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124 results for “temperature adaptation”
Projection of temperature-related mortality in 854 European cities under climate change and adaptation scenarios
<p>This repository contains the data and results from the paper <strong>Estimating future heat-related and cold-related mortality under climate change, demographic and adaptation scenarios in 854 European cities</strong> published in <em>Nature Medicine</em> (<a href="https://doi.org/10.1038/s41591-024-03452-2">https://doi.org/10.1038/s41591-024-03452-2</a>).</p> <p>It provides projections of excess death rates and burden for the period 2015-2099 for five age groups in 854 cities across 30 countries, under three Shared Socioeconomic Pathway (SSP) scenarios, and four adaptation scenarios. The results include point estimates for five-year periods and four global warming levels, along with 95% empirical confidence intervals. </p> <p>The fully reproducible analysis code using the data and producing the results included in this repository is provided in <a href="https://github.com/PierreMasselot/EUcityProj" target="_blank" rel="noopener">GitHub</a>. The results can be visualised and explored in a dedicated <a href="https://ehm-lab.shinyapps.io/vistemphip/">Shiny app</a>.</p> <h3>Content</h3> <p>This repository contains three zip files, each with an internal codebook:</p> <ul> <li><em>data.zip</em>: contains the input data necessary to run the analysis. It includes historical and projected daily temperature at the city level, age-group specific projections of population and survival rates at the country level, and exposure-response functions extracted from another Zenodo repository (<a href="https://doi.org/10.5281/zenodo.10288665" target="_blank" rel="noopener">https://doi.org/10.5281/zenodo.10288665</a>). This file also include a script showing how each dataset was extracted for the purpose of this projection study.</li> <li><em>results_csv.zip</em>: contains the full results from the health impact projections. It includes one file for each combination of geographical level (city, country, region or European wide) and scale of reporting (five year periods or global warming levels). </li> <li><em>results_parquet.zip</em>: contains the same information as the <em>results_csv.zip</em> but in a parquet format. This allows for more efficient storage and data reading.</li> </ul> <p>It is recommended to only download <em>results_csv.zip</em> for a quick exploration of the results, or only <em>results_parquet.zip</em> when the results are to be loaded into a software for deeper analysis.</p> <p> </p>
Locally adaptive temperature response of vegetative growth in Arabidopsis thaliana
<p>We investigated early vegetative growth of natural <em>Arabidopsis thaliana</em> accessions in cold, non-freezing temperatures, similar to temperatures these plants naturally encounter in fall at northern latitudes.</p> <p>Dataset includes:<br> - rosette area measurements over 3 weeks in a 16ºC and a 6ºC treatment. First phenoptying time point is at 14 days after stratification. Measurements were take twice per day.<br> These data are in file <a href="https://zenodo.org/api/files/54fc7139-99a8-4e7f-af87-d6754031f5d9/rawdata_combined_annotation.txt?versionId=7b707f81-723f-4059-b72b-9dfb9f5ddd2e">rawdata_combined_annotation.txt</a> and go together with <a href="https://zenodo.org/api/files/54fc7139-99a8-4e7f-af87-d6754031f5d9/outliers.csv?versionId=7287c919-1ed1-4b65-8e25-a75bb312c8fa">outliers.csv</a>, which contains outlying datapoints.</p> <p>- Seed Size measurements.<br> These data are in file <a href="https://zenodo.org/api/files/54fc7139-99a8-4e7f-af87-d6754031f5d9/seed_size_swedes_lab_updated.csv?versionId=fb739477-862b-45cb-8074-7a1d8e1650bb">seed_size_swedes_lab_updated.csv </a><br> </p> <p>The remainnig files are required to rerun the analyses and recreate figures.<br> Scripts to do so can be found in https://github.com/picla/growth_16C_6C/</p> <p><a href="https://zenodo.org/api/files/54fc7139-99a8-4e7f-af87-d6754031f5d9/1001genomes-accessions.csv?versionId=ee605038-bd9e-448f-9c96-1a8e980c1755">1001genomes-accessions.csv</a>: lists all accession from the 1001genomes project and their respective subpopulations.</p> <p><a href="https://zenodo.org/api/files/54fc7139-99a8-4e7f-af87-d6754031f5d9/2029_modified_MN_SH_wc2.0_30s_bilinear.csv?versionId=73c6c2bf-97bd-425f-bf7e-14b5a7cb162f">2029_modified_MN_SH_wc2.0_30s_bilinear.csv</a>: contains climate data for each accession, downloaded and prcocessed from www.worldclim.org</p> <p><a href="https://zenodo.org/api/files/54fc7139-99a8-4e7f-af87-d6754031f5d9/metabolic_distance.csv?versionId=8456f998-d0dc-4a80-b96f-c0c66c1c9731">metabolic_distance.csv</a>: contains the metabolic distance as calculated in Weiszmann et al. (https://www.biorxiv.org/content/10.1101/2020.09.24.311092v1)</p> <p><a href="https://zenodo.org/api/files/54fc7139-99a8-4e7f-af87-d6754031f5d9/RNAseq_samples.txt?versionId=6ae1518b-1a70-440d-b0bd-0ccdcb66665e">RNAseq_samples.txt</a>: sample description of the RNA-seq samples (data is downloadable from <a href="http://www.ncbi.nlm.nih.gov/bioproject/807069">http://www.ncbi.nlm.nih.gov/bioproject/807069)</a></p> <p><a href="https://zenodo.org/api/files/54fc7139-99a8-4e7f-af87-d6754031f5d9/ZAT12_downregulated_table10.csv?versionId=c6f7aa54-cb07-4378-a5a0-de12c6979b9b">ZAT12_downregulated_table10.csv</a>, <a href="https://zenodo.org/api/files/54fc7139-99a8-4e7f-af87-d6754031f5d9/ZAT12_upregulated_table9.csv?versionId=911a2aa2-f08f-4a20-85de-cfa7c58b73a8">ZAT12_upregulated_table9.csv</a>, <a href="https://zenodo.org/api/files/54fc7139-99a8-4e7f-af87-d6754031f5d9/CBF_regulon_DOWN_ParkEtAl2015.txt">CBF_regulon_DOWN_ParkEtAl2015.txt</a>, <a href="https://zenodo.org/api/files/54fc7139-99a8-4e7f-af87-d6754031f5d9/CBF_regulon_UP_ParkEtAl2015.txt?versionId=f7cacbda-eea6-4ac9-8f71-5ba74e3a67c4">CBF_regulon_UP_ParkEtAl2015.txt, </a><a href="https://zenodo.org/api/files/54fc7139-99a8-4e7f-af87-d6754031f5d9/CBF2_downregulated_table8.csv">CBF2_downregulated_table8.csv, </a><a href="https://zenodo.org/api/files/54fc7139-99a8-4e7f-af87-d6754031f5d9/CBF2_upregulated_table7.csv">CBF2_upregulated_table7.csv, </a><a href="https://zenodo.org/api/files/54fc7139-99a8-4e7f-af87-d6754031f5d9/HSFC1_regulon_ParkEtAl2015.txt">HSFC1_regulon_ParkEtAl2015.txt</a>: these files list genes that are involve din cold acclimation as described by Park et al. (https://onlinelibrary.wiley.com/doi/10.1111/tpj.12796), and Vogel et al.(https://onlinelibrary.wiley.com/doi/10.1111/j.1365-313X.2004.02288.x).</p> <p><strong>Material and Methods</strong></p> <p><em><strong>Rosette growth</strong></em></p> <p>Seeds of 249 natural accessions (Suppl. Data 1) of <em>Arabidopsis thaliana</em> described in the 1001 genomes project <a href="https://paperpile.com/c/UDgV3V/DUBI">(1001 Genomes Consortium 2016)</a> were sown on sieved (6 mm) substrate (Einheitserde ED63). Pots were filled with 71.5 g ±1.5 g of soil to assure homogenous packing. The prepared pots were all covered with blue mats <a href="https://paperpile.com/c/UDgV3V/1WUv">(Junker et al. 2014)</a> to enable a robust performance of the high-throughput image analysis algorithm. Seeds were stratified (4 days at 4ºC in darkness) after which they germinated and left to grow for 2 weeks at 21ºC (relative humidity: 55 %; light intensity: 160 µmol m-2 s-1; 14 h light). The temperature treatments were started by transferring the seedlings to either 6 °C or 16 °C. To simulate natural conditions temperatures fluctuated diurnally between 16-21 °C, 0.5-6 °C and 8-16 °C for the 21 °C initial growth conditions and the 6 °C and 16 °C treatments, respectively (<a href="https://docs.google.com/document/d/1Bmr7p24ZMh4yPFVV5oPeH2-T5S41TOFDS3au8JhtwsU/edit#fig_design">Fig.2</a>). Light intensity was kept constant at 160 µmol m-2 s-1 throughout the experiment. Relative humidity was set at 55% but in colder temperatures it rose uncontrollably to maximum 95%. Daylength was 9h during the 16°C and 6°C treatments.</p> <p>Each temperature treatment was repeated in three independent experiments. Five replicate plants were grown for every genotype per experiment. Plants were randomly distributed across the growth chamber with an independent randomisation pattern for each experiment. During the temperature treatments (14 DAS – 35 DAS), plants were photographed twice a day (1 hour. after/before lights switched on/off), using an RGB camera (IDS uEye UI-548xRE-C; 5MP) mounted to a robotic arm. At 35 DAS, whole rosettes were harvested, immediately frozen in liquid nitrogen and stored at -80 °C until further analysis. Rosette areas were extracted from the plant images using Lemnatec OS (LemnaTec GmbH, Aachen, Germany) software.</p> <p><em><strong>Seed size</strong></em></p> <p>We used the seeds produced by <a href="https://paperpile.com/c/UDgV3V/Jqsd">(Kerdaffrec et al. 2016)</a> and limited our measurements to the set of 123 Swedish accessions that overlapped with our growth dataset. After seed stratification for four days at 4ºC in darkness, mother plants were grown for 8 weeks at 4ºC under long-day conditions (16h light; 8h dark) to ensure proper vernalization. Temperature was raised to 21ºC (light) and 16ºC (dark) for flowering and seed ripening. Seeds were kept in darkness at 16ºC and 30% relative humidity, from the harvest until seed size measurements. For each genotype three replicates were pooled and about 200-300 seeds were sprinkled on 12 x 12 cm square, transparent Petri dishes. Image acquisition was performed as described in <a href="https://paperpile.com/c/UDgV3V/WH1e">(Exposito-Alonso et al. 2018)</a> by scanning dishes on a cluster of eight Epson V600 scanners. The resulting 1200 dpi .tiff images were analyzed in the Fiji software. Images were converted to 8-bit binary images and thresholded with the <em>setAutoThreshold("Defaultdark”) </em>command, and seed area was measured in squared mm by running the <em>Analyse Particles</em> command (inclusion parameters: size=0.04-0.25 circularity=0.70-1.00).</p> <p> </p> <p> </p> <p> </p> <p> </p>
Thermal adaptation in Aedes aegypti does not constrain temperature-sensitive growth of bacteria or dengue virus
<p>Data set and R script used for the following manuscript : </p> <p><strong>Thermal adaptation in <em>Aedes aegypti</em> does not constrain temperature-sensitive growth of bacteria or dengue virus</strong></p> <p><span lang="EN-US">Alida Kropf<sup>1*#</sup>, Stéphanie Dabo<sup>2</sup>, Marine Amann<sup>3</sup>, Louis Lambrechts<sup>2</sup>, Jacob C Koella<sup>1</sup></span></p> <p><span lang="EN-US">PROCEEDINGS OF THE ROYAL SOCIETY B THE ROYAL SOCIETY B BIOLOGICAL SCIENCES</span></p> <p><strong><em><span lang="IT-CH">DOI: 10.1098/rspb.2025-0832.R1 </span></em></strong></p>
Adaptation to environmental temperature in divergent clades of the nematode Pristionchus pacificus
<p><span>Because of ongoing climate change, populations of organisms are being subjected to stressful temperatures more often. This is especially problematic for ectothermic organisms, which are likely to be more sensitive to changes in temperature. Therefore, we need to know if ectotherms have adapted to environmental temperature and, if so, what are the evolutionary mechanisms behind such adaptation. Here, we use the nematode <em>Pristionchus pacificus</em> as a case study to investigate thermal adaptation on the Indian Ocean island of La Réunion, which experiences a range of temperatures from coast to summit. We study the evolution of high temperature tolerance by constructing a phylogenetic tree of strains collected from many different thermal niches. We show that populations of <em>P. pacificus</em> at low altitudes have higher fertility at warmer temperatures. Most likely, this phenotype has arisen recently and at least twice independently, consistent with parallel evolution. We also studied low temperature tolerance and showed that populations from high altitudes have increased their fertility at cooler temperatures. </span><span>Together, these data indicate that <em>P. pacificus</em> strains on La Réunion are subject to divergent selection, adapting to hot and cold niches at the coast and summit of the volcano.</span><span> </span><span>Precisely defining these thermal niches provides essential information for models that predict the impact of future climate change on these populations.</span></p>
Data from: Range-edge populations of seaweeds show niche unfilling and poor adaptation to increased temperatures
<p>Data used for the study entitled "Range-edge populations of seaweeds show niche unfilling and poor adaptation to increased temperatures". These are the distribution data collected from literature and personal communications to complete the GBIF and OBIS distributional records of the Atlantic European coast, the weekly growth data taken from the study individuals as well as the binomial survival data used for the graphs of the last week of the experiment.</p>
Temperature adaptation and its impact on the shape of performance curves in Drosophila populations
<p><span>Understanding how species adapt to different temperatures is crucial to predict their response to global warming, and thermal performance curves (TPCs) have been employed recurrently to study this topic. Nevertheless, fundamental questions regarding how thermodynamic constraints and evolution interact to shape TPCs in lineages inhabiting different environments remain unanswered. Here, we study </span><span><em>Drosophila</em> <em>simulans</em></span><span> along a latitudinal gradient spanning 3,000 km to test </span><span>opposing hypotheses based on thermodynamic constraints ('<em>hotter</em>-<em>is</em>-<em>better</em>') versus biochemical adaptation ('jack-of-all-temperatures') as primary determinants of TPCs variation across populations. </span><span>We compare thermal responses in metabolic rate and the egg-to-adult survival as descriptors of organismal performance and fitness, respectively, and show that different descriptors of TPCs vary in tandem with mean environmental temperatures, providing strong support to <em>hotter</em>-<em>is</em>-<em>better</em>. Thermodynamic constraints also resulted in a strong negative association between maximum performance and thermal breadth. </span><span>Lastly, we show that descriptors of TPCs for metabolism and </span><span>egg-to-adult survival </span><span>are highly correlated, providing evidence of coadaptation and that curves for </span><span>egg-to-adult survival </span><span>are systematically narrower and displaced towards lower temperatures. Taken together, results support the pervasive role of thermodynamics constraining thermal responses in <em>Drosophila</em> populations along a latitudinal gradient, that are only partly compensated by evolutionary adaptation. </span></p>
Data for: A mosquito parasite is locally adapted to its host but not temperature
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Adaptation to environmental temperature in divergent clades of the nematode Pristionchus pacificus
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Temperature adaptation and its impact on the shape of performance curves in Drosophila populations
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Temperature-specific repeatability of evolution and its implications for genomic predictions of adaptation to warming
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Data from: Range-edge populations of seaweeds show niche unfilling and poor adaptation to increased temperatures
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Data from: Temperature variability and metabolic adaptation in terrestrial and aquatic ectotherms
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Adult sex-ratio bias does not lead to detectable adaptive offspring sex allocation via nest-site choice in a turtle with temperature-dependent sex determination
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Data from: Landscape genomics and a common garden trial reveal adaptive differentiation to temperature across Europe in the tree species Alnus glutinosa
The adaptive potential of tree species to cope with climate change has important ecological and economic implications. Many temperate tree species experience a wide range of environmental conditions, suggesting high adaptability to new environmental conditions. We investigated adaptation to regional climate in the drought-sensitive tree species Alnus glutinosa (Black alder), using a complementary approach that integrates genomic, phenotypic and landscape data. A total of 24 European populations were studied in a common garden and through landscape genomic approaches. Genotyping-By-Sequencing was used to identify SNPs across the genome, resulting in 1990 SNPs. Although a relatively low percentage of putative adaptive SNPs was detected (2.86% outlier SNPs), we observed clear associations among outlier allele frequencies, temperature, and plant traits. In line with the typical drought avoiding nature of A. glutinosa, leaf size varied according to a temperature gradient and significant associations with multiple outlier loci were observed, corroborating the ecological relevance of the observed outlier SNPs. Moreover, the lack of isolation-by-distance, the very low genetic differentiation among populations and the high intra-population genetic variation all support the notion that high gene exchange combined with strong environmental selection promotes adaptation to environmental cues.
Sexual selection buffers the negative consequences of population fragmentation on adaptive plastic responses to increasing temperatures
<p class="MsoNormal"><span>Whether sexual selection facilitates or hampers the ability to plastically respond to novel environments might depend on population structure, via its effects on </span><span>sexual interactions and associated fitness payoffs</span><span>. Using experimentally evolved lines </span><span>of the seed beetle <em>Callosobruchus maculatus,</em> we tested whether individuals evolving under different sexual selection (monogamy vs polygamy) and population spatial structure (metapopulation vs undivided populations) treatments differed in their response across developmental thermal conditions (control, hot or stressful) in a range of fitness and fitness-associated traits. We found that individuals from subdivided populations had lower lifetime reproductive success (LRS) at hot temperatures, but only in lines evolving under relaxed sexual selection, revealing a complex interaction between sexual selection, population structure, and thermal environmental stress on fitness. We also found an effect of population structure on several traits, including fertility and adult emergence success, under exposure to high thermal conditions. Finally, we found a strong negative effect of hot and stressful temperatures in fitness and associated traits. Our results show that population structure can exacerbate the impact of a warming climate, potentially leading to declines in population viability, but that sexual selection can buffer the negative influence of population subdivision on adaptation to warm temperatures</span><span>.</span></p>
Data for: Phenotypic adaptation to temperature in the mosquito vector, Aedes aegypti
<p><span>Most models exploring the effects of climate change on </span><span>mosquito-borne disease ignore thermal adaptation. However, if local adaptation leads to changes in mosquito thermal responses, 'one size fits all' models could fail to capture current variation between populations and future adaptive responses to changes in temperature. Here we assess phenotypic adaptation to temperature in <em>Aedes aegypti</em>, the primary vector of dengue, Zika, and chikungunya viruses. First, to explore whether there is any difference in existing thermal response of mosquitoes between populations we used a thermal knockdown assay to examine five populations of <em>Ae. aegypti </em>collected from climatically diverse locations in Mexico, together with a longstanding laboratory strain. We identified significant phenotypic variation in thermal tolerance between populations. Next, to explore whether such variation can be generated by differences in temperature we conducted an experimental passage study by establishing six replicate lines from a single field-derived population of <em>Ae. aegypti </em>from Mexico, maintaining half at 27<strong><span class="nounderlines">°</span></strong>C and the other half at 31<strong><span class="nounderlines">°</span></strong>C. After 10 generations we found a significant difference in mosquito performance, with the lines maintained under elevated temperatures showing greater thermal tolerance. Moreover, these differences in thermal tolerance translated to shifts in the thermal performance curves for multiple life history traits, leading to differences in overall fitness. Together, these novel findings provide compelling evidence that <em>Ae. aegypti </em>populations can and do differ in thermal response, suggesting that simplified thermal performance models might be insufficient for predicting the effects of climate on vector-borne disease transmission. </span></p>
Dataset for: Hug et al. Unexpected behavioural adaptation of yellow fever mosquitoes in response to high temperatures
<p>Dataset for the manuscript: Hug et al. Unexpected behavioural adaptation of yellow fever mosquitoes in response to high temperatures</p>
Interacting impacts of hydrological changes and air temperature warming on lake temperatures highlight the potential for adaptive management: Model output
<p>This archive includes the output from the General Ocean Turbulence Model for a series of simulations that used differing model drivers (inflow discharge, Q, and air temperature, T). The Experiment_output.zip contains text files generated from the GOTM workflow containing modelled water temperatures and the Mod_z.txt are the corresponding depths for these temperatures. </p><p>The file name corresponds to the change made to the driving data from baseline (unchanged conditions), a combination of air temperature <i>increase </i>and flow percentage change e.g. Mod_temp_T_2_Q_1.5 refers to an air temperature increase of 2 degrees Celsius and a flow increase of 50% and a Mod_temp_T_3.5_Q_0.7 refers to an air temperature increase of 3.5 degrees Celsius and a flow decrease of 30%.</p>
Novel mitochondrial genome rearrangements including duplications and extensive heteroplasmy could underlie temperature adaptations in Antarctic notothenioid fishes
<p>Mitochondrial genomes are known for their compact size and conserved gene order, however, recent studies employing long-read sequencing technologies have revealed the presence of atypical mitogenomes in some species. In this study, we assembled and annotated the mitogenomes of five Antarctic notothenioids, including four icefishes (Champsocephalus gunnari, C. esox, Chaenocephalus aceratus, and Pseudochaenichthys georgianus) and the cold-specialized Trematomus borchgrevinki. Antarctic notothenioids are known to harbor some rearrangements in their mt genomes, however the extensive duplications in icefishes observed in our study have never been reported before. In the icefishes, we observed duplications of the protein coding gene ND6, two transfer RNAs, and the control region with different copy number variants present within the same individuals and with some ND6 duplications appearing to follow the canonical Duplication-Degeneration-Complementation (DDC) model in C. esox and C. gunnari. In addition, using long-read sequencing and k-mer analysis, we were able to detect extensive heteroplasmy in C. aceratus and C. esox. We also observed a large inversion in the mitogenome of T. borchgrevinki, along with the presence of tandem repeats in its control region. This study is the first in using long-read sequencing to assemble and identify structural variants and heteroplasmy in notothenioid mitogenomes and signifies the importance of long-reads in resolving complex mitochondrial architectures. Identification of such wide-ranging structural variants in the mitogenomes of these fishes could provide insight into the genetic basis of the atypical icefish mitochondrial physiology and more generally may provide insights about their potential role in cold adaptation.</p>
Data from: Temperature-dependent gene regulatory divergence underlies local adaptation with gene flow in the Atlantic silverside
<p>Gene regulatory divergence is thought to play an important role in adaptation, yet its extent and underlying mechanisms remain largely elusive for local adaptation with gene flow. Local adaptation is widespread in marine species despite generally high connectivity and is often associated with tightly linked genomic architectures, such as chromosomal inversions. To investigate gene regulatory evolution under gene flow and the role of inversions associated with local adaptation to a steep thermal gradient, we generated RNA-seq data from Atlantic silversides (<em>Menidia menidia</em>) from two locally adapted populations and their F1 hybrids, reared under two temperatures. We found substantial divergence in gene expression and thermal plasticity between populations, with up to 31% of genes being differentially expressed. Reduced thermal plasticity, temperature-dependent gene misexpression and the disruption of co-expression networks in hybrids point towards a role of regulatory incompatibilities in local adaptation, particularly under colder temperatures. Chromosomal inversions show an accumulation of regulatory incompatibilities but are not consistently enriched for differentially expressed genes. Together, these results suggest that gene regulation can diverge substantially among populations despite gene flow, partly due to the accumulation of temperature-dependent regulatory incompatibilities within inversions.</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.
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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.