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1,598 results for “genetic diversity”
Relationship between genome-wide and MHC class I and II genetic diversity and complementarity in a nonhuman primate
<p>Although mate choice is expected to favor partners with advantageous genetic properties, the relative importance of genome-wide characteristics, such as overall heterozygosity or kinship, versus specific loci, is unknown. To disentangle genome-wide and locus-specific targets of mate choice, we must first understand congruence in global and local variation within the same individual. This study compares genetic diversity, both absolute and relative to other individuals (e.g., complementarity), assessed across the genome to that found at the major histocompatibility complex (MHC), a hyper-variable gene family integral to immune system function and implicated in mate choice across species. Using DNA from 22 captive olive baboons (<em>Papio anubis</em>), we conducted double digest restriction-site associated DNA sequencing to estimate genome-wide heterozygosity and kinship and sequenced two class I and two class II MHC loci. We found that genome-wide diversity was not associated with MHC diversity, and that diversity at class I MHC loci was not correlated with diversity at class II loci. Additionally, kinship was a significant predictor of the number of MHC alleles shared between dyads at class II loci. Our results provide further evidence of the strong selective pressures maintaining genetic diversity at the MHC in comparison to other randomly selected sites throughout the genome. Furthermore, our results indicate that class II MHC disassortative mate choice may mediate inbreeding avoidance in this population. Our study suggests that mate choice favoring genome-wide genetic diversity is not always synonymous with mate choice favoring MHC diversity, and highlights the importance of controlling for kinship when investigating MHC-associated mate choice.</p>
How ancient forest fragmentation and riparian connectivity generate high levels of genetic diversity in a micro-endemic Malagasy tree
<p>This repository contains all the scripts and most of the intermediary files necessary to replicate the analyses of the preprint "<strong>How ancient forest fragmentation and riparian connectivity generate high levels of genetic diversity in a micro-endemic Malagasy tree</strong>" submitted to Molecular Ecology and available at:</p> <p><a href="https://www.biorxiv.org/content/10.1101/2020.11.25.394544v1">https://www.biorxiv.org/content/10.1101/2020.11.25.394544v5</a></p> <p>Within each of the different zipped folders a readme.txt file briefly explains how the analyses are organized.</p> <p>This version of the dataset has been revised in agreement with the manuscript revision to answer the comments of the first two rounds of reviews in Peer Community In Evolutionary Biolology (PCI-EvolBiol; <a href="https://evolbiol.peercommunityin.org/">https://evolbiol.peercommunityin.org/</a>) by M. Navascues (Recommender), Katharina Budde (reviewer) and Yurena Arjona (reviewer), as well as two rounds of reviews in Molecular Ecology. All PCIevolbiol comments, response and changes are documented on the PCIevolbiol website.</p>
FIGURE 1 in Genetic diversity in two threatened species of guitarfish (Elasmobranchii: Rhinobatidae) from the Brazilian and Argentinian coasts: an alert for conservation
FIGURE 1 | Median-joining network of mtCR haplotypes for A. Pseudobatos horkelii and B. Pseudobatos percellens. Haplotypes are represented by circles with size proportional to frequency in the total sample. All hatch marks correspond to one mutation. Samples from northern Argentina (AR), Torrinha/RS (RS), Florianópolis/SC (SC), Pontal do Paraná/PR (PR), Cananéia/ SP (SP1), Mongaguá/SP (SP2), Santos/SP (SP3), Rio de Janeiro/RJ(RJ).
FIGURE 2 in Genetic diversity in two threatened species of guitarfish (Elasmobranchii: Rhinobatidae) from the Brazilian and Argentinian coasts: an alert for conservation
FIGURE 2 | Graph of the Bayesian analysis of population structure of mtCR for A. Pseudobatos horkelii and B. Pseudobatos percellens. Samples from northern Argentina (AR), Torrinha/RS (RS), Florianópolis/SC (SC), Pontal do Paraná/PR (PR), Cananéia/ SP (SP1), Mongaguá/SP (SP2), Santos/SP (SP3), Rio de Janeiro/RJ(RJ).
Global patterns of nuclear and mitochondrial genetic diversity in marine fishes
<p>Genetic diversity is a fundamental component of biodiversity. Examination of global patterns of genetic diversity can help highlight mechanisms underlying species diversity, though a recurring challenge has been that patterns may vary by molecular marker. Here, we compiled 6862 observations of genetic diversity from 492 species of marine fish and tested among hypotheses for diversity gradients: the founder effect hypothesis, the kinetic energy hypothesis, and the productivity-diversity hypothesis. We fit generalized linear mixed effect models (GLMMs) and explored the extent to which various macroecological drivers (latitude, longitude, temperature (SST), and chlorophyll-a concentration) explained variation in genetic diversity. We found that mitochondrial genetic diversity followed geographic gradients similar to those of species diversity, being highest near the Equator, particularly in the Coral Triangle, while nuclear genetic diversity did not follow clear geographic patterns. Despite these differences, all genetic diversity metrics were correlated with chlorophyll-a concentration, while mitochondrial diversity was also positively associated with SST. Our results provide support for the kinetic energy hypothesis, which predicts that elevated mutation rates at higher temperatures increase mitochondrial but not necessarily nuclear diversity, and the productivity-diversity hypothesis, which posits that resource-rich regions support larger populations with greater genetic diversity. Overall, these findings reveal how environmental variables can influence mutation rates and genetic drift in the ocean, caution against using mitochondrial macro-genetic patterns as proxies for whole-genome diversity, and aid in defining global gradients of genetic diversity.</p>
Data from: Genome-wide association mapping within a local Arabidopsis thaliana population more fully reveals the genetic architecture for defensive metabolite diversity
<p>A paradoxical finding from genome-wide association studies (GWAS) in plants is that variation in metabolite profiles typically maps to a small number of loci, despite the complexity of underlying biosynthetic pathways. This discrepancy may partially arise from limitations presented by geographically diverse mapping panels. Properties of metabolic pathways that impede GWAS by diluting the additive effect of a causal variant, such as allelic and genic heterogeneity and epistasis, would be expected to increase in severity with the geographic range of the mapping panel. We hypothesized that a population from a single locality would reveal an expanded set of associated loci. We tested this in a French <em>Arabidopsis thaliana</em> population (< 1 km transect) by profiling and conducting GWAS for glucosinolates, a suite of defensive metabolites that have been studied in depth through functional and genetic mapping approaches. For two distinct classes of glucosinolates, we discovered more associations at biosynthetic loci than previous GWAS with continental-scale mapping panels. Candidate genes underlying novel associations were supported by concordance between their observed effects in the TOU-A population and previous functional genetic and biochemical characterization. Local populations complement geographically diverse mapping panels to reveal a more complete genetic architecture for metabolic traits.</p>
Genetic diversity and efficacy of natural selection in spiders with pre-copulatory sexual cannibalism
<p>Factors that increase reproductive variance among individuals act to reduce effective population size (Ne), which accelerates loss of genetic diversity and decreases efficacy of purifying selection. These factors include sexual cannibalism, offspring investment, and mating system. Pre-copulatory sexual cannibalism where the female consumes the male prior to mating exacerbates this effect. We performed comparative transcriptomics in two spider species, the cannibalistic Trechaleoides biocellata and the non-cannibalistic T. keyserlingi, to generate genomic evidence to support these predictions. First, we estimated heterozygosity and found that genetic diversity is relatively lower in the cannibalistic species. Second, we calculated dN/dS ratios as a measure of purifying selection, higher dN/dS ratio indicated relaxed purifying selection in the cannibalistic species. These results are consistent with the hypothesis that sexual cannibalism impacts operational sex ratio and demographic processes, which interact with evolutionary forces to shape the genetic structure of populations. However, other factors such as the mating system and life-history traits contribute to shape Ne. Comparative analyses across multiple contrasting species-pairs would be required to disentangle these effects. Our study highlights that extreme behaviours such as pre-copulatory cannibalism may have profound eco-evolutionary effects. </p>
Fig. 2 in Genetic diversity of Egyptian populations of the African Common Toad (Sclerophrys regularis, Reuss 1833)
Fig. 2. Phylogenetic tree of African Common Toad, using COI haplotypes based on the Maximum Likelihood method. Numbers refer to localities mentioned in the text: 1. Sharm El-Shaikh; 2. Arish; 3. Ismailia; 4. Damietta; 5. Alexandria; 6. Matrouh; 7. Gharbiya; 8. Cairo; 9. SiwaOasis; 10. Bani Sweif; 11. Menia; 12. Sohag; 13. Qena; 14. Aswan.
Multinational evaluation of genetic diversity indicators for the Kunming-Montreal Global Biodiversity Framework
<p>Under the recently adopted Kunming-Montreal Global Biodiversity Framework, 196 Parties committed to report the status of genetic diversity for all species. To facilitate reporting, three genetic diversity indicators were developed, two of which focus on processes contributing to genetic diversity conservation: maintaining genetically distinct populations and ensuring populations are large enough to maintain genetic diversity. The major advantage of these indicators is that they can be estimated with or without DNA-based data. However, demonstrating their feasibility requires addressing the methodological challenges of using data gathered from diverse sources, across diverse taxonomic groups, and for countries of varying socioeconomic status and biodiversity levels. Here, we assess the genetic indicators for 919 taxa, representing 5,271 populations across nine countries, including megadiverse countries and developing economies. Eighty-three percent of taxa assessed had data available to calculate at least one indicator. Our results show that although the majority of species maintain most populations, 58% of species have populations too small to maintain genetic diversity. Moreover, genetic indicator values suggest that IUCN Red List status and other initiatives fail to assess genetic status, highlighting the critical importance of genetic indicators.</p>
Fig. 3 in Assessing genetic diversity of three species of potato tuber moths (Gelechiidae, Lepidoptera) in the Ecuadorian highlands
Fig. 3. Distribution of 5 haplotypes and sequence identity between each pair of Symmetrischema tangolias haplotypes. St-H1 was present in all 4 provinces; St-H2 was present in 3 provinces; the other 3 haplotypes were present only in 1 province for each haplotype. Arrows point to province(s) instead of a specific sampling location.
Fig. 1 in Assessing genetic diversity of three species of potato tuber moths (Gelechiidae, Lepidoptera) in the Ecuadorian highlands
Fig. 1. Use of pheromone traps to collect potato tuber moths in Cacha, Chimborazo, and Tishinguirí, Bolívar: (A) potato crops are grown in mountainous regions of Ecuador where smallholder terrace farming is predominant; (B) low-cost pheromone traps were made of plastic bottles; a species-specific lure is fixed to the bottle cap using a string, and thumb-sized holes were carved to allow moths to fly into the bottle that was filled with soapy water; (C) 3 different traps were placed (pointed by arrows) in each field at least 100 m apart to catch different moths.
Fig. 5 in Assessing genetic diversity of three species of potato tuber moths (Gelechiidae, Lepidoptera) in the Ecuadorian highlands
Fig. 5. Distribution of 3 haplotypes and sequence identity between each pair of Phthorimaea operculella haplotypes. Po-H1 was present in all 4 provinces, Po-H3 was present only in Cotopaxi and Chimborazo; Po-H2 was limited to Tungurahua.
Fig. 2 in Assessing genetic diversity of three species of potato tuber moths (Gelechiidae, Lepidoptera) in the Ecuadorian highlands
Fig. 2. Alignment of 5 COI haplotype sequences of Symmetrischema tangolias samples. KX443104.1 is a reference sequence from GenBank. Sequences of these 5 haplotypes were deposited in GenBank with accession numbers MN223391 to MN223395.
Fig. 4 in Assessing genetic diversity of three species of potato tuber moths (Gelechiidae, Lepidoptera) in the Ecuadorian highlands
Fig. 4. Alignment of 3 unique COI haplotype sequences of Phthorimaea operculella. MF121882 is a reference sequence from GenBank. Sequences of these 3 haplotypes were deposited in GenBank with accession numbers MN205567 to MN205569.
Fig. 2 in Genetic diversity of Serianthes nelsonii on Guam and Rota
Fig. 2. Individual-based genetic structure elucidated by admixture analysis (STRUCTURE) and distributions of genetic ancestry when the number of clusters ranged from K = 2 to 5. Each bar represents an individual of Serianthes nelsonii in the study. Different colors represent different genetic ancestry groups. The y-axis aids in estimating the percentage of each genetic ancestry group within an individual. Abbreviations of Rota population indicate sampled locations: a. I Chego/Saligai; b. Guayaungan/Sisiao; c. Ca'an; d. Talo; and e. As Igua.
Figure 1 in Genetic diversity of Serianthes nelsonii on Guam and Rota
Figure 1. Sampling sites for Serianthes nelsonii in this study. A. Sampling site of the S. nelsonii mother tree and seedlings in Ritidian, Guam. Seedlings were found under the mother plant. B. Sampling sites of S. nelsonii on Rota indicating three mature plant sites (a. I Chego/Saligai; b. Guayaungan/Sisiao; and c. Ca'an) and two out-planting sites (d. Talo and e. As Igua).
Fig. 3 in Haplotype variation in the Physa acuta group (Basommatophora): genetic diversity and distribution in Serbia Abstract
Fig. 3: Haplotype networks from 43 Physa acuta group specimens, obtained using statistical parsimony (TCS). Circles represent specific haplotypes; the size of the circles reflects the number of individuals with a particular haplotype (not to scale); the dots between the circles represent mutational steps.
Fig. 2 in Haplotype variation in the Physa acuta group (Basommatophora): genetic diversity and distribution in Serbia Abstract
Fig. 2: Phylogenetic trees based on mt16S rDNA, obtained using the Maximum Likelihood (ML) method. Bootstrap values are indicated below the branches. Scale bar indicates the number of substitutions per site.
Fig. 1 in Genetic Diversity In Peripheral And Central Populations Of Rusty-Necklaced Partridge (Alectoris Magna) Based On Mitochondrial And Microsatellite Dna
Fig. 1. Rusty-necklaced partridge sampling sites: 1 = Lanzhou, 2 = Jingyuan, 3 = Haiyuan, 4 = Dingxi, 5 = Huining, 6 = Wushan, 7 = Beidao, 8 = Lixian
Fig. 2 in Low Level Genetic Diversity of Opalinid Morphotypes from the Digestive Tract of Hoplobatrachus rugulosus (Batrachia, Amphibia) in Thailand
Fig. 2. Scanning electron micrographs of opaline cells fixed in 2.5% glutaraldehyde. All opaline cells are covered with flagella throughout their body. (A) Opalinid cell with somatic ridges caused by the flagellar metachronal beating clearly defined in a spiral arrangement. (B) Fan-shaped opalinid cell with a broad anterior end and tapering posterior. (C) Uniformly elongated opalinid cell with a slightly tapering posterior end. (D) Fan-shaped opalinid cell of a similar morphotype to B but of a smaller size. Scale bar: A, C and D: 50 μm; B: 10 μm.
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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)
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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.