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76 results for “Genome-wide selection”
Data from: Genome-wide analysis of colonization history and concomitant selection in Arabidopsis lyrata
The high climatic variability in the past hundred thousand years has affected the demographic and adaptive processes in many species, especially in boreal and temperate regions undergoing glacial cycles. This has also influenced the patterns of genome-wide nucleotide variation, but the details of these effects are largely unknown. Here we study the patterns of genome-wide variation to infer colonization history and patterns of selection of the perennial herb species Arabidopsis lyrata, in locally adapted populations from different parts of its distribution range (Germany, UK, Norway, Sweden, and USA) representing different environmental conditions. Using site frequency spectra based demographic modelling we found strong reduction in the effective population size of the species in general within the past 100 000 years, with more pronounced effects in the colonizing populations. We further found that the northwestern European A. lyrata populations (UK and Scandinavian) are more closely related to each other than with the Central European populations, and coalescent based population split modelling suggests that western European and Scandinavian populations became isolated relatively recently after the glacial retreat. We also highlighted loci showing evidence for local selection associated with the Scandinavian colonization. The results presented here give new insights into post-glacial Scandinavian colonization history and its genome-wide effects.
Variant Call File (VCF) for Genome-wide polymorphism and genic selection in feral and domesticated lineages of Cannabis sativa
<p>A comprehensive understanding of the degree to which genomic variation is maintained by selection versus drift and gene flow is lacking in many important species such as <em>Cannabis</em> <em>sativa </em>(<em>C. sativa</em>), one of the oldest known crops to be cultivated by humans worldwide. We generated whole genome resequencing data across diverse samples of feralized (escaped domesticated lineages) and domesticated lineages of <em>C. sativa</em>. We performed analyses to examine population structure, and genome wide scans for FST, balancing selection, and positive selection. Our analyses identified evidence for sub-population structure and further support the Asian origin hypothesis of this species. Feral plants sourced from the U.S. exhibited broad regions on chromosomes 4 and 10 with high <span>𝐹̅</span>ST which may indicate chromosomal inversions maintained at high frequency in this sub-population. Both our balancing and positive selection analyses identified loci that may reflect differential selection for traits favored by natural selection and artificial selection in feral versus domesticated sub-populations. In the U.S. feral sub-population, we found six loci related to stress response under balancing selection and one gene involved in disease resistance under positive selection, suggesting local adaptation to new climates and biotic interactions. In the marijuana sub-population, we identified the gene <em>SMALLER TRICHOMES</em> <em>WITH VARIABLE BRANCHES 2 </em>to be under positive selection which suggests artificial selection for increased tetrahydrocannabinol yield. Overall the data generated, and results obtained from our study help to form a better understanding of the evolutionary history in <em>C. sativa</em>.</p>
The phylogeny of Triticeae Dumort. (Poaceae): resolution and reticulation based on a genome-wide selection of nuclear loci.
<p>Chloroplast-genome and nuclear-locus phylogenetic datasets for the wheat tribe Triticeae.</p>
Data from: Genetic diversity, linkage disequilibrium and selection signatures in Chinese and Western pigs revealed by genome-wide SNP markers
To investigate population structure, linkage disequilibrium (LD) pattern and selection signature at the genome level in Chinese and Western pigs, we genotyped 304 unrelated animals from 18 diverse populations using porcine 60 K SNP chips. We confirmed the divergent evolution between Chinese and Western pigs and showed distinct topological structures of the tested populations. We acquired the evidence for the introgression of Western pigs into two Chinese pig breeds. Analysis of runs of homozygosity revealed that historical inbreeding reduced genetic variability in several Chinese breeds. We found that intrapopulation LD extents are roughly comparable between Chinese and Western pigs. However, interpopulation LD is much longer in Western pigs compared with Chinese pigs with average r20.3 values of 125 kb for Western pigs and only 10.5 kb for Chinese pigs. The finding indicates that higher-density markers are required to capture LD with causal variants in genome-wide association studies and genomic selection on Chinese pigs. Further, we looked across the genome to identify candidate loci under selection using FST outlier tests on two contrast samples: Tibetan pigs versus lowland pigs and belted pigs against non-belted pigs. Interestingly, we highlighted several genes including ADAMTS12, SIM1 and NOS1 that show signatures of natural selection in Tibetan pigs and are likely important for genetic adaptation to high altitude. Comparison of our findings with previous reports indicates that the underlying genetic basis for high-altitude adaptation in Tibetan pigs, Tibetan peoples and yaks is likely distinct from one another. Moreover, we identified the strongest signal of directional selection at the EDNRB loci in Chinese belted pigs, supporting EDNRB as a promising candidate gene for the white belt coat color in Chinese pigs. Altogether, our findings advance the understanding of the genome biology of Chinese and Western pigs.
Data from: Genome-wide differentiation in closely related populations: the roles of selection and geographic isolation
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Data from: Genetic diversity, linkage disequilibrium and selection signatures in Chinese and Western pigs revealed by genome-wide SNP markers
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Data from: Genome-wide association mapping of phenotypic traits subject to a range of intensities of natural selection in Timema cristinae
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Data from: Genome-wide analysis of colonization history and concomitant selection in Arabidopsis lyrata
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Data from: Experimental evidence of genome-wide impact of ecological selection during early stages of speciation-with-gene-flow
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Data from: Genome-wide analyses suggest parallel selection for universal traits may eclipse local environmental selection in a highly mobile carnivore
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Data from: Strong selection genome-wide enhances fitness trade-offs across environments and episodes of selection
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Variant Call File (VCF) for Genome-wide polymorphism and genic selection in feral and domesticated lineages of Cannabis sativa
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Genome-wide association study in quinoa reveals selection pattern typical for crops with a short breeding history
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Data from: Selection, genome-wide fitness effects and evolutionary rates in the model legume Medicago truncatula
Sequence data for >20 000 annotated genes from 56 accessions of Medicago truncatula were used to identify potential targets of positive selection, the determinants of evolutionary rate variation and the relative importance of positive and purifying selection in shaping nucleotide diversity. Based upon patterns of intraspecific diversity and interspecific divergence, c. 50–75% of nonsynonymous polymorphisms are subject to strong purifying selection and 1% of the sampled genes harbour a signature of positive selection. Combining polymorphism with expression data, we estimated the distribution of fitness effects and found that the proportion of deleterious mutations is significantly greater for expressed genes than for genes with undetected transcripts (nonexpressed) in a previous RNA-seq experiment and greater for broadly expressed genes than those expressed in only a single tissue. Expression level is the strongest correlate of evolutionary rates at nonsynonymous sites, and despite multiple genomic features being significantly correlated with evolutionary rates, they explain less than 20% of the variation in nonsynonymous rates (dN) and <15% of the variation in either synonymous rates (dS) or dN:dS. Among putative targets of selection were genes involved in defence against pathogens and herbivores, genes with roles in mediating the relationship with rhizobial symbionts and one-third of annotated histone-lysine methyltransferases. Adaptive evolution of the methyltransferases suggests that positive selection in gene expression may have occurred through evolution of enzymes involved in epigenetic modification.
Genetic diversity and signatures of selection in 15 Chinese indigenous dog breeds revealed by genome-wide SNPs
<p><span><span><span><span><span><span><span><span><span><span><span><a name="_Hlk15722205">There are dozens of recognized indigenous dog breeds in China. However, these breeds have not had extensive studies to describe their population structure, genomic linkage disequilibrium (LD) patterns, and selection signatures. </a>Here, <a name="_Hlk15722444">we systematically surveyed the genomes </a>of 169 unrelated dogs that were from<a name="_Hlk15722467">15 diverse Chinese dog breeds</a>. Canine 170K SNP chips were used to<a name="_Hlk15722535">compare the genomic structures of Chinese and Western dogs</a>. The genotyping data of 170K SNP chips in Western dogswere downloadedfrom the LUPA (a European initiative of canine genome project) database. Chinese indigenous dogs had lower LD and shorter accumulative runs of homozygosity (ROH) in the genome. The genetic distances between individuals within each Chinese breed were larger than those within Western breeds. Principal component analysis (PCA) and neighbor-joining (NJ)-tree analysis indicated distinct phylogenetic affinities between Chinese and Western dogs. <a name="_Hlk15722638">We found evidence for historical introgression of Western dogs</a>into Chinese Kazakhstan shepherd and Mongolia Xi dogs. We suggested that Greenland sledge dog, Spanish Papillon, and European Eurasier have Chinese dog lineages. The <i>d<sub>i</sub></i>statistic estimation identified genome-wide selection signatures of each Chinese breed and three breed groups. This study highlights several candidate genes that have undergone natural selection and might be responsible for breed-typical phenotypes. Several genes, e.g. <i>EPAS1</i>and <i>DNAH9</i>, showed signatures of natural selection in Qinghai-Tibetan plateau dogs and are important for genetic adaptation to high altitude. <i>RBP7</i>,<i>NMNAT1</i>,<i>SLC2A5,</i>and <i>H6PD</i>genes exhibit signatures of natural selection in Chinese mountain hounds and are likely associated with hunting abilities (endurance and night vision). Moreover, the selective sweep analysis suggested that <i>NOL8</i>,<i>KRT9</i>, <i>RORB</i>and <i>CAMTA1</i>might be candidate genes for dog running speed. The resultsabout genomic and population structures, and <a name="_Hlk15722685">selection signatures of Chinese dog breeds reinforce the conclusion that </a>Chinese indigenous dogs with great variations of phenotypes are important resources for identifying genes responsible for complex traits.</span></span></span></span></span></span></span></span></span></span></span></p>
Data from: The evolutionary history of Xiphophorus fish and their sexually selected sword: a genome-wide approach using restriction site-associated DNA sequencing
Next-generation sequencing (NGS) techniques are now key tools in the detection of population genomic and gene expression differences in a large array of organisms. However, so far few studies have utilized such data for phylogenetic estimations. Here, we use NGS data obtained from genome-wide restriction site-associated DNA (RAD) (∼66000 SNPs) to estimate the phylogenetic relationships among all 26 species of swordtail and platyfish (genus Xiphophorus) from Central America. Past studies, both sequence and morphology-based, have differed in their inferences of the evolutionary relationships within this genus, particularly at the species-level and among monophyletic groupings. We show that using a large number of markers throughout the genome, we are able to infer the phylogenetic relationships with unparalleled resolution for this genus. The relationships among all three major clades and species within each of them are highly resolved and consistent under maximum likelihood, Bayesian inference and maximum parsimony. However, we also highlight the current cautions with this data type and analyses. This genus exhibits a particularly interesting evolutionary history where at least two species may have arisen through hybridization events. Here, we are able to infer the paternal lineages of these putative hybrid species. Using the RAD-marker-based tree we reconstruct the evolutionary history of the sexually selected sword trait and show that it may have been present in the common ancestor of the genus. Together our results highlight the outstanding capacity that RAD sequencing data has for resolving previously problematic phylogenetic relationships, particularly among relatively closely related species.
The genome-wide signature of short-term temporal selection
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Genome-wide patterns of selection-drift variation strongly associate with organismal traits across the green plant lineage
<p>Gene alignments and trees</p>
Data from: Disruptive selection without genome-wide evolution across a migratory divide
Transcontinental migration is a fascinating example of how animals can respond to climatic oscillation. Yet, quantitative data on fitness components are scarce, and the resulting population genetic consequences are poorly understood. Migratory divides, hybrid zones with a transition in migratory behaviour, provide a natural setting to investigate the micro-evolutionary dynamics induced by migration under sympatric conditions. Here, we studied the effects of migratory programme on survival, trait evolution and genome-wide patterns of population differentiation in a migratory divide of European barn swallows. We sampled a total of 824 individuals from both allopatric European populations wintering in central and southern Africa, respectively, along with two mixed populations from within the migratory divide. While most morphological characters varied by latitude consistent with Bergmann's rule, wing length co-varied with distance to wintering grounds. Survival data collected during a 5-year period provided strong evidence that this covariance is repeatedly generated by disruptive selection against intermediate phenotypes. Yet, selection-induced divergence did not translate into genome-wide genetic differentiation as assessed by microsatellites, mtDNA and >20 000 genome-wide SNP markers; nor did we find evidence of local genomic selection between migratory types. Among breeding populations, a single outlier locus mapped to the BUB1 gene with a role in mitotic and meiotic organization. Overall, this study provides evidence for an adaptive response to variation in migration behaviour continuously eroded by gene flow under current conditions of nonassortative mating. It supports the theoretical prediction that population differentiation is difficult to achieve under conditions of gene flow despite measurable disruptive selection.
Data from: Disruptive selection without genome-wide evolution across a migratory divide
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