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157 results for “Evolutionary Studies”
Figure 1 in Phylogenetic biome conservatism as a key concept for an integrative understanding of evolutionary history: Galliformes and Falconiformes as study cases
Figure 1. Schematic explanatory example for transition categories considered in this study: transition with biome conservatism; transition with colonization; and transition with loss of ancestral biome occupation. Note that ancestral biome occupation (for node A) is the same above and below, whereas biome occupations for derived nodes B (above) and C (below) differ.
A Bayesian extension of phylogenetic generalized least squares (PGLS): incorporating uncertainty in the comparative study of trait relationships and evolutionary rates
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Data from: Methodological artefacts cause counter-intuitive evolutionary conclusions in a simulation study
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Taxon-specific or universal? Using target capture to study the evolutionary history of a rapid radiation
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Chromosome-level genome of the peach fruit moth Carposina sasakii (Lepidoptera: Carposinidae) provides a resource for evolutionary studies on moths
<p>Here we provide scripts and parameters for genome assembly and annotation, as well as the manually annotated circadian genes of <i>period</i> (PER), <i>timeless</i> (TIM), <i>Clock</i> (CLK), <i>cycle</i> (CYC) and cryptochrome (CRY), five detoxification gene families of cytochrome P450 monooxygenase (P450s), glutathione S-transferase (GSTs), carboxyl/cholinesterases (CCEs), UDP-glycosyltransferases (UGTs) and ATP-binding cassette (ABC) transporters, IR, OR, OBP, GR genes from the genome of <span class="fontstyle01"><span>the peach fruit moth (PFM), </span></span><span class="fontstyle01"><span><i>Carposina sasakii</i></span></span><span class="fontstyle01"><span> Matsumura (Lepidoptera: Carposinidae, superfamily Copromorphoidea) and genomes of its related species.</span></span></p>
Data from: A phylogenomic framework, evolutionary timeline and genomic resources for comparative studies of decapod crustaceans
Comprising over 15 000 living species, decapods (crabs, shrimp and lobsters) are the most instantly recognizable crustaceans, representing a considerable global food source. Although decapod systematics have received much study, limitations of morphological and Sanger sequence data have yet to produce a consensus for higher-level relationships. Here, we introduce a new anchored hybrid enrichment kit for decapod phylogenetics designed from genomic and transcriptomic sequences that we used to capture new high-throughput sequence data from 94 species, including 58 of 179 extant decapod families, and 11 of 12 major lineages. The enrichment kit yields 410 loci (greater than 86 000 bp) conserved across all lineages of Decapoda, more clade-specific molecular data than any prior study. Phylogenomic analyses recover a robust decapod tree of life strongly supporting the monophyly of all infraorders, and monophyly of each of the reptant, 'lobster' and 'crab' groups, with some results supporting pleocyemate monophyly. We show that crown decapods diverged in the Late Ordovician and most crown lineages diverged in the Triassic–Jurassic, highlighting a cryptic Palaeozoic history, and post-extinction diversification. New insights into decapod relationships provide a phylogenomic window into morphology and behaviour, and a basis to rapidly and cheaply expand sampling in this economically and ecologically significant invertebrate clade.
Global Sensitivity Analysis is Not Always Beneficial for Evolutionary Computation: A Study in Engineering Design
<p>This Zenodo repository contains all the results generated for the book chapter "Global Sensitivity Analysis is Not Always Beneficial for Evolutionary Computation: A Study in Engineering Design".</p>
The Community Coevolution Model with application to the study of evolutionary relationships between genes based on phylogenetic profiles
<p>Organismal traits can evolve in a coordinated way, with correlated patterns of gains and losses reflecting important evolutionary associations. Discovering these associations can reveal important information about the functional and ecological linkages among traits. Phylogenetic profiles treat individual genes as traits distributed across sets of genomes and can provide a fine-grained view of the genetic underpinnings of evolutionary processes in a set of genomes. Phylogenetic profiling has been used to identify genes that are functionally linked, and to identify common patterns of lateral gene transfer in microorganisms. However, comparative analysis of phylogenetic profiles and other trait distributions should take into account the phylogenetic relationships among the organisms under consideration.</p> <p>Here we propose the Community Coevolution Model (CCM), a new coevolutionary model to analyze the evolutionary associations among traits, with a focus on phylogenetic profiles. In the CCM, traits are considered to evolve as a community with interactions, and the transition rate for each trait depends on the current states of other traits. Surpassing other comparative methods for pairwise trait analysis, CCM has the additional advantage of being able to examine multiple traits as a community to reveal more dependency relationships. We also develop a simulation procedure to generate phylogenetic profiles with correlated evolutionary patterns that can be used as benchmark data for evaluation purposes.</p> <p>A simulation study demonstrates that CCM is more accurate than other methods including the Jaccard Index and three tree-aware methods. The parameterization of CCM makes the interpretation of the relations between genes more direct, which leads to Darwin's scenario being identified easily based on the estimated parameters. We show that CCM is more efficient and fits real data better than other methods resulting in higher likelihood scores with fewer parameters. An examination of 3786 phylogenetic profiles across a set of 659 bacterial genomes highlights linkages between genes with common functions, including many patterns that would not have been identified under a non-phylogenetic model of common distribution. We also applied the CCM to 44 proteins in the well-studied Mitochondrial Respiratory Complex I and recovered associations that mapped well onto the structural associations that exist in the complex.</p>
Data from: Skeletal mineralogy of marine organisms shaped by seawater temperature and evolutionary history - a case study of cheilostome bryozoans
<p>The record of CaCO<sub>3</sub> biominerals serves as a valuable repository documenting Earth's evolutionary history and environmental changes. An in-depth understanding of the mineralogical diversity within calcifying organisms is essential for interpreting the evolutionary record of CaCO<sub>3</sub> and evaluating the adaptability of biomineralizers to past and future environmental change. To offer insights into the relative importance of environment vs. phylogenetic history in determining mineralogy, this study explores the modern-day global distribution of mineralogies in cheilostome bryozoans.</p> <p>Cheilostome bryozoans vary considerably in their mineral composition: in our dataset 65% of the species possess purely calcite skeletons, 15% exclusively employ aragonite, and 20% exhibit mixed (i.e., calcite and aragonite) mineralogies. Temperature is the predominant measured environmental factor influencing bryozoan skeletal mineralogy, accounting for 20% of its variability across species, when phylogenetic relatedness is unaccounted for. Bryozoans in lower latitudes, characterized by higher seawater temperatures, have higher aragonite concentrations. By accounting for phylogenetic structure using a subset of 87 species for which we have topological information, 40% of the observed mineralogical variability could be attributed to present-day temperature. In contrast, depth and salinity played minor roles, explaining less than 1% of the mineralogical variation each.</p> <p>This study emphasizes the influence of evolutionary history on the mineralogical variability of calcifying organisms, even when it can be shown that a single environmental factor (temperature) explains a substantial amount of this variability. When confronted with changing temperature, calcifiers such as bryozoans are likely to respond in diverse ways, depending on the species, given their phylogenetic relatedness and the external conditions they meet.</p>
Simulated datasets analysed in Rota et al. study "A simple method for data partitioning based on relative evolutionary rates"
<p>Simulated datasets analysed in Rota et al. study "A simple method for data partitioning based on relative evolutionary rates". AS refers to datasets simulated on an asymmetrical trees and SS to those simulated on a symmetrical tree. The datasets are in phylip format. Having 'miss' in the name of a file refers to missing 25% of the data.</p>
Figure 15 in The suprageneric groups of the Pimplinae (Hymenoptera: Ichneumonidae): a cladistic re-evaluation and evolutionary biological study
Figure 15. Cladogram resulting from secondary analysis: section 2 (of 9), Delomeristini.
Anguimorpha as a model group for studying the comparative heart morphology among Lepidosauria: Evolutionary window on the ventricular septation
<p>The group Anguimorpha represents one of the most unified squamate clades in terms of body plan, ecomorphology, ecophysiology and evolution. On the other hand, the anguimorphs vary between different habitats and ecological niches. Therefore, we focused on the group Anguimorpha to test a possible correlation between heart morphology and ecological niche with respect to phylogenetic position in Squamata with <em>Sphenodon</em>, <em>Salvator</em>, and <em>Pogona</em> as the outgroups. The chosen lepidosaurian species were investigated by microCT. Generally, all lepidosaurs had two well-developed atria with complete interatrial septum and one ventricle divided by ventricular septa to three different areas. The ventricles of all lepidosaurians had a compact layer and abundant trabeculae. The compact layer and trabeculae were developed in accordance with the particular ecological niche of the species; the trabeculae in nocturnal animals with low metabolism, such as <em>Sphenodon, Heloderma</em> or <em>Lanthanotus</em>, were more massive. On the other hand, athletic animals, such as varanids or <em>Salvator</em>, had ventricle compartmentalization divided by three incomplete septa. A difference between varanids and <em>Salvator</em> was found in compact layer thickness: thicker in monitor lizards and possibly linked to their mammalian-like high blood pressure, and the level of ventricular septation. In summary: heart morphology varied among clades in connection with the ecological niche of particular species and it reflects the phylogenetic position in the model clade Anguimorpha. In the absence of fossil evidence, this is the closest approach to understanding heart evolution and septation in clades with different cardiac compartmentalization levels. </p>
Multi-gene phylogeny of North American clear-winged moths (Lepidoptera: Sesiidae): A foundation for future evolutionary study of a speciose mimicry complex
<p>Sesiids are a diverse group of predominantly diurnal moths, many of which are Batesian mimics of Hymenoptera. However, their diversity and relationships are poorly understood. A multi-gene phylogenetic analysis of 48 North American sesiid species confirmed the traditional taxonomic tribal ranks, demonstrated the paraphyly of <em>Carmenta</em> and <em>Synanthedon</em> with respect to several other genera, and ultimately provided minimal phylogenetic resolution within and between North American and European groups. Character support from each gene suggested inconsistency between the phylogenetic signal of the <em>CAD</em> gene and that of the other four genes. However, removal of <em>CAD</em> from subsequent phylogenetic analyses did not substantially change the initial phylogenetic results or return <em>Carmenta</em> and <em>Synanthedon</em> as reciprocally monophyletic, suggesting it was not impacting the overall phylogenetic signal. The lack of resolution using genes that are typically informative at the species level for other lepidopterans suggests a surprisingly rapid radiation of species in <em>Carmenta</em>/<em>Synanthedon</em>. This group also exhibits a wide range of mimicry strategies and hostplant usage, which could be fertile ground for future study.</p>
Data from: Skeletal mineralogy of marine organisms shaped by seawater temperature and evolutionary history - a case study of cheilostome bryozoans
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Development of a homeolog-specific gene editing system in an evolutionary model for the study of polyploidy in nature
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Multi-gene phylogeny of North American clear-winged moths (Lepidoptera: Sesiidae): A foundation for future evolutionary study of a speciose mimicry complex
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Data from: Phylogenomics disentangles the evolutionary history of spruces (Picea) in the Qinghai-Tibetan Plateau: implications for the design of population genetic studies and species delimitation of conifers
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Anguimorpha as a model group for studying the comparative heart morphology among Lepidosauria: Evolutionary window on the ventricular septation
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Data from: A phylogenomic framework, evolutionary timeline and genomic resources for comparative studies of decapod crustaceans
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Chromosome-level genome of the peach fruit moth Carposina sasakii (Lepidoptera: Carposinidae) provides a resource for evolutionary studies on moths
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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.