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6 results for “Neutral and adaptive loci”
Neutral and adaptive loci reveal fine-scale population structure in Eleginops maclovinus from North Patagonia
<p>Patagonia is an understudied area, especially when it comes to population genomic studies with relevance to fishery management. However, the dynamic and heterogeneous landscape in this area can harbor important but cryptic genetic population structure. Once such information is revealed, it can be integrated into the management of infrequently investigated species. <i>Eleginops maclovinus</i> is a protandrous hermaphrodite species with economic importance for local communities that is currently managed as a single genetic unit. In this study, we sampled five locations distributed across a salinity cline from Northern Patagonia to investigate the genetic population structure of <i>E</i>. <i>maclovinus</i>. We use Restriction-site Associated DNA (RAD) sequencing and outlier tests to obtain 11,712 neutral, 338 adaptive loci, and 78 loci associated to environmental variables. We identified a spatial pattern of structuration with gene flow and spatial selection by environmental association. Neutral and adaptive loci showed two and three genetic groups, respectively. The effective population sizes estimated ranged from 572 to 14,454 and were influenced more by locality than salinity cline. We found loci putatively associated with salinity suggesting that salinity may act as a selective driver in <i>E</i>. <i>maclovinus</i> populations. These results suggest a complex interaction between genetic drift, geneflow, and natural selection in this area. Our findings suggest that at least two to three genetic units exist in this area, and the information should be integrated into the management of this species. We discuss the significance of these results for fishery management and suggest future directions to improve our understanding of how <i>E</i>. <i>maclovinus</i> is adapted to the dynamic waters of Northern Patagonia.</p>
Weak coupling among barrier loci and waves of neutral and adaptive introgression across an expanding hybrid zone
<p>Hybridization can serve as an evolutionary stimulus, but we have little understanding of introgression at early stages of hybrid zone formation. We analyze reproductive isolation and introgression between a range-limited and a widespread species. Reproductive barriers are estimated based on differences in flowering time, ecogeographic distributions, and seed set from crosses. We find an asymmetrical mating barrier due to cytonuclear incompatibility that is consistent with observed clusters of coincident and concordant tension zone clines (barrier loci) for mtDNA haplotypes and nuclear SNPs. These groups of concordant clines are spread across the hybrid zone, resulting in weak coupling among barrier loci and extensive introgression. Neutral clines had nearly equal introgression into both species' ranges, while putative cases of adaptive introgression had exceptionally wide clines with centers shifted towards one species. Analyses of cline shape indicate that secondary contact was initiated within the last 800 generations with the per-generation dispersal between 200 and 400 meters, and provide some of the first estimates of the strength of selection required to account for observed levels of adaptive introgression. The weak species boundary between these species appears to be in early stages of dissolution, and ultimately will precipitate genetic swamping of the range-limited species.</p>
Weak coupling among barrier loci and waves of neutral and adaptive introgression across an expanding hybrid zone
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Neutral and adaptive loci reveal fine-scale population structure in Eleginops maclovinus from North Patagonia
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Data from: Genetic depletion at adaptive but not neutral loci in an endangered bird species
Many endangered species suffer from the loss of genetic diversity, but some populations may be able to thrive even if genetically depleted. To investigate the underlying genetic processes of population bottlenecks, we apply an innovative approach for assessing genetic diversity in the last known population of the endangered Pale-headed Brushfinch (Atlapetes pallidiceps) in Ecuador. First, we measure genetic diversity at eleven neutral microsatellite loci and adaptive SNP variation in five Toll-like receptor (TLR) immune system genes. Bottleneck tests confirm genetic drift as the main force shaping genetic diversity in this species and indicate a 99 % reduction in population size dating back several hundred years. Second, we compare contemporary microsatellite diversity with historic museum samples of A. pallidiceps, finding no change in genetic diversity. Third, we compare genetic diversity in the Pale-headed Brushfinch with two co-occurring-related brushfinch species (Atlapetes latinuchus, Buarremon torquatus), finding a reduction of up to 91% diversity in the immune system genes but not in microsatellites. High TLR diversity is linked to decreased survival probabilities in A. pallidiceps. Low TLR diversity is thus probably an adaptation to the specific selection regime within its currently very restricted distribution (approximately 200 ha), but could severely restrict the adaptive potential of the species in the long run. Our study illustrates the importance of investigating both neutral and adaptive markers to assess the effect of population bottlenecks and for recommending specific management plans in endangered species.
Data from: Genetic depletion at adaptive but not neutral loci in an endangered bird species
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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.
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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.