Find research datasets worth reusing
Search datasets from major research repositories and use ShareScore to quickly assess how well each record supports discovery, access, and reuse.
80
datasets available to search
ShareScore release 0.7.1
Dataset results
80 results for “geographic isolation”
Rapid diversification of gray mangroves (Avicennia marina) driven by geographic isolation and extreme environmental conditions in the Arabian Peninsula
<p><span>Biological systems occurring in ecologically heterogeneous and spatially discontinuous habitats provide an ideal opportunity to investigate the relative roles of neutral and selective factors in driving lineage diversification. The gray mangroves (<em>Avicennia marina</em>) of Arabia occur at the northern edge of the species' range and are subject to variable, often extreme, environmental conditions, as well as to historic large fluctuations in habitat availability and connectivity resulting from Quaternary glacial cycles. Here, we analyze fully sequenced genomes sampled from 20 locations across the Red Sea, the Arabian Sea, and the Persian/Arabian Gulf (PAG) to reconstruct the evolutionary history of the species in the region and to identify adaptive mechanisms of lineage diversification. Population structure and phylogenetic analyses revealed marked genetic structure and highly supported clades among and within the seas surrounding the Arabian Peninsula. Demographic modeling showed times of divergence consistent with recent periods of geographic isolation and low marine connectivity during glaciations, revealing the presence of (cryptic) glacial refugia in the Red Sea and the PAG. Significant migration was detected within the Red Sea and the PAG, and across the Strait of Hormuz to the Arabian Sea, suggesting gene flow upon secondary contact among Arabian mangrove populations. Genetic‐environment association analyses revealed high levels of adaptive divergence and detected signs of multi-loci local adaptation driven by temperature extremes and hypersalinity. These results support a process of rapid diversification resulting from the combined effects of historical factors and ecological selection and reveal mangrove peripheral environments as relevant drivers of lineage diversity.</span></p>
Data from: Rampant dispersal without gene-flow: Reproductively and geographically isolated lineages of the Supertramp lizard Lamprolepis smaragdina permeate the lesser Sunda Archipelago
Open the record for dataset details and reuse information.
Rapid diversification of gray mangroves (Avicennia marina) driven by geographic isolation and extreme environmental conditions in the Arabian Peninsula
Open the record for dataset details and reuse information.
Data from: Distributional shifts – not geographic isolation – as a probable driver of montane species divergence
As biodiversity hotspots, montane regions have been a focus of research to understand the divergence process. Like their oceanic counterparts, the diversity of the "sky islands" might be ascribed to geographic isolation of mountaintops. However, because the sky islands, and especially those in northern latitudes, are subject to extreme climatic events such as the glacial cycles that drove both altitudinal and geographical shifts in species' distributions, the dynamic colonization process is also a possible factor driving divergence. Here we test these two hypotheses (i.e., isolation versus colonization) in a flightless montane grasshopper, Melanoplus oregonensis, which is a member of a diverse group that radiated across the Rocky Mountains of North America. Using approximate Bayesian computation (ABC) and spatially explicit simulations that account for spatial heterogeneity and temporal shifts in species distributions, we show that a colonization model of the sky islands from refugial populations provides a significantly better fit to the empirical genetic data than a model of the geographic isolation among sky islands. Moreover, support for the colonization model holds irrespective of whether the movement of individuals was modeled as a diffusion process or was informed by differences in habitat suitabilities across the landscape. With validation analyses to confirm the models provide a good fit to the data, as well as general power and quality analyses, the research not only adds to a growing body of work on the complex dynamics underlying montane biodiversity, but it also provides much needed evaluation of competing hypotheses based on explicit models of the divergence process, as opposed to inferences about diversification drivers from species diversity patterns.
Foliar endophyte diversity in eastern Asia-eastern North America disjunct tree species – Influences of host identity, environment, phylogeny, and geographic isolation
<p><span>The well-known eastern Asia (EA) and eastern North America (ENA) floristic disjunction provides a unique system for biogeographic and evolutionary studies. Despite considerable interest in the disjunction, few studies have investigated the patterns and their underlying drivers of allopatric divergence in sister species or clades isolated in the two areas. Endophyte diversity and assembly in disjunct sister taxa, as an ecological trait, may have played an important role in the processes of allopatric evolution, but no studies have examined endophytes in these disjunct lineages. In this study, we compared foliar endophytes (including both fungi and bacteria) in 17 EA-ENA disjunct species pairs from genera representing conifers and major clades of angiosperms, as well as 23 species of </span><em>Cornus</em> from the US and China. We sequenced the ITS of fungi and 16S rDNA of bacteria to understand the composition of the endophyte community and gain insights into the relative roles of geographic isolation, host identity, phylogeny, and environment in shaping endophytic diversity patterns. We detected a much richer fungal than bacterial community in leaves of all species. Beta diversity varied greatly among individuals within species, between species, among genera, and among three natural environmental conditions. Based on a principal coordinates analysis, we found no close clustering of endophyte communities in samples from the same host plant species, from the same genus, or from the same geographic origin (i.e. EA or ENA) (when plants were grown in the same common garden), but we did detect clustering of samples from plants grown in the same environment (i.e., same geographic location). We observed separation of microbes in plant samples of the same species grown in different locations/environments. However, pooled samples across all species from the common garden with the same geographic origin (EA vs. ENA) showed a moderate level of dissimilarity in fungal endophytes between EA and ENA. An overall significant correlation between endophyte community dissimilarity and phylogenetic distance was detected among the disjunct genera but not among species of <em>Cornus</em>. However, significant correlation between order, family, and genera of endophytes and phylogenetic distance of Cornus species was observed. We also found no significant differences in Foliar Endophytic Fungal (FEF) communities between counterparts of disjunct species pairs in EA and ENA in most genera except in <em>Liriodendron</em> and <em>Cornus</em>, although the beta diversity within genera is high. Our results suggest important roles of host identity and environment (geographic locations), and a likely minor role of phylogenetic divergence and biogeographic isolation in shaping the pattern of foliar endophyte diversity and assembly in the EA-ENA disjunct genera, as well as in <em>Cornus</em>. The results further suggest that the sister taxa in EA and ENA are likely different in their foliar endophyte composition when growing in their native habitats due to differences in geographic locations and local environments, which is potentially a factor driving allopatric divergence of species functional features. This hypothesis can be tested by analysis of samples from native habitats.</p>
Divided by the range: evidence for geographic isolation of the highly mobile Emu (Dromaius novaehollandiae)
<p>Conserving evolutionary processes is becoming increasingly important in conservation management as environmental changes threaten wild populations. Characterising genetically distinct populations and assessing connectivity across the landscape enables wildlife managers to prioritise conservation efforts with limited resources. In the NSW North Coast bioregion of Australia, one of the last remaining coastal populations of the Emu (<em>Dromaius novaehollandiae</em>) has been state-listed as an Endangered Population, owing to its geographic isolation and small census size. Using mitochondrial and nuclear genetic markers, we examined the spatial genetic structure of Emus across south-eastern Australia and assessed the effective population size (<em>N</em><sub><em>e</em></sub>) and genetic diversity of the NSW North Coast Emu to inform management. We show significant genetic divergence between the NSW North Coast Emu and other localities based on thousands of highly resolving nuclear markers, which was not explained by geographic distance. Among NSW North Coast Emus, we found less genetic diversity and a critically low effective population size (<em>N</em><sub><em>e</em></sub> = 14.84 and 22.49 based on independent methods). Together, these findings suggest that the NSW North Coast Emu is at risk of further losses of genetic diversity and inbreeding depression. Incorporating genetic data into the design of captive-release and translocation projects would refine management plans for this locally important population and monitor risks to its long-term survival.</p>
Strain diversity of human-residential Lactiplantibacillus plantarum across children cohorts of two ethnic groups geographically isolated
<p>This file includes seven genes, groEL-ileS-murC-murE-pheS-pyrG-recA, and has been used for multi-site sequence typing (MLST) studies.</p>
Data for: Geographic isolation reduces genetic diversity of a wide-ranging terrestrial vertebrate, Canis lupus
<p>Genetic diversity is theorized to decrease in populations closer to a species' range edge, where habitat may be suboptimal. However, generalist species capable of long-range dispersal may maintain sufficient gene flow to counteract this, though the presence of significant barriers to dispersal (e.g., large water bodies, human-dominated landscapes) may still lead to, and exacerbate, the edge effect. We used microsatellite data for 2,426 gray wolves (<em>Canis</em> <em>lupus</em>) from 24 sub-populations (groups) to model how allelic richness and expected heterozygosity varied with two measures of range edge (mainland-island position, latitude, and distance from range center) across >7.3 million km<sup>2</sup> of northern North America. We found that allelic richness and expected heterozygosity of island groups was measurably less than that of mainland groups and that these differences increased with the island's distance to the species' range center in the study area. Our results demonstrate how multiple axes of geographic isolation (distance from range center and island habitation) can act synergistically to erode the genetic diversity of wide-ranging terrestrial vertebrate populations despite the counteracting influence of long-range dispersal ability. These findings emphasize how geographic isolation is a potential threat to the genetic diversity and viability of terrestrial vertebrate populations even among species capable of long-range dispersal. </p> <p>This dataset is comprised of four separate sub-datasets, sourced from Carmichael et al. (2007), Musiani et al. (2007), McNay (2006), and a manuscript in progress (referred to as "MacNulty" in the data files, to be first published in Frevol et al. 2023). The raw data are comprised of sample IDs, latitude and longitude points indicating where the sample was collected or recorded, and microsatellite genetic information. To aid in re-use, the raw genetic data has also been formatted and presented for use with common population genetics software (Genepop, MICROCHECKER, Genetix, FSTAT). The dataset also includes spatial data files of the sub-populations described in the study, allelic richness and expected heterozygosity data derived from the raw and spatial data, and the R script used to create the models. </p> <ul> <li>Carmichael LE, Krizan J, Nagy JA, et al (2007) Historical and ecological determinants of genetic structure in arctic canids. Molecular Ecology 16:3466–3483. https://doi.org/10.1111/j.1365-294X.2007.03381.x</li> <li>McNay ME (2006) Preliminary results of parentage analysis using microsatellite markers from an exploited wolf population in central Alaska. Alaska Department of Fish and Game, Division of Wildlife Conservation, Juneau, Alaska</li> <li>Musiani M, Leonard JA, Cluff HD, et al (2007) Differentiation of tundra/taiga and boreal coniferous forest wolves: genetics, coat colour and association with migratory caribou. Molecular Ecology 16:4149–4170. https://doi.org/10.1111/j.1365-294X.2007.03458.x</li> </ul>
Geographic isolation alone does not explain divergence of a group of orchid species across Brazil's campos rupestres sky-islands
<p class="MsoNormal">Mountains play a crucial role in the origin and maintenance of Neotropical biodiversity, but there are still unanswered questions about the diversification of the <em><span>campos rupestres</span></em> (CR), an herbaceous-shrubby sky-island vegetation in Eastern South America. For orchids distributed across this disjunct rock habitat, difficulties with distinguishing morphological taxa add an additional challenge to disentangling the history of divergence. Here, we combined the power of ddRAD genomic data with broad sampling of <em>Bulbophyllum</em> sect. <em>Didactyle</em> (Orchidaceae), across the CR and other Neotropical outcrops, to estimate evolutionary relationships and reconstruct the biogeography of the group's diversification. Although genetic lineages generally align with geographic disjunctions, we also observe distantly related lineages within some previously recognized species. For such taxa, their lack of monophyly and a shared regional divergence pattern suggests a complex history that may include unrecognized diversity. When viewed through the lens of morphological variability, our study raises intriguing questions about the persistence and permeability of species barriers among orchid populations. These results, in addition to the recency of the divergence history of <em>B.</em> sect. <em>Didactyle,</em> provide insights about hypothesized community level versus species-specific paths of diversification across the Neotropical sky-islands of the CR.</p>
Divided by the range: evidence for geographic isolation of the highly mobile Emu (Dromaius novaehollandiae)
Open the record for dataset details and reuse information.
Data from: Distributional shifts – not geographic isolation – as a probable driver of montane species divergence
Open the record for dataset details and reuse information.
Geographic isolation alone does not explain divergence of a group of orchid species across Brazil’s campos rupestres sky-islands
Open the record for dataset details and reuse information.
Data from: Replicate geographic transects across a hybrid zone reveal parallelism and differences in the genetic architecture of reproductive isolation
Open the record for dataset details and reuse information.
Data for: Geographic isolation reduces genetic diversity of a wide-ranging terrestrial vertebrate, Canis lupus
Open the record for dataset details and reuse information.
Foliar endophyte diversity in eastern Asia-eastern North America disjunct tree species – Influences of host identity, environment, phylogeny, and geographic isolation
Open the record for dataset details and reuse information.
Genomic variation in the American pika: signatures of geographic isolation and implications for conservation
<p>Distributional responses by alpine taxa to repeated, glacial-interglacial cycles throughout the last two million years have significantly influenced the spatial genetic structure of populations. These effects have been exacerbated for the American pika (<i>Ochotona princeps</i>), a small alpine lagomorph constrained by thermal sensitivity and a limited dispersal capacity. As a species of conservation concern, long-term lack of gene flow has important consequences for landscape genetic structure and levels of diversity within populations. Here, we use reduced representation sequencing (ddRADseq) to provide a genome-wide perspective on patterns of genetic variation across pika populations representing distinct subspecies. To investigate how landscape and environmental features shape genetic variation, we collected genetic samples from distinct geographic regions as well as across finer spatial scales in two geographically proximate mountain ranges of eastern Nevada.</p> <p> </p> <p> </p>
Data from: Phylogenetic diversity of two geographically overlapping species in the lichen genus Sticta (Ascomycota: Peltigeraceae): isolation by distance, environment, or fragmentation?
<p><span><b>Aim:</b> To test whether the degree of phylogenetic diversity differs in two congeneric, morphologically similar lichens that are both widespread and with a similar geographical range (Neotropics and Hawaii), but differ in altitudinal and habitat preferences, and whether the two species underwent isolation by distance (IBD), environment (IBE), or fragmentation (IBF).</span></p> <p><span><b>Location:</b> South and Central America, Caribbean, Hawaii, Azores.</span></p> <p><span><b>Taxon:</b> <i>Sticta</i> (Peltigeraceae).</span></p> <p><span><b>Methods:</b> Analysis of 395 specimens across the study area; ITS barcoding marker; maximum likelihood tree reconstruction within a broad taxonomic framework; TCS haplotype networks; Mantel test of genetic vs. geographic, environmental, and fragmentation distances; statistical comparison of BIOclim variables.</span></p> <p><span><b>Results:</b><b> </b><i>Sticta andina</i> exhibited high phenotypic variation and high reticulate phylogenetic diversity across its range, whereas the phenotypically more uniform <i>S. scabrosa</i> contained two main haplotypes, one unique to Hawaii (subsp. <i>hawaiiensis</i>). <i>Sticta andina</i> was restricted to well-preserved andine forests and paramos, habitats fragmented due to disruptive topology, whereas <i>S. scabrosa</i> was found in lowland to lower montane forests in rather exposed microsites, representing a more continuous habitat. These differences were statistically significant for several BIOclim variables. Mantel tests on genetic vs. geographic and environmental distances demonstrated that <i>S. scabrosa</i> followed a pattern of IBD across its full range but not within continental Central and South America. In contrast, <i>S. andina</i> did not exhibit IBD but showed weak, yet significant patterns of IBE at continental level and IBF in the northern Andes.</span></p> <p><b>Main Conclusions:</b> Autecology indirectly drives phylogenetic diversity in the two studied species. In the low altitude species, <i>S. scabrosa</i>, phylogenetic diversity is low and shows no correlation with geographic or environmental distances, except for the differentiation of the Hawaiian subspecies. We attribute this to rapid expansion and effective gene flow between populations across a more or less continuously distributed niche representing partially exposed microsites, including disturbed and anthropogenic vegetation, such as planted trees. In contrast, in the high altitude species, <i>S. andina</i>, phylogenetic diversity is high and correlated with both environmental niche differentiation (IBE) and fragmentation caused by the final Andean uplift (IBF). Therefore, an autoecological preference for high altitudes increases the likelihood for higher phylogenetic diversity.</p>
Data from: Geographic isolation and larval dispersal shape seascape genetic patterns differently according to spatial scale
Genetic variation, as a basis of evolutionary change, allows species to adapt and persist in different climates and environments. Yet, a comprehensive assessment of the drivers of genetic variation at different spatial scales is still missing in marine ecosystems. Here, we investigated the influence of environment, geographic isolation, and larval dispersal on the variation in allele frequencies, using an extensive spatial sampling (47 locations) of the striped red mullet (Mullus surmuletus) in the Mediterranean Sea. Univariate multiple regressions were used to test the influence of environment (salinity and temperature), geographic isolation, and larval dispersal on Single Nucleotide Polymorphisms (SNPs) allele frequencies. We used Moran's Eigenvector Maps (db-MEMs) and Asymmetric Eigenvector Maps (AEMs) to decompose geographic and dispersal distances in predictors representing different spatial scales. We found that salinity and temperature had only a weak effect on the variation in allele frequencies. Our results revealed the predominance of geographic isolation to explain variation in allele frequencies at large spatial scale (> 1,000km) while larval dispersal was the major predictor at smaller spatial scale (< 1,000km). Our findings stress the importance of including spatial scales to understand the drivers of spatial genetic variation. We suggest that larval dispersal allows to maintain gene flows at small to intermediate scale, while at broad scale, genetic variation may be mostly shaped by adult mobility, demographic history or multi-generational stepping stone dispersal. These findings bring out important spatial scale considerations to account for in the design of a protected areas network that would efficiently enhance protection and persistence capacity of marine species.
Data from: Phylogeography, genetic structure and population divergence time of cheetahs in Africa and Asia: evidence for long-term geographic isolates
The cheetah (Acinonyx jubatus) has been described as a species with low levels of genetic variation. This has been suggested to be the consequence of a demographic bottleneck 10 000–12 000 years ago (ya) and also led to the assumption that only small genetic differences exist between the described subspecies. However, analysing mitochondrial DNA and microsatellites in cheetah samples from most of the historic range of the species we found relatively deep phylogeographic breaks between some of the investigated populations, and most of the methods assessed divergence time estimates predating the postulated bottleneck. Mitochondrial DNA monophyly and overall levels of genetic differentiation support the distinctiveness of Northern-East African cheetahs (Acinonyx jubatus soemmeringii). Moreover, combining archaeozoological and contemporary samples, we show that Asiatic cheetahs (Acinonyx jubatus venaticus) are unambiguously separated from African subspecies. Divergence time estimates from mitochondrial and nuclear data place the split between Asiatic and Southern African cheetahs (Acinonyx jubatus jubatus) at 32 000–67 000 ya using an average mammalian microsatellite mutation rate and at 4700–44 000 ya employing human microsatellite mutation rates. Cheetahs are vulnerable to extinction globally and critically endangered in their Asiatic range, where the last 70–110 individuals survive only in Iran. We demonstrate that these extant Iranian cheetahs are an autochthonous monophyletic population and the last representatives of the Asiatic subspecies A. j. venaticus. We advocate that conservation strategies should consider the uncovered independent evolutionary histories of Asiatic and African cheetahs, as well as among some African subspecies. This would facilitate the dual conservation priorities of maintaining locally adapted ecotypes and genetic diversity.
Data from: Examining the full effects of landscape heterogeneity on spatial genetic variation: a multiple matrix regression approach for quantifying geographic and ecological isolation
Understanding the effects of landscape heterogeneity on spatial genetic variation is a primary goal of landscape genetics. Ecological and geographic variables can contribute to genetic structure through geographic isolation, in which geographic barriers and distances restrict gene flow, and ecological isolation, in which gene flow among populations inhabiting different environments is limited by selection against dispersers moving between them. Although methods have been developed to study geographic isolation in detail, ecological isolation has received much less attention, partly because disentangling the effects of these mechanisms is inherently difficult. Here, I describe a novel approach for quantifying the effects of geographic and ecological isolation using multiple matrix regression with randomization. I explored the parameter space over which this method is effective using a series of individual-based simulations and found that it accurately describes the effects of geographic and ecological isolation over a wide range of conditions. I also applied this method to a set of real-world datasets to show that ecological isolation is an often overlooked but important contributor to patterns of spatial genetic variation and to demonstrate how this analysis can provide new insights into how landscapes contribute to the evolution of genetic variation in nature.
ScienceDex guides
Understand access before you commit
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.