Update of the geographic range of Humboldt's squirrel monkeys (Saimiri cassiquiarensis cassiquiarensis Lesson, 1840) using a model-based approach.

Saimiri cassiquiarensis cassiquiarensis (Cebidae) is a primate subspecies with a wide distribution in the Amazonian region of Brazil, Colombia, and Venezuela. However, the boundaries of its geographic range remain poorly defined. This study presents new occurrence localities for this subspecies and updates its distribution using a compiled data set of 140 occurrence records based on literature, specimens vouchered in scientific collections, and new field data to produce model-based range maps. After cleaning our data set, we updated the subspecies' extent of occurrence, which was used in model calibration. We then modeled the subspecies' range using a maximum entropy algorithm (MaxEnt). The final model was adjusted using a fixed threshold, and we revised this polygon based on known geographic barriers and parapatric congeneric ranges. Our findings indicate that this subspecies is strongly associated with lowland areas, with consistently high daily temperatures. We propose modifications to all range boundaries and estimate that 3% of the area of occupancy (AOO, as defined by IUCN) has already been lost due to deforestation, resulting in a current range of 224,469 km2. We also found that 54% of their AOO is currently covered by protected areas (PAs). Based on these results, we consider that this subspecies is currently properly classified as Least Concern, because it occupies an extensive range, which is relatively well covered by PAs, and is currently experiencing low rates of deforestation.

Saimiri cassiquiarensis cassiquiarensis (Cebidae) é uma subespécie de primata com ampla distribuição na região amazônica do Brasil, Colômbia e Venezuela. No entanto, os limites de sua distribuição geográfica permanecem mal definidos. Este estudo apresenta novas localidades de ocorrência para essa subespécie e atualiza sua distribuição usando 140 registros de ocorrência compilados com base na literatura, espécimes depositados em coleções científicas e novos registros de campo para produzir mapas de distribuição baseados em modelos. Após a limpeza do nosso banco de dados, atualizamos a extensão de ocorrência da subespécie, que foi usada na calibração do modelo. Em seguida, modelamos a área de distribuição da subespécie usando um algoritmo de entropia máxima (MaxEnt). O modelo final foi ajustado usando um limiar fixo e revisamos esse polígono com base em barreiras geográficas conhecidas e na distribuição de congêneres parapátricas. Nosso modelo sugere que a espécie é fortemente associada a áreas planas, com temperaturas diárias consistentemente altas. Propomos modificações em todos os limites da área de distribuição e estimamos que 3% da área de ocupação (AOO, conforme definida pela IUCN) da subespécie já foi perdida devido ao desmatamento, resultando em uma área de distribuição atual de 224,469 km2. Também estimamos que 54% de sua AOO encontra­se atualmente coberta por áreas protegidas. Com base nesses resultados, consideramos que a subespécie está apropriadamente classificada como Pouco Preocupante, pois ocupa uma área extensa, que é relativamente bem coberta por áreas protegidas e atualmente apresenta baixas taxas de desmatamento.

Phylogeography, genetic diversity, and intraspecific genetic structure of the black-horned capuchin (Sapajus nigritus).

Recent molecular studies have clarified the overarching taxonomy of capuchin monkeys, but intraspecific genetic diversity remains unexplored for most capuchin species. One example is Sapajus nigritus, the southernmost capuchin monkey, found in Brazil and Argentina; its phenotypic diversity has been recognized as two geographic subspecies, but the intraspecific genetic structure of this taxon is poorly known. Here, we sampled across most of this species' geographic distribution, producing a newly sequenced data set for genetic analyses that included 78 individuals from 14 populations. We investigated the intraspecific diversity, genetic structure, and evolutionary history using three mitochondrial markers. Our results indicated that S. nigritus populations exhibited high levels of genetic structure. We found strong support for two monophyletic clades within this species with a deep phylogenetic split, and clear separation from other related taxa. Vicariance events seem to have played a prevalent role in shaping S. nigritus genetic differentiation. The Paraíba do Sul River may have driven the deep divergence between southern and northern clades, whereas the Tietê River may have had a weaker, more recent effect on the divergence of populations within the southern clade.

New records of Amblyomma ticks parasitizing neotropical primates in Brazil.

Amblyomma is an important tick genus for animal and human health, with some species being the vectors of zoonotic pathogens, such as Rickettsia rickettsii, in the Neotropical region. Knowing their hosts may help to understand the distribution of these agents and decrease the occurrence of clinical cases. Primates are intelligent and adaptable animals that can get close to humans in the search for food. So, they may be an important epidemiological link for the spread of these ticks. Beyond that, primates also suffer from these infections, serving as sentinels for different diseases. Thus, the present study aims to report the parasitism by Amblyomma spp. on six species of Neotropical primates from different locations in Brazil. The 337 collected ticks were morphologically identified using stereomicroscopes and taxonomic keys, and six distinct species of ticks were identified. We report here the first record of nymphs of the tick species Amblyomma cajennense sensu stricto on Alouatta belzebul, a male of Amblyomma fuscum on Alouatta guariba clamitans, nymphs of Amblyomma sculptum on Leontopithecus chrysopygus and Callithrix aurita, as well as nymphs of Amblyomma geayi on Saimiri collinsi. Of the 337 tick specimens collected, 256 (75,96%) were nymphs. The importance of primates in the life cycle of these species remains to be elucidated.

Framework of the Alu Subfamily Evolution in the Platyrrhine Three-Family Clade of Cebidae, Callithrichidae, and Aotidae.

The history of Alu retroposons has been choreographed by the systematic accumulation of inherited diagnostic nucleotide substitutions to form discrete subfamilies, each having a distinct nucleotide consensus sequence. The oldest subfamily, AluJ, gave rise to AluS after the split between Strepsirrhini and what would become Catarrhini and Platyrrhini. The AluS lineage gave rise to AluY in catarrhines and to AluTa in platyrrhines. Platyrrhine Alu subfamilies Ta7, Ta10, and Ta15 were assigned names based on a standardized nomenclature. However, with the subsequent intensification of whole genome sequencing (WGS), large scale analyses to characterize Alu subfamilies using the program COSEG identified entire lineages of subfamilies simultaneously. The first platyrrhine genome with WGS, the common marmoset (Callithrix jacchus; [caljac3]), resulted in Alu subfamily names sf0 to sf94 in an arbitrary order. Although easily resolved by alignment of the consensus sequences, this naming convention can become increasingly confusing as more genomes are independently analyzed. In this study, we reported Alu subfamily characterization for the platyrrhine three-family clade of Cebidae, Callithrichidae, and Aotidae. We investigated one species/genome from each recognized family of Callithrichidae and Aotidae and of both subfamilies (Cebinae and Saimiriinae) of the family Cebidae. Furthermore, we constructed a comprehensive network of Alu subfamily evolution within the three-family clade of platyrrhines to provide a working framework for future research. Alu expansion in the three-family clade has been dominated by AluTa15 and its derivatives.

Cebidae Alu Element Alignments and a Complex Non-Human Primate Radiation.

Phylogenetic relationships among Cebidae species of platyrrhine primates are presently under debate. Studies prior to whole genome sequence (WGS) availability utilizing unidirectional Alu repeats linked Callithrix and Saguinus as sister taxa, based on a limited number of genetic markers and specimens, while the relative positions of Cebus, Saimiri and Aotus remained controversial. Multiple WGS allowed computational detection of Alu-genome junctions, however random mutation and evolutionary decay of these short-read segments prevented phylogenetic resolution. In this study, WGS for four Cebidae genomes of marmoset, squirrel monkey, owl monkey and capuchin were analyzed for full-length Alu elements and each locus was compared to the other three genomes in all possible combinations using orthologous region sequence alignments. Over 2000 candidates were aligned and subjected to visual inspection. Approximately 34% passed inspection and were considered shared in their respective category, 48% failed due to the target being present in all four genomes, having N's in the sequence or other sequence quality anomalies, and 18% were determined to represent near parallel insertions (NP). Wet bench locus specific PCR confirmed the presence of shared Alu insertions in all phylogenetically informative categories, providing evidence of extensive incomplete lineage sorting (ILS) and an abundance of Alu proliferation during the complex radiation of Cebidae taxa.

Signatures of adaptive evolution in platyrrhine primate genomes.

The platyrrhine family Cebidae (capuchin and squirrel monkeys) exhibit among the largest primate encephalization quotients. Each cebid lineage is also characterized by notable lineage-specific traits, with capuchins showing striking similarities to Hominidae such as high sensorimotor intelligence with tool use, advanced cognitive abilities, and behavioral flexibility. Here, we take a comparative genomics approach, performing genome-wide tests for positive selection across five cebid branches, to gain insight into major periods of cebid adaptive evolution. We uncover candidate targets of selection across cebid evolutionary history that may underlie the emergence of lineage-specific traits. Our analyses highlight shifting and sustained selective pressures on genes related to brain development, longevity, reproduction, and morphology, including evidence for cumulative and diversifying neurobiological adaptations across cebid evolution. In addition to generating a high-quality reference genome assembly for robust capuchins, our results lend to a better understanding of the adaptive diversification of this distinctive primate clade.

Anatomy applied to image diagnosis of the hind limb in the black-striped capuchin (Sapajus libidinosus Spix, 1823).

The knowledge of anatomy and imaging exams emerges as an important tool in the study of evolutionary processes of a species, in the elaboration of diagnosis, and the successful choice of the appropriate clinical and surgical procedures. Therefore, this study aims to describe the osteology of the hind limb of Sapajus libidinosus by means of gross, radiographic, and tomographic images. Four cadavers were used in the macroscopic analysis and five animals for the imaging exams, of which four were eventually euthanized and added to the macroscopic study. For imaging exams, they were kept anesthetized. All bones of the hind limb were documented, their structures were described, and compared with data in the literature from human and nonhuman primates. We have performed Student's t test for independent samples. There was no statistical difference between the sexes regarding the length of the hind limb bones. The coxal bone was largely well described using imaging methods. A small penile bone was present at the tip of the penis and it could be identified by all analysis methods. The femur, as well as the tibia and fibula, were not well portrayed in their proximal and distal epiphyses by radiography (Rx). However, they were well identified on tomography. No third trochanter was observed in the femur and the patella had a triangular shape. All the structures described by gross anatomy of the tarsus and metatarsus could be identified by Rx and tomography. More subtle structures, such as the popliteal notch on the tibia, and the gluteal tuberosity pectineal line and facies aspera on the coxal bone, were not identified by medical imaging. S. libidinosus presented anatomical characteristics that were similar to those of larger New World and Old World monkeys, including man. This suggests it's value as an experimental model for studies in recent primates.

Diet, activity patterns, and home range use in forest and cultivated areas for one wild group of endangered crested capuchin monkeys (Sapajus robustus) in Reserva Natural Vale, Espírito Santo, Brazil.

Robust capuchin monkeys (Sapajus spp.) are distributed widely in the Neotropics and may be able to survive in modified landscapes because of their omnivorous, opportunistic diet. The poorly known and endangered crested capuchin monkey (Sapajus robustus) is endemic to the Atlantic Forest in Bahia, Minas Gerais and Espírito Santo states, Brazil. We collected data on diet and home range for a crested capuchin group with access to forest and cultivated areas. We hypothesized that with access to cultivated exotic fruit, capuchins would use cultivated areas more for feeding during the season of fruit scarcity in the surrounding forest and have a small home range size because of higher fruit availability. Both the forest and the cultivated areas peaked in fruit availability in the wet season, with a low proportion of trees producing fruit in the dry season; cultivated areas had a higher proportion of trees in fruit compared to the forest throughout the study. While monkeys consumed exotic fruits like jackfruit and oil palm, we recorded more samples of them eating forest fruits than exotic fruits in all but 1 month, and they consumed a more diverse array of forest fruits (56 species) but only six exotic species. Home range size was relatively small compared with other studies: 120.5 ha across the year (wet season 102 ha, dry season 111.5 ha). Natural and human-intensified fruit sources in a protected area without hunting may have allowed monkeys to maintain a smaller home range size. The group composition changed during the study; this also likely influenced home range use. Studies focused on robust capuchin groups that utilize agricultural or cultivated foods may underestimate home range needs for groups without access to human-intensified food sources. Studying crested capuchin ecology in additional locations will be important for establishing a sound species conservation program.

Recently Integrated Alu Elements in Capuchin Monkeys: A Resource for Cebus/Sapajus Genomics.

Capuchins are platyrrhines (monkeys found in the Americas) within the Cebidae family. For most of their taxonomic history, the two main morphological types of capuchins, gracile (untufted) and robust (tufted), were assigned to a single genus, Cebus. Further, all tufted capuchins were assigned to a single species, Cebus apella, despite broad geographic ranges spanning Central and northern South America. In 2012, tufted capuchins were assigned to their genus, Sapajus, with eight currently recognized species and five Cebus species, although these numbers are still under debate. Alu retrotransposons are a class of mobile element insertion (MEI) widely used to study primate phylogenetics. However, Alu elements have rarely been used to study capuchins. Recent genome-level assemblies for capuchins (Cebus imitator; [Cebus_imitator_1.0] and Sapajus apella [GSC_monkey_1.0]) facilitated large scale ascertainment of young lineage-specific Alu insertions. Reported here are 1607 capuchin specific and 678 Sapajus specific Alu insertions along with candidate oligonucleotides for locus-specific PCR assays for many elements. PCR analyses identified 104 genus level and 51 species level Alu insertion polymorphisms. The Alu datasets reported in this study provide a valuable resource that will assist in the classification of archival samples lacking phenotypic data and for the study of capuchin phylogenetic relationships.

Botfly Parasitism on Two Primates of the Cebidae Family in Peru.

Botflies (Diptera:Oestridae) are a diverse group of insect parasites that affect various vertebrate species. There are previous reports of myiasis affecting wild primates in Central and South America; however, information about botfly parasitism in Peruvian primates is scarce. We present data from two Cebidae primate specimens: a rescued large-headed capuchin monkey (Sapajus macrocephalus) housed at Taricaya Rescue Center, in Tambopata, Peru, and a free-ranging white-fronted capuchin monkey (Cebus albifrons aequatorialis) inhabiting Cerros de Amotape National Park. The first specimen had a larva identified as Dermatobia hominis, whereas Cuterebra baeri larvae infested the second. In both cases we initially identified the parasite species through their morphologic features before confirming the identification with genetic analysis through the cytochrome C oxidase subunit 1 mitochondrial gene sequencing of the larvae. Further field studies on the primate-parasite dynamics are needed to understand the impact of botfly myiasis on primate populations.

Frequency of enteroparasites in Cebidae and Callitrichidae primates at the Zoológico de Cali, Colombia: zoonotic implications / [Frecuencia de enteroparásitos en primates Cebidae y Callitrichidae del Zoológico de Cali, Colombia: implicaciones zoonóticas].

Introduction: Enteroparasites can cause problems in animals kept under human care in zoos and shelters. Wild animals have low parasitic loads but when sheltered in closed places they can be higher and lead to clinical manifestations, which increases the cost of medical treatments and care. On the other hand, some enteroparasites can represent a potential risk of zoonotic infection for their animal keepers, visitors, and other zoo animals. In addition, they could affect recovery programs for endangered species. Objectives: To establish the presence and prevalence of potentially zoonotic enteroparasites in primates of the Cebidae and Callitrichidae families at the Zoológico de Cali from September to November, 2017. Materials and methods: We conducted a prospective cross-sectional study. Serial samples from 50 individuals belonging to seven species and two primate families were analyzed by ova and parasite test, flotation, and Kinyoun stain between September and November, 2017. Results: In order of frequency, the parasite genera found in the seven primate species evaluated were Blastocystis spp., Trichomonas spp., Giardia spp., Entamoeba spp., Strongyloides spp., Cyclospora sp., and Trichuris sp. Conclusions: At least six of the parasite genera found have potential zoonotic implications. It is necessary to establish what are the infection sources at the Zoológico de Cali and implement management protocols to reduce the risk of transmission to both humans and other animals in the collection. Additionally, we offer relevant information on the zoonotic potential of each of the enteroparasites found.

Introducción. Los enteroparásitos pueden generar problemas en animales bajo cuidado humano en zoológicos y centros de acogida. Los animales silvestres presentan bajas cargas parasitarias, pero estas pueden ser mayores y llevar a manifestaciones clínicas cuando se trata de animales resguardados en recintos, lo que aumenta los gastos en tratamientos y cuidados médicos. Por otro lado, algunos enteroparásitos pueden causar infecciones zoonóticas en los cuidadores, los visitantes y otros animales del zoológico, así como afectar los programas de recuperación de especies amenazadas de extinción. Objetivos. Determinar la presencia y prevalencia de enteroparásitos con potencial de transmisión zoonótica en primates de las familias Cebidae y Callitrichidae del Zoológico de Cali, entre septiembre y noviembre de 2017. Materiales y métodos. Se hizo un estudio transversal prospectivo, para lo cual se recolectaron muestras seriadas de 50 individuos pertenecientes a siete especies de dos familias de primates y se analizaron mediante examen coprológico, flotación y coloración Kinyoun, entre septiembre y noviembre de 2017. Resultados. Según su prevalencia, los géneros de parásitos hallados en las siete especies de primates evaluadas, fueron Blastocystis spp., Trichomonas spp., Giardia spp., Entamoeba spp., Strongyloides spp., Cyclospora sp. y Trichuris sp. Conclusiones. Por lo menos, seis de los géneros de parásitos identificados tienen implicaciones zoonóticas, lo cual hace necesario establecer las posibles vías de infección de los primates del Zoológico de Cali e implementar protocolos de manejo que reduzcan el riesgo de transmisión a los humanos y a otros animales de la colección. Además, se presenta la información relevante sobre el potencial zoonótico de los enteroparásitos hallados.

Frecuencia de enteroparásitos en primates Cebidae y Callitrichidae del Zoológico de Cali, Colombia: implicaciones zoonóticas / Frequency of enteroparasites in Cebidae and Callitrichidae primates at the Zoológico de Cali, Colombia: Zoonotic implications

Resumen | Introducción. Los enteroparásitos pueden generar problemas en animales bajo cuidado humano en zoológicos y centros de acogida. Los animales silvestres presentan bajas cargas parasitarias, pero estas pueden ser mayores y llevar a manifestaciones clínicas cuando se trata de animales resguardados en recintos, lo que aumenta los gastos en tratamientos y cuidados médicos. Por otro lado, algunos enteroparásitos pueden causar infecciones zoonóticas en los cuidadores, los visitantes y otros animales del zoológico, así como afectar los programas de recuperación de especies amenazadas de extinción. Objetivos. Determinar la presencia y prevalencia de enteroparásitos con potencial de transmisión zoonótica en primates de las familias Cebidae y Callitrichidae del Zoológico de Cali, entre septiembre y noviembre de 2017. Materiales y métodos. Se hizo un estudio transversal prospectivo, para lo cual se recolectaron muestras seriadas de 50 individuos pertenecientes a siete especies de dos familias de primates y se analizaron mediante examen coprológico, flotación y coloración Kinyoun, entre septiembre y noviembre de 2017. Resultados. Según su prevalencia, los géneros de parásitos hallados en las siete especies de primates evaluadas, fueron Blastocystis spp., Trichomonas spp., Giardia spp., Entamoeba spp., Strongyloides spp., Cyclospora sp. y Trichuris sp. Conclusiones. Por lo menos, seis de los géneros de parásitos identificados tienen implicaciones zoonóticas, lo cual hace necesario establecer las posibles vías de infección de los primates del Zoológico de Cali e implementar protocolos de manejo que reduzcan el riesgo de transmisión a los humanos y a otros animales de la colección. Además, se presenta la información relevante sobre el potencial zoonótico de los enteroparásitos hallados.

Abstract | Introduction: Enteroparasites can cause problems in animals kept under human care in zoos and shelters. Wild animals have low parasitic loads but when sheltered in closed places they can be higher and lead to clinical manifestations, which increases the cost of medical treatments and care. On the other hand, some enteroparasites can represent a potential risk of zoonotic infection for their animal keepers, visitors, and other zoo animals. In addition, they could affect recovery programs for endangered species. Objectives: To establish the presence and prevalence of potentially zoonotic enteroparasites in primates of the Cebidae and Callitrichidae families at the Zoológico de Cali from September to November, 2017. Materials and methods: We conducted a prospective cross-sectional study. Serial samples from 50 individuals belonging to seven species and two primate families were analyzed by ova and parasite test, flotation, and Kinyoun stain between September and November, 2017. Results: In order of frequency, the parasite genera found in the seven primate species evaluated were Blastocystis spp.,Trichomonas spp., Giardia spp., Entamoeba spp., Strongyloides spp., Cyclospora sp., and Trichuris sp. Conclusions: At least six of the parasite genera found have potential zoonotic implications. It is necessary to establish what are the infection sources at the Zoológico de Cali and implement management protocols to reduce the risk of transmission to both humans and other animals in the collection. Additionally, we offer relevant information on the zoonotic potential of each of the enteroparasites found.

The nomenclature of the blond capuchin, Cebus flavius (Schreber, 1799) (Mammalia, Primates, Cebidae).

I review the nomenclatural history of the blond capuchin, Cebus flavius (Schreber), a Brazilian monkey species. The name was published in 1799, not 1774 as generally cited, so the species is correctly known as Cebus flavius (Schreber, 1799).

Wild Blonde Capuchins (Sapajus flavius) Perform Anointing Behaviour Using Toxic Secretions of a Millipede (Spirobolida: Rhinocricidae).

Defensive secretions of millipedes are remarkable for containing toxic quinones known to efficiently repell hematophagous arthropods. Here we show that Endangered blonde capuchin monkeys make use of such secretions. We (i) describe the anointing behavior performed by the monkeys (ii) identify the millipede species used in the process (iii) describe the volatile chemical composition of its secretion. The blonde capuchin monkeys selectively searched for millipedes hidden under the ground. We observed three bouts of anointing behavior, performed by 13 individuals of all age classes (from adults to independent infants), both solitarily (1 event) and socially (10 events). The only millipede species used by the monkeys is an undescribed species of the genus Poecilocricus (Spirobolida, Rhinocricidae). The volatile chemical composition of the secretions was predominantly comprised of a mixture of benzoquinones and hydroquinones. The social nature of the behavior and time of the observations (mosquito season), suggest that social bonding and mosquito avoidance is linked to the anointing behavior of the monkeys.

Genetic variability of the sws1 cone opsin gene among New World monkeys.

Vision is a major sense for Primates and the ability to perceive colors has great importance for the species ecology and behavior. Visual processing begins with the activation of the visual opsins in the retina, and the spectral absorption peaks are highly variable among species. In most Primates, LWS/MWS opsins are responsible for sensitivity to long/middle wavelengths within the visible light spectrum, and SWS1 opsins provide sensitivity to short wavelengths, in the violet region of the spectrum. In this study, we aimed to investigate the genetic variation on the sws1 opsin gene of New World monkeys (NWM) and search for amino acid substitutions that might be associated with the different color vision phenotypes described for a few species. We sequenced the exon 1 of the sws1 opsin gene of seven species from the families Callitrichidae, Cebidae, and Atelidae, and searched for variation at the spectral tuning sites 46, 49, 52, 86, 90, 93, 114, 116, and 118. Among the known spectral tuning sites, only residue 114 was variable. To investigate whether other residues have a functional role in the SWS1 absorption peak, we performed computational modeling of wild-type SWS1 and mutants A50I and A50V, found naturally among the species investigated. Although in silico analysis did not show any visible effect caused by these substitutions, it is possible that interactions of residue 50 with other sites might have some effect in the spectral shifts in the order of ~14 nm, found among the NWM. We also performed phylogenetic reconstruction of the sws1 gene, which partially recovered the species phylogeny. Further studies will be important to uncover the mutations responsible for the phenotypic variability of the SWS1 of NWM, and how spectral tuning may be associated with specific ecological features such as preferred food items and habitat use.

The terminal ventricle of Saguinus leucopus (Primate).

The terminal ventricle is a dilation of the ventricular system located within the spinal cord, which is enveloped in ependymal cells that are involved in the dynamic of the cerebrospinal liquid. In the present study, four Saguinus leucopus specimens were dissected, two males and two females, whose spinal cords were extracted and histologically processed via hematoxylin and eosin stains of cuts at the conus medullaris. The S. leucopus' terminal ventricle was observed at the conus medullaris, and had an average diameter of 241.38 µm. Thus, the presence of the terminal ventricle in the S. leucopus at the level of the conus medullaris was established.

Viral diversity in oral cavity from Sapajus nigritus by metagenomic analyses.

Sapajus nigritus are non-human primates which are widespread in South America. They are omnivores and live in troops of up to 40 individuals. The oral cavity is one of the main entry routes for microorganisms, including viruses. Our study proposed the identification of viral sequences from oral swabs collected in a group of capuchin monkeys (n = 5) living in a public park in a fragment of Mata Atlantica in South Brazil. Samples were submitted to nucleic acid extraction and enrichment, which was followed by the construction of libraries. After high-throughput sequencing and contig assembly, we used a pipeline to identify 11 viral families, which are Herpesviridae, Parvoviridae, Papillomaviridae, Polyomaviridae, Caulimoviridae, Iridoviridae, Astroviridae, Poxviridae, and Baculoviridae, in addition to two complete viral genomes of Anelloviridae and Genomoviridae. Some of these viruses were closely related to known viruses, while other fragments are more distantly related, with 50% of identity or less to the currently available virus sequences in databases. In addition to host-related viruses, insect and small vertebrate-related viruses were also found, as well as plant-related viruses, bringing insights about their diet. In conclusion, this viral metagenomic analysis reveals, for the first time, the profile of viruses in the oral cavity of wild, free ranging capuchin monkeys.

Sensitivity of the polyDetect computational pipeline for phylogenetic analyses.

Alu elements are powerful phylogenetic markers. The combination of a recently-developed computational pipeline, polyDetect, with high copy number Alu insertions has previously been utilized to help resolve the Papio baboon phylogeny with high statistical support. Here, the polyDetect method was applied to the highly contentious Cebidae phylogeny within New World monkeys (NWM). The polyDetect method relies on conserved homology/identity of short read sequence data among the species being compared to accurately map predicted shared Alu insertions to each unique flanking sequence. The results of this comprehensive assessment indicate that there were insufficient sequence homology/identity stretches in non-repeated DNA sequences among the four Cebidae genera analyzed in this study to make this strategy phylogenetically viable. The ~20 million years of evolutionary divergence of the Cebidae genera has resulted in random sequence decay within the short read data, obscuring potentially orthologous elements in the species tested. These analyses suggest that the polyDetect pipeline is best suited to resolving phylogenies of more recently diverged lineages when high-quality assembled genomes are not available for the taxa of interest.

Long-term population monitoring of the threatened and endemic black-headed squirrel monkey (Saimiri vanzolinii) shows the importance of protected areas for primate conservation in Amazonia.

Population monitoring of endangered species is essential to the improvement of their management and conservation plans. The black-headed squirrel monkey (Saimiri vanzolinii) is a vulnerable species on the IUCN Red List and has extreme geographical endemism, exhibiting the smallest known distribution among Neotropical primates (ca. 870 km2 ), over 90% of which occurs in white-water flooded forests within the Mamirauá Sustainable Development Reserve (MSDR), Brazilian Amazonia. To assess the effectiveness of this protected area in conserving the species, we conducted population monitoring of black-headed squirrel monkeys across five consecutive years (2009-2013) on nine trails 2 km each. Each year samples included both low and high river water periods. We used the distance sampling method, recording the distance to each observed social group as well as counting component individuals. We also calculated annual encounter rates based on the number of individuals sighted every 10 km traveled. Densities ranged from 256 individuals/km2 (2011) to 453 individuals/km2 (2013), and no seasonal differences were detected. Population size was estimated to be 147,848 mature individuals. Encounter rates ranged from 100 individuals/10 km (2010) to 179 individuals/10 km (2013); no significant difference among years was found. We found that S. vanzolinii populations remained stable throughout the years, which indicates that the MSDR has been playing an essential role on protecting this species. Due to difficulties of fulfilling assumptions of the distance sampling method, we consider the encounter rate analysis to be more effective for monitoring this and other Saimiri species. Given the critical endemism and worrying conservation status of S. vanzolinii, we suggest that monitoring of the species population should be carried out regularly.

ATLANTIC-PRIMATES: a dataset of communities and occurrences of primates in the Atlantic Forests of South America.

Primates play an important role in ecosystem functioning and offer critical insights into human evolution, biology, behavior, and emerging infectious diseases. There are 26 primate species in the Atlantic Forests of South America, 19 of them endemic. We compiled a dataset of 5,472 georeferenced locations of 26 native and 1 introduced primate species, as hybrids in the genera Callithrix and Alouatta. The dataset includes 700 primate communities, 8,121 single species occurrences and 714 estimates of primate population sizes, covering most natural forest types of the tropical and subtropical Atlantic Forest of Brazil, Paraguay and Argentina and some other biomes. On average, primate communities of the Atlantic Forest harbor 2 ± 1 species (range = 1-6). However, about 40% of primate communities contain only one species. Alouatta guariba (N = 2,188 records) and Sapajus nigritus (N = 1,127) were the species with the most records. Callicebus barbarabrownae (N = 35), Leontopithecus caissara (N = 38), and Sapajus libidinosus (N = 41) were the species with the least records. Recorded primate densities varied from 0.004 individuals/km2 (Alouatta guariba at Fragmento do Bugre, Paraná, Brazil) to 400 individuals/km2 (Alouatta caraya in Santiago, Rio Grande do Sul, Brazil). Our dataset reflects disparity between the numerous primate census conducted in the Atlantic Forest, in contrast to the scarcity of estimates of population sizes and densities. With these data, researchers can develop different macroecological and regional level studies, focusing on communities, populations, species co-occurrence and distribution patterns. Moreover, the data can also be used to assess the consequences of fragmentation, defaunation, and disease outbreaks on different ecological processes, such as trophic cascades, species invasion or extinction, and community dynamics. There are no copyright restrictions. Please cite this Data Paper when the data are used in publications. We also request that researchers and teachers inform us of how they are using the data.