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385 results for “Conservation genetics”
The conservation genetics of Iris lacustris (Dwarf Lake Iris), a Great Lakes endemic
<p><em>Iris lacustris</em>, a northern Great Lakes endemic, is a rare species known from 165 occurrences across Lake Michigan and Huron in the United States and Canada. Due to multiple factors, including habitat loss, lack of seed dispersal, patterns of reproduction, and forest succession, the species is threatened. Early population genetic studies using isozymes and allozymes recovered no to limited genetic variation within the species. To better explore genetic variation across the geographic range of <em>I. lacustris </em>and to identify units for conservation, we used tunable Genotyping-by-Sequencing (tGBS) with 171 individuals across 24 populations from Michigan and Wisconsin, and because the species is polyploid, we filtered the single nucleotide polymorphism (SNP) matrices using polyRAD to recognize diploid and tetraploid loci. Based on multiple population genetic approaches, we resolved three to four population clusters that are geographically structured across the two ranges of the species. The species migrated from west to east across its geographic range, and minimal genetic exchange has occurred among populations. Four units for conservation are recognized, but nine adaptive units were identified, providing evidence for local adaptation across the geographic range of the species. Population genetic analyses with all, diploid, and tetraploid loci recovered similar results, which suggests that methods may be robust to variation in ploidy level. </p>
Population genetics of caribou in the Alaska-Yukon border region: implications for designation of conservation units and small herd persistence
<p>Better knowledge of genetic relationships between the Fortymile caribou herd and its neighbors is needed for conservation decision-making in Canada. Here, we contribute the first fine-scale analysis of genetic population structure in nine contiguous caribou herds at the geographic boundaries between Barren-ground and Northern Mountain caribou, and at the Alaska-Yukon border. Using pairwise differentiation metrics, STRUCTURE, and discriminant analysis of principal components (DAPC) to analyze 15 microsatellite loci in 379 caribou, we found complex patterns of genetic differentiation. The Fortymile was the only herd assigned to more than one genetic cluster, indicative of its history as a larger herd whose range expansions and gene flow to other herds were likely important to maintaining diversity across a functioning genetic metapopulation. Some small herds (Chisana, Klaza, and White Mountains) were genetically distinct, while others (Hart River, Clear Creek, Mentasta) exhibited little differentiation from herds they occasionally overlap, including herds assigned to different conservation units (DUs). This genetic connectivity does not result from demographic connectivity, as episodic contact during rut, rather than herd switching, is the likely mechanism. Unusually, one small herd (White Mountains) maintained genetic differentiation despite rut overlap with Fortymile. Our data reveal that some herds with different ecological and behavioral attributes are demographically independent but nonetheless genetically connected. Thus, we suggest that managing caribou for an appropriate level of genetic connectivity, while also supporting herd persistence, will be essential to conserve caribou genetic diversity in the region.</p>
Collecting baleen whale blow samples by drone: a minimally intrusive tool for conservation genetics
<p>In coastal British Columbia, Canada, marine megafauna such as humpback whales (<em>Megaptera novaeangliae</em>) and fin whales (<em>Balaenoptera physalus velifera</em>) have been subject to a history of exploitation and near extirpation. While their populations have been in recovery, significant threats are posed by proposed natural resource ventures in this region, in addition to the compounding effects of increasingly severe marine heatwaves. Genetic tools play a vital role in informing conservation efforts, but the associated collection of tissue biopsy samples can be challenging for the investigators and disruptive to the ongoing behaviour of the targeted whales. Here we evaluate a minimally intrusive approach based on collecting exhaled breath condensate, or respiratory 'blow' samples, from baleen whales using an unoccupied aerial system (UAS), within Gitga'at First Nation territory for conservation genetics. Minimal behavioural responses to the sampling technique were observed, with no response detected 87% of the time (of 112 UAS deployments). DNA from whale blow (<em>n</em> = 88 samples) was extracted, and DNA profiles consisting of 10 nuclear microsatellite loci, sex identification, and mitochondrial (mt) DNA haplotypes, were constructed. An average of 7.5 microsatellite loci per individual were successfully genotyped. The success rates for mtDNA and sex assignment were 80% and 89% respectively. Thus, this minimally intrusive sampling method can be used to describe genetic diversity and generate genetic profiles for individual identification. The results of this research show the potential of UAS-collected whale blow for conservation genetics from a remote location.</p>
Data from: Genetic diversity and divergence in the fountain darter (Etheostoma fonticola): implications for conservation of an endangered species
<p>The endangered fountain darter Etheostoma fonticola is found only in the Comal and San Marcos rivers in the Guadalupe River basin in central Texas, USA. Comal River fountain darters were believed to be extir- pated following a severe drought in the 1950s and were reintroduced in the early 1970s using 457 darters from the San Marcos River. In this study we used 23 microsatellite loci to describe and evaluate the genetic diversity, population structure and effective population size (Ne) of fountain darters. We also evaluated the genetic effect of the Comal River reintroduction and the influence of low-head dams (dams) on dispersal in both rivers. Bayesian analysis of individual genotypes and Analysis of Molecular Variation supported two distinct populations concordant with the two rivers. Estimates of Ne were much smaller (<10 %) than census size (Nc) in both rivers but did not indicate the populations are at risk of an immediate and rapid loss of genetic diversity. Coalescent-based estimates of the genetically effective number of founders (Nf) for the Comal River averaged about 49 darters and, together with the indices of genetic diversity and the bottleneck test (heterozygosity excess) results, were consistent with a founder event following the reintroduction in the Comal River. Finally, our results regarding the influence of dams on fountain darter dispersal were equivocal and did not support a conclusion. We recommend this issue be examined further as part of the fountain darter recovery program.</p>
Modelling the genetic aetiology of complex disease: human-mouse conservation of noncoding features and disease-associated loci
<p>Understanding the genetic aetiology of loci associated with disease is crucial for developing preventative measures and effective treatments. Mouse models are used extensively to understand human pathobiology and mechanistic functions of disease-associated loci. However, the utility of mouse models is limited by evolutionary divergence in transcription regulation for pathways of interest. Here, we summarise the conservation of genomic (exonic and multi-cell regulatory) features and complex disease associated variant sites between humans and mice. Our results highlight the importance of understanding evolutionary divergence in transcription regulation when interpreting functional studies using mice as models for human disease variants.</p>
Data accessibility for conservation implications of genetic structure in the narrowest endemic quillwort from the Eastern Amazon
<p>The quillwort <em>Isoetes cangae</em> is a critically endangered species occurring in a single lake in Serra dos Carajás, Eastern Amazon. Low genetic diversity and small effective population sizes (N<sub>e</sub>) is expected for narrow endemic species (NES). Here, we evaluated genetic diversity, population structure, and N<sub>e</sub> of <em>I. cangae </em>to provide information for conservation programs. Conservation biology studies centered in a single‐species show some limitations but they are still useful considering the limited time and resources available for the protection of species at risk of extinction. Our analyses were based on 55 individuals collected from the Amendoim lake and 35,638 neutral SNPs. Our results indicated a single panmictic population, moderate levels of genetic diversity, and effective population size (N<sub>e</sub>) in the order of thousands, contrasting the expected for NES. Negative FIS values were also found, suggesting that <em>I. cangae</em> is not under risk of inbreeding depression. Our findings imply that <em>I. cangae </em>contains enough genetic diversity to ensure evolutionary potential, all individuals should be treated as one demographic unit.</p>
Data from: Conservation and convergence of genetic architecture in the adaptive radiation of anolis lizards
<p>The G matrix, which quantifies the genetic architecture of traits, is often viewed as an evolutionary constraint. However, G can evolve in response to selection and may also be viewed as a product of adaptive evolution. Convergent evolution of G in similar environments would suggest that G evolves adaptively, but it is difficult to disentangle such effects from phylogeny. Here, we use the adaptive radiation of Anolis lizards to ask whether convergence of G accompanies the repeated evolution of habitat specialists, or ecomorphs, across the Greater Antilles. We measured G in seven species representing three ecomorphs (trunk-crown, trunk-ground, and grass-bush). We found that the overall structure of G does not converge. Instead, the structure of G is well conserved and displays a phylogenetic signal consistent with Brownian motion. However, several elements of G showed signatures of convergence, indicating that some aspects of genetic architecture have been shaped by selection. Most notably, genetic correlations between limb traits and body traits were weaker in long-legged trunk-ground species, suggesting effects of recurrent selection on limb length. Our results demonstrate that common selection pressures may have subtle but consistent effects on the evolution of G, even as its overall structure remains conserved.</p>
Fig. 1 in Chloroplast genome of the conserved Aster altaicus var. uchiyamae B2015-0044 as genetic barcode
Fig. 1. Plastid genomic map of Aster altaicus var. uchiyamae.
Genetic variability, management, and conservation implications of the critically endangered Brazilian pitviper Bothrops insularis
<p>Information on demographic, genetic, and environmental parameters of wild and captive animal populations has proven to be crucial to conservation programs and strategies. Genetic approaches in conservation programs of Brazilian snakes remain scarce despite their importance for critically endangered species, such as <i>Bothrops insularis</i>, the golden lancehead, which is endemic to Ilha da Queimada Grande, coast of São Paulo State, Brazil. This study aims to (i) characterize the genetic diversity of <i>ex-situ</i> and <i>in-situ</i> populations of <i>B. insularis</i> using heterologous microsatellites; (ii) investigate genetic structure among and within these populations; and (iii) provide data for the conservation program of the species. Twelve informative microsatellites obtained from three species of the <i>B. neuwiedi</i> group were used to access genetic diversity indexes of <i>ex-situ</i> and <i>in-situ</i> populations. Low-to-medium genetic diversity parameters were found. Both populations showed low — albeit significant — values of system of mating inbreeding coefficient, whereas only the <i>in-situ</i> population showed a significant value of pedigree inbreeding coefficient. Significant values of genetic differentiation indexes suggest a small differentiation between the two populations. Discriminant analysis of principal components (DAPC) recovered five clusters. No geographic relationship was found in the island, suggesting the occurrence of gene flow. Also, our data allowed the establishment of six preferential breeding couples, aiming to minimize inbreeding and elucidate uncertain parental relationships in the captive population. In a conservation perspective, continuous monitoring of both populations is demanded: it involves the incorporation of new individuals from the island into the captive population to avoid inbreeding and to achieve the recommended allelic similarity between the two populations. At last, we recommend that the genetic data support researches as a base to maintain a viable and healthy captive population, highly genetically similar to the <i>in-situ</i> one, which is crucial for considering a reintroduction process into the island.</p>
Male diversity matters: Genetic structuring of insular male date palm (Phoenix dactylifera L.) revealed valuable breeding and conservation resources
Most male date palms available for pollinating different female cultivars have mainly originated from seed propagation resulting in many different local males that represent a source of genetic diversity. Favorable fruit production is related to quality of pollen and its compatibility with a certain female variety. Therefore, the genetic characterization of the male pollen as a superior one for each female cultivar should be the first step to establish an intensive program to produce superior males through different procedures. In this study, the genetic diversity and population structure of 72 male date palm accessions were investigated using 15 microsatellite loci. A total number of 125 alleles was detected with an average of 8.33 alleles per locus. Bayesian model-based clustering analysis indicated the presence of two differentiated endemic male date palm genetic clusters, continental and insular, with the presence of introduced accessions originating from the Middle East. The diversity analysis in the insular region of Tunisia, which had never been performed before, revealed that this germplasm enclosed valuable endemic resources supporting the hypothesis of the presence of wild material. These findings are crucial for identifying interesting genotypes that can be integrated into international coordinated actions of Phoenix dactylifera L. breeding programs as well as for the protection and conservation of valuable resources.
Genetic restoration of black rhinoceroses in South Africa: conservation implications
<p>Globally, wildlife populations are becoming increasingly small and isolated. Both processes contribute to an elevated risk of extinction, notably due to genetic factors related to inbreeding depression and a loss of adaptive potential. Wildlife translocation is a valuable conservation tool to reintroduce species to previously occupied areas, or augment existing populations with genetically divergent animals, thereby improving the viability of endangered populations. However, understanding the genetic implications of mixing gene pools is key to avoid the risk of outbreeding depression, and to maximise translocation effectiveness. In this study we used mitochondrial and microsatellite DNA collected from 110 black rhinoceroses (Diceros bicornis minor) in Kruger National Park, South Africa, to determine levels of genetic diversity, inbreeding and relatedness. We compared this diversity with the two source populations (KwaZulu-Natal, South Africa and Zambezi River, Zimbabwe) using data from previously published studies, and assessed changes in the relative contribution of source lineages since their reintroduction in the 1970s. Our results show that Kruger's black rhinoceroses are genetically more diverse than those from KwaZulu-Natal, with levels closer to those from the Zambezi Valley. Furthermore, our findings indicate a relative increase in the Zimbabwean lineage since reintroduction, suggesting a possible selective advantage. From a conservation perspective, our results demonstrate the benefits of mixing multiple source populations to restore gene flow, improve genetic diversity and thereby help protect small, isolated populations from extinction.</p>
Supplementary data for "Testing the efficacy of different molecular tools for parasite conservation genetics: a case study using horsehair worms (Phylum Nematomorpha)"
<p>Supplementary data for "Testing the efficacy of different molecular tools for parasite conservation genetics: a case study using horsehair worms (Phylum Nematomorpha)"</p> <p>alignments: alignments used for BEAST ("bayes") and PopArt ("popart"). The "popart" folder also has a traits file per each species.</p> <p>bayesian_plots: TSVs ("tsv") and PDF files ("ogs") generated by BEAST. The "tsv" folder also has the scripts for plotting the results in R.</p> <p>easysfs: scripts, population file and results from the VCF to SFS conversione done by easySFS.</p> <p>fineRADstructure: fineRADstructure input files and output PDF plots ("plots") for <em>C. formosanus</em> ipyrad and Stacks ("stacks") data. </p> <p>logs: logs for ipyrad, ModelTest, PGDspider, PopArt ("popart") and Stacks ("stacks"). The "popart" folder also have the generated networks in a TXT file. The "stacks" folder also has ODS files for calculating the amount of loci per each M/n fixed value.</p> <p>snapclust: STR files used with R for snapclust. Scripts included.</p> <p>stairway_plot: input (blueprint files) and outputs for Stairway Plot 2 analyses. The <em>C. formosanus</em> folder ("chordodes") also has scripts for R plotting.</p> <p>vcfs: VCF and HDF5 files used in this study. Also scripts for filtering/converting data and plotting the PCA with ipyrad (activate python first!) for <em>C. formosanus</em>.</p> <p>"acutogordius" = <em>A. taiwanensis</em><br> "chordodes" = <em>C. formosanus</em><br> "gordius" = <em>G. chiashanus</em></p>
Phylogeography and genetic variation in Western Jacob's ladder (Polemonium occidentale) provide insights into the origin and conservation of rare species in the Great Lakes region
<p>The perennial herb Western Jacob's Ladder (<em>Polemonium</em> <em>occidentale</em>, Polemoniaceae) is widespread in the mountains of western North America but reappears as a disjunct in the Great Lakes Region in Minnesota and Wisconsin, USA as the narrow endemic<em> P. occidentale </em>subsp. <em>lacustre</em>. This distribution is shown by a diverse assemblage of angiosperms. It has been hypothesized that these species became isolated just after the Last Glacial Maximum, but this has not been tested. Additionally, the genetic diversity and population connectivity of the endemic Great Lakes flora has been understudied, with important conservation implications. Using Genotyping-by-sequencing, we examined the relationship of <em>P</em>. <em>occidentale</em> subsp. <em>lacustre</em> to its closest relatives, relationships among all known populations, and genetic diversity within these populations. <em>Polemonium</em> <em>occidentale</em> subsp. <em>lacustre</em> represents an isolated, unique lineage that diverged from its closest relatives 1.3 ma and arrived in the Great Lakes Region by at least 38 ka. Nearly all extant populations diverged prior to the Last Glacial Maximum, are largely genetically distinct, and show relatively little within-population genetic diversity. Clonality may mitigate reduction in diversity due to drift. Mixed population signal between Wisconsin and some Minnesota populations may be due to gene flow during the Late Pleistocene. While populations of <em>Polemonium</em> <em>occidentale</em> subsp. <em>lacustre</em> may be relictual from a now-extinct western relative, it is best treated as a distinct species. Conservation efforts should focus more on ensuring that current populations remain rather than maintaining large population sizes across a few populations. However, encouraging habitat heterogeneity may accomplish both simultaneously.</p>
Data and R scripts from: Using conservation genetics to prioritise management options for an endangered songbird
<p>Genetic data can be highly informative for answering questions relevant to practical conservation efforts but remain one of the most neglected aspects of species recovery plans. Framing genetic questions with reference to practical and tractable conservation objectives can help bypass this limitation of the application of genetics in conservation. Using a single-nucleotide polymorphism dataset from reduced-representation sequencing (DArTSeq), we conducted a genetic assessment of remnant populations of the endangered forty-spotted pardalote (<em>Pardalotus</em> <em>quadragintus</em>), a songbird endemic to Tasmania, Australia. Our objectives were to inform strategies for conservation of genetic diversity in the species and estimate effective population sizes and patterns of inter-population movement to identify management units relevant to population conservation and habitat restoration. We show population genetic structure and identify two small populations on mainland Tasmania as 'satellites' of larger Bruny Island populations connected by migration. Our data identify management units for conservation objectives relating to genetic diversity and habitat restoration. Although our results do not indicate the immediate need to genetically manage populations, the small effective population sizes we estimated for some populations indicate that they are vulnerable to genetic drift, highlighting the urgent need to implement habitat restoration to increase population size and to conduct genetic monitoring. We discuss how our genetic assessment can be used to inform management interventions for the forty-spotted pardalote, and show that by assessing contemporary genetic aspects, valuable information for conservation planning and decision-making can be produced to guide actions that account for genetic diversity and increase chances of recovery in species of conservation concern.</p>
Genomic tools for comparative conservation genetics among three recently diverged stag beetles (Lucanus, Lucanidae)
<p>We are witnessing a rapid decline in global biodiversity. International protocols and local conservation laws have been installed to counter such an unprecedented rate of decline. However, quantitatively evaluating how much biodiversity has been lost due to climatic and anthropogenic effects and how much biodiversity has been restored due to conservation efforts remain challenging. We applied a comparative conservation genomic approach to statistically and quantitatively address these questions using three geographical taxa from a stag beetle species complex. We found that the three sky-island taxa formed three independently evolving units without detectable post-divergence gene flow; furthermore, the three taxa, which have been divergent from each other since the mid-Pleistocene, have experienced episodes of demographic decline in the past. More importantly, even though idiosyncratic anthropogenic exploitations have been hypothesized to impact the recent demographic history (< 100 years) differently, we found a shared pattern of continuous decline in effective population size among the three geographical taxa. We argue that future empirical studies should include more taxa, in addition to the focal species, that may or may not be affected by the focal historical events to avoid making biased conservation plans.</p>
Repeated mapped tree inventory data in a tree plantation for pedunculate oak (Quercus robur) genetic conservation
<p>We performed replicated, repeated mapped tree inventory measures (x,y, height, diameter, vitality, etc.) to allow analysis of the spatial and temporal structure in 1 ha planted pedunculate oak (Quercus robur) stand established in 2003 to resemble the oak-hornnbeam forests for genetic conservation purposes in Po Valley (Foresta Carpaneta). Two inventories were carried out in 2009 and 2019. The use of replicated, repeated, and mapped tree measures allows the examination of true changes in spatial pattern processes through time in this forest type.</p>
Data from: Patterns of intra- and inter-population genetic diversity in Alaskan coho salmon: implications for conservation
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Y-SNP data for Y-chromosome genetic characterization of Tibetan antelope supporting conservation efforts
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Data from: Genome-wide diversity in lowland and highland maize landraces from southern South America: Population genetics insights to assist conservation
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Data from: Behavioral syndromes shape evolutionary trajectories via conserved genetic architecture
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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.