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325 results for “Landscape genetics”
Data from: Absence of genetic isolation across highly fragmented landscape in the ant Temnothorax nigriceps
<p><strong>This README accompanies data_genotyping.txt</strong></p> <p> </p> <p><strong><em>Associate publication : </em></strong></p> <p>Absence of genetic isolation across highly fragmented landscape in the ant Temnothorax nigriceps</p> <p>M. Cordonnier<sup>a</sup>, D. Felten<sup>a</sup>, A. Trindl<sup>a</sup>, J. Heinze<sup>a</sup>*, A. Bernadou<sup>a</sup>*</p> <p><sup>a</sup>Lehrstuhl für Zoologie / Evolutionsbiologie, Univ. Regensburg</p> <p>*Equal contribution</p> <p> </p> <p>****************************** CONTENTS *******************************</p> <p>The data can be readily imported in any statistical package or spreadsheet program. Please, contact me if you need the file formatted in other ways.</p> <p> </p> <p>This file includes a description of the variables.</p> <p>***********************************************************************</p> <p>Variable names and descriptions</p> <p> </p> <p><strong>Sample:</strong> ID of the sampled nest</p> <p><strong>Location:</strong> Population of the sampled nest</p> <p> </p> <p><strong>List of genotypes </strong></p> <p>Microsatellite primers used in the study</p> <table> <tbody> <tr> <td> </td> <td> <p>Annealing temperature [°C]</p> </td> <td> <p>Orientation</p> </td> <td> <p>Sequence of primers</p> </td> </tr> <tr> <td> <p>LX GT218</p> </td> <td> <p>57</p> </td> <td> <p>Forward</p> </td> <td> <p>5’-GTTCTTGCGCGGATGCATAC-3’</p> </td> </tr> <tr> <td> <p>Reverse</p> </td> <td> <p>5’-TGTACTCGCGTGTCTATCGG-3’</p> </td> </tr> <tr> <td> <p>Ant3993</p> </td> <td> <p>57</p> </td> <td> <p>Forward</p> </td> <td> <p>5’-TGATCCGCTCTTAAAATTTAGATGGA-3’</p> </td> </tr> <tr> <td> <p>Reverse</p> </td> <td> <p>5’-ACTTTCCGCRGCATTAAACATTTTCTT-3’</p> </td> </tr> <tr> <td> <p>L-18</p> </td> <td> <p>57</p> </td> <td> <p>Forward</p> </td> <td> <p>5’-TGAATTTGGATGGCGGTAGAC-3’</p> </td> </tr> <tr> <td> <p>Reverse</p> </td> <td> <p>5’-ACCTAATGCACGCTTTAGAAT-3’</p> </td> </tr> <tr> <td> <p>LXA GT1</p> </td> <td> <p>57</p> </td> <td> <p>Forward</p> </td> <td> <p>5’-GTGGCGACCAATTCTGCAAG-3’</p> </td> </tr> <tr> <td> <p>Reverse</p> </td> <td> <p>5’-GCAGGACCAGCATCAAATGACAG-3’</p> </td> </tr> <tr> <td> <p>2MS17</p> </td> <td> <p>55</p> </td> <td> <p>Forward</p> </td> <td> <p>5’-CAGCCTCTATTTTGTTCGAAG-3’</p> </td> </tr> <tr> <td> <p>Reverse</p> </td> <td> <p>5’-TTTACTGCGGCTCCATAATC-3’</p> </td> </tr> <tr> <td> <p>2MS46</p> </td> <td> <p>55</p> </td> <td> <p>Forward</p> </td> <td> <p>5’-GCTCACTACTATGCTGCCAGC-3’</p> </td> </tr> <tr> <td> <p>Reverse</p> </td> <td> <p>5’-CTTTCCTGCAAACCACGTGT-3’</p> </td> </tr> <tr> <td> <p>2MS60</p> </td> <td> <p>55</p> </td> <td> <p>Forward</p> </td> <td> <p>5’-TATGCGCCGGACAATAATCGC-3’</p> </td> </tr> <tr> <td> <p>Reverse</p> </td> <td> <p>5’-GTTCATTGTCCGAGGCGCAGC-3’</p> </td> </tr> <tr> <td> <p>2MS67</p> </td> <td> <p>55</p> </td> <td> <p>Forward</p> </td> <td> <p>5’-GAAGATTCGTCAGGATGCAGC-3’</p> </td> </tr> <tr> <td> <p>Reverse</p> </td> <td> <p>5’-AACTCTCGCTGGCAAGCGAGC-3’</p> </td> </tr> <tr> <td> <p>2MS82</p> </td> <td> <p>55</p> </td> <td> <p>Forward</p> </td> <td> <p>5’-AAAAGAGCATGCAACAGGTCAGC-3’</p> </td> </tr> <tr> <td> <p>Reverse</p> </td> <td> <p>5’-TTTCTTAAGTCGCAAGCGAGC-3’</p> </td> </tr> <tr> <td> <p>2MS87</p> </td> <td> <p>55</p> </td> <td> <p>Forward</p> </td> <td> <p>5’-GGAACCTCACTCAACCTCGGT-3’</p> </td> </tr> <tr> <td> <p>Reverse</p> </td> <td> <p>5’-ACGCGGACTACTTTAACCGGA-3’</p> </td> </tr> <tr> <td> <p>2MS91</p> </td> <td> <p>55</p> </td> <td> <p>Forward</p> </td> <td> <p>5’-AAAGTCTCGGAGTGGCTTTGC-3’</p> </td> </tr> <tr> <td> <p>Reverse</p> </td> <td> <p>5’-ATTCTCGTCCATTTGTTCTAA-3’</p> </td> </tr> <tr> <td> <p>Ant11893</p> </td> <td> <p>55</p> </td> <td> <p>Forward</p> </td> <td> <p>5’-CAGGCTCGGRACGTTAATGC-3’</p> </td> </tr> <tr> <td> <p>Reverse</p> </td> <td> <p>5’-GGTGCCGACGTCTAGCTAGC-3’</p> </td> </tr> </tbody> </table> <p> </p> <p>Missing data are encoded “-9”.</p> <p> </p> <p>****************************** CONTACTING *****************************</p> <p>Contact me at:</p> <p> </p> <p>Marion Cordonnier</p> <p>e-mail: marion.cordonnier@hotmail.com</p> <p> </p> <p>***********************************************************************</p> <p> </p>
Data and modeling results for publication: Landscape genetics indicate recently increased habitat fragmentation in African forest-associated chafers
<ul> <li>DNA sequences: <em>cox1</em> and ITS1 alignments</li> <li>spatial records (in hypervolume archive)</li> <li>spatial principal component 1-3 used for <em>hypervolume</em> models (in hypervolume archive)</li> <li>Present and past species distribution models (SDMs): <ul> <li><em>biomod2</em> ensemble SDMs <ul> <li>Present</li> <li>Holocene Altithermal</li> <li>Last Glacial Maximum</li> </ul> </li> <li><em>biomod2</em> SDMs for single PMIP3 models <ul> <li>Present</li> <li>Holocene Altithermal</li> <li>Last Glacial Maximum</li> </ul> </li> <li><em>hypervolume</em> SDMs</li> </ul> </li> <li>landscape connectivity models <ul> <li>circuitscape (for F0, F1, and F2)</li> <li>least cost corridors and paths (for F0, F1, and F2)</li> </ul> </li> </ul>
Mountain landscape connectivity and subspecies appurtenance shape genetic differentiation in natural plant populations of the snapdragon (Antirrhinum majus L.)
<p>This dataset provides the raw data for the population genetic analyses for the article: "Mountain landscape connectivity and subspecies appurtenance shape genetic differentiation in natural plant populations of the snapdragon (Antirrhinum majus L.)" by Benoit Pujol; Juliette Archambeau; Aurore Bontemps; Mylène Lascoste; Sara Marin; and Alexandre Meunier found in the journal "Botany Letters", Vol 164 pp. 111-119 (DOI: 10.1080/23818107.2017.1310056).</p> <p>Link to journal open access article: http://www.tandfonline.com/doi/pdf/10.1080/23818107.2017.1310056</p> <p>Link to Zenodo article reporsitory: https://zenodo.org/record/801169</p> <p>The datafile includes three data sheets:</p> <p>Data, which contains for each plant : the name of the population, the name of the sampled individual, the subspecies, the latitude of the population, the longitude of the population, the altitudinal elevation of the population in meters, and the microsatellite genotype of each plant. Genotype data is recorded by locus (two columns for the two alleles at one locus). Locus name is found as the title of the column. The record for each allele is its allele size.</p> <p>valleys 1 and valleys 2, which contains the association between populations and valleys following the two scenarios that we analyzed in the paper.</p> <p>Microsatelite loci were developed during previous work: see the following paper for more details: Debout, G., E. Lhuillier, P.-J. Malé, B. Pujol, and C. Thébaud. 2012. Development and characterization of 24 polymorphic microsatellite loci in two Antirrhinum majus subspecies (Plantaginaceae) using pyrosequencing technology. Conservation Genetics Resources 4:75-79.</p>
Data from: Context matters: the landscape matrix determines the population genetic structure of temperate forest herbs across Europe
<p>Context. Plant populations in agricultural landscapes are mostly fragmented and their functional connectivity often depends on seed and pollen dispersal by animals. However, little is known about how the interactions of seed and pollen dispersers with the agricultural matrix translate into gene flow among plant populations.</p> <p>Objectives. We aimed to identify effects of the landscape structure on the genetic diversity within, and the genetic differentiation among, spatially isolated populations of three temperate forest herbs. We asked, whether different arable crops have different effects, and whether the orientation of linear landscape elements relative to the gene dispersal direction matters.</p> <p>Methods. We analysed the species' population genetic structures in seven agricultural landscapes across temperate Europe using microsatellite markers. These were modelled as a function of landscape composition and configuration, which we quantified in buffer zones around, and in rectangular landscape strips between, plant populations.</p> <p>Results. Landscape effects were diverse and often contrasting between species, reflecting their association with different pollen- or seed dispersal vectors. Differentiating crop types rather than lumping them together yielded higher proportions of explained variation. Some linear landscape elements had both a channelling and hampering effect on gene flow, depending on their orientation.</p> <p>Conclusions. Landscape structure is a more important determinant of the species' population genetic structure than habitat loss and fragmentation <i>per se</i>. Landscape planning with the aim to enhance the functional connectivity among spatially isolated plant populations should consider that even species of the same ecological guild might show distinct responses to the landscape structure.</p>
Bauder Et Al. - Landscape features fail to explain spatial genetic structure
<p> RMarkdown script and data in an Excel sheet to evaluate spatial genetic structure in white-tailed deer across Ohio and compare the support for isolation by distance (IBD) and isolation by landscape resistance (IBR) models in explaining this structure. We used genetic data from 619 individual deer from 24 counties across Ohio tested at 11 microsatellites and haplotypes from a 547-bp fragment of the mitochondrial DNA control region. We used spatial and non-spatial genetic clustering tests to evaluate genetic structure in both types of genetic data and empirically optimized landscape resistance surfaces to compare IBD and IBR using microsatellite data.</p> <p>v2 (BauderEtAl_Files_for_archiving2.zip) includes additional and updated files not in v1. </p>
Data for: Inferring population connectivity in Eastern Massasauga Rattlesnakes (Sistrurus catenatus) using landscape genetics
<p>Assessing the environmental factors that influence the ability of a threatened species to move through the landscape can be used to identify conservation actions that connect isolated populations. However, direct observations of species' movement are often limited making the development of alternate approaches necessary. Here we use landscape genetic analyses to assess the impact of landscape features on the movement of individuals between local populations of a threatened snake, the Eastern Massasauga Rattlesnake (<em>Sistrurus catenatus</em>). We linked connectivity data with habitat information from two landscapes of similar size: a large region of unfragmented habitat and a previously studied fragmented landscape consisting of isolated patches of habitat. We used this analysis to identify features of the landscape where modification or acquisition would enhance population connectivity in the fragmented region. We found evidence that current connectivity is impacted by both contemporary landcover features, especially roads, and inherent landscape features such as elevation. Next, we derived estimates of expected movement ability using a recently developed pedigree-based approach and Least Cost Paths through the unfragmented landscape. We then used our pedigree and resistance map to estimate resistance polygons of the potential extent for <em>S. catenatus</em> movement in the fragmented landscape. These polygons identify possible sites for future corridors connecting currently isolated populations in this landscape by linking the impact of future habitat modification or land acquisition to dispersal ability in this species. Overall, our study shows how modeling landscape resistance across differently fragmentated landscapes can identify habitat features that affect contemporary movement in threatened species in fragmented landscapes and how this information can be used to guide mitigation actions whose goal is to connect isolated populations.</p>
Data from: Spatial replication is important for developing landscape genetic inferences for a wetland salamander
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Data from: Functional connectivity and home range inferred at a microgeographic landscape genetics scale in a desert-dwelling rodent
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Data from: Context matters: the landscape matrix determines the population genetic structure of temperate forest herbs across Europe
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Data for: Inferring population connectivity in Eastern Massasauga Rattlesnakes (Sistrurus catenatus) using landscape genetics
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Data from: A landscape genetics approach reveals species-specific connectivity patterns for stream insects in fragmented habitats
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Effects of Corridors on Genetics of a Butterfly in a Landscape Experiment
To investigate the possible role of landscape connectivity on the genetic structure of isolated populations, we examined the effects of habitat corridors on the population genetics of a vagile butterfly species, Junonia coenia, within a largescale, experimental system. Using allozyme electrophoresis, a total of nine loci were identified and scored, six of which exhibited polymorphism. Our data demonstrated consistently higher levels of expected (He) and observed (Ho) heterozygosity in butterflies sampled from patches connected by corridors compared to unconnected patches. A t-test comparing He and Ho in connected versus unconnected patches found a marginally significant difference in one locus, the glycolytic enzyme phosphoglucose isomerase (PGI). Connected patches exhibited overall lower FST values compared to unconnected patches, indicating potentially increased levels of gene flow due to corridors. Our results support previous investigations on dispersal and population size for J. coenia, and show that higher dispersal through corridors promotes genetic variability at a locus (PGI) implicated in dispersal and fitness in butterflies.
Data from: Adaptive landscape genetics and malaria across divergent island bird populations
Environmental conditions play a major role in shaping the spatial distributions of pathogens, which in turn can drive local adaptation and divergence in host genetic diversity. Haemosporidians, such as plasmodium (malaria) are a strong selective force, impacting survival and fitness of hosts, with geographic distributions largely determined by habitat suitability for their insect vectors. Here, we have tested whether patterns of fine-scale local adaptation to malaria are replicated across discrete, ecologically differing island populations of Berthelot's pipits Anthus berthelotii. We sequenced TLR4, an innate immunity gene that is potentially under positive selection in <i>Berthelot's pipits</i>, and two SNPs previously identified as being associated with malaria infection in a genome-wide association study (GWAS) in Berthelot's pipits in the Canary Islands. We determined the environmental predictors of malaria infection, using these to estimate variation in malaria risk on Porto Santo, and found some congruence with previously identified environmental risk factors on Tenerife. We also found a negative association between malaria infection and a TLR4 variant in Tenerife. In contrast, one of the GWAS SNPs showed an association with malaria risk in Porto Santo, but in the opposite direction to that found in the Canary Islands GWAS. Together, these findings suggest that disease-driven local adaptation may be an important factor in shaping variation among island populations.
Data from: Landscape genetics reveals unique and shared effects of urbanization for two sympatric pool-breeding amphibians
Metapopulation-structured species can be negatively affected when landscape fragmentation impairs connectivity. We investigated the effects of urbanization on genetic diversity and gene flow for two sympatric amphibian species, spotted salamanders (Ambystoma maculatum) and wood frogs (Lithobates sylvaticus), across a large (>35,000 km2) landscape in Maine, USA, containing numerous natural and anthropogenic gradients. Isolation by distance (IBD) patterns differed between the species. Spotted salamanders showed a linear and relatively high variance relationship between genetic and geographic distance (r = 0.057; p < 0.001); whereas, wood frogs exhibited a strongly non-linear and lower variance relationship (r = 0.429; p < 0.001). Scale dependence analysis of IBD found gene flow has its most predictable influence (strongest IBD correlations) at distances up to 9 km for spotted salamanders and up to 6 km for wood frogs. Estimated effective migration surfaces revealed contrasting patterns of high and low genetic diversity and gene flow between the two species. Population isolation, quantified as the mean IBD residuals for each population, was associated with local urbanization and less genetic diversity in both species. The influence of geographic proximity and urbanization on population connectivity was further supported by distance-based redundancy analysis and multiple matrix regression with randomization. Resistance surface modelling found interpopulation connectivity to be influenced by developed land cover, light roads, interstates, and topography for both species, plus secondary roads and rivers for wood frogs. Our results highlight the influence of anthropogenic landscape features within the context of natural features and broad spatial genetic patterns, in turn supporting the premise that while urbanization significantly restricts interpopulation connectivity for wood frogs and spotted salamanders, specific landscape elements have unique effects on these two sympatric species.
Analysing landscape effects on dispersal networks and gene flow with genetic graphs
<p>Graph-theoretic approaches have relevant applications in landscape genetic analyses. When species form populations in discrete habitat patches, genetic graphs can be used i) to identify direct dispersal paths followed by propagules or ii) to quantify landscape effects on multigenerational gene flow. However, the influence of their construction parameters remains to be explored. Using a simulation approach, we constructed genetic graphs using several pruning methods (geographical distance thresholds, topological constraints, statistical inference) and genetic distances to weight graph links (F<sub>ST</sub>, D<sub>PS</sub>, Euclidean genetic distances). We then compared the capacity of these different graphs to i) identify the precise topology of the dispersal network and ii) to infer landscape resistance to gene flow from the relationship between cost-distances and genetic distances. Although not always clear-cut, our results showed that methods based on geographical distance thresholds seem to better identify dispersal networks in most cases. More interestingly, our study demonstrates that a subselection of pairwise distances through graph pruning (thereby reducing the number of data points) can counter-intuitively lead to improved inferences of landscape effects on dispersal. Finally, we showed that genetic distances such as the D<sub>PS</sub> or Euclidean genetic distances should be preferred over the F<sub>ST</sub> for landscape effect inference as they respond faster to landscape changes.</p>
Data from: Landscape genetic inferences vary with sampling scenario for a pond breeding amphibian
A critical decision in landscape genetic studies is whether to use individuals or populations as the sampling unit. This decision affects the time and cost of sampling and may affect ecological inference. We analyzed 334 Columbia spotted frogs at 8 microsatellite loci across 40 sites in northern Idaho to determine how inferences from landscape genetic analyses would vary with sampling design. At all sites, we compared a proportion available sampling scheme (PASS), in which all samples were used, to resampled datasets of 2-11 individuals. Additionally, we compared a population sampling scheme (PSS) to an individual sampling scheme (ISS) at 18 sites with sufficient sample size. We applied an information theoretic approach with both restricted maximum likelihood and maximum likelihood estimation to evaluate competing landscape resistance hypotheses. We found that PSS supported a low-density forest model (0.87) and ISS supported this model as well as additional models when testing hypotheses of landcover types that create the greatest resistance to gene flow for Columbia spotted frogs. Increased sampling density and study extent, seen by comparing PSS to PASS, showed a change in model support from a model of only low-density forest to a model of only high-density forest. As number of individuals increased, model support converged at 7 individuals for ISS to PSS. ISS may be useful to increase study extent and sampling density, but may lack power to provide strong support for the correct model with microsatellite datasets. Our results highlight the importance of additional research on sampling design effects on landscape genetics inference.
Data from: Comparative landscape genetics of two frugivorous bats in a biological corridor undergoing agricultural intensification
Agricultural intensification in tropical landscapes poses a new threat to the ability of biological corridors to maintain functional connectivity for native species. We use a landscape genetics approach to evaluate impacts of expanding pineapple plantations on two widespread and abundant frugivorous bats in a biological corridor in Costa Rica. We hypothesize that the larger, more mobile Artibeus jamaicensis will be less impacted by pineapple than the smaller Carollia castanea. In 2012 and 2013, we sampled 735 bats in 26 remnant forest patches surrounded by different proportions of forest, pasture, crops and pineapple. We used 10 microsatellite loci for A. jamaicensis and 16 microsatellite loci for C. castanea to estimate genetic diversity and gene flow. Canonical correspondence analyses indicate that land cover type surrounding patches has no impact on genetic diversity of A. jamaicensis. However, for C. castanea, both percentage forest and pineapple surrounding patches explained a significant proportion of the variation in genetic diversity. Least-cost transect analyses (LCTA) and pairwise G″st suggest that for A. jamaicensis, pineapple is more permeable to gene flow than expected, while as expected, forest is the most permeable land cover for gene flow of C. castanea. For both species, LCTA indicate that development may play a role in inhibiting gene flow. The current study answers the call for landscape genetic research focused on tropical and agricultural landscapes, highlights the value of comparative landscape genetics in biological corridor design and management and is one of the few studies of biological corridors in any ecosystem to implement a genetic approach to test corridor efficacy.
Data from: Genetic analysis of red deer (Cervus elaphus) administrative management units in a human-dominated landscape - patterns of genetic diversity, population structure and gene flow
<p><span><span>Red deer (</span><span><em>Cervus elaphus</em></span><span>) throughout central Europe are</span> impacted by different anthropogenic activities including habitat fragmentation, selective hunting, and translocations<span>. This has substantial influences on genetic diversity and the long-term conservation of local populations of this species. Here we use genetic samples from 480 red deer individuals to assess the genetic diversity and differentiation of the 12 administrative management units located in Schleswig Holstein, the northernmost federal state in Germany. </span></span><span><span>We applied multiple analytical approaches and show that the history of local populations (i.e., translocations, culling of individuals outside of designated red deer zones, and anthropogenic infrastructures) has led to comparably low levels of genetic diversity. The mean expected heterozygosity was below 0.6 and we observed on average 4.2 alleles across 12 microsatellite loci. Effective population sizes below the recommended level of 50 were estimated for multiple local populations. </span></span><span><span>Our estimates of genetic structure and gene flow show that red deer in northern Germany are best described as a complex network of asymmetrically connected subpopulations, with high genetic exchange among some local populations and reduced connectivity of others. Genetic diversity was also correlated with population densities of neighboring management units. </span></span></p> <p><span><span>Based on these findings, we suggest that connectivity among existing management units needs to be considered in the practical management of the species, which means that some administrative management units should be managed together, while the effective isolation of other units needs to be mitigated.</span></span></p>
Landscape genetics Afromontane forest birds - microsatellite data
<p><a name="_Hlk61564128"></a><span><span><span><span><span><span><span><span><span><span><span><span><span><span><span>Species confined to naturally fragmented habitats may exhibit intrinsic population complexity which may challenge interpretations of species response to anthropogenic landscape transformation. In South Africa, where native forests are naturally fragmented, forest‐dependent birds have undergone range declines since 1992, most notably among insectivores. These insectivores appear sensitive to the quality of natural matrix habitats, and it is unknown whether transformation of the landscape matrix has disrupted gene flow in these species</span></span></span></span></span></span></span></span></span></span></span></span></span></span></span><span><span><span><span><span><span><span><span><span><span><span><span><span><span><span>. We undertook a landscape genetics study of four forest‐dependent insectivorous songbirds across southeast South Africa. Microsatellite data were used to conduct a priori optimization of landscape resistance surfaces (land cover, rivers and dams, and elevation) using cost‐distances along least‐cost pathway (LCP), and resistance distances (IBR). We detected pronounced declines in effective population sizes over the past two centuries for the endemic forest specialist </span></span></span></span></span></span></span></span></span></span></span></span></span></span></span><em>Cossypha dichroa</em><span><span><span><span><span><span><span><span><span><span><span><span><span><span><span> and </span></span></span></span></span></span></span></span></span></span></span></span></span></span></span><em>Batis capensis</em><span><span><span><span><span><span><span><span><span><span><span><span><span><span><span>, alongside recent gene flow disruption in </span></span></span></span></span></span></span></span></span></span></span></span></span></span></span><em>B. capensis</em><span><span><span><span><span><span><span><span><span><span><span><span><span><span><span>, </span></span></span></span></span></span></span></span></span></span></span></span></span></span></span><em>C. dichroa</em><span><span><span><span><span><span><span><span><span><span><span><span><span><span><span> and </span></span></span></span></span></span></span></span></span></span></span></span></span></span></span><em>Pogonocichla stellata</em><span><span><span><span><span><span><span><span><span><span><span><span><span><span><span>. Landscape resistance modelling showed both native forest and dense thicket configuration facilitates gene flow in </span></span></span></span></span></span></span></span></span></span></span></span></span></span></span><em>P. stellata</em><span><span><span><span><span><span><span><span><span><span><span><span><span><span><span>, </span></span></span></span></span></span></span></span></span></span></span></span></span></span></span><em>B. capensis</em><span><span><span><span><span><span><span><span><span><span><span><span><span><span><span> and </span></span></span></span></span></span></span></span></span></span></span></span></span></span></span><em>C. dichroa</em><span><span><span><span><span><span><span><span><span><span><span><span><span><span><span>. Facultative dispersal of </span></span></span></span></span></span></span></span></span></span></span></span></span></span></span><em>P. stellata</em><span><span><span><span><span><span><span><span><span><span><span><span><span><span><span> through dense thicket likely aided resilience against historic landscape transformation, whereas combined forest‐thicket degradation adversely affected the forest generalist </span></span></span></span></span></span></span></span></span></span></span></span></span></span></span><em>B. capensis</em><span><span><span><span><span><span><span><span><span><span><span><span><span><span><span>. By contrast, </span></span></span></span></span></span></span></span></span></span></span></span></span></span></span><em>Phylloscopus ruficapilla</em><span><span><span><span><span><span><span><span><span><span><span><span><span><span><span> appears least reliant upon landscape features to maintain gene flow and was least impacted by anthropogenic landscape transformation. Collectively, gene flow in all four species is improved at lower elevations, along river valleys, and riparian corridors— where </span></span></span></span></span></span></span></span></span></span></span></span></span></span></span><span><span><span><span><span><span><span><span><span><span><span><span><span><span><span>native forest and dense thicket better persist. Consistent outperformance of LCP over IBR land‐cover models for </span></span></span></span></span></span></span></span></span></span></span></span></span></span></span><em>P. stellata</em><span><span><span><span><span><span><span><span><span><span><span><span><span><span><span>, </span></span></span></span></span></span></span></span></span></span></span></span></span></span></span><em>B. capensis</em><span><span><span><span><span><span><span><span><span><span><span><span><span><span><span> and </span></span></span></span></span></span></span></span></span></span></span></span></span></span></span><em>C. dichroa</em><span><span><span><span><span><span><span><span><span><span><span><span><span><span><span> demonstrates the benefits of wildlife corridors for South African forest‐dependent bird conservation, to ameliorate the extinction debts from past and present anthropogenic forest exploitation.</span></span></span></span></span></span></span></span></span></span></span></span></span></span></span></p>
Data and R codes from: Exploring the effect of 195 years-old locks on species movement: Landscape genetics of painted turtles in the Rideau Canal, Canada
<p>Aquatic systems have been extensively altered by human structures (e.g., construction of dams/canals) and these have major impacts on the connectivity of wildlife populations through the loss and isolation of suitable habitats. Habitat loss and isolation affect gene flow and influence the persistence of populations in time and space by restricting movements. Isolation can result in higher inbreeding, lower genetic diversity, and greater genetic structure, which may render populations more vulnerable to environmental changes, and thus to extinction. Given the ubiquity and the persistence of dams and canals in space and time, it is crucial to understand their effects on the population genetics of aquatic species. Here, we documented the genetic diversity and structure of painted turtle (<em>Chrysemys picta</em>) populations in the Rideau Canal, Ontario, Canada. More specifically, we used 13 microsatellites to evaluate the influence of locks on genetic variation in 822 painted turtles from 22 sites evenly distributed along the 202-km canal. Overall, we found low, but significant, genetic differentiation suggesting that some dispersal is occurring throughout the canal. In addition, we showed that locks contribute to the genetic differentiation observed in the system. Clustering analysis revealed two distinct genetic groups whose boundary is associated with a series of six locks. Our results illustrate how artificial waterways, such as canal systems, can influence population genetic structure. We highlight the importance of adopting management plans that can mitigate the impacts of human infrastructure and preserve gene flow across the landscape to maintain viable populations.</p>
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.