BackgroundTiti monkeys, Callicebus, comprise the most species-rich primate genus—34 species are currently recognised, five of them described since 2005. The lack of molecular data for titi monkeys has meant that little is known of their phylogenetic relationships and divergence times. To clarify their evolutionary history, we assembled a large molecular dataset by sequencing 20 nuclear and two mitochondrial loci for 15 species, including representatives from all recognised species groups. Phylogenetic relationships were inferred using concatenated maximum likelihood and Bayesian analyses, allowing us to evaluate the current taxonomic hypothesis for the genus.ResultsOur results show four distinct Callicebus clades, for the most part concordant with the currently recognised morphological species-groups—the torquatus group, the personatus group, the donacophilus group, and the moloch group. The cupreus and moloch groups are not monophyletic, and all species of the formerly recognized cupreus group are reassigned to the moloch group. Two of the major divergence events are dated to the Miocene. The torquatus group, the oldest radiation, diverged c. 11 Ma; and the Atlantic forest personatus group split from the ancestor of all donacophilus and moloch species at 9–8 Ma. There is little molecular evidence for the separation of Callicebus caligatus and C. dubius, and we suggest that C. dubius should be considered a junior synonym of a polymorphic C. caligatus.ConclusionsConsidering molecular, morphological and biogeographic evidence, we propose a new genus level taxonomy for titi monkeys: Cheracebus n. gen. in the Orinoco, Negro and upper Amazon basins (torquatus group), Callicebus Thomas, 1903, in the Atlantic Forest (personatus group), and Plecturocebus n. gen. in the Amazon basin and Chaco region (donacophilus and moloch groups).Electronic supplementary materialThe online version of this article (doi:10.1186/s12983-016-0142-4) contains supplementary material, which is available to authorized users.

The pygmy marmoset, Cebuella pygmaea, the smallest of the New World monkeys, has one of the largest geographical distributions of the Amazonian primates. Two forms have been recognized: Cebuella pygmaea pygmaea (Spix, 1823), and C. p. niveiventris Lönnberg, 1940. In this study, we investigated if the separation of pygmy marmosets into these two clades can be corroborated by molecular data. We also examine and compare coloration of the pelage in light of the new molecular results. We analyzed the mtDNA cytochrome b gene and, for the first time for any Neotropical primate, we used a reduced representation genome sequencing approach (ddRADseq) to obtain data for recently collected, geographically representative samples from the Rio Japurá, a northern tributary of the Rio Solimões and from the Javarí, Jutaí, Juruá, Madeira and Purus river basins, all tributaries south of the Solimões. We estimated phylogenies and diversification times under both maximum likelihood and Bayesian inference criteria. Our analysis showed two highly supported clades, with intraclade divergences much smaller than interclade divergences, indicating two species of Cebuella: one from the Rio Japurá and one to the south of Solimões. The interpretation of our results in light of the current taxonomy is not trivial however. Lönnberg stated that the type of Spix's pygmy marmoset (type locality 'near Tabatinga') was obtained from the south of the Solimões, and his description of the distinct niveiventris from Lago Ipixuna, south of the Solimões and several hundred kilometres east of Tabatinga, was based on a comparison with specimens that he determined as typical pygmaea that were from the upper Rio Juruá (south of the Solimões). As such it remains uncertain whether the name pygmaea should be applicable to the pygmy marmosets north of the Rio Solimões (Tabatinga type locality) or south (near Tabatinga but across the Solimões). Finally, our analysis of pelage coloration revealed three phenotypic forms: (1) south of the Rio Solimoes, (2) Eirunepé-Acre, upper Juruá basin; and (3) Japurá. More samples from both sides of Solimões in the region of Tabatinga will be necessary to ascertain the exact type locality for Spix's pygmaea and to resolve the current uncertainties surrounding pygmy marmoset taxonomy.

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ABSTRACT. Although the genus Tursiops has a worldwide distribution and is globally well-studied, some dolphin populations continue to face high risks of decline. Hence, it is necessary to assess the genetic diversity and structure of this genus to properly assess its conservation status and to implement appropriate management actions. In Brazil, genetic studies on this group remain rare, particularly for populations inhabiting offshore waters. Saint Peter and Saint Paul Archipelago (SPSPA) is a small group of islands located in the MidAtlantic Ridge, where recent studies of the Tursiops truncatus group indicate that individuals are resident throughout the year around the archipelago, exhibiting considerable site fidelity. A previous study with this group indicated that the individuals form an isolated population. To test this hypothesis, and describe the genetic diversity of SPSPA individuals, we assessed 12 microsatellite loci and a portion of the mitochondrial control region. Bayesian analysis revealed that SPSPA bottlenose dolphins form a unique population. In a phylogeographic perspective, we found that individuals from SPSPA shared mtDNA haplotypes with inshore and offshore individuals from North Atlantic, suggesting that they are not currently isolated from their conspecifics. Mirroring mtDNA findings, microsatellite analysis revealed that most of the pairs of individuals sampled seem to be unrelated (83.8%) and no indication of inbreeding, what would be expected if a small population such as SPSPA was reproductively isolated.

Amazonia has the richest primate fauna in the world. Nonetheless, the diversity and distribution of Amazonian primates remain little known and the scarcity of baseline data challenges their conservation. These challenges are especially acute in the Amazonian arc of deforestation, the 2500 km long southern edge of the Amazonian biome that is rapidly being deforested and converted to agricultural and pastoral landscapes. Amazonian marmosets of the genus Mico are little known endemics of this region and therefore a priority for research and conservation efforts. However, even nascent conservation efforts are hampered by taxonomic uncertainties in this group, such as the existence of a potentially new species from the Juruena–Teles Pires interfluve hidden within the M. emiliae epithet. Here we test if these marmosets belong to a distinct species using new morphological, phylogenomic, and geographic distribution data analysed within an integrative taxonomic framework. We discovered a new, pseudo-cryptic Mico species hidden within the epithet M. emiliae, here described and named after Horacio Schneider, the pioneer of molecular phylogenetics of Neotropical primates. We also clarify the distribution, evolutionary and morphological relationships of four other Mico species, bridging Linnean, Wallacean, and Darwinian shortfalls in the conservation of primates in the Amazonian arc of deforestation.

The criteria to classify the diversity of Neotropical Primates have recently taken the discussion boards due to the reappraisal on the phylogenetic relationship of some groups. Such controversial and arbitrary decisions, however, can hamper conservation actions in as much as it becomes difficult to prioritise and set meaningful targets. It is the case for dwarf marmosets from central Amazonia. Today, the classification of dwarf marmosets in Mico or Callibella genus has not been satisfactorily settled. Aiming to contribute to the taxonomic and conservation assessment of dwarf marmosets, we conducted new data collection during 3‐year fieldwork in the Aripuanã River, where the species was discovered. We present the first phylogenomic analysis of the evolutionary relationships between marmosets, new data from mitochondrial DNA and morphology, as well new records to clarify geographic distribution. With this new evidence, we support dwarf marmosets as the genus Callibella. We further discuss the implications for the conservation of this marmoset.

Deltamys is a monotypic sigmodontine rodent from the Pampas of South America. In addition to the formally recognized D. kempi that inhabits lowlands, an undescribed form Deltamys sp. 2n=40 was recently found in the highlands of southeastern Brazil. In the present study, we perform a phylogeographic reassessment of Deltamys and describe a third form of the genus, endemic to the Brazilian Araucaria Forest. We describe this new species based on an integrative analysis, using complete cytochrome b DNA sequences, karyology and morphology. Bayesian tree recovered two allopatric clades (lowlands vs. highlands) and three lineages: (i) the lowland D. kempi, (ii) the highland Deltamys sp. 2n=40, and (iii) Deltamys araucaria sp. n. Deltamys araucaria sp. n. is karyotypically (2n=34) and morphologically distinguishable from D. kempi (2n=37-38), showing a tawnier dorsum/flank pelage, presence of a protostyle, M1 alveolus positioned anteriorly to the posterior margin of the zygomatic plate, and several other distinguishing characteristics. A phylogeographic assessment of D. kempi recovered two haplogroups with significant differences in skull measurements. This phylogeographic break seems to have been shaped by the Patos Lagoon estuarine channel. The diversification in Deltamys might have been triggered by dispersal of older lineages over different altitudinal ranges in the Paraná geological basin.

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.