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36 results for “primate diversity”
Relationship between genome-wide and MHC class I and II genetic diversity and complementarity in a nonhuman primate
<p>Although mate choice is expected to favor partners with advantageous genetic properties, the relative importance of genome-wide characteristics, such as overall heterozygosity or kinship, versus specific loci, is unknown. To disentangle genome-wide and locus-specific targets of mate choice, we must first understand congruence in global and local variation within the same individual. This study compares genetic diversity, both absolute and relative to other individuals (e.g., complementarity), assessed across the genome to that found at the major histocompatibility complex (MHC), a hyper-variable gene family integral to immune system function and implicated in mate choice across species. Using DNA from 22 captive olive baboons (<em>Papio anubis</em>), we conducted double digest restriction-site associated DNA sequencing to estimate genome-wide heterozygosity and kinship and sequenced two class I and two class II MHC loci. We found that genome-wide diversity was not associated with MHC diversity, and that diversity at class I MHC loci was not correlated with diversity at class II loci. Additionally, kinship was a significant predictor of the number of MHC alleles shared between dyads at class II loci. Our results provide further evidence of the strong selective pressures maintaining genetic diversity at the MHC in comparison to other randomly selected sites throughout the genome. Furthermore, our results indicate that class II MHC disassortative mate choice may mediate inbreeding avoidance in this population. Our study suggests that mate choice favoring genome-wide genetic diversity is not always synonymous with mate choice favoring MHC diversity, and highlights the importance of controlling for kinship when investigating MHC-associated mate choice.</p>
Fig. 1 in Prevalence and genetic diversity of Enterocytozoon bieneusi in nonhuman primates in Northern and Central China
Fig. 1. Phylogenetic tree of E. bieneusi genotypes identified in this study and known genotypes based on the Neighbor-Joining analysis of the internal transcribed spacer of the rRNA gene. The numbers on the branches represent percent bootstrapping values from 500 replicates, with values of>70.0% shown in the tree. The genotypes identified in this study were marked, with △ for known genotypes and ▴ for the novel genotypes.
Fig. 3 in Mammalian Diversity And Matses Ethnomammalogy In Amazonian Peru Part 1: Primates
Fig. 3. Dorsal and ventral cranial views of Pithecia monachus showing the anatomical endpoints of measurements defined in the text.
Fig. 2 in Mammalian Diversity And Matses Ethnomammalogy In Amazonian Peru Part 1: Primates
Fig. 2. Faunal inventory sites and collecting localities within the Yavarí-Ucayali interfluve (see appendix 2 for geographic coordinates and other information). Inset: Faunal inventory sites in or near the Tamshiyacu-Tahuayo watersheds (EBQB 5 Estación Biológica Quebrada Blanco).
Fig. 1 in Mammalian Diversity And Matses Ethnomammalogy In Amazonian Peru Part 1: Primates
Fig. 1. The Yavarí-Ucayali interfluve (shaded) in relation to surrounding geographical features of western Amazonia.
Relationship between genome-wide and MHC class I and II genetic diversity and complementarity in a nonhuman primate
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Data from: A RAD-sequencing approach to genome-wide marker discovery, genotyping, and phylogenetic inference in a diverse radiation of primates
Until recently, most phylogenetic and population genetics studies of nonhuman primates have relied on mitochondrial DNA and/or a small number of nuclear DNA markers, which can limit our understanding of primate evolutionary and population history. Here, we describe a cost-effective reduced representation method (ddRAD-seq) for identifying and genotyping large numbers of SNP loci for taxa from across the New World monkeys, a diverse radiation of primates that shared a common ancestor ~20-26 mya. We also estimate, for the first time, the phylogenetic relationships among 15 of the 22 currently-recognized genera of New World monkeys using ddRAD-seq SNP data using both maximum likelihood and quartet-based coalescent methods. Our phylogenetic analyses robustly reconstructed three monophyletic clades corresponding to the three families of extant platyrrhines (Atelidae, Pitheciidae and Cebidae), with Pitheciidae as basal within the radiation. At the genus level, our results conformed well with previous phylogenetic studies and provide additional information relevant to the problematic position of the owl monkey (Aotus) within the family Cebidae, suggesting a need for further exploration of incomplete lineage sorting and other explanations for phylogenetic discordance, including introgression. Our study additionally provides one of the first applications of next-generation sequencing methods to the inference of phylogenetic history across an old, diverse radiation of mammals and highlights the broad promise and utility of ddRAD-seq data for molecular primatology.
The effect of tropical forest modification on primate population density and diversity
<b>Description: </b><p>This data represents orang-utan nest survey data, collected to investigate the effects of habitat disturbance on orang-utan populations. Our surveys were conducted in and around the SAFE project site, including areas of Ulu Segama forest reserves and surrounding oil palm estates, covering a total study area of ca. 13,000ha. We conducted nest surveys between April and August 2017, using the standing crop method. Transects were surveyed once by teams of two to four people walking at a steady pace of roughly 0.5km/hr. The data primarily contains perpendicular distances from directly under each nest we encountered to the transect line. We assigned a decay category to each nest, ranging from 1 (new nest) to 5 (heavily degraded). Additionally we recoded the location of each nest, the height of the nest and DBH of the host tree. </p><p><b>Project: </b>This dataset was collected as part of the following SAFE research project: <a href="https://www.safeproject.net/projects/project_view/30"><b>The effect of tropical forest modification on primate population density and diversity.</b></a></p><p><b>Funding: </b>These data were collected as part of research funded by: </p><ul><li>NERC - Human Modified Tropical Forest (HMTF) (Standard grant, NE/K016407/1, <a href=" http://lombok.nerc-hmtf.info/"> http://lombok.nerc-hmtf.info/</a>)</li><li>Primate Society of Great Britain (Conservation grant, NA, <a href="http://www.psgb.org/conservation_grants.php">http://www.psgb.org/conservation_grants.php</a>)</li></ul><p>This dataset is released under the CC-BY 4.0 licence, requiring that you cite the dataset in any outputs, but has the additional condition that you acknowledge the contribution of these funders in any outputs.</p><p></p><p><b>Permits: </b>These data were collected under permit from the following authorities:</p><ul><li>Sabah Biodiversity Centre (Research licence JKM/MBS.1000-2/2 JLD.4(104))</li></ul><p></p><p><b>XML metadata: </b>GEMINI compliant metadata for this dataset is available <a href="https://www.safeproject.net/datasets/xml_metadata?id=5109892">here</a></p><p><b>Files: </b>This consists of 1 file: Orangutan_Transect_Data.xlsx</p><p><b>Orangutan_Transect_Data.xlsx</b></p><p>This file contains dataset metadata and 1 data tables:</p><ol><li><p><b>Orang-utan nest survey data</b> (described in worksheet Distance_data)</p><p>Description: Data from orang-utan nest surveys, using the standing crop method to collect perpendicular distances of orang-utan nests from line transects.</p><p>Number of fields: 13</p><p>Number of data rows: 677</p><p>Fields: </p><ul><li><b>Region</b>: Area in which the survey took place (Field type: id)</li><li><b>Habitat_Type</b>: Habitat type of the transect location (Field type: id)</li><li><b>Transect</b>: Transect ID (Field type: location)</li><li><b>TranLenght</b>: Transect length (Field type: numeric)</li><li><b>Side</b>: Side of the transect nest was located (L = left, R= Right and OT= On transect) (Field type: categorical)</li><li><b>Dist</b>: Perpendicular distance from direct under nest to the transect line (Field type: numeric)</li><li><b>Slope</b>: Angle of slope from transect line (measured to compensate for measuring perpendicular distance of steel slopes) (Field type: numeric)</li><li><b>Class</b>: Age class of east nest (From 1 = new nest to 5 = very old nest) (Field type: numeric)</li><li><b>Nest_Height</b>: Height of each nest in host tree (Field type: numeric trait)</li><li><b>DBH</b>: DBH of host tree (Field type: numeric)</li><li><b>Lat_Y</b>: Nest location latitude (Field type: latitude)</li><li><b>Long_X</b>: Nest location longitude (Field type: longitude)</li><li><b>Elevation</b>: Height above sea leave at each nest location (Field type: numeric)</li></ul></li></ol><p><b>Date range: </b>2017-04-01 to 2017-08-28</p><p><b>Latitudinal extent: </b>4.5607 to 4.7828</p><p><b>Longitudinal extent: </b>117.4636 to 117.7008</p><p><b>Taxonomic coverage: </b><br> All taxon names are validated against the GBIF backbone taxonomy. If a dataset uses a synonym, the accepted usage is shown followed by the dataset usage in brackets. Taxa that cannot be validated, including new species and other unknown taxa, morphospecies, functional groups and taxonomic levels not used in the GBIF backbone are shown in square brackets.</p><div> -  Animalia <br> -  -  Chordata <br> -  -  -  Mammalia <br> -  -  -  -  Primates <br> -  -  -  -  -  Hominidae <br> -  -  -  -  -  -  <i>Pongo</i> <br> -  -  -  -  -  -  -  <i>Pongo pygmaeus</i> <br></div><p></p>
Data from: A RAD-sequencing approach to genome-wide marker discovery, genotyping, and phylogenetic inference in a diverse radiation of primates
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Data from: Low genetic diversity and strong population structure shaped by anthropogenic habitat fragmentation in a critically endangered primate, Trachypithecus leucocephalus
Habitat fragmentation may strongly impact population genetic structure and reduce the genetic diversity and viability of small and isolated populations. The white-headed langur (Trachypithecus leucocephalus) is a critically endangered primate species living in a highly fragmented and human-modified habitat in southern China. We examined the population genetic structure and genetic diversity of the species and investigated the environmental and anthropogenic factors that may have shaped its population structure. We used 214 unique multi-locus genotypes from 41 social groups across the main distribution area of T. leucocephalus, and found strong genetic structure and significant genetic differentiation among local populations. Our landscape genetic analyses using a causal modelling framework suggest that a large habitat gap and geographical distance represent the primary landscape elements shaping genetic structure, yet high levels of genetic differentiation also exist between patches separated by a small habitat gap or road. This is the first comprehensive study that has evaluated the population genetic structure and diversity of T. leucocephalus using nuclear markers. Our results indicate strong negative impacts of anthropogenic land modifications and habitat fragmentation on primate genetic connectivity between forest patches. Our analyses suggest that two management units of the species could be defined, and indicate that habitat continuity should be enforced and restored to reduce genetic isolation and enhance population viability.
Data from: A DNA metabarcoding study of a primate dietary diversity and plasticity across its entire fragmented range
In tropical regions, most primary ecosystems have been replaced by mosaic landscapes in which species must cope with a large shift in the distribution of their habitat and associated food resources. Primates are particularly vulnerable to habitat modifications. Most species persist in small fragments surrounded by complex human-mediated matrices whose structure and connectivity may strongly influence their dispersal and feeding behavior. Behavioral plasticity appears to be a crucial parameter governing the ability of organisms to exploit the resources offered by new matrix habitats and thus to persist in fragmented habitats. In this study, we were interested in the dietary plasticity of the golden-crowned sifaka (Propithecus tattersalli), an endangered species of lemur, found only in the Daraina region in north-eastern Madagascar. We used a DNA-based approach combining the barcoding concept and Illumina next-generation sequencing to (i) describe the species diet across its entire range and (ii) evaluate the influence of landscape heterogeneity on diet diversity and composition. Faeces from 96 individuals were sampled across the entire species range and their contents were analyzed using the trnL metabarcoding approach. In parallel, we built a large DNA reference database based on a checklist of the plant species of the Daraina region. Our results suggest that golden-crowned sifakas exhibit remarkable dietary diversity with at least 130 plant species belonging to 80 genera and 49 different families. We highlighted an influence of both habitat type and openness on diet composition suggesting a high flexibility of foraging strategies. Moreover, we observed the presence of numerous cultivated and naturalized plants in the faeces of groups living in forest edge areas. Overall, our findings support our initial expectation that P. tattersalli is able to cope with the current level of alteration of the landscape and confirm our previous results on the distribution and the dispersal ability of this species.
Data from: Macronutrient signature of dietary generalism in an ecologically diverse primate in the wild
A question of considerable importance is why some animals are able to succeed on a wide range of diets while others are more tightly constrained. Theory predicts that generalists should show a flexible response for macronutrient acquisition in the face of ecologically-driven constraint on the nutritional balance of available foods, which in the modelling framework of nutritional geometry has been quantitatively characterized as an "equal distance" regulatory model. This prediction, which has empirical support from several laboratory studies on insects, has not been tested for any generalist animal in the wild, nor for any vertebrate. We performed the first such test, using 281 dawn-to-dusk focal animal observations over three years (2013-2015) of Rhesus macaques monkeys (Macaca mulatta tcheliensis), a primate that is second only to humans in ecological generalism. Results showed, as predicted, that macronutrient regulation conformed closely to the equal distance pattern, and differed markedly from the other, ecologically more-specialized primate species that have been studied to date. The same was independently true for lactating and non-lactating macaques, but lactating females had substantially higher intake of macronutrients, as well as the non-nutritional food components, indigestible fiber and tannins. This demonstrates that equal distance regulation by non-lactating monkeys was not an artefact of constraint such as restricted food availability or an upper limit to the ingestion of dietary fiber or plant tannins, but a strategic regulatory response to variation in dietary macronutrient balance. We discuss implications of our results for the most generalist primate of all, humans.
Figure 4 in Phylogeography and evolutionary lineage diversity in the small-eared greater galago, Otolemur garnettii (Primates: Galagidae)
Figure 4. Summary of results from five different species-delimitation analyses for dataset 1, comprising 76 samples of partial cytochrome b (402 bp).
Figure 1 in Phylogeography and evolutionary lineage diversity in the small-eared greater galago, Otolemur garnettii (Primates: Galagidae)
Figure 1. Illustrations of the recently recognized Otolemur garnettii subspecies (A), their geographic range according to the IUCN red list (B), and localities sampled in this study (C). It is worth noting that illustrations represent the extremes of variation found in the subspecies and the overall range of distribution should be interpreted as areas in which they might be expected to occur. Otolemur g. lasiotis, in particular, is known to occur in highly discontinuous distributions.
Figure 2. Haplotype median joining network estimated from dataset 1, comprising 76 in Phylogeography and evolutionary lineage diversity in the small-eared greater galago, Otolemur garnettii (Primates: Galagidae)
Figure 2. Haplotype median joining network estimated from dataset 1, comprising 76 samples of partial cytochrome b (402 bp).
Data from: Low genetic diversity and strong population structure shaped by anthropogenic habitat fragmentation in a critically endangered primate, Trachypithecus leucocephalus
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Data from: Interactions between plants and primates shape community diversity in a rainforest in Madagascar
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Data from: The role of rivers as geographical barriers in shaping genetic differentiation and diversity of Neotropical primates
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Mapping the diversity of cetacean and primate cultural heritage
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Data from: A DNA metabarcoding study of a primate dietary diversity and plasticity across its entire fragmented range
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