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.
275
datasets available to search
ShareScore release 0.9.0
Dataset results
275 results for “refugia”
Evaluating refugia in recent human evolution in Africa: Supplementary information
<p><em>Homo sapiens</em> have adapted to an incredible diversity of habitats around the globe. This capacity to adapt to different landscapes is clearly expressed within Africa, with Late Pleistocene <em>Homo sapiens</em> populations occupying savannahs, woodlands, coastlines and mountainous terrain. As the only area of the world where <em>Homo sapiens</em> have clearly persisted through multiple glacial-interglacial cycles, Africa is the only continent where classic refugia models can be formulated and tested to examine and describe changing patterns of past distributions and human phylogeographies. The potential role of refugia has frequently been acknowledged in the Late Pleistocene palaeoanthropological literature, yet explicit identification of potential refugia has been limited by the patchy nature of palaeoenvironmental and archaeological records, and the low temporal resolution of climate or ecological models. Here, we apply potential climatic thresholds on human habitation, rooted in ethnographic studies, in combination with high resolution model datasets for precipitation and biome distributions to identify persistent refugia spanning the Late Pleistocene (130-10 thousand years ago). We present two alternate models suggesting that between 27-66% of Africa may have provided refugia to Late Pleistocene human populations, and examine variability in precipitation, biome, and ecotone distributions within these refugial zones.</p>
Data from: Influence of topographic features and vegetation on climate refugia in the boreal plains
<ol> <li>Climate-change refugia can be defined by the strength of influence of physiographic and biotic properties on local atmospheric conditions relative to regional averages. In flatter landscapes, thermal heterogeneity and decoupling may be limited. We sought to quantify the magnitude of climate decoupling produced by topographic variation and vegetation in North America's boreal-parkland-grassland transition zone.</li> <li>We deployed iButton data loggers at four hill and 12 river valley systems along a latitudinal gradient in Alberta, Canada (N = 240) between 2014 and 2018. We modelled monthly temperature metrics by season as a function of topography and percent vegetation cover using general linear mixed effect models.</li> <li>Summer T<sub>max</sub> varied ~6 <sup>o</sup>C across the entire elevation gradient sampled, and ~3.5 <sup>o</sup>C within the range of topographic conditions sampled, after accounting for latitude. We found that canopy cover type had a negative effect on most temperature metrics, with coniferous forests having the strongest effect on T<sub>min </sub>and T<sub>ave</sub>. Spatial predictions derived from models based on iButton sensors resulted in similar regional patterns compared to a gridded climate product (ClimateNA), but the difference between them increased with potential solar radiation, vegetation cover and terrain roughness.</li> <li>We observed that local T<sub>max</sub> on steep, north-facing slopes with relatively low levels of potential solar radiation were 0.5 – 1.5 <sup>o</sup>C cooler than the surrounding landscape on average, while terrain roughness may further contribute to 0.5 – 0.7 <sup>o</sup>C. When combined, these local landscape characteristics may compensate for expected warming by the end of the century. Topographic and vegetation characteristics that are related to colder local climates should be considered in the evaluation of future climate-change impacts and to identify potential refugia from climate-change.</li> </ol>
Data from: Underlying geology and climate interactively shape climate change refugia in mountain streams
<p>Identifying climate-change refugia is a key adaptation strategy for reducing global warming impacts. Knowledge of the effects of underlying geology on thermal regime along climate gradients and the ecological responses to the geology-controlled thermal regime is essential to plan appropriate climate adaptation strategies. In the present study, the dominance of volcanic rocks in the watershed is used as a landscape-scale surrogate for cold groundwater inputs to clarify the importance of underlying geology in stream ecosystems along climate gradients. First, using hundreds of monitoring stations distributed across multiple catchments, we explored the relationship between watershed geology and the mean summer water temperature of mountain streams along climate gradients in the Japanese archipelago. Mean summer water temperature was explained by the interaction between the watershed geology and climate in addition to independent effects. The cooling effect supported by volcanic rocks reached up to 3.3°C among study regions, which was more pronounced in streams with less summer precipitation or lower air temperatures. Next, we examined the function of volcanic streams as cold refugia under contemporary and future climatic conditions. Community composition analyses revealed that volcanic streams hosted distinct stream communities composed of more cold-water species compared with non-volcanic streams. Scenario analyses based on multiple GCMs and RCPs revealed a geology-related pattern of thermal habitat loss for cold-water species. Non-volcanic streams rapidly declined in thermally suitable habitats for lotic sculpins even under the lowest emission scenario (RCP 2.6). In contrast, most volcanic streams will be sustained below the thermal threshold, especially for low and mid-level emission scenarios (RCP 2.6, 4.5). However, the distinct stream community in volcanic streams and geology-dependent habitat loss for lotic sculpins was not uniform and was more pronounced in streams with less summer precipitation or lower air temperatures. These findings highlight that underlying geology, climate variability, and their interaction should be considered simultaneously for effective management of climate-change refugia in mountain streams. </p>
Data from: European common frog (Rana temporaria) recolonised Switzerland from multiple glacial refugia in northern Italy via trans- and circum-Alpine routes
<p><span>The high mountain ranges of western Europe had a profound effect on the biotic recolonisation of Europe from glacial refugia. The Alps present a particularly interesting case because they form an absolute barrier to dispersal for most taxa, obstructing recolonisation from multiple refugia in northern Italy. Here we investigate the effect of the European Alps on the phylogeographic history of the European common frog <i>Rana temporaria</i>. Based on partial <i>cytochrome b </i>and <i>COXI </i>sequences from Switzerland, we find two mitochondrial lineages roughly north and south of the alpine ridge, with contact zones between them in eastern and western Switzerland. The northern haplogroup falls within the previously identified western European haplogroup, while the southern haplogroup is unique to Switzerland. We find that the lineages diverged ~110 kya, at approximately the onset of the last glacial glaciation; this indicates that they are from different glacial refugia. Phylogenetic analyses suggest that the northern and southern haplogroups colonised Switzerland via trans- and circum-alpine routes from at least two separate refugia in northern Italy. Our results illustrate how a complex recolonisation history of the central European Alps can arise from the semi-permeable barrier created by high mountains.</span></p>
Phylogeographical break and limited connectivity between multiple refugia in panantarctic moss species
<p><span><strong>Aim</strong>:</span><span> Historical biogeography of the Antarctic terrestrial biota remains poorly studied and understood. We aim to advance this through a range-wide, multilocus analysis of a pan-Antarctic moss species, in the context of its age, range dynamics, phylogeographical structure, and location of possible long-term refugia. </span></p> <p><span><strong>Location</strong>:</span><span> Continental and maritime Antarctic, South America (Patagonia), Australasia.</span></p> <p><span><strong>Taxon</strong>:</span><span> <em>Syntrichia sarconeurum</em> Ochyra & R.H. Zander (Pottiaceae).</span></p> <p><span><strong>Methods</strong>:</span><span> We used a comprehensive, range-wide and taxonomically-informed sampling, and multilocus sequencing of nuclear and plastid DNA regions. Temporal evolutionary framework, regional genetic diversification and diversity were assessed with phylogenetic and phylogeographic reconstructions, molecular dating, haplotype networks, mismatch analysis, and S-DIVA reconstruction of past events and ancestral areas.</span></p> <p><span><strong>Results</strong>:</span><span> Intercontinental disjunction between Australia and Antarctica/S. America was dated to 3.77 Ma, while diversification of extant <em>Syntrichia sarconeurum</em> lineages had taken place since roughly 1.36 Ma. Antarctic populations contained two high-frequency, allopatric cpDNA haplotypes, which highlighted separation of the continental populations. <em>ITS</em> data showed higher diversification and revealed three main lineages with a main genetic break mostly concordant with plastid data. <em>ITS</em> also showed contrasting diversity between the Antarctic continent and maritime Antarctic/Patagonia.</span></p> <p><span><strong>Main conclusions</strong>:</span><span> Age of the Antarctic range of <em>Syntrichia sarconeurum</em> potentially reaches back to mid-Pliocene, while diversification of extant genetic lineages was linked with recurrent macroenvironmental changes of the Pleistocene. Significant phylogeographical structure displays a major genetic break, which coincides with a known boundary in the terrestrial biota and suggests constrained population connectivity. <em>S. sarconeurum</em> persisted <em>in situ</em> over several glacial periods in refugia both in the peripheral maritime Antarctic and within the Antarctic continent. Disparity in genetic diversity among these areas hypothetically reflects asymmetric changes of reproduction mode in the past. Finally, nested topology of Patagonian subclades and ancestry analysis indicates that South American populations were secondary and originated through multiple dispersal from the Antarctic region.</span></p>
Data from: In both directions: Expansions of European land snails to the north and south from glacial refugia
<p><strong>Aim</strong>: The location of glacial refugia and the timing of postglacial colonisations remain of interest because together they inform about the ability of species to track shifting climates. In the associated paper, we tested a hypothesis that a central European forest land snail species survived in a northern refugium, which was proposed based on fossil finds indirectly dated to the Last Glacial Maximum and Late Glacial. We assessed the credibility of our results by comparing them to those obtained from three other, broadly sympatric land snail species.</p> <p><strong>Location</strong>: Central Europe and the Balkans.</p> <p><strong>Taxon</strong>: Pulmonate land snails: <em>Monachoides incarnatus</em> (Hygromiidae) and <em>Helix pomatia</em>, <em>Helix thessalica,</em> and <em>Caucasotachea vindobonensis</em> (Helicidae).</p> <p><strong>Methods</strong>: We used continuous phylogeographic analysis of mitochondrial data to trace the origin of postglacially expanding lineages and direct radiocarbon dating to verify the presumed glacial presence of <em>M. incarnatus</em> on the territories of Czechia and Slovakia. Geolocated concatenated sequences of partial 16S rRNA and cytochrome c oxidase subunit I were analysed using BEAST 1.10.4. and conclusions were drawn from the reconstructed geographic positions of internal nodes in the resulting phylogenetic trees.</p> <p><strong>Data</strong>: Input files for the phylogeograpic analyses, containing the sequence alignments and analysis settings, and the trees summarizing the results of the analyses.</p>
Data from: Climate refugia along Lake Superior's shores: Disjunct arctic-alpine plants rely on cool shoreline temperatures but are unlikely to persist under climate warming
<p>Climate refugia can serve as remnant habitat or stepping stones for species dispersal under climate warming. The largest freshwater lake by surface area, Lake Superior, USA and Canada, serves as a model system for understanding cooling-mediated local refugia, as its cool water temperatures and wave action have maintained shoreline habitats suitable for southern disjunct populations of arctic-alpine plants since deglaciation. Here we seek to explain spatial patterns and environmental drivers of arctic-alpine plant refugia along Lake Superior's shores, and assess future risk to refugia under moderate (+3.5 °C) and warmest (+5.7 °C) climate warming scenarios. First, we examined how the interactive effects of summer surface water temperatures and wind affected onshore temperatures, resulting in areas of cooler refugia. Second, we developed an ecological niche model for presence of disjunct arctic-alpine refugia (pooling 1253 occurrences from 58 species) along the lake's shoreline. Third, we fit species distribution models for 20 of the most common arctic-alpine disjunct species and predicted presence to identify refugia hotspots. Finally, we used the two climate warming scenarios to predict changes in presence of refugia and disjunct hotspots. Bedrock type, elevation above water, inland distance, July land surface temperature from MODIS/Terra satellite, and near-shore depth of water were the best predictors of disjunct occurrences. Overall, we predicted 2,236 km of the shoreline (51%) as disjunct refugia habitat for at least one species under current conditions, but this was reduced to 20% and 7% with moderate (894 km) and warmest (313 km) climate change projections.</p>
Fig. 2 in Phylogeography and potential glacial refugia of terrestrial gastropod Faustina faustina (Rossmässler, 1835) (Gastropoda: Eupulmonata: Helicidae) inferred from molecular data and species distribution models
Fig. 2 Haplotype distribution for nuclear markers: ITS-2 (left) and 28S rRNA (right)
Shapefiles showing the locations of long-term climate change refugia and hotspots identified in the FutureMARES report "D6.3, Climate ready strategies for nature-based solutions"
<p>Shapefiles created for the report "D6.3, Climate ready strategies for nature-based solutions", a deliverable report from the Horizon Europe project FutureMARES</p> <p>These shapefiles summarise long-term patterns that emerge from the spatial-meta analysis of physical-biogeochemical and species distribution modelling data, providing an overview of the distribution of climate change refugia and climate change hotspots across six European case study areas between 2026 - 2069, and across the five scenarios considered in the FutureMARES project (Global Sustainability RCP2.6, National Enterprise RCP8.5, World Market RCP8.5, Status Quo RCP2.6 and Status Quo RCP8.5). </p> <p>Filenames refer to the case study area and scenario each set of shapefiles belong to. Details of the modelling datasets used in each of these analyses, the meta-analysis method and shapefile creation can be found in the relevant chapter in the report "D6.3, Climate ready strategies for nature-based solutions".</p>
An explicit test of Pleistocene survival in peripheral versus nunatak refugia in two high mountain plant species
<p>Pleistocene climate fluctuations had profound influence on the biogeographic history of many biota. As large areas in higher latitudes and high mountain ranges were covered by glaciers, biota were forced either to peripheral refugia (and possibly beyond to lowland refugia) or to interior refugia (nunataks), but nunatak survival remains controversial as it solely relies on correlative genetic evidence. Here, we test the nunatak hypothesis using two high alpine plant species of contrasting pollination modes (insect-pollinated Pedicularis aspleniifolia and wind-pollinated Carex fuliginosa) in the European Alps, a geographic model system to study Pleistocene biogeography. Employing the iDDC (integrative distributional, demographic and coalescent) approach, which couples species distribution modelling, spatial and temporal demographic simulation and Approximate Bayesian Computation, we explicitly test three hypotheses of glacial survival: (1) peripheral survival only, (2) nunatak survival only, and (3) nunatak plus peripheral survival. In P. aspleniifolia the nunatak plus peripheral survival hypothesis was supported by Bayes Factors (BF > 100), whereas in C. fuliginosa the peripheral survival only hypothesis, though best supported, could not be unambiguously distinguished from the nunatak plus peripheral survival hypothesis (BF = 5.58). These results are consistent with current habitat preferences (P. aspleniifolia extends to higher elevations) and the potential for genetic swamping, i.e., replacement of local genotypes via hybridization with immigrating genotypes (expected to be higher in the wind-pollinated C. fuliginosa). Although the persistence of plants on nunataks during glacial periods has been debated and studied over decades, this is one of the first studies to explicitly test the hypothesis instead of solely using correlative evidence.</p>
Ancient bears provide insights into Pleistocene ice age refugia in Southeast Alaska
<p>During the Late Pleistocene, major parts of North America were periodically covered by ice sheets. However, there are still questions about whether ice-free refugia were present in the Alexander Archipelago along the Southeast (SE) Alaska coast during the Last Glacial Maximum (LGM). Numerous subfossils have been recovered from caves in SE Alaska, including American black (<em>Ursus</em> <em>americanus</em>) and brown (<em>U</em>. <em>arctos</em>) bears, which today are found in the Alexander Archipelago but are genetically distinct from mainland bear populations. Hence, these bear species offer an ideal system to investigate long-term occupation, potential refugial survival, and lineage turnover. Here we present genetic analyses based on 99 new complete mitochondrial genomes from ancient and modern brown and black bears spanning the last ~45,000 years. Black bears form two SE Alaskan subclades that diverged >100,00 years ago, one preglacial and one postglacial. All postglacial ancient brown bears are closely related to modern brown bears in the archipelago, while a single preglacial brown bear is found in a distantly related clade. A hiatus in the bear subfossil record around the LGM and the deep split of their pre- and post-glacial subclades fail to support a hypothesis of continuous occupancy in SE Alaska throughout the LGM for either species. Our results are consistent with an absence of refugia along the SE Alaska coast but indicate that vegetation quickly expanded after deglaciation, allowing bears to recolonize the area after a short-lived LGM peak.</p>
Data for: Thermal refugia and persistence of Texas horned lizards (Phrynosoma cornutum) in small towns
<p class="MsoNormal">Vegetation loss is a primary cause of habitat degradation and results in a decline in reptile species abundance due to loss of refuge from predators and hot temperatures, and foraging opportunities. Texas horned lizards (<em>Phrynosoma cornutum</em>) have disappeared from many areas in Texas, especially from urbanized areas, probably in large part due to loss of suitable habitat. This species still occurs in some small towns in Texas that still contain suitable habitat. Long-term data from Kenedy and Karnes City, Texas indicate that when study sites experienced significant shrub and vegetation removal horned lizards declined by 79%. We hypothesize the decline was due to the degradation of the thermal landscape for these lizards. We determined the preferred temperature range (<em>T<sub>set25 </sub></em>−<em>T<sub>set75</sub></em>) of lizards at our study sites and took field measurements of body temperature (<em>T<sub>b</sub></em>). Temperature loggers were also placed in three microhabitats across our study sites. Shrubs and vegetation provided the highest quality thermal environment, especially for about 5 hours midday when temperatures in the open and buried under the surface in the open exceeded the lizards' critical maximum temperature (<em>CT<sub>max</sub></em>) or were above their preferred temperature range. Horned lizard density was positively related to the thermal quality of the habitat across our sites. Texas horned lizards in these towns require a heterogeneous mix of closely spaced microhabitats and especially thermal refugia, such as shrubs and vegetation along fence lines and in open fields. Maintaining thermal refugia is one of the most important and practical conservation actions that can be taken to help small ectotherms persist in modified human landscapes and cope with increasing temperatures due to climate change.</p>
Phylogenetic endemism and ancestral area inference reveal historical refugia in the Greater Cape Floristic Region
Open the record for dataset details and reuse information.
Data from: Seeking temporal refugia to heat stress: Increasing nocturnal activity despite predation risk
Open the record for dataset details and reuse information.
Data from: European common frog (Rana temporaria) recolonised Switzerland from multiple glacial refugia in northern Italy via trans- and circum-Alpine routes
Open the record for dataset details and reuse information.
Data from: Climate refugia along Lake Superior’s shores: Disjunct arctic-alpine plants rely on cool shoreline temperatures but are unlikely to persist under climate warming
Open the record for dataset details and reuse information.
Data from: The potential role of temperate Japanese regions as refugia for the coral Acropora hyacinthus in the face of climate change
Open the record for dataset details and reuse information.
Data from: Multiple glacial refugia and contemporary dispersal shape the genetic structure of an endemic amphibian from the Pyrenees
Open the record for dataset details and reuse information.
Modelling 21st-century refugia and the impact of climate change on Amazonia's largest primates
Open the record for dataset details and reuse information.
Data from: Drivers of kelp forest refugia during successive disturbance events
Open the record for dataset details and reuse information.
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.