How many Pygmy Marmoset (Cebuella Gray, 1870) species are there? A taxonomic re-appraisal based on new molecular evidence

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 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

Ancient DNA of the pygmy marmoset type specimen Cebuella pygmaea (Spix, 1823) resolves a taxonomic conundrum

The pygmy marmoset, the smallest of the anthropoid primates, has a broad distribution in Western Amazonia. Recent studies using molecular and morphological data have identified two distinct species separated by the Napo and Solimões-Amazonas rivers. However, reconciling this new biological evidence with current taxonomy, i.e., two subspecies, Cebuella pygmaea pygmaea (Spix, 1823) and Cebuella pygmaea niveiventris (Lönnberg, 1940), was problematic given the uncertainty as to whether Spix’s pygmy marmoset (Cebuella pygmaea pygmaea) was collected north or south of the Napo and Solimões-Amazonas rivers, making it unclear to which of the two newly revealed species the name pygmaea would apply. Here, we present the first molecular data from Spix’s type specimen of Cebuella pygmaea, as well as novel mitochondrial genomes from modern pygmy marmosets sampled near the type locality (Tabatinga) on both sides of the river. With these data, we can confirm the correct names of the two species identified, i.e., C. pygmaea for animals north of the Napo and Solimões-Amazonas rivers and C. niveiventris for animals south of these two rivers. Phylogenetic analyses of the novel genetic data placed into the context of cytochrome b gene sequences from across the range of pygmy marmosets further led us to re-evaluate the geographical distribution for the two Cebuella species. We dated the split of these two species to 2.54 million years ago. We discuss additional, more recent, subdivisions within each lineage, as well as potential contact zones between the two species in the headwaters of these rivers

Four New Species Of Spiny Rats Of The Genus Proechimys (Rodentia : Echimyidae) From The Western Amazon Of Brazil

Volume: 111Start Page: 436End Page: 47

A taxonomic reassessment of Cacajao melanocephalus Humboldt (1811), with the description of two new species

The author of the last published systematic review of Cacajao recognized 2 subspecies of black-headed uakaris (black uakaris): Cacajao melanocephalus melanocephalus and C. m. ouakary. As a result of a series of black uakari surveys and collecting expeditions to several tributaries of the Rio Negro and of morphological and molecular analyses of museum specimens and specimens we collected during field expeditions, we reassess their taxonomy. We describe a newly discovered species of black uakari from the Rio Aracá, a left bank tributary of the Rio Negro, Amazonas, Brazil. We also show that ouakary is a junior synonym of melanocephalus and provide a new name and a new description for Cacajao melanocephalus melanocephalus in the Pico da Neblina region of Brazil and Venezuela. Based on genetic, morphological, and ecological evidence, we propose that there are 3 species of black uakaris. We named the Rio Aracá species Cacajao ayresi sp. nov. (Ayres uakari) in honor of the late José Márcio Ayres, a pioneer in uakari research and conservation. We named the Neblina black uakari Cacajao hosomi, after the Yanomami word for uakaris. The new taxonomic arrangement provided here implies that the conservation status of black uakaris needs to be reassessed

Spatial and temporal patterns of diversification on the Amazon : a test of the riverine hypothesis for all diurnal primates of Rio Negro and Rio Branco in Brazil

The role of Amazonian rivers as drivers of speciation through vicariance remains controversial. Here we explore the riverine hypothesis by comparing spatial and temporal concordances in pattern of diversification for all diurnal primates of Rio Negro and its largest tributary, Rio Branco. We built a comprehensive comparative phylogenetic timetree to identify sister lineages of primates based on mitochondrial cytochrome b DNA sequences from 94 samples, including 19 of the 20 species of diurnal primates from our study region and 17 related taxa from elsewhere. Of the ten primate genera found in this region, three had populations on opposite banks of Rio Negro that formed reciprocally monophyletic clades, with roughly similar divergence times (Cebus: 1.85 Ma, HPD 95% 1.19–2.62; Callicebus: 0.83 Ma HPD 95% 0.36–1.32, Cacajao: 1.09 Ma, 95% HPD 0.58–1.77). This also coincided with time of divergence of several allopatric species of Amazonian birds separated by this river as reported by other authors. Our data offer support for the riverine hypothesis and for a Plio-Pleistocene time of origin for Amazonian drainage system. We showed that Rio Branco was an important geographical barrier, limiting the distribution of six primate genera: Cacajao, Callicebus, Cebus to the west and Pithecia, Saguinus, Sapajus to the east. The role of this river as a vicariant agent however, was less clear. For example, Chiropotes sagulata on the left bank of the Rio Branco formed a clade with C. chiropotes from the Amazonas Department of Venezuela, north of Rio Branco headwaters, with C. israelita on the right bank of the Rio Branco as the sister taxon to C. chiropotes + C. sagulata. Although we showed that the formation of the Rio Negro was important in driving diversification in some of our studied taxa, future studies including more extensive sampling of markers across the genome would help determine what processes contributed to the evolutionary history of the remaining primate genera

On a new species of titi monkey (Primates: Plecturocebus Byrne et al., 2016), from Alta Floresta, southern Amazon, Brazil

The taxonomy of the titi monkeys (Callicebinae) has recently received considerable attention. It is now recognised that this subfamily is composed of three genera with 33 species, seven of them described since 2002. Here, we describe a new species of titi, Plecturocebus, from the municipality of Alta Floresta, Mato Grosso, Brazil. We adopt an integrative taxonomic approach that includes phylogenomic analyses, pelage characters, and locality records. A reduced representation genome-wide approach was employed to assess phylogenetic relationships among species of the eastern Amazonian clade of the Plecturocebus moloch group. Using existing records, we calculated the Extent of Occurrence (EOO) of the new species and estimated future habitat loss for the region based on predictive models. We then evaluated the species’ conservation status using the IUCN Red list categories and criteria. The new species presents a unique combination of morphological characters: (1) grey agouti colouration on the crown and dorsal parts; (2) entirely bright red-brown venter; (3) an almost entirely black tail with a pale tip; and (4) light yellow colouration of the hair on the cheeks contrasting with bright red-brown hair on the sides of the face. Our phylogenetic reconstructions based on maximum-likelihood and Bayesian methods revealed well-supported species relationships, with the Alta Floresta taxon as sister to P. moloch + P. vieirai. The species EOO is 10,166,653 ha and we predict a total habitat loss of 86% of its original forest habitat under a “business as usual” scenario in the next 24 years, making the newly discovered titi monkey a Critically Endangered species under the IUCN A3c criterion. We give the new titi monkey a specific epithet based on: (1) clear monophyly of this lineage revealed by robust genomic and mitochondrial data; (2) distinct and diagnosable pelage morphology; and (3) a well-defined geographical distribution with clear separation from other closely related taxa. Urgent conservation measures are needed to safeguard the future of this newly discovered and already critically endangered primate

Nine karyomorphs for spiny rats of the genus Proechimys (Echimyidae, Rodentia) from North and Central Brazil

Spiny rats of the genus Proechimys are morphologically diverse, widely distributed and have diploid numbers ranging from 2n = 14-16 to 2n = 62. In this paper we present cytogenetical data and brief comments on morphological and biogeographical issues related to spiny rats. In our sample of 42 spiny rats collected from 12 Brazilian Amazonian tropical rainforest and the Cerrado (Brazilian savanna) sites we detected nine karyological entities: four different karyomorphs with 2n = 30, three with 2n = 28, one with 2n = 15 and one with 2n = 44. Based on qualitative morphological characters these karyomorphs can be allocated to five species within the goeldii, guyannensis and longicaudatus species groups

Edge effects and landscape matrix use by a small mammal community in fragments of semideciduous submontane forest in Mato Grosso, Brazil

A community of small mammals was studied in seasonal semideciduous submontane forest in the state of Mato Grosso, Brazil. This study evaluated the use of edge and matrix pasture, by different small mammal species. Overall, 31 areas were studied, with a total sampling effort of 33,800 trap x nights. Only seven of the 25 species captured in the study sites were able to use the pasture matrix; we classified these species as generalists. Fourteen species were found to be intermediate in habits, being able to use forest edges. We found only four species habitat specialists, occurring only on transect lines in the interior of the fragment, at least 150 m from the edge. Transects located in the pasture matrix and 50 m from the edge had significantly lower species richness and abundance than transects located in the fragment edge or in the interior of the fragment. All transects located within the fragment had similar species richness and abundance, but transects located 50 m from the edge had slightly lower, but non-significant, species richness than transects located 100 m apart from edges. Rarefaction curves demonstrated that only medium-sized fragments (100 300 ha) reached an asymptote of species accumulation. The other areas require further sampling, or more sampling transect, before species accumulation curves stabilize, due to a continued increase in species number