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1,467 results for “Genetic structure”
Data from: The role of ecological factors in determining phylogeographic and population genetic structure of two sympatric island skinks (Plestiodon kishinouyei and P. stimpsonii)
We conducted comparative phylogeographic and population genetic analyses of Plestiodon kishinouyei and P. stimpsonii, two sympatric skinks endemic to islands in the southern Ryukyus, to explore different factors that have influenced population structure. Previous phylogenetic studies using partial mitochondrial DNA (mtDNA) indicate similar divergence times from their respective closest relatives, suggesting that differences in population structure are driven by intrinsic attributes of either species rather than the common set of extrinsic factors that both presumably have been exposed to throughout their history. In this study, analysis of mtDNA sequences and microsatellite polymorphism demonstrate contrasting patterns of phylogeography and population structure: P. kishinouyei exhibits a lower genetic variability and lower genetic differentiation among islands than P. stimpsonii, consistent with recent population expansion. However, historical demographic analyses indicate that the relatively high genetic uniformity in P. kishinouyei is not attributable to recent expansion. We detected significant isolation-by-distance patterns among P. kishinouyei populations on the land bridge islands, but not among P. stimpsonii populations occurring on those same islands. Our results suggest that P. kishinouyei populations have maintained gene flows across islands until recently, probably via ephemeral Quaternary land bridges. The lower genetic variability in P. kishinouyei may also indicate smaller effective population sizes on average than that of P. stimpsonii. We interpret these differences as a consequence of ecological divergence between the two species, primarily in trophic level and habitat preference.
Data from: Evaluation of genetic diversity and population structure of five Chinese indigenous donkey breeds using microsatellite markers
China had the largest population of raising donkeys in the world, however the number of Chinese indigenous donkey decreased dramatically due to the increase of agriculture mechanization in the last century. The species has still been important in China because of its edible and medical value, therefore the survey on its genetic diversity in China is necessary for its conservation and utilization. In this study, 15 microsatellite markers were used to evaluate genetic diversity and population structure of five Chinese indigenous donkey breeds. The mean values of expected heterozygosity, allelic richness, and total number of alleles for all the tested Chinese donkeys were 0.70, 6.04, and 6.28 respectively, suggesting that the genetic diversity of Chinese indigenous donkeys is rich. The Bayesian analysis and principal component analysis plot yielded the same clustering result, which revealed that Guanzhong donkey was the most differentiated breed in all detected samples, and Jinnan (JN) and Guangling (GL) were genetically closed together. Additionally, our results indicated that the heterozygote deficit was severe in two Chinese indigenous donkey breeds (GL and JN), and it warned us that animal conservation activities on this species should be considered carefully in near future.
Figure 3 from: Zhao L, Wang S, Qu F, Liu Z, Gao T (2022) A genetic assessment of the population structure and demographic history of Odontamblyopus lacepedii (Perciformes, Amblyopinae) from the northwestern Pacific. ZooKeys 1088: 1-15. https://doi.org/10.3897/zookeys.1088.70860
Figure 3 Phylogenetic network of all haplotypes.
Figure 1 from: Zhao L, Wang S, Qu F, Liu Z, Gao T (2022) A genetic assessment of the population structure and demographic history of Odontamblyopus lacepedii (Perciformes, Amblyopinae) from the northwestern Pacific. ZooKeys 1088: 1-15. https://doi.org/10.3897/zookeys.1088.70860
Figure 1 Sampling locations of Odontamblyopus lacepedii in the present study.
Clonality and genetic structure of an endangered aquatic plant, Typha minima, in the French Alps: consequences for conservation
<p>Genetic data on Typha minima populations obtained with AFLP markers.</p> <p>The data was used in the article "Clonality and genetic structure of an endangered aquatic plant, Typha minima, in the French Alps: consequences for conservation, by Irène Till-Bottraud, Jacky Girel, Erwan Roussel, Delphine Rioux, Lucie Fiorese, Noémie Fort and published in Alpine Botany in 2022</p>
Data from: Does a coexisting congener affect the genetic structure and selfing rate via reproductive interference?
<p>Data archived here were used for analyses in Katsuhara et al. "Does a coexisting congener affect the genetic structure and selfing rate via reproductive interference?" Data is in two worksheets.</p>
Figure 1 from: Muhammad F, Lü Z-m, Liu L, Gong L, Du X, Shafi M, Kaleri HA (2018) Genetic structure of Octopus minor around Chinese waters as indicated by nuclear DNA variations (Mollusca, Cephalopoda). ZooKeys 775: 1-14. https://doi.org/10.3897/zookeys.775.24258
Figure 1 Map showing the collection locations.
Figure 5 from: Liu L, Zhang X, Li C, Zhang H, Yanagimoto T, Song N, Gao T (2019) Population genetic structure of Marbled Rockfish, Sebastiscus marmoratus (Cuvier, 1829), in the northwestern Pacific Ocean. ZooKeys 830: 127-144. https://doi.org/10.3897/zookeys.830.30586
Figure 5 The heatmap of Fst genetic distances based on mtDNA control sequences of populations.
Figure 3 from: Liu L, Zhang X, Li C, Zhang H, Yanagimoto T, Song N, Gao T (2019) Population genetic structure of Marbled Rockfish, Sebastiscus marmoratus (Cuvier, 1829), in the northwestern Pacific Ocean. ZooKeys 830: 127-144. https://doi.org/10.3897/zookeys.830.30586
Figure 3 Median-joining network of S.marmoratus haplotypes.
Figure 1 from: Liu L, Zhang X, Li C, Zhang H, Yanagimoto T, Song N, Gao T (2019) Population genetic structure of Marbled Rockfish, Sebastiscus marmoratus (Cuvier, 1829), in the northwestern Pacific Ocean. ZooKeys 830: 127-144. https://doi.org/10.3897/zookeys.830.30586
Figure 1 Sampling sites of S.marmoratus.
Functional characterization of 3D-protein structures informed by human genetic diversity - data
<p>Supplementary data for https://www.biorxiv.org/content/early/2017/08/29/182287</p>
Figure 5 in Genetic structure and population dynamics of the silver pheasant (Lophura nycthemera) in southern China
Figure 5. The test for STRUCTURE analysis.
Data from: Spatial and temporal genetic structure of a river-resident Atlantic salmon (Salmo salar) after millennia of isolation
The river-resident Salmo salar ("småblank") has been isolated from other Atlantic salmon populations for 9,500 years in upper River Namsen, Norway. This is the only European Atlantic salmon population accomplishing its entire life cycle in a river. Hydropower development during the last six decades has introduced movement barriers and changed more than 50% of the river habitat to lentic conditions. Based on microsatellites and SNPs, genetic variation within småblank was only about 50% of that in the anadromous Atlantic salmon within the same river. The genetic differentiation (FST) between småblank and the anadromous population was 0.24. This is similar to the differentiation between anadromous Atlantic salmon in Europe and North America. Microsatellite analyses identified three genetic subpopulations within småblank, each with an effective population size Ne of a few hundred individuals. There was no evidence of reduced heterozygosity and allelic richness in contemporary samples (2005–2008) compared with historical samples (1955–56 and 1978–79). However, there was a reduction in genetic differentiation between sampling localities over time. SNP data supported the differentiation of småblank into subpopulations and revealed downstream asymmetric gene flow between subpopulations. In spite of this, genetic variation was not higher in the lower than in the upper areas. The meta-population structure of småblank probably maintains genetic variation better than one panmictic population would do, as long as gene flow among subpopulations is maintained. Småblank is a unique endemic island population of Atlantic salmon. It is in a precarious situation due to a variety of anthropogenic impacts on its restricted habitat area. Thus, maintaining population size and avoiding further habitat fragmentation are important.
Data from: Long distance dispersal and genetic structure of natural populations: an assessment of the inverse isolation hypothesis in peat mosses
It is well accepted that the shape of the dispersal kernel, especially its tail, has a substantial effect on the genetic structure of species. Theory predicts that dispersal by fat-tailed kernels reshuffles genetic material and thus preserves genetic diversity during colonization. Moreover, if efficient long distance dispersal is coupled with random colonization, an inverse isolation effect is predicted to develop in which increasing genetic diversity per colonizer is expected with increasing distance from a genetically variable source. By contrast, increasing isolation leads to decreasing genetic diversity when dispersal is via thin-tailed kernels. Here we use a well-established model group for dispersal biology (peat mosses: genus Sphagnum) with a fat-tailed dispersal kernel, and the natural laboratory of the Stockholm archipelago to study the validity of the inverse isolation hypothesis in spore-dispersed plants in island colonization. Population genetic structure of three species (S. fallax, S. fimbriatum and S. palustre) with contrasting life histories and ploidy levels were investigated on a set of islands using microsatellites. Our data show (φ'st, AMOVA, IBD) that dispersal of the two most abundant species can be well approximated by a random colonization model. We find that genetic diversity per colonizer on islands increases with distance from the mainland for S. fallax and S. fimbriatum. By contrast, S. palustre deviates from this pattern, owing to its restricted distribution in the region affecting its source pool strength. Therefore, the inverse isolation effect appears to hold in natural populations of peat mosses and, likely, in other organisms with small diaspores.
Figure 4 from: Osikowski A, Georgiev D, Hofman S, Falniowski A (2015) Does the genetic structure of spring snail Bythinella (Caenogastropoda, Truncatelloidea) in Bulgaria reflect geological history? ZooKeys 518: 67-86. https://doi.org/10.3897/zookeys.518.10035
Figure 4 - Geographical distribution of COI clades. Compare with Figure 3.
Data from: Fragmentation shapes nest density and social structure but not genetic diversity of Temnothorax crassispinus (Formicidae)
<p><strong>This README accompanies data_fragmentation_T.crassispinus.xlsx</strong></p> <p> </p> <p><strong><em>Associate publication : </em></strong></p> <p> </p> <p>Fragmentation shapes nest density and social structure but not genetic diversity of <em>Temnothorax crassispinus</em> (Formicidae)</p> <p>M. Cordonnier, T. Lindner, J. Heinze</p> <p>Lehrstuhl für Zoologie / Evolutionsbiologie, Univ. Regensburg</p> <p> </p> <p>****************************** CONTENTS *******************************</p> <p>The data can be readily imported in any statistical package or spreadsheet program. Please, contact me if you need the file formatted in other ways.</p> <p> </p> <p>This file includes a description of the variables.</p> <p>***********************************************************************</p> <p>Variable names and descriptions</p> <p> </p> <p><strong>Sheet 1</strong></p> <p>ID nest: identity of the nest of the genotyped worker</p> <p>2MS46 to GT-1: complete genotype of the worker. Missing data: “-9”</p> <p>Q1_inter & Q2_inter: Q-values resulting from the Bayesian clustering (interspecific level)</p> <p>ID_inter: species identity based on genotype (TC: <em>Temnothorax crassispinus</em>, TN: <em>T. nylanderi</em>; H: intermediate)</p> <p>Q1_intra & Q2_intra: Q-values resulting from the Bayesian clustering (intraspecific level)</p> <p>ID_intra: population identity based on genotype (TC1: <em>Temnothorax crassispinus</em>, cluster1; TC2: <em>T. crassispinus</em>, cluster2)</p> <p>ID_sequencing_C1-J-2183/C2-N-3661: species identity based on sequencing for primers C1-J-2183/C2-N-3661 (TC: <em>Temnothorax crassispinus</em>, TN: <em>T. nylanderi</em>)</p> <p>ID_sequencing_LCO1490 ⁄ HCO2198: species identity based on sequencing for primers LCO1490 ⁄ HCO2198 (TC: <em>Temnothorax crassispinus</em>, TN: <em>T. nylanderi</em>)</p> <p> </p> <p><strong>Sheet 2</strong></p> <p>Idpatch: identity of the forest patch</p> <p>Latitude, longitude: geographic coordinates of the forest patch</p> <p>Date, Hour: Sampling time of the forest patch</p> <p>TC_Nest-density: number of <em>T. crassispinus </em>nests sampled per people in 30 minutes in the forest patch</p> <p>Prop_Queenright_nests: proportion of queenright nests in the forest patch</p> <p>Gen_div: averaged number of alleles per <em>T. crassispinus</em> nest in the forest patch</p> <p>Connect1 & Connect5: distance to the closest patch and mean distance to the five closest patches</p> <p>Nbneig200 & Nbneig400: number of neighboring forest patches at 200 and 400 meters from the focal forest patch</p> <p>area: size of the forest patch</p> <p>shape: shape of the forest patch (perimeter/surface)</p> <p> </p> <p> </p> <p>****************************** CONTACTING *****************************</p> <p>Contact me at:</p> <p> </p> <p>Marion Cordonnier</p> <p>e-mail: marion.cordonnier@hotmail.com</p> <p> </p> <p>***********************************************************************</p> <p> </p> <p> </p>
Interest Balance Auto-immune Population in Patients With Focal Epilepsy of Unknown Cause, Not Structural, Not Genetics, Newly Diagnosed
ClinicalTrials.gov study NCT02885207. IPD Sharing: NO. Countries: 1. Publications: 0.
SNP data: Population genetic structure in bull sharks (Carcharhinus leucas)
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Data from: Long distance dispersal and genetic structure of natural populations: an assessment of the inverse isolation hypothesis in peat mosses
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Data from: Genetic diversity and population structure of Urochloa grass accessions from Tanzania using simple sequence repeat (SSR) markers
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Allen Brain Atlas
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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
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