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230 results for “Divergent evolution”
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 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>
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>
Data from: Natural selection and repeated patterns of molecular evolution following allopatric divergence
Background: Geographic speciation is a major force in generating biodiversity. However, how genomes diverge over time after geographic isolation has halted gene flow has remained unclear. We examine genome-wide divergence of putatively single-copy orthologous genes (POGs) from transcriptomes in 20 allopatric species/variety pairs from diverse angiosperm clades. Sixteen of these pairs reflect the well-known eastern Asia – eastern North America floristic disjunction; these species have been isolated for different lengths of time, from the Miocene to Pleistocene. Results: Molecular evolutionary analyses revealed that >90% of the genes examined are under purifying selection and <10% are under positive selection, and this pattern was observed for all taxon pairs, despite differences in divergence time. The divergence level at synonymous sites shared by most POGs in each taxon pair predicts the divergence time between the species/varieties. Divergence time estimates were positively correlated with abundance of genes under moderate purifying selection, but negatively correlated with abundance of genes under strong purifying selection. We identified 200 genes under strong positive selection across the species pairs, with 14 shared by 10-15 pairs and one shared by all taxon pairs. An additional 15 loci annotated to biological processes responding to various stimuli were present in 1-3 pairs.Conclusions: Our results suggest a common "most genes conserved–few genes adaptive" genomic architecture for the taxon pairs, which may be a key for maintaining a balance between the ability to conserve ancestral functions and the ability to evolve new features beneficial for new adaptations. As geographic isolation proceeds through time, the evolutionary trajectory of some genes changed from strong purifying selection to more relaxed selection. The allopatric divergence of these taxon pairs involved both neutral and adaptive evolution of functional genes.
Historical museum samples enable the examination of divergent and parallel evolution during invasion
<p>During the Anthropocene, Earth has experienced unprecedented habitat loss, native species decline, and global climate change. Concurrently, greater globalisation is facilitating species movement, increasing the likelihood of alien species establishment and propagation. There is a great need to understand what influences a species' ability to persist or perish within a new or changing environment. Examining genes that may be associated with a species' invasion success or persistence informs invasive species management, assists with native species preservation, and sheds light on important evolutionary mechanisms that occur in novel environments. This approach can be aided by coupling spatial and temporal investigations of evolutionary processes. Here we use the common starling, <i>Sturnus vulgaris,</i> to identify parallel and divergent evolutionary change between contemporary native and invasive range samples and their common ancestral population. To do this, we use reduced-representation sequencing of native samples collected recently in north-western Europe and invasive samples from Australia, together with museum specimens sampled in the UK during the mid-19<sup>th</sup> Century. We found evidence of parallel selection on both continents, possibly resulting from common global selective forces such as exposure to pollutants. We also identified divergent selection in these populations, which might be related to adaptive changes in response to the novel environment encountered in the introduced Australian range. Interestingly, signatures of selection are equally as common within both invasive and native range contemporary samples. Our results demonstrate the value of including historical samples in genetic studies of invasion and highlight the ongoing and occasionally parallel role of adaptation in both native and invasive ranges.</p>
Figure 5. Bayesian phylogeny, with species divergence age estimates reconstructed with BEAST using all the 26 in Complete mitochondrial genomes from museum specimens clarify millipede evolution in the Eastern Arc Mountains
Figure 5. Bayesian phylogeny, with species divergence age estimates reconstructed with BEAST using all the 26 mitochondrial genomes generated in this study. The dataset was supplemented with Thyropygus sp. and Abacion magnum as outgroups, derived from GenBank. GenBank accession numbers are provided in parentheses. Blue bars indicate the 95% highest probability density intervals for node ages. Age estimation for lineage divergence was based on a general arthropod mitochondrial DNA substitution rate and should be considered with caution. *Thyropygus sp. (red font) is very likely to be a misidentification; for more information, see the Discussion.
Fig. 2 in Biodiversity Interslope Divergence Of Oribatid Mites At "Evolution Canyon", Mount Carmel, Israel
Fig. 2. Plot showing distribution of different phylogenetic groups according to two identified differentiating factors at "EC". Factor 1 was identified with the interslope distribution and, factor 2, with
Fig. 1 in Biodiversity Interslope Divergence Of Oribatid Mites At "Evolution Canyon", Mount Carmel, Israel
Fig. 1. Linkage distance between stations at "EC" based on the Sørensen similarity index. Amalgamation rule: Ward's method
Evolution of the correlated genomic variation landscape across a divergence continuum in the genus Castanopsis
<p>The heterogeneous landscape of genomic variation has been well documented in population genomic studies. However, disentangling the intricate interplay of evolutionary forces influencing the genetic variation landscape over time remains challenging. In this study, we assembled a chromosome-level genome for <em>Castanopsis eyrei</em> and sequenced the whole genomes of 276 individuals from 12 <em>Castanopsis</em> species, spanning a broad divergence continuum. We found highly correlated genomic variation landscapes across these species. Furthermore, variations in genetic diversity and differentiation along the genome were strongly associated with recombination rates and gene density. These results suggest that long-term linked selection and conserved genomic features have contributed to the formation of a common genomic variation landscape. By examining how correlations between population summary statistics change throughout the species divergence continuum, we determined that background selection alone does not fully explain the observed patterns of genomic variation; the effects of recurrent selective sweeps must be considered. We further revealed that extensive gene flow has significantly influenced patterns of genomic variation in <em>Castanopsis</em> species. The estimated admixture proportion correlated positively with recombination rate and negatively with gene density, supporting a scenario of selection against gene flow. Additionally, putative introgression regions exhibited strong signals of positive selection, an enrichment of functional genes, and reduced genetic burdens, indicating that adaptive introgression has played a role in shaping the genomes of hybridizing species. This study provides insights into how different evolutionary forces have interacted in driving the evolution of the genomic variation landscape.</p>
Figure 6 in Past ecosystems drive the evolution of the early diverged Symphyta (Hymenoptera: Xyelidae) since the earliest Eocene
Figure 6. (A) Map of the Eocene world with vegetation simulated by BIOME4 (modified from Herold et al., 2014) and distribution of extant Xyelidae (from https://v3.boldsystems.org, last access: 7 November 2021). (B) World map of the Cretaceous period at 105 Ma with xyelid localities indicated. (C) World map of the Jurassic period at 170 Ma with xyelid localities indicated. (D) World map of the Triassic period at 220 Ma with xyelid localities indicated (B, C, D; ' PALEOMAP project).
Figure 5 in Past ecosystems drive the evolution of the early diverged Symphyta (Hymenoptera: Xyelidae) since the earliest Eocene
Figure 5. Proxyelia pankowskii gen. et sp. nov. Holotype FOBU14313. (A) Detailed photograph of head. (B) Interpretative line drawing of antenna. (C) Detailed photograph of pterostigma. (D) Interpretative line drawing of venation with cell (in bold) and vein names labeled. (E) Detailed view of apical part of abdomen. Scale bars: 1 mm.
Figure 1 in Past ecosystems drive the evolution of the early diverged Symphyta (Hymenoptera: Xyelidae) since the earliest Eocene
Figure 1. Photograph of Paleoxyela nearctica gen. et sp. nov. Holotype UCM 18643. Scale bar: 5 mm. (' Talia Karim).
Figure 2 in Past ecosystems drive the evolution of the early diverged Symphyta (Hymenoptera: Xyelidae) since the earliest Eocene
Figure 2. Paleoxyela nearctica gen. et sp. nov. Holotype UCM 18643. (A) Detailed photograph of head and thorax. (B) Detailed photograph of right wings. (C) Detailed photograph of left wings. Scale bars: 1 mm. (' Talia Karim).
Figure 3 in Past ecosystems drive the evolution of the early diverged Symphyta (Hymenoptera: Xyelidae) since the earliest Eocene
Figure 3. Paleoxyela nearctica gen. et sp. nov. Holotype UCM 18643. (A) Interpretative line drawing of right wing venation with cell (in bold) and vein names labeled. (B) Interpretative line drawing of venation of left wings with cell (in bold) and vein names labeled. Scale bars: 1 mm.
Evolution of allele frequencies in two chicken lines divergently selected for meat ultimate pH
<p>Two lines of chicken were divergently selected during 5 generations for high or low meat ultimate pH. Genotypes at about 50K SNPs were obtained for a sample of individuals in each line and at each generation (including the founder population G0). The present dataset provides the allele frequencies for all SNP and generations in the two lines, at plink frq.strat format. The position of the SNP on the chicken genome are provided in another file at plink .map format.</p> <p>These data were first ued in the following publication:</p> <p>Le Bihan-Duval, E., Hennequet-Antier, C., Berri, C., Beauclercq, S. A., Bourin, M. C., Boulay, M., ... & Boitard, S. (2018). Identification of genomic regions and candidate genes for chicken meat ultimate pH by combined detection of selection signatures and QTL. <em>BMC genomics</em>, <em>19</em>(1), 294.</p>
Fig. 6. Divergence times estimated from a in Ecological and geographical speciation in Lucilia bufonivora: The evolution of amphibian obligate parasitism
Fig. 6. Divergence times estimated from a concatenated data set of per, COX1 and ITS2 sequences for the Lucilia bufornivora species group. Substitution model and relaxed clock models were unlinked for each gene. The tree was calibrated by setting the root to the node age corresponding to the split between Luciilinae and Calliphorinae subfamilies (~19 mya) as estimated by Wallman et al. (2005). Blue bars represent 95% highest posterior density (HPD) of each node age. (For interpretation of the references to colour in this figure legend, the reader is referred to the Web version of this article.)
Linked collectors and determiners for: Species delimitation in the Gehyra nana (Squamata: Gekkonidae) complex: cryptic and divergent morphological evolution in the Australian Monsoonal Tropics, with the description of four new species.
Natural history specimen data linked to collectors and determiners held within, "Species delimitation in the Gehyra nana (Squamata: Gekkonidae) complex: cryptic and divergent morphological evolution in the Australian Monsoonal Tropics, with the description of four new species". Claims or attributions were made on Bionomia by volunteer Scribes, <a href="https://bionomia.net/dataset/5f73d28a-b9b5-4297-91c5-e14ce6f4db0b">https://bionomia.net/dataset/5f73d28a-b9b5-4297-91c5-e14ce6f4db0b</a> using specimen data from the dataset aggregated by the Global Biodiversity Information Facility, <a href="https://gbif.org/dataset/5f73d28a-b9b5-4297-91c5-e14ce6f4db0b">https://gbif.org/dataset/5f73d28a-b9b5-4297-91c5-e14ce6f4db0b</a>. Formatted as a Frictionless Data package.
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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.
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DANDI Archive for NWB datasets
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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.