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74 results for “evolutionary processes”
Eco-evolutionary processes underlying early warning signals of population declines
<p>Datasets for the paper appearing in Journal of Animal ecology : "Eco-evolutionary processes underlying early warning signals of population declines". Also GitHub repository link :<a href="https://github.com/GauravKBaruah/ECO-EVO-EWS-DATA">https://github.com/GauravKBaruah/ECO-EVO-EWS-DATA</a></p>
Data from: Spatial processes and evolutionary models: a critical review
Evolution is a fundamentally population level process in which variation, drift, and selection produce both temporal and spatial patterns of change. Statistical model fitting is now commonly used to estimate which kind of evolutionary process best explains patterns of change through time, using models like Brownian motion, stabilizing selection (Ornstein-Uhlenbeck), and directional selection on traits measured from stratigraphic sequences or on phylogenetic trees. But these models assume that the traits possessed by a species are homogeneous. Spatial processes such as dispersal, gene flow, and geographic range changes can produce patterns of trait evolution that do not fit the expectations of standard models, even when evolution at the local-population level is governed by drift or a typical OU model of selection. The basic properties of population level processes (variation, drift, selection, and population size) are reviewed and the relationship between their spatial and temporal dynamics is discussed. Typical evolutionary models used in palaeontology incorporate the temporal component of these dynamics, but not the spatial. Range expansions and contractions introduce rate variability into drift processes, range expansion under a drift model can drive directional change in trait evolution, and spatial selection gradients can create spatial variation in traits that can produce long-term directional trends and punctuation events depending on the balance between selection strength, gene flow, extirpation probability, and model of speciation. Using computational modelling that spatial processes can create evolutionary outcomes that depart from basic population-level notions from these standard macroevolutionary models.
Incorporating evolutionary and threat processes into crop wild relatives conservation
<p>Crop wild relatives (CWR) intra- and interspecific diversity is essential for crop breeding and food security. However, intraspecific genetic diversity, which is central given the idiosyncratic threats to species in landscapes, is usually not considered in planning frameworks. Here, we introduce an approach to develop proxies of genetic differentiation to identify conservation areas, applying systematic conservation planning tools that produce hierarchical prioritizations of the landscape. It accounts for: (i) evolutionary processes, including historical and environmental drivers of genetic diversity, and (ii) threat processes, considering taxa-specific tolerance to human-modified habitats, and their extinction risk status. Our results support the development of national strategies for the conservation and use of CWR in Mexico and inform public policy to mitigate threat processes to CWR. Although we focus on Mesoamerican CWR within Mexico, our methodology offers opportunities to effectively guide conservation and monitoring strategies to safeguard the evolutionary resilience of any taxa, including in regions of complex evolutionary histories and mosaic landscapes.</p>
Processed data for "Characterising the evolutionary dynamics of cancer proliferation in single-cell clones with SPRINTER"
<p>This dataset contains the processed data for the figures and analyses performed in the publication "Characterising the evolutionary dynamics of cancer proliferation in single-cell clones with SPRINTER" from Lucas O., Ward S., Zaidi R., Bunkum A., ..., Zaccaria S. Nature genetics, in press, 2024.</p> <p>The processed data are separated into three respective folders:</p> <ul> <li>GT contains all the data related to the analysis of the generated ground truth datasets;</li> <li>NSCLC contains all the data related to the analysis of the NSCLC dataset;</li> <li>TNBC_HGSC contains all the data related to the analysis of the TNBC and HGSC datasets. </li> </ul>
Figure 8 in The giraffe (Giraffa camelopardalis) cervical vertebral column: a heuristic example in understanding evolutionary processes?
Figure 8. These graphs compare the measured individual cervical vertebrae lengths of fossil Giraffids (Table 4), compared with extant giraffes and the 'other ungulate' group used in this study. The measurement of total vertebral column lengths (TVLs) for the fossil giraffids were generated from the regressions derived for extant giraffes or 'other ungulates', whereas the lengths of the individual cervical vertebrae were taken from the literature (see Table 4). Note that the specimens for Giraffa sp., Samotherium, and Paleotragus germaini appear to scale in a manner similar to extant giraffes, whereas those of Paleotragus primaevus, Climacoceras, and Canthumeryx appear to fall within the range of ungulates that do not demonstrate cervical elongation.
Figure 6 in The giraffe (Giraffa camelopardalis) cervical vertebral column: a heuristic example in understanding evolutionary processes?
Figure 6. Graphs of total vertebral column length plotted against the body lengths of C2–C7 vertebrae of all of the extant specimens studied. Other ungulates represent all species studied except the giraffe, camel, and llama. Note that for all specimens of the giraffe the vertebral lengths are longer than one would predict on the basis of a generalized ungulate regression, and scale more steeply than the ungulates. The dotted line on the ungulate plot is an extension of the ungulate regression that allows us to establish a comparison with the camel.
Figure 9 in The giraffe (Giraffa camelopardalis) cervical vertebral column: a heuristic example in understanding evolutionary processes?
Figure 9. These graphs compare the measured individual cervical vertebrae lengths of fossil Giraffids (Table 4) with extant giraffes and the 'other ungulate' group used in this study. The measurement of normalized vertebral column lengths for the fossil giraffids were generated from the regressions derived for extant giraffes or 'other ungulates', whereas the lengths of the individual cervical vertebrae were taken from the literature (see Table 4). Note that the specimens for Giraffa sp., Samotherium, and Paleotragus germaini appear to scale in a manner similar to extant giraffes, whereas those of Paleotragus primaevus, Climacoceras, and Canthumeryx appear to fall within the range of ungulates that do not demonstrate cervical elongation.
Figure 5 in The giraffe (Giraffa camelopardalis) cervical vertebral column: a heuristic example in understanding evolutionary processes?
Figure 5. Graph of total cervical vertebral length (TCL) vs. individual vertebral length of all the extant specimens studied. Note the way in which the giraffe cervical vertebrae scale in accordance with those seen in the other extant ungulates studied, with the only exception being the youngest giraffe (which was excluded from the regression analysis, but was placed on the graph for comparison).
Figure 2 in The giraffe (Giraffa camelopardalis) cervical vertebral column: a heuristic example in understanding evolutionary processes?
Figure 2. Photographs of the lateral aspect of non-articulated giraffe vertebrae C6, C7, T1, and T2, demonstrating the osteological differences between cervical and thoracic vertebrae. Note the size of the transverse foramen in C7, the lack of a transverse foramina in T1 and T2, and the longer spinous process of T1 compared with C6 and C7.
Figure 4 in The giraffe (Giraffa camelopardalis) cervical vertebral column: a heuristic example in understanding evolutionary processes?
Figure 4. Upper panel: the percentage contribution of the remaining vertebral regions to the vertebral column length minus that of the cervical of giraffes aged from calf to adult (ages are estimates). Lower panel: the percentage contributions of the remaining vertebral regions to the vertebral column length minus that of the cervical of the extant ungulates studied, in comparison with the adult giraffes. The percentage occupied by the various spinal regions in the giraffe falls into the same ranges observed in other ungulates when the cervical vertebrae are not included. Key: l, lumbar; s, sacral; t, thoracic.
Figure 3 in The giraffe (Giraffa camelopardalis) cervical vertebral column: a heuristic example in understanding evolutionary processes?
Figure 3. Upper panel: the percentage contribution of the vertebral regions to the entire length of the vertebral column of giraffes aged from calf to adult (ages are estimates). In the calf, the cervical vertebrae occupy approximately 45% of the total vertebral length. As the animal matures, this increases to between 52 and 54%. Lower panel: the percentage contribution of the vertebral regions to the entire length of the vertebral column of the extant ungulates studied, compared with the adult giraffe. Note that only in the giraffes do the cervical vertebrae occupy more than half of the entire vertebral column. Key: c, cervical; l, lumbar; s, sacral; t, thoracic.
Figure 1 in The giraffe (Giraffa camelopardalis) cervical vertebral column: a heuristic example in understanding evolutionary processes?
Figure 1. Photograph of the left aspect of giraffe vertebrae C6–T2, demonstrating how they are articulated in a living individual, and the differences between cervical and thoracic vertebrae. Note the size of the transverse foramen in C7 and the longer spinous process of T1 compared with C6 and C7.
Incorporating evolutionary and threat processes into crop wild relatives conservation
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Data from: Spatial processes and evolutionary models: a critical review
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Scripts and data sets associated with: On testing homogeneity of the evolutionary process using alignments of homologous sequences
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Ecological network structure in response to community assembly processes over evolutionary time
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Data from: How Bank Vole-PUUV Interactions Influence the Eco-Evolutionary Processes Driving Nephropathia Epidemica Epidemiology—An Experimental and Genomic Approach
<p><strong>Abstract: </strong>In Europe, Puumala virus (PUUV) is responsible for nephropathia epidemica (NE), a mild form of hemorrhagic fever with renal syndrome (HFRS). Despite the presence of its reservoir, the bank vole, on most of French territory, the geographic distribution of NE cases is heterogeneous and NE endemic and non-endemic areas have been reported. In this study we analyzed whether bank vole-PUUV interactions could partly shape these epidemiological differences. We performed crossed-experimental infections using wild bank voles from French endemic (Ardennes) and non-endemic (Loiret) areas and two French PUUV strains isolated from these areas. The serological response and dynamics of PUUV infection were compared between the four cross-infection combinations. Due to logistical constraints, this study was based on a small number of animals. Based on this experimental design, we saw a stronger serological response and presence of PUUV in excretory organs (bladder) in bank voles infected with the PUUV endemic strain. Moreover, the within-host viral diversity in excretory organs seemed to be higher than in other non-excretory organs for the NE endemic cross-infection but not for the NE non-endemic cross-infection. Despite the small number of rodents included, our results showed that genetically different PUUV strains and in a lesser extent their interaction with sympatric bank voles, could affect virus replication and diversity. This could impact PUUV excretion/transmission between rodents and to humans and in turn at least partly shape NE epidemiology in France.</p>
Contrasting patterns of sequence variation in steelhead populations reflect distinct evolutionary processes
<p>Multiple evolutionary processes influence genome‐wide allele frequencies and quantifying effects of genetic drift, and multiple forms of selection remain challenging in natural populations. Here, we investigate variation at major effect loci in contrast to patterns of neutral drift across a wide collection of steelhead (<em>Oncorhynchus mykiss</em>) populations that have declined in abundance due to anthropogenic impacts. Whole‐genome resequencing of 74 populations of steelhead revealed genome‐wide patterns (~8 million SNPs) consistent with expected neutral population structure. However, allelic variation at major effect loci associated with adult migration timing (chromosome 28: GREB1L/ROCK1) and age at maturity (chromosome 25: SIX6) reflected how selection has acted on phenotypic variation in contrast with neutral structure. Variation at major effect loci was influenced by evolutionary processes with differing signals between the strongly divergent Coastal and Inland lineages, while allele frequencies within and among populations within the Inland lineage have been driven by local natural selection as well as recent anthropogenic influences. Recent anthropogenic effects appeared to have influenced the frequency of major effect alleles including artificial selection for specific traits in hatchery stocks with subsequent gene flow into natural populations. Selection from environmental factors at various scales has also likely influenced variation for major effect alleles. These results reveal evolutionary mechanisms that influence allele frequencies at major effect loci that are critical for conservation of phenotypic traits and life history variation of this protected species.</p>
Global biogeography and diversification of a group of brown seaweeds (Phaeophyceae) driven by clade-specific evolutionary processes
<p class="BodyA"><span><b>Aim:</b> Historical processes that shaped current diversity patterns of seaweeds remain poorly understood. Using Dictyotales, a globally distributed order of brown seaweeds as a model, we test if historical biogeographical and diversification patterns are comparable across clades. Dictyotales contain some 22 genera, three of which, <i>Dictyota</i>, <i>Lobophora</i> and <i>Padina</i>, are exceptionally diverse. Specifically we test if the evolutionary processes in these clades that shaped their latitudinal diversity patterns are in line with the tropical conservatism, the out-of-the-tropics, and diversification rate hypotheses.</span></p> <p class="BodyA"><span><b>Location:</b> Global coastal benthic marine environments.</span></p> <p class="BodyA"><span><b>Taxon:</b> Dictyotales (Phaeophyceae)</span></p> <p class="BodyA"><span><b>Methods:</b> Species diversity was inferred using DNA-based species delineation, addressing cryptic diversity and circumventing taxonomic problems. A six-gene time-calibrated phylogeny, distribution data of 3,755 specimens, and probabilistic modeling of geographic range evolution was used to infer historical biogeographical patterns. The phylogeny was tested against different trait dependent models in order to compare diversification rates for different geographical units as well as different thermal affinities.</span></p> <p class="BodyA"><span><b>Results:</b> The Dictyotales originated in the Middle Jurassic and reach a current peak of species diversity in the Central Indo-Pacific. Ancestral range estimation points to a southern hemisphere origin of Dictyotales corresponding to the tropical southern Tethys Sea. Our results demonstrate that diversification rates were generally higher in tropical regions, but increased diversification rates in different clades are driven by different processes. Three major clades underwent a major diversification burst in the early Cenozoic, with <i>Dictyota </i>and <i>Padina </i>expanding their distribution into temperate regions, while <i>Lobophora</i> retained a predominantly tropical niche.</span></p> <p><b>Main conclusions:</b> Our results are consistent with both the tropical conservatism hypothesis, in which clades originate and remain in the tropics (<i>Lobophora</i>), and the out-of-the-tropics scenario, where taxa originate and expand towards the temperate regions while preserving their presence in the tropics (<i>Dictyota</i>, <i>Padina</i>).</p>
Ecological and evolutionary processes shape belowground springtail communities along an elevational gradient
<p> The data sets were analyzed during the current study. Data from: Ecological and evolutionary processes shape belowground springtail communities along an elevational gradient</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)
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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.