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275 results for “refugia”
Quantitative estimates of glacial refugia for chimpanzees (Pan troglodytes) since the Last Interglacial (120,000 BP)
<p>Paleoclimate reconstructions have enhanced our understanding of how past climates have shaped present-day biodiversity. We hypothesize that the geographic extent of Pleistocene forest refugia and suitable habitat fluctuated significantly in time during the late Quaternary for chimpanzees (Pan troglodytes). Using bioclimatic variables representing monthly temperature and precipitation estimates, past human population density data and an extensive database of georeferenced presence points, we built a model of changing habitat suitability for chimpanzees at fine spatio-temporal scales dating back to the Last Interglacial (120,000 BP). Our models cover a spatial resolution of 0.0467 degrees (approximately 5.19 km2 grid cells) and a temporal resolution of between1,000–4,000 years . Using our model, we mapped habitat stability over time using three approaches, comparing our modelled stability estimates to existing knowledge of Afrotropical refugia, as well as contemporary patterns of major keystone tropical food resources used by chimpanzees, figs (Moraceae) and palms (Arecacae). Results show habitat stability congruent with known glacial refugia across Africa, suggesting their extents may have been underestimated for chimpanzees, with potentially up to ~60,000 km2 of previously unrecognized glacial refugia. The refugia we highlight coincide with higher species richness for figs and palms. Our results provide spatio-temporally explicit insights into the role of refugia across the chimpanzee range, forming the empirical foundation for developing and testing hypotheses about behavioural, ecological and genetic diversity with additional data. This methodology can be applied to other species and geographic areas when sufficient data are available.</p>
Figure 3. Likelihood trees generated from the X in Forest monkeys and Pleistocene refugia: a phylogeographic window onto the disjunct distribution of the Chlorocebus lhoesti species group
Figure 3. Likelihood trees generated from the X- and Y-chromosomal datasets. Bootstrap values of 50 and above (100 replicates, 'fast' stepwise addition) are included throughout the trees. The dashed ovals indicate the consistent recovery of a lhoesti group monophyly. One Chlorocebus solatus sample (CS026) is derived from a female (XX), and therefore is not represented in the Y-chromosomal tree.
Figure 1 in Forest monkeys and Pleistocene refugia: a phylogeographic window onto the disjunct distribution of the Chlorocebus lhoesti species group
Figure 1. Present ranges of the lhoesti group relative to two putative Pleistocene refugia and the Congo River Basin. Species distributions follow Kingdon (1997), and refuges follow Grubb (2001). Harrison (1988) hypothesized that the evolutionary dispersal of the lhoesti group followed an eastward path around the Congo Basin, along either its northern or southern rim. In contrast, Kaplin (2002) suggested that the lhoesti group ancestor may have spread through the basin, with its present distribution being the result of a vicariant event.
Key triggers of adaptive genetic variability of sessile oak [Q. petraea (Matt.) Liebl.] from the Balkan refugia: outlier detection and association of SNP loci from ddRAD-seq data
<p>Knowledge on the genetic composition of <em>Quercus petraea</em> in south-eastern Europe is limited despite the species' significant role in the re-colonisation of Europe during the Holocene, and the diverse climate and physical geography of the region. Therefore, it is imperative to conduct research on adaptation in sessile oak to better understand its ecological significance in the region. While large sets of SNPs have been developed for the species, there is a continued need for smaller sets of SNPs that are highly informative about the possible adaptation to this varied landscape. By using double digest restriction site associated DNA sequencing data from our previous study, we mapped RAD-tag sequences to the <em>Quercus robur</em> reference genome and identified a set of SNPs putatively related to drought stress-response. A total of 179 individuals from eighteen natural populations at sites covering heterogeneous climatic conditions in the southeastern natural distribution range of <em>Q. petraea</em> were genotyped. The detected highly polymorphic variant sites revealed three genetic clusters with a generally low level of genetic differentiation and balanced diversity among them but showed a north–southeast gradient. Selection tests showed nine outlier SNPs positioned in different functional regions. Genotype-environment association analysis of these markers yielded a total of 53 significant associations, explaining 2.4–16.6% of the total genetic variation. Our work exemplifies that adaptation to drought may be under natural selection in the examined <em>Q. petraea</em> populations.</p>
Data from: Multiple refugia from penultimate glaciations in East Asia demonstrated by phylogeography and ecological modelling of an insect pest
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Quantitative estimates of glacial refugia for chimpanzees (Pan troglodytes) since the Last Interglacial (120,000 BP)
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Riparian buffers provide refugia during secondary forest succession
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The role of multiple Pleistocene refugia in promoting diversification in the Pacific Northwest
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Climatic refugia and reduced extinction correlate with underdispersion in mammals and birds in Africa
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Limited migration from physiological refugia constrains the rescue of native gastropods facing an invasive predator
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Data from: Integrating genomic data and simulations to evaluate alternative species distribution models and improve predictions of glacial refugia and future responses to climate change
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When resilience is not enough: 2022 extreme marine heatwave threatens climatic refugia for a habitat-forming Mediterranean octocoral
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Data from: Multiple glacial refugia and contemporary dispersal shape the genetic structure of an endemic amphibian from the Pyrenees
<p>Historical factors (colonization scenarios, demographic oscillations) and contemporary processes (population connectivity, current population size) largely contribute to shaping species' present-day genetic diversity and structure. In this study, we use a combination of mitochondrial and nuclear DNA markers to understand the role of Quaternary climatic oscillations and present-day gene flow dynamics in determining the genetic diversity and structure of the newt <i>Calotriton asper </i>(Al. Dugès, 1852), endemic to the Pyrenees. Mitochondrial DNA did not show a clear phylogeographic pattern and presented low levels of variation. In contrast, microsatellites revealed five major genetic lineages with admixture patterns at their boundaries. Approximate Bayesian computation analyses and linear models indicated that the five lineages likely underwent separate evolutionary histories and can be tracked back to distinct glacial refugia. Lineage differentiation started around the Last Glacial Maximum at three focal areas (western, central and eastern Pyrenees) and extended through the end of the Last Glacial Period in the central Pyrenees, where it led to the formation of two more lineages. Our data revealed no evidence of recent dispersal between lineages, whereas borders likely represent zones of secondary contact following expansion from multiple refugia. Finally, we did not find genetic evidence of sex-biased dispersal. This work highlights the importance of integrating past evolutionary processes and present-day gene flow and dispersal dynamics, together with multilocus approaches, to gain insights into what shaped the current genetic attributes of amphibians living in montane habitats.</p>
High genomic diversity in the bank vole at the northern apex of a range expansion: the role of multiple colonizations and end-glacial refugia
<p>The history of repeated northern glacial cycling and southern climatic stability has long dominated explanations for how genetic diversity is distributed within temperate species in Eurasia and North America. However, growing evidence indicates the importance of cryptic refugia for northern colonization dynamics. An excellent geographic region to assess this is Fennoscandia, where recolonization at the end of the last glaciation was restricted to specific routes and temporal windows. We used genomic data to analyze genetic diversity and colonization history of the bank vole (<i>Myodes glareolus</i>) throughout Europe (> 800 samples) with Fennoscandia as the northern apex. We inferred that bank voles colonized Fennoscandia multiple times by two different routes; with three separate colonizations via a southern land-bridge route deriving from a 'Carpathian' glacial refugium and one via a north-eastern route from an 'Eastern' glacial refugium near the Ural Mts. Clustering of genome-wide SNPs revealed tremendous diversity in Fennoscandia, with eight genomic clusters: three of Carpathian origin and five Eastern. Time estimates revealed that the first of the Carpathian colonizations occurred before the Younger Dryas (YD), meaning that the first colonists survived the YD in Fennoscandia. Results also indicated that introgression between bank and northern red-backed voles (<i>Myodes rutilus</i>) took place in Fennoscandia just after end-glacial colonization. Therefore, multiple colonizations from the same and different cryptic refugia, temporal and spatial separations and interspecific introgression have shaped bank vole genetic variability in Fennoscandia. Together, these processes drive high genetic diversity at the apex of the northern expansion in this model species.</p>
Multiple drainage reversal episodes and glacial refugia in a Patagonian fish revealed by sequenced microsatellites
<p>The rise of the southern Andes and the Quaternary glacial cycles influenced the landscape of Patagonia, affecting the phylogeographic and biogeographic patterns of its flora and fauna. Here we examine the phylogeography of the freshwater fish, Percichthys trucha, using 53 sequenced microsatellite DNA markers. Fish (N=835) were collected from 16 river systems (46 locations) spanning the species range on both sides of the Andes. Eleven watersheds drain to the Pacific, five of which are trans-Andean (headwaters east of Andes). The remaining five drainages empty into the Atlantic. Three analytical approaches (neighbour-joining tree, hierarchical AMOVAs, STRUCTURE) revealed evidence of historic drainage reversals: Fish from four of the five trans-Andean systems (Puelo, Futalaufquen/Yelcho, Baker, Pascua) exhibited greater genetic similarity with Atlantic draining systems than with Pacific systems with headwaters west of Andes. Present-day drainage (Pacific vs. Atlantic) explained only 5% of total genetic variance, while ancestral drainage explained nearly 27% of total variance. Thus, the phylogeographic structure of Percichthys trucha is consistent with episodes of drainage reversal in multiple systems and suggests a major role for deglaciation in the genetic and indeed the geographic distribution of P. trucha in Patagonia. The study emphasizes the significant role of historical processes in the current pattern of genetic diversity and differentiation in a fish from a southern temperate region.</p>
Reconstructing hotspots of genetic diversity from glacial refugia and subsequent dispersal in Italian common toads (Bufo bufo)
<p>Genetic diversity feeds the evolutionary process and allows populations to adapt to environmental changes. However, we still lack a thorough understanding of why hotspots of genetic diversity are so 'hot'. Here, we analysed the relative contribution of bioclimatic stability and genetic admixture between divergent lineages in shaping spatial patterns of genetic diversity in the common toad <i>Bufo bufo</i> along the Italian peninsula. We combined population genetic, phylogeographic and species distribution modelling (SDM) approaches to map ancestral areas, glacial refugia, and secondary contact zones. We consistently identified three phylogeographic lineages, distributed in northern, central and southern Italy. These lineages expanded from their ancestral areas and established secondary contact zones, before the last interglacial. SDM identified widespread glacial refugia in peninsular Italy, sometimes located under the present-day sea-level. Generalized linear models indicated genetic admixture as the only significant predictor of the levels of population genetic diversity. Our results show that glacial refugia contributed to preserving both levels and patterns of genetic diversity across glacial-interglacial cycles, but not to their formation, and highlight a general principle emerging in Mediterranean species: higher levels of genetic diversity mark populations with substantial contributions from multiple genetic lineages, irrespective of the location of glacial refugia.</p>
Data from: Seeking temporal refugia to heat stress: Increasing nocturnal activity despite predation risk
<p>Flexibility in activity timing may enable organisms to quickly adapt to environmental changes. Under global warming, diurnally adapted endotherms may achieve a better energy balance by shifting their activity towards cooler nocturnal hours. However, this shift may expose animals to new or increased environmental challenges (e.g., increased predation risk, reduced foraging efficiency). We analysed a large dataset of activity data from 47 ibex (<em>Capra ibex</em>) in two protected areas, characterized by varying levels of predation risk (presence vs absence of the wolf – <em>Canis lupus</em>). We found that ibex increased nocturnal activity following warmer days and during brighter nights. Despite the considerable sexual dimorphism typical of this species and the consequent different predation-risk perception, males and females demonstrated consistent responses to heat in both predator-present and predator-absent areas. This supports the hypothesis that shifting activity towards nighttime may be a common strategy adopted by diurnal endotherms in response to global warming. As nowadays different pressures are pushing mammals towards nocturnality, our findings emphasize the urgent need to integrate knowledge of temporal behavioural modifications into management and conservation planning.</p>
Spatial priorities for climate-change refugia and connectivity for British Columbia (Version 1.1)
<p>Climate-informed conservation priorities in British Columbia (Version 1.1)</p> <p>Territorial acknowledgement:</p> <p>We respectfully acknowledge that we live and work across diverse unceded territories and treaty lands and pay our respects to the First Nations, Inuit and Métis ancestors of these places. We honour our connections to these lands and waters and reaffirm our relationships with one another.</p> <p><br>Suggested citation:</p> <p>Stolar, J., D. Stralberg, I. Naujokaitis-Lewis, S.E. Nielsen, and G. Kehm. 2024. Spatial priorities for climate-change refugia and connectivity for British Columbia (Version 1.1). Place of publication: University of Alberta, Edmonton, Canada. doi: 10.5281/zenodo.10603162</p> <p>Corresponding author: stolar@ualberta.ca</p> <p><br>Summary:</p> <p>The purpose of this project is to identify spatial locations of (a) vulnerabilities within British Columbia’s current network of protected areas and (b) priorities for conservation and management of natural landscapes within British Columbia under a range of future climate-change scenarios. This involved adaptation and implementation of existing continental- and provincial-scale frameworks for identifying areas that have potential to serve as refugia from climate change or corridors for species migration.</p> <p>Outcomes of this work include the provision of practical guidance for protected areas network design and vulnerabilities identification under climate change, with application to other regions and jurisdictions. Project results, in the form of multiple spatial prioritization scenarios, may be used to evaluate the resilience of the existing protected area network and other conservation designations to better understand the risks to British Columbia’s biodiversity in our changing climate.</p> <p><br>Description:</p> <p>These raster layers represent different scenarios of Zonation rankings of conservation priorities for climate resilience and connectivity between current and 2080s conditions for a provincial-scale analysis. Input conservation features included metrics of macrorefugia (forward and backward climate velocity (km/year), overlapping future and current habitat suitability for ~900 rare species in BC), microrefugia (presence of old growth ecosystems, drought refugia, glaciers/cool slopes/wetlands, and geodiversity), and connectivity. Please see details in the accompanying report.</p> <p><br>File nomenclature:</p> <p>.zip folder (Stolar_et_al_2024_CiCP_Zenodo_upload_Version_1.1.zip):<br>Contains the files listed below.</p> <p>Macrorefugia (2080s_macrorefugia.tif):<br>Scenarios for each taxonomic group (equal weightings for all species) (Core-area Zonation Function)<br>Climate-type velocity + species scenarios from above (Core-area Zonation; equal weightings)</p> <p>Microrefugia (microrefugia.tif):<br>Scenario with old growth forest habitat, landscape geodiversity, wetlands/cool slopes/glaciers, drought refugia (Core-area Zonation; equal weightings)</p> <p>Overall scenario (2080s_macro_micro_connectivity.tif):<br>Inputs from above (with equal weightings) + connectivity metrics (each weighted at 0.1) (Additive Benefit Function Zonation)</p> <p>Conservation priorities (Conservation_priorities_2080s.tif):<br>Overall scenario from above extracted to regions of low human footprint.</p> <p>Restoration priorities (Restoration_priorities_2080s.tif):<br>Overall scenario from above extracted to regions of high human footprint.</p> <p>Accompanying report (Stolar_et_al_2024_CiCP_Zenodo_upload_Version_1.1.pdf):<br>Documentation of rationale, methods and interpretation.</p> <p>READ_ME file (READ_ME_PLEASE.txt):<br>Metadata.</p> <p><br>Legend interpretation:</p> <p>Ranked Zonation priorities increase from 0 (lowest) to 1 (highest).</p> <p>Raster information:</p> <p>Columns and Rows: 1597, 1368<br>Number of Bands: 1<br>Cell Size (X, Y): 1000, 1000<br>Format: TIFF<br>Pixel Type: floating point <br>Compression: LZW</p> <p><br>Spatial reference:</p> <p>XY Coordinate System: NAD_1983_Albers<br>Linear Unit: Meter (1.000000)<br>Angular Unit: Degree (0.0174532925199433)<br>false_easting: 1000000<br>false_northing: 0<br>central_meridian: -126<br>standard_parallel_1: 50<br>standard_parallel_2: 58.5<br>latitude_of_origin: 45<br>Datum: D_North_American_1983</p> <p><br>Extent:</p> <p>West -139.061502 East -110.430823 <br>North 60.605550 South 47.680823 </p> <p><br>Disclaimer: </p> <p>The University of Alberta (UofA) is furnishing this deliverable "as is". UofA does not provide any warranty of the contents of the deliverable whatsoever, whether express, implied, or statutory, including, but not limited to, any warranty of merchantability or fitness for a particular purpose or any warranty that the contents of the deliverable will be error-free.</p> <p><br>Funding:<br> <br>We gratefully acknowledge the financial support of Environment and Climate Change Canada, the Province of British Columbia through the Ministry of Water, Land and Resource Stewardship) and the Ministry of Environment and Climate Change Strategy, the BC Parks Living Lab for Climate Change and Conservation, and the Wilburforce Foundation.</p>
Modelling 21st-century refugia and the impact of climate change on Amazonia's largest primates
<p>Edaphic and vegetation conditions can render climatically suitable sites inadequate for a species to persist, constraining the amount of suitable habitat and the possibilities of tracking preferred climatic conditions as they shift in response to climate change. We combined climatic and remotely sensed data to model current and future distributions of nine extant taxa of ateline primates across the Amazon basin. We used the models to identify and quantify potential range changes and refugia of suitable habitats from the present to the latter half of the 21st century.<strong> </strong>We applied an ensemble forecasting approach for species distribution models using 596 spatially rarefied occurrences. We parameterised these models by combining reflectance data from a basin‐wide Landsat TM/ETM+ image composite, three sets of bioclimatic layers containing data for the current period, and two different (moderate and worst-case) climate change scenarios for 2041-2070. Eight out of nine taxa are likely to experience pronounced range losses, with seven of them predicted to lose over 50% of their currently suitable habitats irrespective of climate change scenarios. Modelled ateline richness exhibited a broad decrease in high-richness areas and a possible redistribution along the northernmost parts of western Amazonia. Refugia from 21st-century climate change for the whole complex was mostly concentrated in western Amazonia, especially in its southern part. We identified hotspots of vulnerability to climate change and 21st-century refugia for all Amazonian atelines while accounting for habitat characteristics that are important to guarantee the continued existence of suitable habitats for these strictly arboreal taxa. Increasing the understanding of climate change impacts on Amazonia's largest primates can help to inform spatial conservation planning decisions and management to sustain forest-dwelling biodiversity over large areas such as Amazonia.</p>
Supporting data for identifying microclimate tree seedling refugia in post-wildfire landscapes
<p>High-severity wildfire in arid regions has caused ecological state change, transforming previously forested areas into shrublands. This dramatically alters the climatic envelope for tree seedlings, rendering the likelihood of returning post-wildlife landscapes to their previous state relatively low. We used a combination of sUAS imagery, satellite data and in-situ microclimate data recordings, together with a machine learning approach, to model monthly near-ground minimum, mean and max temperature as well as relative humidity and vapor pressure deficit in a previously forested area, which is now dominated by shrubs species. Spatially explicit models predicted recorded microclimate well (<i>r</i> = <span>0.73 to 0.97), and projections of models highlighted the solar buffering capacity of existing vegetation to alter the maximum temperature in the hottest month by ~12<sup>o</sup>C, increase relative humidity by ~20% and reduced vapor pressure deficit by 0.3mbar in locations 2m apart. By harnessing these microclimate refugia, the success rate of reforestation efforts in post-wildfire landscapes could be substantially increased and mitigate seedlings from climate warming at local scales.</span></p>
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
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.