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275 results for “refugia”
Data from: Will Current Protected Areas Harbour Refugia for Threatened Arctic Vegetation Types until 2050? A First Assessment
<p>We present predictions of Arctic vegetation for 2050 based on a combination of climate models (namely, EC-Earth3-Veg, IPSL-CM6A-LR, and MRI-ESM2-0), emission scenarios (names, SSP126 and SSP585) and tree dispersal rate scenarios (unrestricted, 20km and 5km) based on the methods of Pearson et al. (2013) and the new raster version of the Circumpolar Arctic Vegetation Map (CAVM) (Raynolds et al. 2019). We additionally present a dataset summarising total areas for each vegetation type in the CAVM and the forecasted models based on the computation of zonal histograms in ArcGIS (zonal_histogram_results.csv), for the total Arctic as well as only within protected areas, defined by the Map of Arctic Protected Areas (CAFF and PAME 2017). We also present a potential map of refugia for what we deem the realistic model (IPSL, SSP585, 20 km tree dispersal) as a raster file. Refugia were identified as regions where the vegetation remained the same between the CAVM and the predictions. Additionally, we present a map of model agreement, showing the degree to which other models agree with the vegetation classification for our refugia.</p> <p>All predictions named according to the tree dispersal rate, climate model, and emissions scenario, preceded by the term "pred". For example: "pred_unres_mri_585" represents the unrestricted tree dispersal, MRI-ESM-0 climate model, and SSP585 scenario-based prediction. The MRI-ESM-0 x SSP585 combination had gaps in data which results in a lack of predictions in some areas; this affects 3 models.</p> <p>Further details and all code associated with these datasets are found <a href="https://github.com/PlekhanovaElena/Arctic_vegetation_prediction">here</a>.</p>
Shapefiles showing the locations of long-term climate change refugia and hotspots identified in the FairSeas report "A Climate Resilient Path for Ireland's Marine Protected Areas Network"
<p>Shapefiles created for the report "A Climate Resilient Path for Ireland’s Marine Protected Areas Network", an addendum chapter to "Revitalising Our Seas report: Identifying<br>Areas of Interest for Marine Protected Area Designation in Irish Waters"</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 Ireland's National Marine Planning Framework between 2026 - 2069, and across the two emissions scenarios considered in the report (RCP4.5 and RCP8.5). </p> <p>Filenames refer to the specific analysis each set of shapefiles belong to: Benthic habitats, benthic megafauna, pelagic habitats, pelagic megafauna and forage fish. Details of the modelling datasets used in each of these analyses, the meta-analysis method and shapefile creation can be found in Annex A1 in the report "A Climate Resilient Path for Ireland’s Marine Protected Areas Network".</p>
Soil geochemistry and microbial community data from glaciated and potential glacial refugia sites in the McMurdo Dry Valleys, Antarctica (1993-2019)
A study was conducted to examine soil microbial communities and associated geochemical parameters at potential glacial refugia and glaciated control sites throughout the McMurdo Dry Valleys region of Antarctica. Soil samples were collected as part of ongoing long-term monitoring efforts by the McMurdo Dry Valleys Long Term Ecological Research program (MCM LTER). The oldest samples used in this study were collected during the 1993-1994 austral summer, and the newest from the 2018-2019 austral summer. "Refugia" sites were selected based on geographical positions and elevations indicative of potential glacial refugia status. Each refugia site was paired with a lower elevation "glaciated" site in the same dry valley that was not likely to have functioned as a refugium. Six replicate soils per sampling site were sequenced with 16S primers following Earth Microbiome Project protocols, filtered using the DADA2 pipeline, and clustered to amplicon sequence variant using the SILVA reference database to generate the microbial classification table included herein. Soil samples were also analyzed for various geochemical parameters as part of this study, which include P, K, NO3-, gravimetric water content, percent organic matter, pH, and electroconductivity.
Figure 2 in Forest monkeys and Pleistocene refugia: a phylogeographic window onto the disjunct distribution of the Chlorocebus lhoesti species group
Figure 2. All possible patterns of relationships among the lhoesti group species. A, topology consistent with a vicariant scenario in which the distribution of a widespread common ancestor fragments into three segments – nearly simultaneously – as the result of habitat deterioration associated with a Pleistocene glacial cycle. B, topology consistent with an alternative vicariant scenario, in which ancestral populations of Chlorocebus preussi and Chlorocebus solatus remain in contact for a short time after the divergence of Chlorocebus lhoesti, because the former two stocks range within the same Pleistocene refuge. C, tree consistent with a dispersal hypothesis in which early C. preussi populations (following divergence from C. solatus) migrate along the northern rim of the Congo Basin, and found a new lineage (C. lhoesti) in the Albertine region (see Fig. 1). D, tree consistent with a dispersal hypothesis in which early C. solatus populations (following divergence from C. preussi) conduct a similar transcontinental migration, but along the southern rim of the Congo Basin (see Fig. 1).
Climatic refugia and reduced extinction correlate with underdispersion in mammals and birds in Africa
Macroevolutionary patterns, often inferred from metrics of community relatedness, are often used to ascertain major evolutionary processes shaping communities. These patterns have been shown to be informative of biogeographic barriers, of habitat suitability and invasibility (especially with regards to environmental filtering), and of regions that function as evolutionary cradles (i.e., sources of diversification) or museums (i.e., regions of reduced extinction). Here, we analysed continental datasets of mammal and bird distributions to identify primary drivers of community evolution on the African continent for mostly-endothermic vertebrates. We find that underdispersion (i.e., relatively low phylogenetic diversity compared to species richness) closely correlates with specific ecoregions that have been identified as climatic refugia in the literature, regardless of whether these specific regions have been touted as cradles or museums. Using theoretical models of identical communities that differ only with respect to extinction rates, we find that even small suppressions of extinction rates can result in underdispersed communities, supporting the hypothesis that climatic stability can lead to underdispersion. We posit that large-scale patterns of under- and overdispersion between regions of similar species richness are more reflective of a particular region's extinction potential, and that the very nature of refugia can lead to underdispersion via the steady accumulation of species richness through diversification within the same ecoregion during climatic cycles. Thus, patterns of environmental filtering can be obfuscated by environments that coincide with biogeographic refugia, and considerations of regional biogeographic history are paramount for inferring macroevolutionary processes. --
Riparian buffers provide refugia during secondary forest succession
<p>Aim Secondary forests regenerating from human disturbance are increasingly becoming a predominant forest type in many regions, and they play a significant role in forest community dynamics. Understanding the factors that underlie the variation in species responses during secondary succession is important for understanding community assembly and biodiversity monitoring and management. Because species vary in ecology and behavior, responses to ecosystem change should vary among species. Here, we show that habitat type (riparian, upland), phylogeny, and species traits mediate anuran and lizard probability of occurrence and species richness in pasture and secondary forest. Location Sarapiquí and Osa Peninsula, Costa Rica. Methods We used phylogenetic occupancy models to estimate assemblage-level and species-specific responses to forest succession in 30 chronosequence sites that include pasture, secondary forest regenerating from pasture, and mature forest sites. Results For the majority of species, we found increasing probability of occurrence in upland habitats as forest regenerated from pasture to secondary forest and similar probability of occurrence in riparian habitats across pasture, secondary forest, and mature forest sites. Species' responses to forest stage were phylogenetically correlated, and the trend was especially strong for anuran response to pasture sites. Anurans with lotic larval habitat had a positive occupancy response to pasture upland habitat and anurans with lentic larval habitat had a variable response to different forest stages compared to mature forest.</p>
The role of multiple Pleistocene refugia in promoting diversification in the Pacific Northwest
<p>Pleistocene glacial cycles drastically changed the distributions of taxa endemic to temperate rainforests in the Pacific Northwest, with many experiencing reduced habitat suitability during glacial periods. In this study, we investigate whether glacial cycles promoted intraspecific divergence and whether subsequent range changes led to secondary contact and gene flow. For seven invertebrate species endemic to the PNW, we estimated Species Distribution Models (SDMs) and projected them onto current and historical climate conditions to assess how habitat suitability changed during glacial cycles. Using single nucleotide polymorphism (SNP) data from these species, we assessed population genetic structure and used a machine-learning approach to compare models with and without gene flow between populations upon secondary contact after the Last Glacial Maximum (LGM). Finally, we estimated divergence times and rates of gene flow between populations. SDMs suggest that there was less suitable habitat in the North Cascades and Northern Rocky Mountains during glacial compared to interglacial periods, resulting in reduced habitat suitability and habitat fragmentation during the LGM. Our genomic data identify population structure in all taxa and support gene flow upon secondary contact in five of the seven taxa. Parameter estimates suggest that population divergences date to the later Pleistocene for most populations. Our results support the role of refugial dynamics in driving intraspecific divergence in the Cascades Range. In these invertebrates, population structure often does not correspond to current biogeographic or environmental barriers. Rather, population structure may reflect refugial lineages that have since expanded their ranges, often leading to secondary contact between once isolated lineages.</p>
When resilience is not enough: 2022 extreme marine heatwave threatens climatic refugia for a habitat-forming Mediterranean octocoral
<p>Climate change is impacting ecosystems worldwide, and the Mediterranean Sea is no exception. Extreme climatic events, such as marine heat waves (MHWs), are increasing in frequency, extent, and intensity during the last decades, which has been associated with an increase in mass mortality events for multiple species. Coralligenous assemblages, where the octocoral <em>Paramuricea clavata</em> lives, are strongly affected by MHWs. The Medes Islands Marine Reserve (NW Mediterranean) was considered a climate refugia for <em>P. clavata</em>, as their populations were showing some resilience to these changing conditions. In this study, we assessed the impacts of the MHWs that occurred between 2016 and 2022 in seven shallow populations of the octocoral <em>P. clavata</em> from a Mediterranean Marine Protected Area. The years that the mortality rates increased significantly were associated with the ones with strong MHWs, 2022 being the one with higher mortalities. In 2022, with 50 MHW days, the proportion of total affected colonies was almost 70%, with a proportion of the injured surface of almost 40%, reaching levels never attained in our study site since the monitoring was started. We also found spatial variability between the monitored populations. Whereas few of them showed low levels of mortality, others lost around 75% of their biomass. The significant impacts documented here raise concerns about the future of shallow <em>P. clavata</em> populations across the Mediterranean, suggesting that the resilience of this species may not be maintained to sustain these populations face the ongoing warming trends.</p>
Stream temperature data for Alaska Sustainable Salmon Fund project 53007 Assessing Thermal Habitat Variability to Identify Refugia in SE Alaska Subsistence Salmon Watersheds
<p>Hourly stream temperature data were collected in eight watersheds in southeast Alaska to better understand within-watershed thermal heterogeneity. Watersheds include: Chilkat, Chilkoot, Klag, Cowee, Peterson (Juneau road system), Saltery, Kadashan, and Klawock. Site latitude and longitude are recorded in the metadata file. Data were collected with HOBO Onset Pro V2 or HOBO TidbiT MX 400 temperature loggers following the protocols in <a href="https://doi.org/10.1016/j.ejrh.2015.07.008">Mauger et al, 2015</a>. Data collection dates range from January 1, 2020 to November 2, 2023, although not all sites cover this entire date range. </p>
Fig. 1 in Mitochondrial Dna Diversity Of The Alpine Newt (Ichthyosaura Alpestris) In The Carpathian Basin: Evidence For Multiple Cryptic Lineages Associated With Pleistocene Refugia*
Fig. 1. Sampling sites and haplotypes found in and around the Carpathian Basin. Sam- ples collected in this study are marked with circles and haplotype codes, and previously
Fig. 5 in Mitochondrial Dna Diversity Of The Alpine Newt (Ichthyosaura Alpestris) In The Carpathian Basin: Evidence For Multiple Cryptic Lineages Associated With Pleistocene Refugia*
Fig. 5. Original drawings by O. Gy. Dely: male (A, B) and female (C, D) Ichthyosaura alpestris alpestris head shape from dorsal (A, C) and lateral (B, D) view
Fig. 4 in Mitochondrial Dna Diversity Of The Alpine Newt (Ichthyosaura Alpestris) In The Carpathian Basin: Evidence For Multiple Cryptic Lineages Associated With Pleistocene Refugia*
Fig. 4. Holotype of Triturus (=Ichthyosaura) alpestris bakonyiensis (Dely, 1964) (HNHM- HER-61.27.1.) from dorsal (A), lateral (B) and ventral (C) view
Fig. 8 in Mitochondrial Dna Diversity Of The Alpine Newt (Ichthyosaura Alpestris) In The Carpathian Basin: Evidence For Multiple Cryptic Lineages Associated With Pleistocene Refugia*
Fig. 8. Original drawings by O. Gy. Dely: female (A–D) and male (E–H) Ichthyosaura alpestris bakonyiensis skull from dorsal (A, E), ventral (B, F), lateral (C, G) and posterior (D, H) view
Fig. 7 in Mitochondrial Dna Diversity Of The Alpine Newt (Ichthyosaura Alpestris) In The Carpathian Basin: Evidence For Multiple Cryptic Lineages Associated With Pleistocene Refugia*
Fig. 7. Original drawings by O. Gy. Dely: female (A–D) and male (E–H) Ichthyosaura alpestris alpestris skull from dorsal (A, E), ventral (B, F), lateral (C, G) and posterior (D, H) view
Fig. 3 in Mitochondrial Dna Diversity Of The Alpine Newt (Ichthyosaura Alpestris) In The Carpathian Basin: Evidence For Multiple Cryptic Lineages Associated With Pleistocene Refugia*
Fig. 3. Median-joining network of the combined mtDNA haplotypes found in and around the Carpathian Basin (drawn with PopArt 1.7). Inset: distribution of Ichthyosaura alpestris in this region. On the network, circles with haplotype names mark haplotypes found in this
Fig. 6 in Mitochondrial Dna Diversity Of The Alpine Newt (Ichthyosaura Alpestris) In The Carpathian Basin: Evidence For Multiple Cryptic Lineages Associated With Pleistocene Refugia*
Fig. 6. Original drawings by O. Gy. Dely: male (A, B) and female (C, D) Ichthyosaura alpestris bakonyiensis head shape from dorsal (A, C) and lateral (B, D) view
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
<p>Climate change poses a threat to biodiversity, and it is unclear whether species can adapt to or tolerate new conditions, or migrate to areas with suitable habitats. Reconstructions of range shifts that occurred in response to environmental changes since the last glacial maximum from species distribution models (SDMs) can provide useful data to inform conservation efforts. However, different SDM algorithms and climate reconstructions often produce contrasting patterns, and validation methods typically focus on accuracy in recreating current distributions, limiting their relevance for assessing predictions to the past or future. We modeled historically suitable habitat for the threatened North American tree green ash (<em>Fraxinus pennsylvanica</em>) using 24 SDMs built using two climate models, three calibration regions, and four modeling algorithms. We evaluated the SDMs using contemporary data with spatial block cross-validation and compared the relative support for alternative models using a novel integrative method based on coupled demographic-genetic simulations. We simulated genomic datasets using habitat suitability of each of the 24 SDMs in a spatially-explicit model. Approximate Bayesian Computation (ABC) was then used to evaluate the support for alternative SDMs through comparisons to an empirical population genomic dataset. Models had very similar performance when assessed with contemporary occurrences using spatial cross-validation, but ABC model selection analyses consistently supported SDMs based on the CCSM climate model, an intermediate calibration extent, and the generalized linear modeling algorithm. Finally, we projected the future range of green ash under four climate change scenarios. Future projections using the SDMs selected via ABC suggest only minor shifts in suitable habitat for this species, while some of those that were rejected predicted dramatic changes. Our results highlight the different inferences that may result from the application of alternative distribution modeling algorithms and provide a novel approach for selecting among a set of competing SDMs with independent data.</p>
Data for Coastal Fog and Low Clouds Provide Intertidal Organisms Refugia During Summer Heat
<p>This repository contains data and code relevant to the paper<br>Coastal Fog and Low Clouds Provide Intertidal Organisms Refugia During Summer Heat<br>by Jessica Lundquist, Autumn Nguyen, Steven Pestana, and Eli Schwat<br>contact person: Jessica Lundquist, University of Washington, jdlund@uw.edu<br>submitted to <em>Geophysical Research Letters</em><br>July 29, 2024</p> <p>Files are as follows:</p> <p>Paper files (note, these are submitted files, and may be modified in the final published version):<br>Lundquist_GRL_Manuscript_July29.pdf Manuscript file, main text and figures, submitted July 29, 2024<br>Lundquist_GRL_SuppInfo_July_29.pdf Supplemental Information file, submitted July 29, 2024</p> <p>Movie files of timelapse photographs from each of the sites:<br>timeLapseCattlePoint_July_Oct_2022.mp4 Images from Cattle Point site, facing Lopez Island<br>timeLapseFHL_facingShaw_July_2022.mp4 Images from Friday Harbor Laboratory (FHL) site, facing Shaw Island<br>timeLapseFHL_facingShaw_July_Nov_2022.mp4 Images from Friday Harbor Laboratory (FHL) site, facing Shaw Island<br>timeLapseMtDallas_view_2022.mp4 Images from Mt. Dallas site, looking towards the coast, with FHL toward the left of the image, and Cattle Point towards the right of the image.</p> <p>Temperature data files:<br>SJI_Tdata_site1.nc Temperature and relative humidity data from Hobo datalogger at Friday Harbor Laboratories Weather station location<br>SJI_Tdata_site2.nc Temperature and relative humidity data from Hobo datalogger at Mt. Dallas location <br>SJI_Tdata_site3.nc Temperature and relative humidity data from Hobo datalogger at Cattle Point location<br>SJI_Tdata_site4.nc Temperature and relative humidity data from Friday Harbor Laboratories Weather Station <br>FHairportdata.txt Raw data from Friday Harbor airport weather station.</p> <p>Reanalysis data files:<br>SJI_strongInv2022.txt File of dates used to select days of strong inversion to assess anomalies<br>500mbHtanomalies.205.175.106.80.157.13.39.23.nc 500hPa height anomaly data for Fig 2e map<br>Tanomaly850mbyycompos.205.175.106.80.157.13.47.49.nc 850hPa temperature anomaly data for Fig 2f map</p> <p><br>Matlab files for plotting figures in paper<br>(note that Matlab software is not required to read these files)<br>TRH2.mat Temperature and relative humidity data from in situ locations for 2022<br>Tides2021_23.mat Friday Harbor tide hight data<br>GOESclouds.mat Cloud height data for the locations with surface observations<br>FHairportdata.mat Temperature data from the Friday Harbor airport<br>Lundquist_GRL_FLCC_figurecode.m Matlab code for using the datafiles above to make all of the figures in the paper</p>
Fig. 5 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. 5 BEAST phylogenetic tree based on the COI sequences. Node values indicate divergence estimated in MYA
Fig. 7 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. 7 Areas of climatic stability over time periods from the LGM through the present, based on summed climatic suitability models for the LGM, mid-Holocene, and present day for three differed GCMs. Stability increase from red to yellow color. White-filled areas show the
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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.