Theropithecus gelada
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA251424 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR5207263_1.fastq.gz | Fastqsanger.gz | |||
| SRR5207263_2.fastq.gz | Fastqsanger.gz | |||
| SRR5207264_1.fastq.gz | Fastqsanger.gz | |||
| SRR5207264_2.fastq.gz | Fastqsanger.gz | |||
| SRR5207265_1.fastq.gz | Fastqsanger.gz |
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Similar Datasets
Project description:Theropithecus gelada Genome Sequencing Project
| PRJNA470999 | ENA
Project description:Theropithecus gelada haplotype 1 genome sequencing
| PRJNA1081469 | ENA
Project description:Theropithecus gelada haplotype 2 genome sequencing
| PRJNA1081468 | ENA
Project description:Background:Baboons (genus Papio) and geladas (Theropithecus gelada) are now generally recognized as close phylogenetic relatives, though morphologically quite distinct and generally classified in separate genera. Primate specific Alu retrotransposons are well-established genomic markers for the study of phylogenetic and population genetic relationships. We previously reported a computational reconstruction of Papio phylogeny using large-scale whole genome sequence (WGS) analysis of Alu insertion polymorphisms. Recently, high coverage WGS was generated for Theropithecus gelada. The objective of this study was to apply the high-throughput "poly-Detect" method to computationally determine the number of Alu insertion polymorphisms shared by T. gelada and Papio, and vice versa, by each individual Papio species and T. gelada. Secondly, we performed locus-specific polymerase chain reaction (PCR) assays on a diverse DNA panel to complement the computational data. Results:We identified 27,700 Alu insertions from T. gelada WGS that were also present among six Papio species, with nearly half (12,956) remaining unfixed among 12 Papio individuals. Similarly, each of the six Papio species had species-indicative Alu insertions that were also present in T. gelada. In general, P. kindae shared more insertion polymorphisms with T. gelada than did any of the other five Papio species. PCR-based genotype data provided additional support for the computational findings. Conclusions:Our discovery that several thousand Alu insertion polymorphisms are shared by T. gelada and Papio baboons suggests a much more permeable reproductive barrier between the two genera then previously suspected. Their intertwined evolution likely involves a long history of admixture, gene flow and incomplete lineage sorting.
| S-EPMC6880559 | biostudies-literature
Project description:Human-primate interfaces are expanding and, despite recent studies on primates from peri-urban environments, little research exists on the impact of agriculture and/or pasture areas on primate social behavior and health. We assessed how crop/pasture areas potentially alter social behavior and health of wild geladas (Theropithecus gelada) frequenting the unprotected area of Kundi (Ethiopia). We predicted that compared to pasture areas, crop areas (i) would be more challenging for geladas (prediction 1) and (ii) would have a greater impact on both aggressive and affiliative behavior, by reducing grooming time and enhancing competition (prediction 2). During January-May 2019 and December 2019-February 2020, we collected data (via scan, focal animal sampling, and video analyses) on direct human disturbance, external signs of pathologies and social behavior of 140 individuals from 14 one-male units and two all-male units. Animals experienced the highest level of human disturbance in crop areas (in line with prediction 1). Individuals from the groups preferentially frequenting crop areas showed the highest prevalence of external signs of pathologies consistent with chemical and biological contamination (alopecia/abnormally swollen parts). We collected 48 fecal samples. Samples from frequent crop users contained the highest rates of parasitic elements/gram (egg/larva/oocyst/cyst) from Entamoeba histolytica/dispar, a parasite common in human settlements of the Amhara region. In crop areas, subjects spent less time grooming but engaged in lower rates of intense aggression (in partial agreement with prediction 2). We speculate that the reduction in social behavior may be a tactic adopted by geladas to minimize the likelihood of detection and maximize food intake while foraging in crops.
| S-EPMC8225520 | biostudies-literature
Project description:BackgroundClimate change coupled with other anthropogenic pressures may affect the extent of suitable habitat for species and thus their distributions. This is particularly true for species occupying high-altitude habitats such as the gelada (Theropithecus gelada) of the Ethiopian highlands. To explore the impact of climate change on species distributions, Species Distribution Modelling (SDM) has been extensively used. Here we model the current and future extent of sutibale habitat for geladas. Our modelling was based on 285 presence locations of geladas, covering their complete current distribution. We used different techniques to generate pseudoabsence datasets, MaxEnt model complexities, and cut-off thresholds to map the potential distribution of gelada under current and future climates (2050 and 2070). We assembled maps from these techniques to produce a final composite map. We also evaluated the change in the topographic features of gelada over the past 200 years by comparing the topography in current and historical settings.ResultsAll model runs had high performances, AUC = 0.87-0.96. Under the current climate, the suitable habitat predicted with high certainty was 90,891 km2, but it decreased remarkably under future climates, -36% by 2050 and - 52% by 2070. However, since the habitats of geladas already extend to mountaintop grasslands, no remarkable range shifts across elevation gradients were predicted under future climates.ConclusionsOur findings indicated that climate change most likely results in a loss of suitable habitat for geladas, particularly south of the Rift Valley. Currently geladas are confined to higher altitudes and steep slopes compared to historical sightings, probably qualifying geladas as refugee species. The difference in topography is potentially associated with anthropogenic pressures that drove niche truncation to higher altitudes, undermining the climatic and topographic niche our models predicted. We recommend protecting the current habitats of geladas even when they are forecasted to become climatically unsuitable in the future, in particular for the population south of the Rift Valley.
| S-EPMC10623689 | biostudies-literature
Project description:The large-bodied, terrestrial primates in the tribe Papionini are among the most intensely studied animals in the world, yet for some members of this tribe we know comparatively little about their evolutionary history and phylogeography. Geladas (Theropithecus gelada Rüppell, 1835), endemic primates of the Ethiopian highlands, are largely unstudied both in genetic diversity and intrageneric phylogeny. Currently, a northern and central subspecies and one isolated southern population are recognized, of which the central is classified as Least Concern, the northern as Vulnerable, and the southern is not yet assessed. The distribution and taxonomy of the subspecies remain poorly defined. Here, we estimate the mitochondrial DNA (mtDNA) diversity and phylogenetic relationships among gelada mtDNA lineages based on samples across the entire species range. We analysed 1.7 kb-long sequences of the mtDNA genome, spanning the cytochrome b gene and the hypervariable region I of the D-loop, derived from 162 faecal samples. We detected five major haplogroups or clades (south, central-1, central-2, north-1, north-2) which diverged between 0.67 and 0.43 million years ago, thus suggesting a rapid radiation, resulting in largely unresolved intrageneric phylogenetic relationships. Both, the northern and central demes contain two similarly valid haplogroups, each with little or no geographic segregation among respective haplogroups. Effective population sizes of the northern and central demes decreased during and after the last glacial maximum but remained stable for the southern deme, although on a very low level. The distribution of haplogroups within the geographic ranges of the putative gelada subspecies indicates that mtDNA sequence information does not allow reliable taxonomic inferences and thus is not sufficient for solving the taxonomic rank of the three demic populations, with the possible exception of the southern population. Nevertheless, due to the genetic differences all three populations deserve conservation efforts, in particular the smallest southern population.
| S-EPMC6107150 | biostudies-other
Project description:Gelada genomes highlight events of gene flow, hybridisation and local adaptation tracked by past climatic changes
| PRJEB72259 | ENA
Project description:To investigate the extent of similarity in epigenetic programming among human, baboon and mouse PSCs, we examined genome-wide patterns of four chromatin modifications (H3K4me3, H3K9me3, H3K27me3, H3K27ac) and DNA methylation in baboon iPSC and ESCs. We show that baboon pluripotent cells (PSCs) recapitulate key molecular features of human PSCs with much greater accuracy than that found in PSCs from non-primate species. Specifically, baboon and human PSCs exhibit significantly greater conservation of gene expression patterns, higher sequence and structural homology among pluripotency factors, more equivalent genome-wide patterns of histone and DNA methylation modifications, and similar maintenance of bivalent programming of developmental genes than that found between human and non-primate PSCs.
2021-01-21 | GSE165186 | GEO