Có 13+ tài liệu thuộc chủ đề "Population genomics"
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Micrococcus luteus. With one of the smallest genomes of free-living actinobacteria, it is found in a wide range of environments, but intraspecies genetic diversity and adaptation strategies to various environments remain unclear. Here, comparative genomics, phylogenomics, and genome-wide association studies were used to investigate the genomic diversity, evolutionary history, and the potential ecological differentiation of the species.. Reconstruction of gene...
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Low impact of different SNP panels from two building-loci pipelines on RAD-Seq. Many building-loci pipelines have been developed to obtain robust single nucleotide polymorphism (SNPs) genotyping datasets using a de novo RAD-seq approach, i.e. Genotyped vs missing data mismatches were the main genotyping difference detected between the two building-loci pipelines or between the de novo and reference genome comparisons.. https://www.earthbiogenome.org....
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RIP) contributing to the rapid diversification of the locus.. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/.. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated in a credit line to the data.. f Linkage disequilibrium r 2 heatmap of the entire region. c TE content variation of...
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Development of a large SNPs resource and a low-density SNP array for brown trout ( Salmo trutta ) population genetics. Background: The brown trout (Salmo trutta) is an economically and ecologically important species for which population genetic monitoring is frequently performed. Here, we used Restriction site Associated DNA sequences (RADs) markers to identify a set of 12,204 informative SNPs positioned...
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Genome-wide divergence among invasive populations of Aedes aegypti in California. Background: In the summer of 2013, Aedes aegypti Linnaeus was first detected in three cities in central California (Clovis, Madera and Menlo Park). Results: Here we report the first population genomics analyses of Ae. one that includes all sample sites in the southern part of the state (South of Tehachapi...
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We found an evidence of admixture between Tibetan chickens and other domestic population. By comparing the genomes of the Tibetan and lowland fowls, we identified genes associated with high-altitude adaptation in Tibetan chickens were mainly involved in energy metabolism, body size maintenance and available food sources.. Since the domestication of the red jungle fowl (Gallus gallus) (approximately 8000 to 5400...
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For both species, population structure inferences were influenced by the percent of missing data.. Conclusions: For studies of non-model species with a reference genome, we recommend combining Stacks output with further filtering (as included in our R pipeline) for population genetic studies, paying particular attention to potential impact of missing data thresholds. 2019 Open Access This article is distributed under...
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We used whole genome sequencing combined with association study of climate to discover the drivers of differentiation in the perennial C4 grass Panicum hallii.. Results: Sequencing of 89 natural accessions of P.hallii revealed complex population structure across the species range. Major population genomic separation was found between subspecies P.hallii var. Conclusions: Both geography and climate adaptation contribute significantly to patterns...
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We identified 145 haplotypes (ranging from 0.5 – 4 Mb in size) in the genome with complete absence or depletion of homozygous animals. Thirty-five haplotypes show a negative effect on at least one of the analysed reproductive traits (total number born, number of stillborn, and number of mummified piglets). For instance, when a homozygous deleterious phenotype leads to very early...
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Background: Mutation load is expected to be reduced in hybrids via complementation of deleterious alleles. While local adaptation of hybrids confounds phenotypic tests for reduced mutation load, it may be possible to assess variation in load by analyzing the distribution of putatively deleterious alleles. engelmannii) hybrid complex, a group likely to suffer from high mutation load and in which hybrids...
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Background: After cereals, root and tuber crops are the main source of starch in the human diet. But domestication of these root and tubers crops is also associated with gigantism of storage organs and changes of habitat.. The genomic diversity in the cultivated species is roughly 30% less important than its wild relatives. Two genes associated with the earliest stages...