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3,773 results for “divergence”
Resources from: Disparate patterns of genetic divergence in three widespread corals across a pan-pacific environmental gradient highlights species-specific adaptation trajectories
<p>The following files are contained in this repository:</p> <p><br> README.Hume_et_al_2022.zenodov4.txt - This document.</p> <p>scripts.Hume_et_al_2022.zenodov4.pdf - Contains the scripts, or locations of the scripts, used to conduct the data analyses detailed in the associated manuscript.</p> <p>acknowledgements_local_authorities.Hume_et_al_2022.zenodov1.pdf - Acknowledgements of local authorities for the collection of samples used in the associated study.</p> <p>TaraPacific_SST_timeseries_mean_productsV2mai2021.Hume_et_al_2022.zenodov1.csv - The historical temperature data set used for the RDA, Mantel tests and gradient Forest analysis.</p> <p>Pocillopora_meandrina_v3_11Islands.raw.Hume_et_al_2022.zenodov2.vcf.genozip - The Pocillopora SNPs referred to as 'raw' in the Methods of the associated manuscript. Compressed using genozip (https://genozip.readthedocs.io/index.html).</p> <p>Pocillopora_meandrina_v3_11Islands.raw.Hume_et_al_2022.zenodov2.vcf.genozip.md5 - md5 of the the Pocillopora raw SNPs.</p> <p>Pocillopora_meandrina_v3_11Islands_maf05_minQ30_biallelic_nomiss.linked.Hume_et_al_2022.zenodov2.vcf.gz - The Pocillopora SNPs referred to as 'linked' in the Methods of the associated manuscript.</p> <p>Pocillopora_meandrina_v3_11Islands_maf05_minQ30_biallelic_nomiss.linked.Hume_et_al_2022.zenodov2.vcf.gz.md5 - md5 of the the Pocillopora linked SNPs.</p> <p>Pocillopora_meandrina_v3_11Islands_maf05_minQ30_biallelic_nomiss_LD02.unlinked.Hume_et_al_2022.zenodov2.vcf.gz - The Pocillopora SNPs referred to as 'unlinked' in the Methods of the associated manuscript.</p> <p>Pocillopora_meandrina_v3_11Islands_maf05_minQ30_biallelic_nomiss_LD02.unlinked.Hume_et_al_2022.zenodov2.vcf.gz.md5 - md5 of the the Pocillopora unlinked SNPs.</p> <p>Porites_lobata_v3_11Islands.raw.Hume_et_al_2022.zenodov2.vcf.genozip - The Pocillopora SNPs referred to as 'raw' in the Methods of the associated manuscript. Compressed using genozip (https://genozip.readthedocs.io/index.html).</p> <p>Porites_lobata_v3_11Islands.raw.Hume_et_al_2022.zenodov2.vcf.genozip.md5 - md5 of the the Pocillopora raw SNPs.</p> <p>Porites_lobata_v3_11Islands_maf05_minQ30_biallelic_nomiss.linked.Hume_et_al_2022.zenodov2.vcf.gz - The Pocillopora SNPs referred to as 'linked' in the Methods of the associated manuscript.</p> <p>Porites_lobata_v3_11Islands_maf05_minQ30_biallelic_nomiss.linked.Hume_et_al_2022.zenodov2.vcf.gz.md5 - md5 of the the Pocillopora linked SNPs.</p> <p>Porites_lobata_v3_11Islands_maf05_minQ30_biallelic_nomiss_LD02.unlinked.Hume_et_al_2022.zenodov2.vcf.gz - The Pocillopora SNPs referred to as 'unlinked' in the Methods of the associated manuscript.</p> <p>Porites_lobata_v3_11Islands_maf05_minQ30_biallelic_nomiss_LD02.unlinked.Hume_et_al_2022.zenodov2.vcf.gz.md5 - md5 of the the Pocillopora unlinked SNPs.</p> <p>PANAMA2021.raw.Hume_et_al_2022.zenodov2.vcf.gz - The Millepora SNPs referred to as 'raw' in the Methods of the associated manuscript.</p> <p>PANAMA2021.raw.Hume_et_al_2022.zenodov2.vcf.gz.md5 - md5 of the the Millepora raw SNPs.</p> <p>Millepora_REF_orthologue_genes.Hume_et_al_2022.zenodov2.csv - The Millepora gene list referred to as 'target genes' in the Methods of the associated manuscript.</p> <p>Mil_transcriptom.Hume_et_al_2022.zenodov2.fa.gz - The Millepora de novo assembled transcriptome.</p> <p>Mil_transcriptom.Hume_et_al_2022.zenodov2.fa.gz.md5 - md5 of the Millepora de novo assembled transcriptome.</p> <p> </p> <p>mtORF Phylogeny</p> <p>TP-Johnston_mtORF-Pocillo.fa = all sequences</p> <p>TP-Johnston_mtORF-Pocillo.mafft.fa = mafft alignment</p> <p>TP-Johnston_mtORF-Pocillo.mafft.ML.nwk = ML tree newick</p> <p> </p> <p>Hellberg genotype network Porites</p> <p>TP-Hellberg_MM32-Porites.nex = all aligned sequences for this locus with indels encoded</p> <p>TP-Hellberg_MM100-Porites.nex = all aligned sequences for this locus with indels encoded</p> <p>TP-Hellberg_ATPaseB.nex = all aligned sequences for this locus with indels encoded,</p> <p>TP-Hellberg_POFAD.nex = POFAD multilocus genotypic distance,</p> <p>TP-Hellberg_Splitstree.nex= Multilocus genotype network in nexus format</p> <p><br> Gradient Forest Analysis</p> <p>Poc_abund.csv - Pocillopora SSH Occurrences per Site er Island</p> <p>Por_abund.csv - Porites SSH Occurrences per Site er Island</p> <p>mean_depth_por.csv - per site per island mean depth among Porites colonies</p> <p>mean_depth_poc.csv - per site per island mean depth among Pocillopora colonies</p>
Population persistence, phenotypic divergence and metabolic adaptation in yarrow (Achillea millefolium L.) along a climate gradient, CA, 1920 to 2023
This dataset provides insights into the persistence and adaptation of yarrow (Achillea millefolium L.) populations over a 100-year period of climate change. The data include plant height measurements and climatic variables (temperature and precipitation) from historical and resurveyed sites spanning a broad environmental gradient (1–3,200 m a.s.l.), alongside metabolic profiles obtained from a common-garden experiment. The dataset captures phenotypic changes in plant growth, metabolic diversity, and site-specific climatic shifts between 1920 and 2020. These data support analyses of how temperature and precipitation interact to shape plant responses over time and allow for exploring patterns of local adaptation in phenotypic and metabolic traits. This comprehensive dataset is valuable for understanding the ecological and evolutionary mechanisms underlying population persistence and can inform conservation strategies under future climate scenarios.
Alignments used in "The evolution of the phenylpropanoid pathway entailed pronounced radiations and divergences of enzyme families"
<p>Alignments used in de Vries et al. (2021) "The evolution of the phenylpropanoid pathway entailed pronounced radiations and divergences of enzyme families" published as</p> <p>(1) a pre-print: https://doi.org/10.1101/2021.05.27.445924</p> <p>(2) in Plant Journal (in press)</p>
Divergent evolution of sleep functions - Joyce et al 2024 Dataset - Part 1 of 4
<p>This is the full experimental dataset associated to "Divergent evolution of sleep functions" by Joyce et al 2024, Nature Communications. See https://lab.gilest.ro/papers/divergent-evolution-of-sleep-functions/ for more information.</p> <p>The dataset contains 86 zip files for a total of about 170GB. Once uncompressed, they will explode 622 ethoscope db files for a total of 330Gb, covering behavioural analysis of more than 11.000 animals. These are the RAW data as collected from the ethoscopes. A separate zip archive with all the R/Python scripts and the metadata is also provided. This also contains confocal images for BRP analysis.</p> <ul> <li>Part 1 of 4: <a href="https://doi.org/10.5281/zenodo.10554851" target="_blank" rel="noopener">10.5281/zenodo.10554851 (this page) </a></li> <li>Part 2 of 4: <a href="https://doi.org/10.5281/zenodo.10557238" target="_blank" rel="noopener">10.5281/zenodo.10557238</a></li> <li>Part 3 of 4: <a href="https://doi.org/10.5281/zenodo.10557310" target="_blank" rel="noopener">10.5281/zenodo.10557310</a></li> <li>Part 4 of 4: <a href="https://doi.org/10.5281/zenodo.10966461" target="_blank" rel="noopener">10.5281/zenodo.10966461 </a></li> </ul>
Genomics of extreme ecological specialists: multiple convergent evolution but no genetic divergence between ecotypes of Maculinea alcon butterflies
<p>Biotic interactions are often acknowledged as catalysers of genetic divergence and eventual explanation of processes driving species richness. We address the question, whether extreme ecological specialization is always associated with lineage sorting, by analysing polymorphisms in morphologically similar ecotypes of the myrmecophilous butterfly <em>Maculinea alcon</em>. The ecotypes occur in either hygric or xeric habitats, use different larval host plants and ant species, but no significant distinctive molecular traits have been revealed so far. We apply genome-wide RAD-sequencing to specimens originating from both habitats across Europe in order to get a view of the potential evolutionary processes at work. Our results confirm that genetic variation is mainly structured geographically but not ecologically — specimens from close localities are more related to each other than populations of each ecotype from distant localities. However, we found two loci for which the association with xeric versus hygric habitats is supported by segregating alleles, suggesting convergent evolution of habitat preference. Thus, ecological divergence between the forms probably does not represent an early stage of speciation, but may result from independent recurring adaptations involving few genes. We discuss the implications of these results for conservation and suggest preserving biotic interactions and main genetic clusters.</p>
Divergent geographic patterns and functional characteristics: Subtle mapping for ponds in the Yangtze River Delta Region
<p>Pond water surfaces (PWS) possess diverse functional types, such as aquaculture, agriculture-water supplement, and ecosystem regulation. However, existing research often treats PWS as a homogeneous aquatic ecosystem; the absence of a comprehensive PWS classification system hinders ours understanding of PWS background characteristics and is detrimental to watershed management. Here, a comprehensive classification system of PWS, including fish aquaculture ponds (FAP), shrimp and crab aquaculture ponds (SCAP), natural ponds (NP), and landscaping ponds (LP) was proposed from remote sensing perspectives. Additionally, interpretation rules were standardized from multi-features including spectrum, shape, topography, and surrounding geographical environments. Subsequently, refined spatiotemporal data product of PWS in the Yangtze River Delta from 2016 to 2022 was generated using Sentinel-2 images with 10 m spatial resolutions. The results indicate that: (1) The spatiotemporal changes exhibited three stages, i.e., “declining – stable – recovery.” The area of PWS decreased from 5186.52 km² to 4920.90 km²in 2016-2017, stabilized at approximately 4500 km² in 2019-2021, and then rebounded to 4834.12 km² in 2022. (2) Regarding different PWS functional types, significant differences were demonstrated in terms of area, surrounding environment, and spatiotemporal changes. Firstly, FAP dominated in terms of area, accounting for 47.81% of the total. Secondly, FAP was widely around rivers and lakes. At the same time, SCAP was concentrated around lakes or along the coast, LP was primarily found in urban areas, and NP was predominantly found in rural areas and mountainous regions; Thirdly, NP decreased as land remediation work progressed continuously, while LP increased due to policy support for urban renewal. Changes in aquaculture were more complex, experiencing a sharp decline from 2016 to 2020 due to reduced market demand but rebounded in 2021-2022 with supportive policies. In summary, the system and data products developed in this study reveal the diverse relationships of "functional type-geographical environment-driving factor" regarding PWS, implicating appropriate planning for aquatic ecosystem.</p>
Selection against admixture and gene regulatory divergence in a long-term primate field study
<p><strong>Selection against admixture and gene regulatory divergence in a long-term primate field study</strong><br> <em>Vilgalys & Fogel et al. (bioRxiv)</em></p> <ul> <li><a href="https://zenodo.org/api/files/7cb721ac-b8e0-4dc0-a91b-fd54cc70f8d7/Panubis1.0_to_hg38.chain.gz">Panubis1.0_to_hg38.chain.gz</a>; <a href="https://zenodo.org/api/files/7cb721ac-b8e0-4dc0-a91b-fd54cc70f8d7/hg38_to_Panubis1.0.chain.gz">hg38_to_Panubis1.0.chain.gz</a>: Liftover chain files between Panubis1.0 and hg38. </li> <li><a href="https://zenodo.org/api/files/7cb721ac-b8e0-4dc0-a91b-fd54cc70f8d7/amboseli_LCLAE_tracts.txt.gz">amboseli_LCLAE_tracts.txt.gz</a>: Local ancestry calls for 442 wild, hybrid baboons studied as part of the Amboseli Baboon Research Project. Local ancestry was called using LCLAE and is represented by a 0 for homozygous yellow ancestry, 2 for homozygous anubis ancestry, and 1 for heterozygous ancestry. Each row in the file has a genomic position (chromosome, start, and end), local ancestry call, and the individual for whom the call was made. </li> <li><a href="https://zenodo.org/api/files/7cb721ac-b8e0-4dc0-a91b-fd54cc70f8d7/masked_yellow_and_anubis.vcf.gz?versionId=25e26878-bca3-4667-9668-9e19424bc23e">masked_yellow_and_anubis.vcf.gz</a>: Genotype calls for non-Amboseli yellow and anubis baboons, after masking to remove putative introgressed ancestry. </li> <li>A time-stamped version of the code is included here, and also available on GitHub at <a href="http://github.com/TaurVil/VilgalysFogel_Amboseli_admixture">github.com/TaurVil/VilgalysFogel_Amboseli_admixture</a>. </li> </ul>
Supporting data and codes for: A new biological species in the Mercurialis annua polyploid complex: functional divergence in inflorescence morphology, hybrid sterility and possible introgression
<p>This GitHub repository includes R codes and datasets for the paper: A new biological species in the Mercurialis annua polyploid complex: functional divergence in inflorescence morphology, hybrid sterility and possible introgression</p>
Case study on hereditary divergence and its impact on glaucoma
<p>The data extracted from the <a href="http://Disgenet.org/">DisGeNET </a>database are processed using available open sources tools (VEP, polyphen, SIFT, and ClueGo). The process of data analysis is given in the book chapter.</p>
Modelled isoscape data for: "Oceanographic and biogeochemical drivers cause divergent trends in the nitrogen isoscape in a changing Arctic Ocean"
<p>The data included in this repository includes the biogeochemical model output of nitrogen isotope fields. These data were generated by simulations with the NEMOv4.0 Ocean General Circulation Model, SI3 sea ice model, and Pelagic Interactions Scheme for Carbon and Ecosystem Studies version 2 (PISCESv2) biogeochemical model. Nitrogen isotopes were integrated within PISCESv2 for the purpoes of this study.</p> <p>All data here are in longitude, latitude and time cordinates. No depth coordinate is provided as all values are averaged over the upper 100 metres of the model.</p> <p> </p> <p>The file names mean the following:<br> </p> <p>ETOPO - refers to how the curvilinear, native grid of the model was re-gridded to a regular 360x180 longitude-latitude grid uisng the etopo60 coordinate system.</p> <p>JRA55 - these are the reanalysis-driven simulations, for which we used the Japanese Atmospheric Reanalysis (JRA55do).</p> <p>future - these are the emissions-driven simulations (historical from 1850-2005, then according to Representative Concentration Pathway 8.5 from 2006-2100.)</p> <p>picontrol - these are parallel to the emissions-driven simulations but do not include the increase in emissions.</p> <p>ndep - refers to if the historical increase in anthropogenic nitrogen deposition was included in the simulation</p> <p>d15Nno3 - isotopic composition of nitrate averaged over the upper 100 metres</p> <p>d15Npom - isotopic composition of particulate organic matter averaged over the upper 100 metres</p> <p>predictors - the average values of salinity, N* and particulate organic matter over the upper 100 metres</p> <p>annualave - annual averages, so that the data are inter-annual</p> <p>1970-1990ave_months - average monthy values over the period 1970-1990.</p>
Divergent evolution between sister species of European green lizards
<p>Annotation and variant calling files (VCFs, heffas) for <em>L. viridis </em>and<em> L. bilineata.</em> The variants have been called with <em>L. viridis</em> genome as reference.</p>
Divergent Evolution of Earth and Venus—Transparent Version
<p>The theory of planetary heat pipes now tells us Venus and Earth may follow separate ways even though they shared a similar beginning. In the context of exoplanet studies, this means rocky planets with a hot surface—or with a thick atmosphere that acts like a blanket—may not exhibit plate tectonics. Also read: <a href="https://doi.org/10.1029/2022GL100987">https://doi.org/10.1029/2022GL100987</a></p>
Microsatellite genotype data and leaf morphological data of the publication "Bidirectional gene flow between Fagus sylvatica L. and F. orientalis Lipsky despite strong genetic divergence"
<p>These data sets were used for analyses in the publication "Bidirectional gene flow between <em>Fagus sylvatica</em> L. and<em> F. orientalis</em> Lipsky despite strong genetic divergence" accepted in Forest Ecology and Management <a href="https://www.sciencedirect.com/journal/forest-ecology-and-management/vol/537/suppl/C">Volume 537</a>, 1 June 2023, 120947, <a href="https://doi.org/10.1016/j.foreco.2023.120947">https://doi.org/10.1016/j.foreco.2023.120947</a></p> <p>For details about the data, please read the corresponding ReadMe files.</p>
Simulation code and simulated data for: Transient polymorphisms in parental care strategies drive divergence of sex roles
<p>This repository contains C++ code, simulated datasets, an R-script for data analysis and a Mathematica notebook for mathetical analysis.</p><p>Datasets are organised into ZIP files named after the corresponding figure in the publication. All of the figures based on simulation data in the manuscript and supplementary materials can be created with the R-script. For further information see the article published in <i>Nature Communications (</i>doi:<i> </i>https://doi.org/10.1038/s41467-023-42607-6).</p><p> </p><p> </p><p> </p>
Processed snRNA-seq data from "Divergent single cell transcriptome and epigenome alterations in ALS and FTD patients with C9orf72 mutation"
<p>Processed snRNA-seq data from "Divergent single cell transcriptome and epigenome alterations in ALS and FTD patients with C9orf72 mutation". All nuclei passed QC and were corrected for background noise using cellBender. Files are in R objects saved in RDS (R Data Serialization) format. This repo contains one Seurat v4 object and one gene-by-cell raw RNA count matrix in sparse matrix format (dgCMatrix).</p>
Multilevel atlas comparisons reveal divergent evolution of the primate brain
<p>Nifti files of 20 mammalian atlases modified into a Common Multilevel Segmentation.</p> <p>(See Figure 1 in Multilevel atlas comparisons reveal divergent evolution of the primate brain; https://www.pnas.org/doi/full/10.1073/pnas.2202491119#sec-3)</p> <p>These nifti files are based on the brain atlases from 18 mammalian species, that were published between the years 2013 and 2021 (see list).</p> <p>The Python script to re-segment the "original" atlases into the modified version (that is shared here) is also available:</p> <p>see Modify_atlases.py</p> <p>Each species folder contains 5 nifti files: 1 for each level of segmentation and 1 for the brain segmentation.</p> <p>The other txt files are the volumetric output extracted using AFNI on each nifti file.</p> <p>Please read the Readme.txt file to credit and cite accordingly all the authors.</p> <p> </p> <p> </p> <p> </p> <p> </p>
FIG. 7 in A new species of Tungurictis Colbert, 1939 (Carnivora, Hyaenidae) from the middle Miocene of Junggar Basin, northwestern China and the early divergence of basal hyaenids in East Asia
FIG. 7. — Tungurictis small sp., IVPP V 11497, left dentary fragment with m1 and m2 alveolus. A, stereo photos of occlusal view; B, lingual view; C, buccal view. Scale bars: 10 mm.
FIG. 5 in A new species of Tungurictis Colbert, 1939 (Carnivora, Hyaenidae) from the middle Miocene of Junggar Basin, northwestern China and the early divergence of basal hyaenids in East Asia
FIG. 5. — Tungurictis peignei, n. sp., IVPP V 25222, holotype, right dentary with p2-m2 (A, stereo photos, occlusal view, C, lingual, and D, buccal views) and IVPP V 11493, left dentary with p2-m1 (B, stereo photos, occlusal view; E, lingual view; F, buccal views). Scale bars: 10 mm.
FIG. 4 in A new species of Tungurictis Colbert, 1939 (Carnivora, Hyaenidae) from the middle Miocene of Junggar Basin, northwestern China and the early divergence of basal hyaenids in East Asia
FIG. 4. — Tungurictis peignei, n. sp., IVPP V 25222, holotype, isolated right I3, mesial view (A), right upper canine, buccal view (B), left P1, and left maxilla with P3-4 (C, stereo photos of occlusal view; D, buccal view). Scale bar: 10 mm.
Fig. 1 in Divergence in energy sources for Prochilodus lineatus (Characiformes: Prochilodontidae) in Neotropical floodplains
Fig. 1. Map of the floodplain of the Upper Paraná River, highlighting the areas sampled in this study. The subsystems sampled were A = Paraná River, B = Baía River and C = Ivinheima River. The numbers indicate sampled sites in each subsystem.
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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.