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26 results for “primate radiation”
Data from: Simulated evolution of mating signal diversification in a primate radiation
<p>Divergence in allopatry and subsequent diversification of mating signals on secondary contact (reinforcement) is a major driver of phenotypic diversity. Observing this evolutionary process directly is often impossible, but simulated evolution can pinpoint key drivers of phenotypic variation. We developed evolutionary simulations in which mating signals, modelled as points in phenotype space, evolve across time under varying evolutionary scenarios. We model mate recognition signals in guenons, a primate radiation exhibiting colourful and diverse face patterns hypothesized to maintain reproductive isolation via mate choice. We simulate face pattern evolution across periods of allopatry and sympatry, identifying the role of key parameters in driving evolutionary endpoints. Results show that diversification in allopatry and assortative mate choice on secondary contact can induce rapid phenotypic diversification, resulting in distinctive (between species) and stereotyped (within species) face patterns, similar to extant guenons. Strong selection against hybrids is key to diversification, with even low levels of hybrid fitness often resulting in merged populations on secondary contact. Our results support a key role for reinforcement by assortative mating in the maintenance of species diversity and support the long-proposed prehistorical scenario for how such striking diversity was produced and maintained in perhaps the most colourful of all mammalian clades.</p>
Figure 6 in The radiation of red colobus monkeys (Primates, Colobinae): morphological evolution in a clade of endangered African primates
Figure 6. Males. Scatter plots of the first discriminant axes (DFs) of species using shape (first 30 principal components; percentages of variance explained by DF in parentheses).
Figure 4 in The radiation of red colobus monkeys (Primates, Colobinae): morphological evolution in a clade of endangered African primates
Figure 4. Males. Scatter plots of the first principal components of shape variables. See Figure 3 for the key.
Figure 1 in The radiation of red colobus monkeys (Primates, Colobinae): morphological evolution in a clade of endangered African primates
Figure 1. Distribution of red colobus taxa (modified from Colyn, 1991). (I) Piliocolobus badius (Kerr, 1792) (western Tropical Africa): (1) Piliocolobus badius ssp. temminckii (Kuhl, 1820), (2) Piliocolobus badius ssp. badius (Kerr, 1792), and (3) Piliocolobus badius ssp. waldroni (Hayman, 1936); (II) Procolobus pennantii (Waterhouse, 1838) (western equatorial Africa): (4) Procolobus pennantii ssp. epieni Grubb and Powell, 1999, (5) Procolobus pennantii ssp. pennantii (Waterhouse, 1838), (6) Procolobus pennantii ssp. preussi (Matschie, 1900), (7) Procolobus pennantii ssp. bouvieri (Rochebrune, 1887); (III) Central African assemblage: (8) Piliocolobus sp. tholloni, (9) Piliocolobus sp. oustaleti, (10) Piliocolobus sp. parmentieri Colyn & Verheyen, 1987, (11) Piliocolobus sp. lulindicus Matschie, 1914 and Piliocolobus sp. foai (de Pousargues, 1899), (12) Piliocolobus sp. langi (Allen, 1925) and Piliocolobus sp. ellioti (Dollman, 1909), (13) Piliocolobus sp. tephrosceles (Elliot, 1907); (IV) Eastern African species: (14) Piliocolobus gordonorum Matschie, 1900, (15) Piliocolobus rufomitratus, (16) Piliocolobus kirkii Gray, 1868. Grey areas are putative Pleistocenic mountain refugia, taken from Mayr & O'Hara (1986).
Figure 3 in The radiation of red colobus monkeys (Primates, Colobinae): morphological evolution in a clade of endangered African primates
Figure 3. Females. Scatter plots of the first principal components (PCs) of shape variables (percentages of variance explained in parentheses). Shape changes at positive extremes of the axes are illustrated using surface rendering with a two-fold magnification (the same magnification is used in all figures). The average shape (origin of the PCA axes) is shown by the upper right corner of the scatter plots in this and other figures. (a) PC1 vs. PC2. (b) PC3 vs. PC4.
Figure 5 in The radiation of red colobus monkeys (Primates, Colobinae): morphological evolution in a clade of endangered African primates
Figure 5. Females. Scatter plots of the first discriminat axes (DAs) of species using shape (first 35 principal components; percentages of variance explained by DA in parentheses). Shape changes predicted by regressing shape coordinates onto DA are illustrated using surface rendering for positive extremes of the axes.
Data from: Simulated evolution of mating signal diversification in a primate radiation
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The structure of species discrimination signals across a primate radiation: Cercopithecus nictitans looking time trials
<p>Data and videos from looking time trials conducted with Cercopithecus nictitans subjects at CERCOPAN sanctuary in 2015.</p>
The structure of species discrimination signals across a primate radiation: Cercopithecus mona looking time trials
<p>Data and videos from looking time trials conducted with Cercopithecus mona subjects at CERCOPAN sanctuary in 2015.</p>
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.
Figure 8 in The radiation of red colobus monkeys (Primates, Colobinae): morphological evolution in a clade of endangered African primates
Figure 8. Males. Phenogram of the species mean shapes. See Figure 7 for further explanation.
Analysis of the proteomic profile in serum of irradiated nonhuman primates treated with Ex-Rad, a radiation medical countermeasure
<p>There are currently four radiation medical countermeasures that have been approved by the United States Food and Drug Administration to mitigate hematopoietic acute radiation syndrome, all of which are repurposed radiomitigators. The evaluation of additional candidate drugs that may also be helpful for use during a radiological/nuclear emergency is ongoing. A chlorobenzyl sulfone derivative (organosulfur compound) known as Ex-Rad, or ON01210, is one such candidate medical countermeasure, being a novel, small-molecule kinase inhibitor that has demonstrated efficacy in the murine model. In this study, nonhuman primates exposed to ionizing radiation were subsequently administered Ex-Rad as two treatment schedules (Ex-Rad I administered 24 and 36 h post-irradiation, and Ex-Rad II administered 48 and 60 h post-irradiation) and the proteomic profiles of serum using a global molecular profiling approach were assessed. We observed that administration of Ex-Rad post-irradiation is capable of mitigating radiation-induced perturbations in protein abundance, particularly in restoring protein homeostasis and immune response and mitigating hematopoietic damage, at least in part after acute exposure. Taken together, restoration of functionally significant pathway perturbations may serve to protect damage to vital organs and provide long-term survival benefits to the afflicted population.</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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Analysis of the proteomic profile in serum of irradiated nonhuman primates treated with Ex-Rad, a radiation medical countermeasure
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Supplementary data for: Primate phylogenomics uncovers multiple rapid radiations and ancient interspecific introgression
<p>Our understanding of the evolutionary history of primates is undergoing continual revision due to ongoing genome sequencing efforts. Bolstered by growing fossil evidence, these data have led to increased acceptance of once controversial hypotheses regarding phylogenetic relationships, hybridization and introgression, and the biogeographical history of primate groups. Among these findings is a pattern of recent introgression between species within all major primate groups examined to date, though little is known about introgression deeper in time. To address this and other phylogenetic questions, here we present new reference genome assemblies for three Old World Monkey species: <i>Colobus angolensis ssp. palliatus </i>(the black and white colobus), <i>Macaca nemestrina </i>(southern pig-tailed macaque), and <i>Mandrillus leucophaeus </i>(the drill). We combine these data with 23 additional primate genomes to estimate both the species tree and individual gene trees using thousands of loci. While our species tree is largely consistent with previous phylogenetic hypotheses, the gene trees reveal high levels of genealogical discordance associated with multiple primate radiations. We use strongly asymmetric patterns of gene tree discordance around specific branches to identify multiple instances of introgression between ancestral primate lineages. In addition, we exploit recent fossil evidence to perform fossil-calibrated molecular dating analyses across the tree. Taken together, our genome-wide data help to resolve multiple contentious sets of relationships among primates, while also providing insight into the biological processes and technical artifacts that led to the disagreements in the first place.</p>
Data from: Next-generation museomics disentangles one of the largest primate radiations
Guenons (tribe Cercopithecini) are one of the most diverse groups of primates. They occupy all of sub-Saharan Africa and show great variation in ecology, behavior, and morphology. This variation led to the description of over 60 species and subspecies. Here, using next-generation DNA sequencing (NGS) in combination with targeted DNA capture, we sequenced 92 mitochondrial genomes from museum-preserved specimens as old as 117 years. We infer evolutionary relationships and estimate divergence times of almost all guenon taxa based on mitochondrial genome sequences. Using this phylogenetic framework, we infer divergence dates and reconstruct ancestral geographic ranges. We conclude that the extraordinary radiation of guenons has been a complex process driven by, among other factors, localized fluctuations of African forest cover. We find incongruences between phylogenetic trees reconstructed from mitochondrial and nuclear DNA sequences, which can be explained by either incomplete lineage sorting or hybridization. Furthermore, having produced the largest mitochondrial DNA dataset from museum specimens, we document how NGS technologies can 'unlock' museum collections, thereby helping to unravel the tree-of-life.
Data from: Species discovery and validation in a cryptic radiation of endangered primates: coalescent-based species delimitation in Madagascar's mouse lemurs
Implementation of the coalescent model in a Bayesian framework is an emerging strength in genetically based species delimitation studies. By providing an objective measure of species diagnosis, these methods represent a quantitative enhancement to the analysis of multilocus data, and complement more traditional methods based on phenotypic and ecological characteristics. Recognized as two species 20 years ago, mouse lemurs (genus Microcebus) now comprise more than 20 species, largely diagnosed from mtDNA sequence data. With each new species description, enthusiasm has been tempered with scientific scepticism. Here, we present a statistically justified and unbiased Bayesian approach towards mouse lemur species delimitation. We perform validation tests using multilocus sequence data and two methodologies: (i) reverse-jump Markov chain Monte Carlo sampling to assess the likelihood of different models defined a priori by a guide tree, and (ii) a Bayes factor delimitation test that compares different species-tree models without a guide tree. We assess the sensitivity of these methods using randomized individual assignments, which has been used in bpp studies, but not with Bayes factor delimitation tests. Our results validate previously diagnosed taxa, as well as new species hypotheses, resulting in support for three new mouse lemur species. As the challenge of multiple researchers using differing criteria to describe diversity is not unique to Microcebus, the methods used here have significant potential for clarifying diversity in other taxonomic groups. We echo previous studies in advocating that multiple lines of evidence, including use of the coalescent model, should be trusted to delimit new species.
Data from: Next-generation museomics disentangles one of the largest primate radiations
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Data from: Species discovery and validation in a cryptic radiation of endangered primates: coalescent-based species delimitation in Madagascar's mouse lemurs
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Supplementary data for: Primate phylogenomics uncovers multiple rapid radiations and ancient interspecific introgression
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.