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79 results for “Genetic admixture”
Data from: Admixture and the organization of genetic diversity in a butterfly species complex revealed through common and rare genetic variants
Detailed information about the geographic distribution of genetic and genomic variation is necessary to better understand the organization and structure of biological diversity. In particular, spatial isolation within species and hybridization between them can blur species boundaries and create evolutionary relationships that are inconsistent with a strictly bifurcating tree model. Here we analyze genome-wide DNA sequence and genetic ancestry variation in Lycaeides butterflies to quantify the effects of admixture and spatial isolation on how biological diversity is organized in this group. We document geographically widespread and pervasive historic admixture, with more restricted recent hybridization. This includes evidence supporting previously known and unknown instances of admixture. The genome composition of admixed individuals varies much more among than within populations, and tree- and genetic ancestry-based analyses indicate that multiple distinct admixed lineages or populations exist. We find that most genetic variants in Lycaeides are rare (minor allele frequency < 0.5%). Because the spatial and taxonomic distributions of alleles reflect demographic and selective processes since mutation, rare alleles, which are presumably younger than common alleles, were spatially and taxonomically restricted compared to common variants. Thus, we show patterns of genetic variation in this group are multifaceted, and we argue that this complexity challenges simplistic notions concerning the organization of biological diversity into discrete, easily delineated, and hierarchically structured entities.
Data from: Genetic admixture supports an ancient hybrid origin of the endangered Hawaiian duck
Speciation is regarded primarily as a bifurcation from an ancestral species into two distinct taxonomic units, but gene flow can create different signals of phylogenetic relationships among different loci. We evaluated several hypotheses that could account for phylogenetic discord between mitochondrial DNA (mtDNA) and nuclear DNA (nuDNA) within Hawaiian ducks (Anas wyvilliana), including stochastic lineage sorting, mtDNA capture, and widespread genomic introgression. Our results best support the hypothesis that the contemporary Hawaiian duck is descended from an ancient hybridization event between the mallard (A. platyrhynchos) and Laysan duck (A. laysanensis). Whereas mtDNA clearly shows a sister-relationship between Hawaiian ducks and mallards, nuDNA is consistent with a genetic mosaic with nearly equal contributions from Laysan ducks and mallards. In addition, coalescent analyses suggest that gene flow from either mallard or Laysan duck, depending on the pre-defined tree topology, is necessary to explain contemporary genetic diversity in Hawaiian ducks, and these estimates are more consistent with ancient, rather than contemporary, hybridization. Time since divergence estimates suggest that the genetic admixture event occurred around the Pleistocene-Holocene boundary, which is further supported by circumstantial evidence from the Hawaiian sub-fossil record. Although the extent of reproductive isolation from either putative parental taxon is not currently known, these species are phenotypically, genetically, and ecologically different, and they meet primary criteria used in avian taxonomy for species designation. Thus, the available data are consistent with an admixed origin, and support the hypothesis that the Hawaiian duck may represent a young hybrid species.
When cultural hints of admixture do not match the genetic ancestry: the case of the Middle Neolithic Paris Basin
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Secondary contacts and genetic admixture shape colonisation by an amphiatlantic epibenthic invertebrate
<p>Research on the genetics of invasive species often focuses on patterns of genetic diversity and population structure within the introduced range. However, a growing body of literature is demonstrating the need to study the native range, and how native genotypes affect both ecological and evolutionary mechanisms within the introduced range. Here we used genotyping-by-sequencing to study both native and introduced ranges [based on 1,653 single nucleotide polymorphisms (SNPs)] of the amphiatlantic marine invertebrate <i>Ciona intestinalis</i>. A previous study using microsatellites analysed samples collected along the Swedish west coast and showed the presence of genetically distinct lineages in deep and shallow waters. Using our SNP data from newly collected samples (285 individuals), we first confirmed the presence of this depth-defined genomic divergence along the Swedish coast. We then used Approximate Bayesian Computation to infer the historical relationship among sites from the North Sea, the English Channel and the northwest Atlantic and found evidence of ancestral divergence between individuals from deep waters off Sweden and individuals from the English Channel. This divergence was followed by a secondary contact that led to a genetic admixture between the ancestral populations (i.e. deep Sweden and English Channel), which originated the genotypes found in shallow Sweden. We then revealed that the colonisation of <i>C. intestinalis</i> in the northwest Atlantic was as a result of an admixture between shallow Sweden and the English Channel genotypes across the introduced range. Our results showed the presence of both past and recent genetic admixture events that together may have promoted the successful colonisations of <i>C. intestinalis</i>. Our study suggests that secondary contacts potentially reshape the evolutionary trajectories of invasive species through the promotion of intraspecific hybridisation and by altering both colonisation patterns and their ecological effects in the introduced range.</p>
Genotype and individual data for genetic structure in Louisiana Iris species reveals patterns of recent and historical admixture
<p><b><span>Premise: </span></b><span>When divergent lineages come into secondary contact reproductive isolation may be incomplete, thus providing an opportunity to investigate how speciation is manifested in the genome. The Louisiana Irises (<i>Iris</i>, series <i>Hexagonae</i>) comprise a group of three or more ecologically and reproductively divergent lineages that can produce hybrids where they come into contact. In this study we sought to estimate standing genetic variation to understand the current distribution of population structure in the Louisiana Irises.</span></p> <p><b><span>Methods:</span></b><span> We used genotyping-by-sequencing techniques to sample the genomes of Louisiana Iris species across their ranges. Twenty populations were sampled (total n=632) across 11,249 loci. Population genetic data were assessed using ENTROPY and PCA models. </span></p> <p><b><span>Results: </span></b><span>We discovered evidence for interspecific gene flow in parts of the range and revealed patterns of population structure at odds with widely accepted nominal taxonomy. Undescribed hybrid populations were discovered that were designated as belonging to the <i>I. brevicaulis</i> lineage. <i>Iris nelsonii </i>shared significant ancestry with only one of the purported parent species, <i>I. fulva, </i>evidence inconsistent with a hybrid origin.</span></p> <p><b><span>Conclusions: </span></b><span>This study provides several key findings important to the investigation of standing genetic variation in the Louisiana Iris species complex. <i>Iris brevicaulis</i> has a large amount of genetic diversity within it relative to the other nominal species. In addition, this study has discovered a previously unknown hybrid zone between <i>I. brevicaulis </i>and <i>I. hexagona</i> along the Texas coast. Finally, <i>I. nelsonii</i> does not appear to have mixed ancestry from three parental taxa as has been the longstanding hypothesis. </span></p>
Data from: Higher genetic diversity in recolonized areas than in refugia of Alnus glutinosa triggered by continent-wide lineage admixture
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Data from: Genetic admixture supports an ancient hybrid origin of the endangered Hawaiian duck
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Genotype and individual data for genetic structure in Louisiana Iris species reveals patterns of recent and historical admixture
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Data from: Admixture and the organization of genetic diversity in a butterfly species complex revealed through common and rare genetic variants
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Data from: Genetic admixture accelerates invasion via provisioning rapid adaptive evolution
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Genetic admixture despite ecological segregation in a North African sparrow hybrid zone (Aves, Passeriformes, Passer domesticus x Passer hispaniolensis)
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Genetic divergence, admixture and subspecific boundaries in a peripheral population of great tit, Parus major (Aves, Paridae)
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Secondary contacts and genetic admixture shape colonisation by an amphiatlantic epibenthic invertebrate
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The genetic legacy of continental scale admixture in Indian Austroasiatic speakers
GEO Series GSE126882. Homo sapiens. 39 samples. Type: Genome variation profiling by SNP array; SNP genotyping by SNP array.
A genetic atlas of human admixture history
GEO Series GSE53626. Homo sapiens. 158 samples. Type: Genome variation profiling by SNP array; SNP genotyping by SNP array.
Genetic analysis of ancestry, admixture, and selection in Bolivian and Totonac populations of the New World
GEO Series GSE29851. Homo sapiens. 47 samples. Type: SNP genotyping by SNP array.
Data from: Genetic substructure and admixture as important factors in linkage disequilibrium-based estimation of effective number of breeders in recovering wildlife populations
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Figure 2 in Rare genetic admixture and unidirectional gene flow between Vipera aspis and Vipera berus at their contact zone in western France
Figure 2. NewHybrids results using Jeffreys priors of V. aspis and V. berus samples collected in the Loire Atlantique department (France). Morphologically intermediate individuals include individual 4.14 which was genetically assigned to V. aspis. The hybridization level of individuals 14 and 71 could not be clearly assigned. BcVa = F1 × Vipera aspis; BcVb = F1 × Vipera berus.
Genetic structure of Mataco-Guaycurú speakers from Argentina and their genetic admixture extent with neighbouring urban populations
<p>Y-STRs haplotype dataset of four Native American groups inhabiting northern Argentina (Wichi, PIlaga, Toba and Mocoví) belonging from Mataco-Guyacurú ethnic group. </p>
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Allen Brain Atlas
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