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262 results for “Genetic variability”
Fig. 2 in Worldwide sampling reveals low genetic variability in populations of the freshwater ciliate Paramecium biaurelia (P. aurelia species complex, Ciliophora, Protozoa)
Fig. 2 Phylog_n_tic tr__ construct_d for Paramecium aurelia compl_x, P. jenningsi compl_x and P. schewiakoffi (two sp_ci_s: P. caudatum and P. multimicronucleatum w_r_ us_d as an outgroup). Th_ tr__ was construct_d on th_ basis of a comparison of s_qu_nc_s from th_ ribosomal ITS1-5.8S-ITS2-5'LSU fragm_nt using th_ maximum lik_lihood m_thod. Bootstrap valu_s for n_ighbor joining, maximum parsimony, maximum lik_lihood, and post_rior probabiliti_s for
Fig. 3 in Worldwide sampling reveals low genetic variability in populations of the freshwater ciliate Paramecium biaurelia (P. aurelia species complex, Ciliophora, Protozoa)
Fig. 3 Phylog_n_tic tr__ construct_d for Paramecium aurelia compl_x, P. jenningsi compl_x and P. schewiakoffi (two sp_ci_s: P. caudatum and P. multimicronucleatum w_r_ us_d as an outgroup). Th_ tr__ was construct_d on th_ basis of a comparison of s_qu_nc_s from th_ mitochondrial COI fragm_nt using th_ maximum lik_lihood m_thod. Bootstrap valu_s for n_ighbor joining, maximum parsimony, maximum lik_lihood, and post_rior probabiliti_s for Bay_sian inf_r_nc_ ar_
Fig. 2. Full length d in Low Genetic Variability In The Recovering Urban Banded Leaf Monkey Population Of Singapore
Fig. 2. Full length d- loop of Presbytis melalophos (1.08kbp) and target region of d-loop (variable site for P. femoralis is position 190). The complete mitochondrial genome of this specimen is published under Sterner et al. (2006), and the specimen is identified as P. melalophos following Groves (2001) and Brandon-Jones et al. (2004).
Fig. 2 in Genetic variability in four samples of Neoplecostomus yapo (Teleostei: Loricariidae) from the rio Paranapanema basin, Brazil
Fig. 2. Lateral view of four specimens of Neoplecostomus yapo from the following localities: A, ribeirão Atlântico, 85.9 mm SL; B) ribeirão Uraí, 93.3 mm SL; C) rio Verde, 96.0 mm SL; and D) rio Fortaleza, 97.4 mm SL (type locality of N. yapo).
Fig. 1 in Genetic variability in four samples of Neoplecostomus yapo (Teleostei: Loricariidae) from the rio Paranapanema basin, Brazil
Fig. 1. Partial map of South America showing the collecting sites of Neoplecostomus yapo. Circle = ribeirão Atlântico, município de Mandaguaçu; triangle = ribeirão Uraí, mun. Londrina; lozenge = rio Fortaleza, mun. Tibagi; and star = rio Verde, mun. Ponta Grossa, Paraná State.
Key triggers of adaptive genetic variability of sessile oak [Q. petraea (Matt.) Liebl.] from the Balkan refugia: outlier detection and association of SNP loci from ddRAD-seq data
<p>Knowledge on the genetic composition of <em>Quercus petraea</em> in south-eastern Europe is limited despite the species' significant role in the re-colonisation of Europe during the Holocene, and the diverse climate and physical geography of the region. Therefore, it is imperative to conduct research on adaptation in sessile oak to better understand its ecological significance in the region. While large sets of SNPs have been developed for the species, there is a continued need for smaller sets of SNPs that are highly informative about the possible adaptation to this varied landscape. By using double digest restriction site associated DNA sequencing data from our previous study, we mapped RAD-tag sequences to the <em>Quercus robur</em> reference genome and identified a set of SNPs putatively related to drought stress-response. A total of 179 individuals from eighteen natural populations at sites covering heterogeneous climatic conditions in the southeastern natural distribution range of <em>Q. petraea</em> were genotyped. The detected highly polymorphic variant sites revealed three genetic clusters with a generally low level of genetic differentiation and balanced diversity among them but showed a north–southeast gradient. Selection tests showed nine outlier SNPs positioned in different functional regions. Genotype-environment association analysis of these markers yielded a total of 53 significant associations, explaining 2.4–16.6% of the total genetic variation. Our work exemplifies that adaptation to drought may be under natural selection in the examined <em>Q. petraea</em> populations.</p>
Fig. 2. Shell morphometric variables. A in Morphology and taxonomic assessment of eight genetic clades of Mercuria Boeters, 1971 (Caenogastropoda, Hydrobiidae), with the description of five new species
Fig. 2. Shell morphometric variables. A. Image of a specimen of Mercuria similis (Draparnaud, 1805) indicating the landmarks (red) and semilandmarks (blue) used for the geometric morphometric analysis (PCA). B–C. Drawings of shells of Mercuria Boeters, 1971, showing the linear measurements made on the shell and protoconch.
Fig. 5 in Additional data on Spinitectus petterae (Nematoda: Rhabditida) from Clarias gariepinus (Siluriformes: Clariidae) in the Vaal River system: conserved morphology or high intraspecific genetic variability?
Fig. 5. Scanning electron micrographs of immature female of Spinitectus petterae Boomker, 1993 collected from Clarias gariepinus (Burchell). A – apical view of cephalic region; B – vulva; C – conical tail end; D – conical tail. Abbrevations: A – anus; CA – caudal papilla; L – labium; MT – mucron tip; PL – pseudolabium.
Fig. 4 in Additional data on Spinitectus petterae (Nematoda: Rhabditida) from Clarias gariepinus (Siluriformes: Clariidae) in the Vaal River system: conserved morphology or high intraspecific genetic variability?
Fig. 4. Illustrations of Spinitectus petterae Boomker, 1993 – male, reproductive structures and tail end. A – lateral aspect of posterior section with left and right spicules, and associated structures; B – tip of left spicule from two views and tip of the right spicule with fleshy extension; C – ventral aspect of posterior section with caudal papillae and cloacal opening. Abbreviation: C – cloacal opening; CCO – cytoplasmic core opening; LS – left spicule; LSB – left spicule blade; LSS – left spicule shaft; M – manubrium; PcP – postcloacal papillae; PP – precloacal papillae; RP – rugosa plates; RS – right spicule; SM – spicule muscle; SP – spicular pouch; VD – vas deferens.
Fig. 7 in Additional data on Spinitectus petterae (Nematoda: Rhabditida) from Clarias gariepinus (Siluriformes: Clariidae) in the Vaal River system: conserved morphology or high intraspecific genetic variability?
Fig. 7. Phylogenetic relationships of Spinitectus spp. based on available cox1 mtDNA for Spinitectus based on Bayesian inference (BI)), with Rhabdochona xiphophori Caspeta-Mandujano, Moravec et Salgado-Maldonado, 2001 as the designated outgroup. Posterior probability (BI) and 1,000 bootstrap replicate (maximum likelihood (ML)) support indicated (BI/ML), nodes with less than 0.5 (50 %) support not annotated. Data shaded in colour from indicated geographical locality or river system, and three haplotypes recorded from the Vaal River system indicated (VRS1–VRS3).
Fig. 2 in Additional data on Spinitectus petterae (Nematoda: Rhabditida) from Clarias gariepinus (Siluriformes: Clariidae) in the Vaal River system: conserved morphology or high intraspecific genetic variability?
Fig. 2. Light and scanning electron micrographs of adult females of Spinitectus petterae Boomker, 1993 collected from Clarias gariepinus (Burchell). A – neck showing spines on annular rings; B – first three rings on neck, rings indicated numerically and spine length measurement illustrated; C – apical view of the cephalic region; D – lateral view of cephalic region; E – apical view of cephalic structures; F – excretory pore; G – diminishing spines; H – posterior end; inlay gonopore with vulva I – posterior end with gonopore, vulva position indicated; J – conical tail tip; K – conical tail and mucron tip. Abbreviations: A – anus; AP – amphid; CP – cephalic papillae; L – labia; MT – mucron tip; PL – pseudolabia; PS – porous structure; OO – oral opening; V – vulva; SL – sublabium.
Fig. 1. A in Additional data on Spinitectus petterae (Nematoda: Rhabditida) from Clarias gariepinus (Siluriformes: Clariidae) in the Vaal River system: conserved morphology or high intraspecific genetic variability?
Fig. 1. A – map of South Africa; B – map of the river systems in the inlay showing the sampling sites where Spinitectus petterae Boomker, 1993 was collected in Clarias gariepinus (Burchell). Abbreviations: 1 – down-stream of the Vaal River Barrage; 2 – in the Vaal Dam reservoir; 3 – down-stream of the Grootdraai Dam; 4 – Crocodile River.
Pollinator loss causes rapid adaptive evolution of selfing and dramatically reduces genome-wide genetic variability
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Genetic variability and telomeres: Insights from a tropical avian hybrid zone
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Genetic variants regulating the immune response improve the prediction of COVID-19 severity provided by clinical variables
<p>Data set generated to evaluate the association between SNPs from genes related to SARS-CoV-2 pathogenesis and their clinical outcome.</p>
Fig. 3. FCAanalysisoftheallozymedataacrosspopulationsof Daphniaatkinsoni and D in Allozyme-Based Genetic Variability Of The Daphnia Atkinsoni-Bolivari Species Complex (Cladocera: Daphniidae) In The Hungarian Great Plain
Fig. 3. FCAanalysisoftheallozymedataacrosspopulationsof Daphniaatkinsoni and D. bolivari.
Data from: Resident-disperser differences and genetic variability affect communities in microcosms
<p>Dispersal is a key process mediating ecological and evolutionary dynamics. Its effects on the dynamics of spatially-structured systems, population genetics, or species range distribution can depend on phenotypic differences between dispersing and non-dispersing individuals. However, scaling up the importance of resident-disperser differences to communities and ecosystems has rarely been considered, in spite of intraspecific phenotypic variability being an important factor mediating community structure and productivity. Here, we used the ciliate <em>Tetrahymena thermophila</em>, in which phenotypic traits are known to differ between residents and dispersers, to test (i) whether these resident-disperser differences affect biomass and composition in competitive communities composed of four other Tetrahymena species, and (ii) whether these effects are genotype-dependent. We found that dispersers led to lower community biomass compared to residents. This effect was highly consistent across the twenty <em>T. thermophila</em> genotypes used, despite intraspecific variability in resident-disperser phenotypic differences. We also found a significant genotypic effect on biomass production, showing that intraspecific variability has consequences for communities. Our study suggests that individual dispersal strategy can scale up to community productivity in a predictable way, opening new perspectives to the functioning of spatially structured ecosystems.</p>
A novel SNP assay reveals increased genetic variability and abundance following translocations to a remnant Allegheny woodrat population
<p><strong>Background</strong>: Allegheny woodrats (<em>Neotoma magister</em>) are found in metapopulations distributed throughout the Interior Highlands and Appalachia. Historically these metapopulations persisted as relatively fluid networks, enabling gene flow between subpopulations and recolonization of formerly extirpated regions. However, over the past 45 years, Allegheny woodrat populations have experienced population declines throughout their range due to a combination of habitat destruction, declining hard mast availability, and roundworm parasitism. In an effort to initiate genetic rescue of a small, genetically depauperate subpopulation in New Jersey, woodrats were translocated from a genetically robust population in Pennsylvania (PA) in 2015, 2016, and 2017. Herein, we assess the efficacy of these translocations to restore genetic diversity within the recipient population. </p> <p><strong>Results</strong>: We designed a novel 134 single nucleotide polymorphism panel, which was used to genotype the six woodrats translocated from PA and 82 individuals from the NJ population captured before and after the translocation events. These data indicated that a minimum of two translocated individuals successfully produced at least 16 offspring, who reproduced as well. Further, population-wide observed heterozygosity rose substantially following the first set of translocations, reached levels comparable to that of populations in Indiana and Ohio, and remained elevated throughout the following years. Abundance also increased during the monitoring period, suggesting Pennsylvania translocations initiated the genetic rescue of the New Jersey population.</p> <p><strong>Conclusions</strong>: Our results indicate, encouragingly, that very small numbers of translocated individuals can successfully restore the genetic diversity of a threatened population. Our work also highlights the risks of managing very small populations, such as when translocated individuals have greater reproductive success relative to residents. Finally, we note that ongoing work with Allegheny woodrats may broadly shape our understanding of genetic rescue within metapopulations and across heterogeneous landscapes.</p>
Data underlying the article: "Excuse me, there is a mutant in my bioactivity soup! A comprehensive analysis of the genetic variability landscape of bioactivity databases and its effect on activity modelling"
<p>This repository contains the data underlying the article: “Excuse me, there is a mutant in my bioactivity soup! A comprehensive analysis of the genetic variability landscape of bioactivity databases and its effect on activity modelling” available as a preprint on ChemRxiv.</p> <p>Main authors: Marina Gorostiola González & Olivier J.M. Béquignon (Leiden University)</p> <p>Senior author: Gerard J.P. van Westen (Leiden University)</p> <p>This analysis was performed using the code available at <a href="https://github.com/CDDLeiden/chembl_variants" target="_blank" rel="noopener">https://github.com/CDDLeiden/chembl_variants</a></p>
Experimental evaluation of genetic variability based on DNA metabarcoding from the aquatic environment: Insights from the Leray COI fragment
<p>Intraspecific genetic variation is important for the assessment of organisms' resistance to changing environments and anthropogenic pressures. Aquatic DNA metabarcoding provides a non-invasive method in biodiversity research, including investigations at the within-species level. Through the analysis of eDNA samples collected from the Peter the Great Gulf of the Japan Sea, in this study we aimed to evaluate the identification of Amplicon Sequence Variants (ASVs) in marine eDNA among abundant species of the <em>Zostera</em> sp. community: <em>Hexagrammos octogrammus</em>, <em>Pholidapus dybowskii</em> (Teleostei: Perciformes), and <em>Pandalus latirostris</em> (Arthropoda: Decapoda). These species were collected from two distant locations to produce mock communities and gather aquatic eDNA both on the community and individual level. Our approach highlights the efficacy of eDNA metabarcoding in capturing haplotypic diversity and the potential for this methodology to track genetic diversity accurately, contributing to conservation efforts and ecosystem management. Additionally, our results elucidate the impact of nuclear mitochondrial DNA segments (NUMTs) on the reliability of metabarcoding data, indicating the necessity for cautious interpretation of such data in ecological studies. Moreover, we analyzed 83 publicly available <em>COI</em> sequence datasets from common groups of multicellular organisms (Mollusca, Echinodermata, Crustacea, Polychaeta, and Actinopterygii). The results reflect the decrease in population diversity that arises from using the metabarcode compared to the <em>COI</em> barcode.</p>
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
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
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.