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165 results for “baboon”
VCF files for 100 high coverage baboon genomes from the Southwest National Primate Research Center
<p>Catalog of SNP and small indel variation in 100 high coverage (>20X) whole genome sequences from baboons (genus <em>Papio</em>) at the Southwest National Primate Research Center (SNPRC). These files use the Panu_2.0 baboon reference genome. See "Analysis of 100 high coverage genomes from a pedigreed captive baboon colony" by Robinson et al. 2019 for further details.</p>
Resources for genomic analyses in baboons (genus Papio)
<p>Resources for genomic analyses in baboons (genus <em>Papio</em>). See "Analysis of 100 high coverage genomes from a pedigreed captive baboon colony" by Robinson et al. 2019 for further details.</p> <p><strong>Panu_2.0_Panu_3.0_chain_files.tar.gz</strong> Chain files for converting coordinates between Panu_2.0 and Panu_3.0. All coordinates in the files below correspond to Panu_2.0, but can be converted to coordinates in the new assembly, Panu_3.0, using the chain files with liftOver (Hinrichs et al. 2006, DOI:10.1093/nar/gkj144).</p> <p><strong>baboon_100_highcoverage_SNPRC_sample_info.txt</strong> Sample information: Sample ID, Sequencing ID, Type, Sex, Fped (%), Admixed, Mean coverage (X). The type, sex, inbreeding coefficient (Fped), and admixture status are all based on the SNPRC pedigree.</p> <p><strong>baboon_24_olive_founders_phased.vcf.gz</strong> Phased VCF files for 24 olive baboon founders. Phasing was performed with Beagle (Browning and Browning 2007, DOI:10.1086/521987), assuming an effective population size of 40,000 individuals (Boissinot et al. 2014, DOI:10.1002/ajpa.22618). SNPs were filtered to remove singletons and thinned so that no two sites were closer than 10 bp. <strong>baboon_24_olive_founders_phased.vcf.gz.tbi</strong> is the index for the VCF file.</p> <p><br> <strong>baboon_ldhelmet_recombination_maps.tar.gz</strong> Fine-scale recombination maps produced with LDhelmet (Chan et al. 2012, DOI:10.1371/journal.pgen.1003090) based on phased genotypes from 24 olive baboon founders. Results from three block penalties are provided (5, 25, 50).</p> <p><strong>baboon_AIMs_33founders_fixed_yellow_olive.txt</strong> List of ancestry informative markers for distinguishing olive and yellow baboon ancestry. These sites represent fixed differences between 7 genetically yellow and 24 genetically olive baboons.</p> <p><strong>baboon_plink_ROH.bed</strong> Coordinates of runs of homozygosity in BED format, inferred with PLINK (Chang et al. 2015, DOI:10.1186/s13742-015-0047-8) using the default behavior of the --homozyg function. The following parameters were used to prune SNPs beforehand: --indep-pairwise 50 5 0.5. The columns are: chromosome, start position, end position, sample name.</p> <p><strong>baboon_LOF_mutations.txt</strong> List of putative LOF mutations annotated with SnpEff (Cingolani et al. 2012, DOI:10.4161/fly.19695). The following mutation types were included: “stop_gained”, “start_lost”, “stop_lost”, “splice_acceptor_variant”, “splice_donor_variant”.</p>
Data from: Conditional fetal and infant killing by male baboons
Sexually selected feticide—the death of infants in utero as a result of male behaviour—has only rarely been described or analysed, although it is presumed to be favoured by the same selective pressures that favour sexually selected infanticide. To test this hypothesis, we measured the frequency of feticide and infanticide by male baboons of the Amboseli basin in Kenya, and examined which characteristics of a male and his environment made him more likely to commit feticide and/or infanticide. We found a dramatic increase in fetal and infant death rates, but no increase in death rates of 1- to 2-year-old individuals, following the immigration of males who stood to benefit from feticide and infanticide. Specifically, fetal and infant death rates were highest following immigrations in which: (i) the immigrant male rapidly attained high rank, (ii) that male remained consistently resident in the group for at least three months, (iii) food availability and social group range overlap was relatively low and (iv) relatively many pregnant females and/or dependent infants were present. Together, these results provide strong evidence for the existence of both sexually selected feticide and infanticide in our population, and they indicate that feticide and infanticide are conditional male behavioural strategies employed under particular circumstances.
Presence of gastrointestinal parasite species of baboons reported in literature
<p>A spreadsheet of the presence (or absence) of parasite species at all study sites that have published data on baboon (<em>Papio</em>) spp. parasite communities. The first tab '2023_Helminths_PrevData' are a list of the macroparasites that have been reported. The second tab '2023_Protozoa_PrevData' are a list of the macroparasites that have been reported. For both these sheets, '1' indicates that a parasite is present, and '0' indicates that a parasite species was not recorded at that study site.</p> <p>The data provided here are collated from all published journal articles and degree theses on baboon parasites up the start of 2023. A list of the publications that contributed are provided in the reference information. </p>
Individual differences in coping styles and associations with social structure in wild baboons (Papio anubis)
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Data from: Extreme behavioural shifts by baboons exploiting risky, resource-rich, human-modified environments
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Data from: When good neighbors don’t need fences: Temporal landscape partitioning among baboon social groups
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Data from: Social bonds do not mediate the relationship between early adversity and adult glucocorticoids in wild baboons
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Data from: The effect of excluding juveniles on apparent adult olive baboons (Papio anubis) social networks
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Data from: To grunt or not to grunt: factors governing call production in female olive baboons, Papio anubis
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Data from: Role of grooming in reducing tick load in wild baboons (Papio cynocephalus)
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Data from: Intergenerational effects of early adversity on survival in wild baboons
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Data from: Higher dominance rank is associated with lower glucocorticoids in wild female baboons: A rank metric comparison
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Data from: Cumulative early life adversity predicts longevity in wild baboons
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Noninvasive measurement of mucosal immunity in a free‐ranging baboon population
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Data from: Measuring fecal testosterone in females and fecal estrogens in males: comparison of RIA and LC/MS/MS methods for wild baboons (Papio cynocephalus).
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Data from: Exaggerated sexual swellings and male mate choice in primates: testing the reliable indicator hypothesis in the Amboseli baboons
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Data from: Consistency in the flight and visual orientation distances of habituated chacma baboons after an observed leopard predation: Do flight initiation distance methods always measure perceived predation risk?
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Data from: Predicting the impacts of climate change on Papio baboon biogeography: are widespread, generalist primates ‘safe’?
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Data from: Social networks predict gut microbiome composition in wild baboons
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