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31 results for “climate test data”
Data from: Oligo-Miocene climate change and mammal body size evolution in the northwest United States a test of Bergmann's Rule
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Data from: A global test of the cold-climate hypothesis for the evolution of viviparity of squamate reptiles
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Assigning occurrence data to cryptic taxa improves climatic niche assessments: biodecrypt, a new tool tested on European butterflies
<p><b><span>Aim</span></b><br> <span>Occurrence data are fundamental to macroecology, but accuracy is often compromised when multiple units are lumped together (e.g. in recently separated cryptic species or citizen science records). Using amalgamated data leads to inaccuracy in species mapping, to biased beta-diversity assessments and to potentially erroneous</span><span>ly</span><span> predicted responses to climate change. We provide a set of R functions (biodecrypt) to objectively attribute undetermined occurrences to the most probable taxon based on a subset of identified records.</span></p> <p><b><span>Innovation</span></b><br> <span>Biodecrypt assumes </span><span>that unknown occurrences can only be attributed at certain distances from </span><span>areas of </span><span>sympatry. </span><span>The </span><span>function draws concave hulls based on the subset of identified records; subsequently, based on hull geometry, it attributes (or not) unknown records to a given taxon. Concavity can be imposed with an alpha value and sea or land areas can be excluded. A cross-validation function tests attribution reliability and another function optimizes the parameters (alpha, buffer, distance ratio between hulls). We applied the procedure to 16 European butterfly complexes recently separated into 33 cryptic species for which most records were amalgamated. We compared niche similarity and divergence between cryptic taxa, and we re-calculated and </span><span>contributed </span><span>updated </span><span>CLIMBER variables for climatic preferences</span><span>.</span></p> <p><b><span>Main conclusions</span></b><br> Biodecrypt showed a cross-validated correct attribution of known records always ≥98% and attributed more than 80% of unknown records to the most likely taxon in parapatric species. The functions determined where records can be assigned even for largely sympatric species, and highlighted areas where further sampling is required. All the cryptic taxa <span>showed significantly diverging climatic niches, </span>reflected in different values of mean temperature and precipitation compared to the values originally provided in the CLIMBER database. The substantial fraction of cryptic taxa existing across different taxonomic groups and their divergence in climatic niches highlights the importance of using reliably assigned occurrence data in macroecology.</p>
Data from: Testing models of speciation from genome sequences: divergence and asymmetric admixture in Island Southeast Asian Sus species during the Plio-Pleistocene climatic fluctuations
In many temperate regions, ice ages promoted range contractions into refugia resulting in divergence (and potentially speciation), while warmer periods led to range expansions and hybridization. However, the impact these climatic oscillations had in many parts of the tropics remains elusive. Here, we investigate this issue using genome sequences of three pig (Sus) species, two of which are found on islands of the Sunda-shelf shallow seas in Island Southeast Asia (ISEA). A previous study revealed signatures of inter-specific admixture between these Sus species (Frantz et al. (2013) Genome sequencing reveals fine scale diversification and reticulation history during speciation in Sus. Genome biology, 14, R107). However, the timing, directionality and extent of this admixture remain unknown. Here we use a likelihood based model comparison to more finely resolve this admixture history and test whether it was mediated by humans or occurred naturally. Our analyses suggest that inter-specific admixture between Sunda-shelf species was most likely asymmetric and occurred long before the arrival of humans in the region. More precisely, we show that these species diverged during the late Pliocene but around 23% of their genomes have been affected by admixture during the later Pleistocene climatic transition. In addition, we show that our method provides a significant improvement over D-statistics which are uninformative about the direction of admixture.
Data from: Evolution of viviparity: a phylogenetic test of the cold-climate hypothesis in Phrynosomatid lizards
The evolution of viviparity is a key life-history transition in vertebrates, but the selective forces favoring its evolution are not fully understood. With >100 origins of viviparity, squamate reptiles (lizards and snakes) are ideal for addressing this issue. Some evidence from field and laboratory studies supports the "cold-climate" hypothesis, wherein viviparity provides an advantage in cold environments by allowing mothers to maintain higher temperatures for developing embryos. Surprisingly, the cold-climate hypothesis has not been tested using both climatic data and phylogenetic comparative methods. Here, we investigate the evolution of viviparity in the lizard family Phrynosomatidae using GIS-based environmental data, an extensive phylogeny (117 species), and recently developed comparative methods. We find significant relationships between viviparity and lower temperatures during the warmest (egg-laying) season, strongly supporting the cold-climate hypothesis. Remarkably, we also find that viviparity tends to evolve more frequently at tropical latitudes, despite its association with cooler climates. Our results help explain this and two related patterns that seemingly contradict the cold-climate hypothesis: the presence of viviparous species restricted to low-elevation tropical regions and the paucity of viviparous species at high latitudes. Finally, we examine whether viviparous taxa may be at higher risk of extinction from anthropogenic climate change.
Data from: Testing models of speciation from genome sequences: divergence and asymmetric admixture in Island Southeast Asian Sus species during the Plio-Pleistocene climatic fluctuations
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Data from: Evolution of viviparity: a phylogenetic test of the cold-climate hypothesis in Phrynosomatid lizards
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Data from: A global test for phylogenetic signal in shifts in flowering time under climate change
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Assigning occurrence data to cryptic taxa improves climatic niche assessments: biodecrypt, a new tool tested on European butterflies
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Aquaplanet experiment data for Webb, M. J., & Lock, A. P. (2020). Testing a physical hypothesis for the relationship between climate sen-sitivity and double-ITCZ bias in climate models.Journal of Advances in Modeling Earth Systems, 12,e2019MS001999.https://doi.org/10.1029/2019MS001999
<p><strong>Aquaplanet experiment data from Webb and Lock (2020)</strong></p> <p><br> Webb, M. J., & Lock, A. P. (2020). Testing a physical hypothesis for the relationship between climate sen-sitivity and double-ITCZ bias in climate models.Journal of Advances in Modeling Earth Systems, 12,e2019MS001999.https://doi.org/10.1029/2019MS001999</p> <p>CSV files containing data from Figs 1(b) and 2(a-d)</p> <p>Figure 2b:</p> <p>APEQ.Precipitation_mmperday.zonal.csv<br> APEQ_2LW_Cloud.Precipitation_mmperday.zonal.csv<br> APEQ_3LW_Cloud.Precipitation_mmperday.zonal.csv</p> <p>Figure 3a:</p> <p>APEQ.w700.zonal.csv<br> APEQ_3LW_Cloud.w700.zonal.csv<br> APEQ_2LW_Cloud.w700.zonal.csv</p> <p>Figure 3b:</p> <p>APEQ.Estimated_Inversion_Strength_K.zonal.csv<br> APEQ_2LW_Cloud.Estimated_Inversion_Strength_K.zonal.csv<br> APEQ_3LW_Cloud.Estimated_Inversion_Strength_K.zonal.csv</p> <p>Figure 3c:</p> <p>APEQ.Net_CRE_Wperm2.zonal.csv<br> APEQ_2LW_Cloud.Net_CRE_Wperm2.zonal.csv<br> APEQ_3LW_Cloud.Net_CRE_Wperm2.zonal.csv</p> <p>Figure 3d:</p> <p>APEQ4K-APEQ.Net_CRE_Feedback_Wperm2perK.zonal.csv<br> APEQ4K_2LW_Cloud-APEQ_2LW_Cloud.Net_CRE_Feedback_Wperm2perK.zonal.csv<br> APEQ4K_3LW_Cloud-APEQ_3LW_Cloud.Net_CRE_Feedback_Wperm2perK.zonal.csv</p> <p>Any queries please contact Mark Webb mark.webb@metoffice.gov.uk</p> <p> </p>
Raw data from the Forests (MDPI) 2020; 11(11):1222 paper: "Seed sourcing strategies considering climate change forecasts: a practical test in Scots pine"
<p>Raw data from the Forests paper: "Seed sourcing strategies considering climate change forecasts: a practical test in Scots pine"</p> <p>Forests. 2020; 11(11):1222. https://doi.org/10.3390/f11111222</p> <p>It comprises data from a multisite (5) provenance test: height (measurements years:1995, 2000 and 2005), dbh (measurements years:1995, 2000 and 2005) and survival (measurements years: 2000 and 2005)</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.