70 research outputs found
Total evidence phylogeny of platyrrhine primates and a comparison of undated and tip-dating approaches
There have been multiple published phylogenetic analyses of platyrrhine primates (New World
monkeys) using both morphological and molecular data, but relatively few that have integrated
both types of data into a total evidence approach. Here, we present phylogenetic analyses of
Recent and fossil platyrrhines, based on a total evidence dataset of 418 morphological characters
and 10.2 kilobases of DNA sequence data from 17 nuclear genes taken from previous studies,
using undated and tip-dating approaches in a Bayesian framework. We compare the results of
these analyses with molecular scaffold analyses using maximum parsimony and Bayesian
approaches, and we use a formal information theoretic approach to identify unstable taxa. After a
posteriori pruning of unstable taxa, the undated and tip-dating topologies appear congruent with
recent molecular analyses and support largely similar relationships, with strong support for
Stirtonia as a stem alouattine, Neosaimiri as a stem saimirine, Cebupithecia as a stem pitheciine,
and Lagonimico as a stem callitrichid. Both analyses find three Greater Antillean subfossil
platyrrhines (Xenothrix, Antillothrix, and Paralouatta) to form a clade that is related to
Callicebus, congruent with a single dispersal event by the ancestor of this clade to the Greater
Antilles. They also suggest that the fossil Proteropithecia may not be closely related to
pitheciines, and that all known platyrrhines older than the Middle Miocene are stem taxa.
Notably, the undated analysis found the Early Miocene Panamacebus (currently recognized as
the oldest known cebid) to be unstable, and the tip-dating analysis placed it outside crown Platyrrhini. Our tip-dating analysis supports a late Oligocene or earliest Miocene (20.8â27.0 Ma)
age for crown Platyrrhini, congruent with recent molecular clock analyses
Microsatellite markers for bearded capuchins (Sapajus libidinosus) : transferability and characterization
Natural Sapajus libidinosus populations are in continuous decline due to fragmentation, habitat loss, and the illegal pet trade. They live in Caatinga scrub forests, which already lost over 50% of their original cover. The lack of studies on S. libidinosus population genetics means that we do not know how they are being affected by this striking habitat loss and other anthropogenic disturbances. Polymorphic markers are not available for the study of S. libidinosus diversity and population genetics. Thus, here we aimed to test the transferability of 14 microsatellite markers to S. libidinosus. These microsatellites were previously isolated from Cebus capucinus (white-faced capuchin), species belonging to the same subfamily (Cebinae) as the study species. We found that six of the tested microsatellite markers (tetra-nucleotide) were cross-amplified in our target species. All loci were polymorphic. The number of alleles varied from 4 to 7, and the expected heterozygosity ranged from 0.588 to 0.869. The microsatellite markers transferred to S. libidinosus and characterised in our study will be valuable tools to evaluate the genetic variability of both wild and captive populations. They will considerably reduce the costs of microsatellite isolations, helping to prioritise currently limited research and conservation budgets in Brazil
The Roosevelt â Rondon expedition marmoset (Mico marcai) : unveiling the conservation status of a data deficient species
The Roosevelt-Rondon Expedition marmoset, Mico marcai, was collected in 1914 and to date, all information on this species comes from three skins brought back by the Expedition and two additional skins collected in the 1990s. It is no surprise then that M.marcai has been classified as Data Deficient (DD). Given that Mico marcaiâs suspected range sits on the path of the advancing Brazilian âArc-of-Deforestationâ, it is urgent that relevant data be collected to assess this taxon. Here we present the first comprehensive field data on the distribution, population size and threats on M. marcai with the goal of removing the species from the DD category. From 2012 to 2015, we surveyed for the species in 11 localities, in and around the Marmelos-AripuanĂŁ interfluve, and estimated density using distance sampling on 10 transects. We also used spatial predictive modelling to project the amount of habitat that will be lost within its range in 18 years under different deforestation scenarios. We found marmosets in 14 localities and calculated its Extent of Occurrence to be 31,073 km2. We walked 271 km and detected 30 marmoset groups, allowing us to estimate their density to be 8.31 individuals/km2 and a total population of 258,217.71 individuals. By a âBusiness as usualâ scenario, 20,181 km2 of habitat will be lost in three marmoset generations (~18 years), compromising 33% of the speciesâ range. Accordingly, M. marcai should be classified as globally Vulnerable under category A3c. Following our study, we propose the Amazonian marmosets, genus Mico, should undergo similar re-assessment as their ranges all fall in the path of the Arc-of-Deforestation.
Keywords: Amazonian marmosets, Conservation Status, Data Deficient, Habitat Loss, Southern Amazoni
Phylogeny, molecular dating and zoogeographic history of the titi monkeys (Callicebus, Pitheciidae) of eastern Brazil
The titi monkeys belong to a genus of New World primates endemic to South America, which were recently reclassified in three genera (Cheracebus, Plecturocebus and Callicebus). The genus Callicebus, which currently includes five species, is endemic to eastern Brazil, occurring in the Caatinga, Savanna, and Atlantic Forest biomes. In the present study, we investigated the validity of these species and inferred their phylogenetic relationships, divergence times, and biogeographic patterns based on the molecular analysis of a concatenated sequence of 11 mitochondrial and nuclear DNA markers, derived from 13 specimens. We ran Maximum Likelihood (ML) and Bayesian Inference (BI) analyses, and estimated genetic distances, divergence times. Ancestral areas were estimated on BioGeoBears. Our results suggest that at about twelve million years ago, the ancestor of all titi monkeys inhabited a wide area that extended from the Amazon forest to the South of the Atlantic forest. A first vicariant event originated Cheracebus in the West of the Amazon and the ancestor of Callicebus and Plectorocebus which, later were separated by a second one. The diversification of Callicebus occurred during the Plio-Pleistocene (beginning at 5 Ma) probably influenced by climatic fluctuations and geological events. Therefore, the results of the present work confirmed the existence of five species that currently inhabit forested areas under increasing threat from human activities. Thus, a reliable diagnosis of the taxonomic status of species living in endangered environments is extremely important for the development of conservation measures
A phylogenomic perspective on the robust capuchin monkey (Sapajus) radiation : first evidence for extensive population admixture across South America
Phylogenetic relationships amongst the robust capuchin monkeys (genus Sapajus) are poorly understood. Morphology-based taxonomies have recognized anywhere from one to twelve different species. The current IUCN (2017) classification lists eight robust capuchins: S. xanthosternos, S. nigritus, S. robustus, S. flavius, S. libidinosus, S. cay, S. apella and S. macrocephalus. Here, we assembled the first phylogenomic data set for Sapajus using ultra-conserved elements (UCEs) to reconstruct a capuchin phylogeny. All phylogenomic analyses strongly supported a deep divergence of Sapajus and Cebus clades within the capuchin monkeys, and provide support for Sapajus nigritus, S. robustus and S. xanthosternos as distinct species. However, the UCE phylogeny lumped the putative species S. cay, S. libidinosus, S. apella, S. macrocephalus, and S. flavius together as a single widespread lineage. A SNP phylogeny constructed from the UCE data was better resolved and recovered S. flavius and S. libidinosus as sister species; however, S. apella, S. macrocephalus, and S. cay individuals were interspersed in a widespread clade with no evidence for monophyly for any of these three morphospecies. STRUCTURE analysis of population clustering revealed widespread admixture among Sapajus populations within the Amazon and even into the Cerrado and Atlantic Forest. Difficulty in assigning species by morphology may be a result of widespread population admixture facilitated through frequent movement across major rivers and even ecosystems by robust capuchin monkeys
eDNA in a bottleneck : obstacles to fish metabarcoding studies in megadiverse freshwater systems
The current capacity of environmental DNA (eDNA) to provide accurate insights into the biodiversity of megadiverse regions (e.g., the Neotropics) requires further evaluation to ensure its reliability for longâterm monitoring. In this study, we first evaluated the taxonomic resolution capabilities of a short fragment from the 12S rRNA gene widely used in fish eDNA metabarcoding studies, and then compared eDNA metabarcoding data from water samples with traditional sampling using nets. For the taxonomic discriminatory power analysis, we used a specifically curated reference dataset consisting of 373 sequences from 258 neotropical fish species (including 47 newly generated sequences) to perform a genetic distanceâbased analysis of the amplicons targeted by the MiFish primer set. We obtained an optimum delimitation threshold value of 0.5% due to lowest cumulative errors. The barcoding gap analysis revealed only a 51.55% success rate in species recovery (133/258), highlighting a poor taxonomic resolution from the targeted amplicon. To evaluate the empirical performance of this amplicon for biomonitoring, we assessed fish biodiversity using eDNA metabarcoding from water samples collected from the Amazon (Adolpho Ducke Forest Reserve and two additional locations outside the Reserve). From a total of 84 identified Molecular Operational Taxonomic Units (MOTUs), only four could be assigned to species level using a fixed threshold. Measures of αâdiversity analyses within the Reserve showed similar patterns in each site between the number of MOTUs (eDNA dataset) and species (netting data) found. However, ÎČâdiversity revealed contrasting patterns between the methods. We therefore suggest that a new approach is needed, underpinned by sound taxonomic knowledge, and a more thorough evaluation of better molecular identification procedures such as multiâmarker metabarcoding approaches and tailorâmade (i.e., orderâspecific) taxonomic delimitation thresholds
Assessing the potential of environmental DNA metabarcoding for monitoring Neotropical mammals : a case study in the Amazon and Atlantic Forest, Brazil
The application of environmental DNA (eDNA) metabarcoding as a biomonitoring tool has greatly increased in the last decade. However, most studies have focused on aquatic macro-organisms in temperate areas (e.g., fishes). We apply eDNA metabarcoding to detect the mammalian community in two high-biodiversity regions of Brazil, the Amazon and Atlantic Forest. We identified critically endangered and endangered mammalian species in the Atlantic Forest and Amazon respectively and found overlap with species identified via camera trapping in the Atlantic Forest. In light of our results, we highlight the potential and challenges of eDNA monitoring for mammals in these highly biodiverse regions
The role of competition in structuring primate communities under different productivity regimes in the Amazon
The factors responsible for the formation of Amazonian primate communities are not well
understood. Here we investigated the influence of interspecific competition in the assembly
of these communities, specifically whether they follow an assembly rule known as "favored
states". According to this rule, interspecific competition influences final species composition,
resulting in functional groups that are equally represented in the community.We
compiled presence-absence data for primate species at 39 Amazonian sites in Brazil, contrasting
two regions with distinct productivity regimes: the eutrophic JuruĂĄ River basin and
the oligotrophic Negro River basin. We tested two hypotheses: that interspecific competition
is a mechanism that influences the structure of Amazonian primate communities, and that
competition has had a greater influence on the structure of primate communities in regions
with low productivity, where resources are more limited. We used null models to test the statistical
significance of the results, and found a non-random pattern compatible with the
favored states rule in the two regions. Our findings suggest that interspecific competition is
an important force driving primate community assembly regardless of productivity regimes
An integrative analysis uncovers a new, pseudo-cryptic species of Amazonian marmoset (Primates: Callitrichidae: Mico) from the arc of deforestation
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 JuruenaâTeles 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
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 JapurĂĄ, a northern tributary of the Rio SolimĂ”es and from the JavarĂ, JutaĂ, JuruĂĄ, Madeira and Purus river basins, all tributaries south of the SolimĂ”es. 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 JapurĂĄ and one to the south of SolimĂ”es. The interpretation of our results in light of the current taxonomy is not trivial however. Lönnberg stated that the type of Spixâs pygmy marmoset (type locality ânear Tabatingaâ) was obtained from the south of the SolimĂ”es, and his description of the distinct niveiventris from Lago Ipixuna, south of the SolimĂ”es 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 JuruĂĄ (south of the SolimĂ”es). As such it remains uncertain whether the name pygmaea should be applicable to the pygmy marmosets north of the Rio SolimĂ”es (Tabatinga type locality) or south (near Tabatinga but across the SolimĂ”es). Finally, our analysis of pelage coloration revealed three phenotypic forms: 1) south of the Rio Solimoes, 2) EirunepĂ©-Acre, upper JuruĂĄ basin; and 3) JapurĂĄ. More samples from both sides of SolimĂ”es in the region of Tabatinga will be necessary to ascertain the exact type locality for Spixâs pygmaea and to resolve the current uncertainties surrounding pygmy marmoset taxonomy
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