxi coronatus. Les donnees suggerent que des nombres importants de lemuriens peuvent encore etre trouves dans certaines parties de la region (E. f. rufus 121 individus par km2, E. mongoz (45), Lepilemur sp. (110), M. murinus (85) et P. v. coronatus (173)). Aucune donnee de densite n'est fournie pour C. medius. En conclusion, Anjamena pourrait constituer une addition importante au reseau des aires protegees dans le nord-ouest de Madagascar dans la mesure ou de hautes densites de population de lemuriens peuvent encore y etre trouvees et, plus particulierement, en raison du fait que P. v. coronatus ne semble exister dans aucune aire protegee.

Data presented here were collected during a 10-month study carried out on the mongoose lemur, Eulemur mongoz, at Anjamena in northwestern Madagascar. Baseline information is provided on behaviour and assessed for seasonal variation. Given the highly seasonal nature of the environment, remarkably little behavioural variation was observed. This may be directly linked to the cathemeral activity pattern, where differential movement into either the diurnal or the nocturnal ‘niche’ could reduce the effect of selective seasonal pressures, thus reducing behavioural and ecological adaptation to seasonal variation. The behavioural mechanisms of reinforcement of the pair bond through close proximity, mutual anogenital marking, paternal participation in the care of offspring and territoriality are all in accord with the general characteristics of monogamy in primates. The feature of mate monopolization by males, proposed as typical of monogamous social systems, seems to be more attributable to females in E. mongoz, as only they exhibit high levels of intrasexual aggression. Female dominance, characteristic of most species of lemur, may thus include more than just female feeding priority in E. mongoz.

Results of a 10 month study of the mongoose lemur (Eulemur mongoz) at Anjamena are presented. The activity pattern is documented in detail for both wet and dry seasons based on observations conducted over the entire 24 h period. E. mongoz was found to be cathemeral throughout the year but exhibited shifts towards more diurnal activity in the wet season and more nocturnal activity in the dry season. The cathemeral activity pattern in the mongoose lemur appears to be coordinated with sunrise, sunset, and day length and modulated by an inhibitory effect of low nocturnal light intensity in the forest during the wet season, resulting in mainly diurnal activity. Temperature and rainfall may also influence the activity pattern. Few advantages to food-related behavior appear to derive from this activity pattern, although resource accessibility may be enhanced by nocturnal behavior in the dry season, leading to reduction in interspecific competition. Cathemerality may also represent a behavioral thermoregulatory mechanism allowing the mongoose lemur to conserve energy by being active during the cool nights of the dry season. In addition, nocturnal behavior in the dry season probably allows avoidance of predation by raptors at the time of year when least protection is afforded by vegetation.

We collected data during a 10-month study carried out on the mongoose lemur, Eulemur mongoz, at Anjamena in northwestern Madagascar, which provide baseline information on seasonal variation in the ecology, home range use and some aspects of the behavior of two neighboring groups. We monitored group size of nine groups in the study area and assessed them for seasonal variation. We present additional information collected during short-term surveys in other areas before and during the study for comparison. The study groups were small family units, and changes in group size were limited to births and emigrations of sexually mature progeny. In spite of clear seasonal changes in climate and vegetation, there is no variation in grouping patterns, so it is not possible to correlate variation in group size with seasonal variation of ecological variables. Comparison with ecological data from other field studies on lemurids reveals differences in food resource distribution in western forests versus other types of Malagasy forest. This distribution of food resources may predict home range size in mixed frugivorous–folivorous lemurs. Small home ranges, mainly in the West, could be correlated with a uniform distribution of food resources. Finally, we suggest that the dry season in the West may not present frugivorous–folivorous lemurs with major problems in finding an adequate food supply. This is supported by the lack of seasonal differences in ranging behavior of mongoose lemurs.

The Malagasy primate family Indriidae comprises three genera with up to 19 species. Cytogenetic and molecular phylogenies of the Indriidae have been performed with special attention to the genus Propithecus. Comparative R-banding and FISH with human paints were applied to karyotypes of representatives of all three genera and confirmed most of the earlier R-banding results. However, additional chromosomal rearrangements were detected. A reticulated and a cladistic phylogeny, the latter including hemiplasies, have been performed. Cladistic analysis of cytogenetic data resulted in a phylogenetic tree revealing (1) monophyly of the family Indriidae, (2) monophyly of the genus Avahi, (3) sister–group relationships between Propithecus diadema and Propithecus edwardsi, and (4) the grouping of the latter with Indri indri, Propithecus verreauxi, and Propithecus tattersalli, and thus suggesting paraphyly of the genus Propithecus. A molecular phylogeny based on complete mitochondrial cytochrome b sequences of 16 species indicated some identical relationships, such as the monophyly of Avahi and the sister–group relationships of the eastern (P. diadema and P. edwardsi) to the western Propithecus species (P. verreauxi, Propithecus coquereli, and P. tattersalli). However, the main difference between the molecular and cytogenetic phylogenies consists in an early divergence of Indri in the molecular phylogeny while in the chromosomal phylogeny it is nested within Propithecus. The similarities and differences between molecular and cytogenetic phylogenies in relation to data on the species’ geographic distributions and mating systems allow us to propose a scenario of the evolution of Indriidae. Chromosomal and molecular processes alone or in combination created a reproductive barrier that was then followed by further speciation processes. Electronic supplementary material The online version of this article (doi:10.1007/s10577-011-9188-5) contains supplementary material, which is available to authorized users.

Background Hybrid zones generally represent areas of secondary contact after speciation. The nature of the interaction between genes of individuals in a hybrid zone is of interest in the study of evolutionary processes. In this study, data from nuclear microsatellites and mitochondrial DNA sequences were used to genetically characterize hybridization between wild mongoose lemurs (Eulemur mongoz) and brown lemurs (E. fulvus) at Anjamena in west Madagascar. Results Two segments of mtDNA have been sequenced and 12 microsatellite loci screened in 162 brown lemurs and mongoose lemurs. Among the mongoose lemur population at Anjamena, we identified two F1 hybrids (one also having the mtDNA haplotype of E. fulvus) and six other individuals with putative introgressed alleles in their genotype. Principal component analysis groups both hybrids as intermediate between E. mongoz and E. fulvus and admixture analyses revealed an admixed genotype for both animals. Paternity testing proved one F1 hybrid to be fertile. Of the eight brown lemurs genotyped, all have either putative introgressed microsatellite alleles and/or the mtDNA haplotype of E. mongoz. Conclusion Introgression is bidirectional for the two species, with an indication that it is more frequent in brown lemurs than in mongoose lemurs. We conclude that this hybridization occurs because mongoose lemurs have expanded their range relatively recently. Introgressive hybridization may play an important role in the unique lemur radiation, as has already been shown in other rapidly evolving animals.

Background The number of species within the Malagasy genus Lepilemur and their phylogenetic relationships is disputed and controversial. In order to establish their evolutionary relationships, a comparative cytogenetic and molecular study was performed. We sequenced the complete mitochondrial cytochrome b gene (1140 bp) from 68 individuals representing all eight sportive lemur species and most major populations, and compared the results with those obtained from cytogenetic studies derived from 99 specimens. Results Interspecific genetic variation, diagnostic characters and significantly supported phylogenetic relationships were obtained from the mitochondrial sequence data and are in agreement with cytogenetic information. The results confirm the distinctiveness of Lepilemur ankaranensis, L. dorsalis, L. edwardsi, L. leucopus, L. microdon, L. mustelinus, L. ruficaudatus and L. septentrionalis on species level. Additionally, within L. ruficaudatus large genetic differences were observed among different geographic populations. L. dorsalis from Sahamalaza Peninsula and from the Ambanja/Nosy Be region are paraphyletic, with the latter forming a sister group to L. ankaranensis. Conclusion Our results support the classification of the eight major sportive lemur taxa as independent species. Moreover, our data indicate further cryptic speciation events within L. ruficaudatus and L. dorsalis. Based on molecular data we propose to recognize the sportive lemur populations from north of the Tsiribihina River, south of the Betsiboka River, and from the Sahamalaza Peninsula, as distinct species.

Endocrine profiles were investigated in wild and captive mongoose lemurs (Eulemur mongoz; Lemuridae) by analysing faecal progestagens and oestrogens. Oestrous cycle characterization was not possible, as most females appeared to conceive during the first oestrus of the breeding season. Conception was preceded by a pseudo-oestrus with no discernible luteal phase. Pseudo-oestrus and oestrus identification was possible by investigating the oestrogen : progestagen ratio. Pregnancy was reliably determined approximately 47 days after conception, when progestagen and oestrogen excretion increased above breeding season concentrations. Gestation was further characterized by high progestagen concentrations and a decline in oestrogen excretion 70–80 days after conception. Post partum, progestagens declined, but oestrogen excretion increased to exceed breeding season concentrations. In the wild group, a nulliparous daughter conceived while still a member of her natal group and aborted after 70–80 days of pregnancy at which time progestagens had declined but oestrogens remained high. Comparisons with other strepsirhine primates suggest that pseudo-oestrus followed by conception at first oestrus may be prevalent in lemurs. Gestational progesterone profiles vary between species, but a delayed increase in oestrogens during pregnancy could be common to all strepsirhines, although oestrogen levels during the final trimester of pregnancy differ between lemurs and lorises. Methodological investigations showed that prolonged storage of faeces in ethanol is viable and that the presence of undigested vegetable matter in the faecal pellets had no effect on the interpretation of hormone profiles.

In 1995, the course “Introduction to Anthropology/Primatology” was organized at the Universite de Mahajanga in collaboration with the Anthropological Institute of the University of Zurich as a pilot project. The defined goals were: (1) presentation of primatology as an interesting and important subject, which may be of special relevance for Madagascar; (2) initiation of a test case to see how it would operate in general; ((3) provision of a starting point for future adjustments and potential extensions. Two questionnaires filled out by students before and after the course showed that they came from all over the island (such that knowledge would potentially be widely distributed later), that they were relatively old for the study level achieved, and that knowledge of the natural richness of Madagascar at the beginning of the lectures was lower than expected. Students judged the course to be interesting and worth following, feeling that it should be offered again; many believed that they had understood quite a lot. In fact, however, some of the messages of the lecture course did not transfer very well. As a pilot project, the course was successful in several realms but failed to catalyze longer term teaching and research activities for various reasons. An evaluation of the experiences made and of results of the questionnaires is presented.