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15,277 results for “GENETICS”
Data from: Evaluating otter reintroduction outcomes using genetic spatial capture-recapture modified for dendritic networks
<p>River otters (Lontra canadensis) were extirpated from New Mexico by the 1950s. A limited reintroduction occurred during 2008–2010 in which 33 otters sourced from Washington (WA) were translocated to the Upper Rio Grande Basin (URG) of New Mexico. We conducted a noninvasive genetic capture-recapture survey during the winter of 2018 by collecting fecal DNA samples from river otter scats found at latrines in the URG dendritic network of perennial waterways. Our objectives were to: 1) estimate genetic diversity and effective population size; 2) genetic divergence from the WA source population and potential connectivity with regionally proximal populations; 3) spatially explicit population density and size; and 4) population growth rate since the founder event. Between February and April 2018, we collected 1,184 fecal DNA samples from 622 individual scats at 20 latrines; genotyping was attempted at 10 otter-specific microsatellite loci for a subsample of 543 samples. A bottlenecking founder effect was strongly supported, which, combined with genetic drift, reduced genetic diversity and effective population size by 20–26% and 106–170%, respectively, compared with the WA source population. Estimated population density from spatial capture-recapture models was 0.23–0.28 otter/km of waterway, or 1 otter/3.57–4.35 km of waterway, corresponding to a total population size of 83–100 otters across 359 km of the perennial dendritic network from La Mesilla, New Mexico to Alamosa National Wildlife Refuge, Colorado. Estimated average annual population growth rate since the founder event was 1.12–1.15/year. Despite successful population establishment, the URG river otter population remains small, is genetically degraded, and does not yet meet the criteria for long-term reintroduction success. Projections suggested that the population could reach the recommended minimum viable population size of ≥400 otters by the years 2030–2033, though sufficient habitat may not exist in the URG Basin to support that many otters. </p>
Conservation genetics of an island-endemic lizard: low Ne and the critical role of intermediate temperatures for genetic connectivity
<p>Island populations are at higher risk of extinction than mainland populations. Therefore, understanding the factors that facilitate connectivity is particularly pressing for the conservation of island taxa. <i>Sceloporus occidentalis becki</i>, the Island Fence Lizard, is an endemic taxon restricted to the Northern Channel Islands, part of a nearshore archipelago in Southern California, USA. Since the Last Glacial Maximum, fence lizard habitat on the Northern Channel Islands has decreased with rising sea levels and increasing temperatures that have reduced the availability of woody vegetation. More recently, the introduction (and subsequent removal) of invasive ungulates over the last 170 years and recovery of vegetation has resulted in further dramatic habitat modification. Given the potential for genetic bottlenecks, the history of habitat alteration, and topographic and landscape complexity, we used landscape and population genetic approaches to characterize patterns of genetic diversity and structure of Island Fence Lizards on Santa Cruz Island, the largest of the Northern Channel Islands. Our analyses revealed shallow population structure across the island, low effective population size (<i>N<sub>e</sub></i> = ~200), and evidence for a recent genetic bottleneck. Landscape genetic analyses showed that connectivity is facilitated by tree canopy cover and shrubland, as well as by intermediate temperatures, emphasizing the importance of woody vegetation and habitats with variable thermal regimes as the climate warms. Combined, these population and landscape genetic analyses suggest that the Island Fence Lizard is of greater conservation concern than currently appreciated, and increased conservation management focus is warranted for this island endemic.</p>
Holocene climate changes explain the spatial pattern in genetic diversity in populations of Cyperus papyrus from Southeast Africa wetlands
<p>Wetlands are one of the most threatened ecosystems in the world because more than 70% of the area worldwide has been lost since 1900. Wetland plant species rely greatly on water for seeds and propagules, which may lead to a downstream unidirectional dispersal and accumulation of genetic diversity downstream. However, several species show no support for unidirectional genetic diversity, revealing the complexity of population dynamics and gene flow in wetlands. Here, we used microsatellite loci to address how the past demographic dynamics shaped the contemporary spatial pattern in genetic diversity and population structure of <em>Cyperus papyrus</em> in wetlands of Southeast Africa. Using spatially explicit analysis and coalescent modelling we found no support for unidirectional dispersal. Instead, we found higher genetic diversity in populations upstream than downstream in the river basin. We also found high admixture among populations, most likely due to connections between adjacent river basins during sporadic floods, and ongoing gene flow due to bird-mediated seed dispersal. Our results suggest stepping-stone migration due to strong isolation-by-distance, but not necessarily unidirectional. Moreover, the past demographic dynamics in the Holocene shaped the current pattern of genetic diversity and structure, leading to higher genetic diversity in populations upstream of the Zambezi river basin. Our results also point to the very low genetic diversity of <em>C</em>. <em>papyrus</em> populations in Southeast Africa and the need for management and conservation strategies to guarantee the long-term persistence of the species in the region.</p>
Data from: Continuous inbreeding affects genetic variation, phenology and reproductive strategy in ex situ cultivated Digitalis lutea
<p>Data from several experiments studying population differences between a wild and a botanic garden population and effects of different hand-pollination treatments on various traits of the short-lived perennial plant <em>Digitalis lutea</em>. Separate spreadsheets contain data on 1) genetic variation using ISSR markers, 2) effects of pollination treatments on seed number and seed mass, 3) differences in germination, 4) various traits studied in a common garden experiment, 5) effects of population and pollination treatments on pollinator visitation.</p> <p>See publication in American Journal of Botany (2022) for details.</p> <p><strong>Abstract:</strong></p> <p><strong>Premise</strong>: Ex situ cultivation is important for plant conservation, but cultivation in small populations may result in genetic changes by drift, inbreeding or unconscious selection. Repeated inbreeding potentially influences not only plant fitness, but also floral traits and interactions with pollinators, which has not yet been studied in an ex situ context.</p> <p><strong>Methods</strong>: We studied the molecular genetic variation of <em>Digitalis lutea</em> L. from a botanic garden population cultivated for 30 years, a frozen seed bank conserving the original genetic structure, and two current wild populations including the source population. In a common garden we studied the effects of experimental inbreeding and between-population crosses on performance, reproductive traits and flower visitation of plants from the garden and a wild population.</p> <p><strong>Results</strong>: Significant genetic differentiation was found between the garden population and the wild population from which the seeds had originally been gathered. After experimental selfing, inbreeding depression was only found in germination and leaf size of plants from the wild population, indicating a history of inbreeding in the smaller garden population. Moreover, garden plants flowered earlier and showed floral traits related to selfing, whereas wild plants showed traits related to attracting pollinators. Bumblebees visited more flowers of outbred than inbred plants and of wild than garden plants.</p> <p><strong>Conclusions</strong>: Our case study suggests that high levels of inbreeding during ex situ cultivation can influence reproductive traits and thus interactions with pollinators. Together with the effects of genetic erosion and unconscious selection this may affect the success of reintroductions into natural habitats.</p> <p> </p>
FIGURE 4 in Genetic diversity of the regionally endangered Chinese ricefish (Oryzias sinensis) in Taiwan, with comments on its conservation status
FIGURE 4. Molecular phylogenetic tree of Chinese ricefish in Taiwan based on combined COI and D-loop sequences constructed with the maximum likelihood method. Bootstrap values less than 50 are not shown.
FIGURE 2 in Genetic diversity of the regionally endangered Chinese ricefish (Oryzias sinensis) in Taiwan, with comments on its conservation status
FIGURE 2. Molecular phylogenetic tree of Chinese ricefish in Taiwan based on the D-loop sequence constructed with the maximum likelihood method (bootstrap values less than 50 not shown). The sample size of each haplotype is given in parentheses after the OTU. Haplotypes from Tzeng et al. (2006) are shown with GenBank accession numbers.
FIGURE 1 in Genetic diversity of the regionally endangered Chinese ricefish (Oryzias sinensis) in Taiwan, with comments on its conservation status
FIGURE 1. Sampling sites in northern Taiwan. Detailed localities and rivers are shown in the upper right image.
FIGRUE 3 in Genetic diversity of the regionally endangered Chinese ricefish (Oryzias sinensis) in Taiwan, with comments on its conservation status
FIGRUE 3. Molecular phylogenetic tree of Chinese ricefish in Taiwan based on COI sequences constructed with the maximum likelihood method. Bootstrap values less than 50 are not shown. Two haplotypes of Chinese ricefish from South Korea from Kim et al. (unpublished data, 2016) are shown with GenBank accession numbers.
Data from: Breeding system and geospatial variation shape the population genetics of Triodanis perfoliata
<p><span>Both intrinsic and extrinsic forces work together to shape connectivity and genetic variation in populations across the landscape. Here we explored how geography, breeding system traits, and environmental factors influence the population genetic patterns of <em>Triodanis perfoliata</em>, a widespread mix-mating annual plant in the contiguous US. By integrating population genomic data with spatial analyses and modeling the relationship between breeding system and genetic diversity, we illustrate the complex ways in which these forces shape genetic variation. Specifically, we used 4,705 single nucleotide polymorphisms to assess genetic diversity, structure, and evolutionary history among 18 populations. Populations with more obligately selfing flowers harbored less genetic diversity (π: R<sup>2</sup> = 0.63, P = 0.01, n = 9 populations), and we found significant population structuring (F<sub>ST</sub> = 0.48). Both geographic isolation and environmental factors played significant roles in predicting the observed genetic diversity: we found that corridors of suitable environment appear to facilitate gene flow between populations, and that environmental resistance is correlated with increased genetic distance between populations. Last, we integrated our genetic results with species distribution modeling to assess likely patterns of connectivity among our study populations. Our landscape and evolutionary genetic results suggest that <em>T. perfoliata</em> experienced a complex demographic and evolutionary history, particularly in the center of its distribution. As such, there is no singular mechanism driving this species' evolution. Together, our analyses support the hypothesis that breeding system, geography, and environmental variables shape the patterns of diversity and connectivity of <em>T. perfoliata</em> in the US. </span></p>
Predation patterns on the tundra – genetic barcoding of scats from two sympatric fox species
<p>In the Arctic tundra, climate-induced emergence of the red fox (Vulpes vulpes), a competitor to the Arctic fox (Vulpes lagopus), is predicted to influence predation patterns of both fox mesopredators. In this study, we i) identified predator species from scats through an established barcoding approach, and ii) explored the use of a cheap, quick barcoding method of fox feces (n = 103). We investigated differences in diet between the red fox (predicted generalist predator) and Arctic fox (predicted specialist predator) over two years with varying prey abundance. We amplified short DNA fragments (< 200 bp) from small rodents, birds and hares. For both predators, there was a high frequency of occurrence of rodents (38 - 69 %) identifying them as primary prey species and birds as secondary prey species (13-31%). This demonstrates the strength of a straightforward DNA barcoding method for dietary analyses in sympatric fox predators, with species-level resolution of prey. Barcoding is a promising tool for future dietary studies, however a few methodological improvements, along with extended sampling, are needed for a more complete assessment of fox predation patterns. Integrating high-resolution dietary analyses has great potential to enhance our understanding of predation patterns in Arctic tundra communities.</p>
Fig. 7 in Broadly Distributed but Genetically Fragmented: Demographic Consequences of Pleistocene Climatic Oscillations in a Common Iberian Grasshopper
Fig. 7. Demographic history of the studied populations of Pantel's grasshopper (Omocestus panteli) inferred using STAIRWAY PLOT. Panels show the median of effective population size (N) over time, estimated assuming a mutation rate of 2.8 × 10−9 and a 1-yr generation time (both axes in a logarithmic scale). Vertical e dashed lines indicate the Last Glacial Maximum (LGM; ca. 21 ka). Number of polymorphic SNPs used to calculate the site frequency spectrum (SFS) indicated in parentheses. Colors correspond to the main genetic cluster at which populations were predominantly assigned according to STRUCTURE analyses for K = 6 (Fig. 3). Population codes as described inTable 1.
Fig. 6 in Broadly Distributed but Genetically Fragmented: Demographic Consequences of Pleistocene Climatic Oscillations in a Common Iberian Grasshopper
Fig. 6. Relationships (A) between genetic diversity (π) and latitude and (B) between long-term effective population size (Ne) and environmental suitability during the last glacial maximum (LGM) inferred by projecting the species-specific environmental niche model (ENM) to LGM bioclimatic conditions under the CCSM4 general atmospheric circulation model.
Fig. 5 in Broadly Distributed but Genetically Fragmented: Demographic Consequences of Pleistocene Climatic Oscillations in a Common Iberian Grasshopper
Fig. 5. Relationship between genetic differentiation (FST) and resistance distances based on environmental suitability during the LGM inferred by projecting the species-specific environmental niche model (ENM) to LGM bioclimatic conditions under the CCSM4 general atmospheric circulation model.
Fig. 3 in Broadly Distributed but Genetically Fragmented: Demographic Consequences of Pleistocene Climatic Oscillations in a Common Iberian Grasshopper
Fig. 3. Results of genetic assignments for populations of the Pantel's grasshopper (Omocestus panteli) based on the Bayesian method implemented in the program STRUCTURE and a discriminant analysis of principal components (DAPC). Each individual is represented by a vertical bar, which is partitioned into K-colored segments showing the individual's probability of belonging to the cluster with that color.Thin vertical black lines separate individuals from different populations. Analyses are based on a dataset of 14,454 SNPs. Population codes as described inTable 1.
Fig. 1 in Broadly Distributed but Genetically Fragmented: Demographic Consequences of Pleistocene Climatic Oscillations in a Common Iberian Grasshopper
Fig. 1. (A) Map showing the geographical location of sampling populations of Pantel's grasshopper (Omocestus panteli), with dot colors indicating their respective levels of genetic diversity (π, in red to blue scale). Dot size is proportional to the number of genotyped individuals (Table 1). (B–D) Projections of the species-specific environmental niche model (ENM) for (B) present and (C–D) last glacial maximum (LGM) bioclimatic conditions under the (C) CCSM4 and (D) MIROC-ESM general atmospheric circulation models. Map in the present shows occurrence points (crosses) used for ENM. Population codes as described in Table 1.
Figure 3 in Cryptic lineages, cryptic barriers: historical seascapes and oceanic fronts drive genetic diversity in supralittoral rockpool beetles (Coleoptera: Hydraenidae)
Figure 3. Haplotype networks for COI and wingless for Ochthebius (Ochthebius) quadricollis. Colours represent the main geographic areas indicated in the legend.
Figure 2. Calibrated phylogenetic tree obtained with BEAST v.1.10.4 in Cryptic lineages, cryptic barriers: historical seascapes and oceanic fronts drive genetic diversity in supralittoral rockpool beetles (Coleoptera: Hydraenidae)
Figure 2. Calibrated phylogenetic tree obtained with BEAST v.1.10.4 of Ochthebius with focus on subgenus Cobalius (purple shade) and quadricollis species group (green shade) (former subgenus 'Calobius'). Numbers at nodes represent posterior probabilities, and 95% highest posterior density are given in blue horizontal rectangles. Calibrations points used in analysis are specified by grey dots.
Figure 5 in Cryptic lineages, cryptic barriers: historical seascapes and oceanic fronts drive genetic diversity in supralittoral rockpool beetles (Coleoptera: Hydraenidae)
Figure 5. Haplotype networks for COI and wingless for Ochthebius (Cobalius) lejolisii. Colours represent the main geographic areas indicated in the legend.
Figure 1 in Cryptic lineages, cryptic barriers: historical seascapes and oceanic fronts drive genetic diversity in supralittoral rockpool beetles (Coleoptera: Hydraenidae)
Figure 1. Distribution of sampling localities 1-57 (as listed in Table 1) and main surface marine currents and potential geographic barriers to dispersal (inset top-right).
Figure 4 in Cryptic lineages, cryptic barriers: historical seascapes and oceanic fronts drive genetic diversity in supralittoral rockpool beetles (Coleoptera: Hydraenidae)
Figure 4. Haplotype networks for COI and wingless for Ochthebius (Cobalius) subinteger. Colours represent the main geographic areas indicated in the legend.
ScienceDex guides
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
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.