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85 results for “evolutionary integration”
Dynamic evolutionary interplay between ontogenetic skull patterning and whole-head integration
<p>Data and code for the analysis in Ollonen et al., 2024, Dynamic evolutionary interplay between ontogenetic skull patterning and whole-head integration, Nature Ecology and Evolution. </p> <p>Raw landmark data, R scripts for the analysis and surface files used for the analysis as well as figure visualisations. </p> <p>Cite the original article, not the dataset citation!!!</p>
Data from: Evolutionary and demographic history of the Californian scrub white oak species complex: an integrative approach
<p>Understanding the factors promoting species formation is a major task in evolutionary research. Here, we employ an integrative approach to study the evolutionary history of the Californian scrub white oak species complex (genus <em>Quercus</em>). To infer the relative importance of geographical isolation and ecological divergence in driving the speciation process, we (i) analyzed inter- and intra-specific patterns of genetic differentiation and employed an approximate Bayesian computation (ABC) framework to evaluate different plausible scenarios of species divergence. In a second step, we (ii) linked the inferred divergence pathways with current and past species distribution models, and (iii) tested for niche differentiation and phylogenetic niche conservatism across taxa. ABC analyses showed that the most plausible scenario is the one considering the divergence of two main lineages followed by a more recent pulse of speciation. Genotypic data in conjunction with species distribution models and niche differentiation analyses support that different factors (geography vs. environment) and modes of speciation (parapatry, allopatry and maybe sympatry) have played a role in the divergence process within this complex. We found no significant relationship between genetic differentiation and niche overlap, which probably reflects niche lability and/or that multiple factors have contributed to speciation. Our study shows that different mechanisms can drive divergence even among closely related taxa representing early stages of species formation and exemplifies the importance of adopting integrative approaches to get a better understanding of the speciation process.</p>
Figure 1. - A in Integrating multiple lines of evidence to better understand the evolutionary divergence of humpback dolphins along their entire distribution range: a new dolphin species in Australian waters?
Figure 1. - A: Diplodus omanensis, 310 mm SL; B: Pagellus affinis, 183 mm SL. Both species were purchased at the West Wharf Fish Harbour, Karachi, Pakistan, 26 May 2012.
Data from: Building on 150 years of knowledge: the freshwater isopod Asellus aquaticus as an integrative eco-evolutionary model system
<p><strong>Introduction</strong></p> <p>This is a literature database with reference information of all papers that use the freshwater isopod <em>Asellus aquaticus</em>; published between the years 1867 and 2020. This database is intended as a starting point for scientists interested in conducting research on and with this organism. The database is currently only available as a single CSV file; future versions may be made available through a more frequently updated SQL database. The database includes specific information about the subject area and content of each paper, as well as bibliographic information. This repository is associated with the paper "Building on 150 years of knowledge: the freshwater isopod<em> Asellus aquaticus</em> as an integrative eco-evolutionary model system", published in Frontiers in Ecology and Evolution.</p> <p><strong>Details on Methods from the electronic supplement:</strong></p> <p>We used the we online search tools of Web of Science (WOS; Clarivate analytics) by searching for the term "asellus aquaticus" in six relevant databases (BIOSIS, CABI, FSTA, Medline, WOS Core Collection and Zoological Records). The database was accessed with a University License (Lund University). We manually downloaded the results and combined them to a single CSV file in Excel (Microsoft). All further processing was done in the statistical programming language R, version 4.0.2 (R Core Team 2020).</p> <p>From the 1238 obtained records we discarded three papers that were published after the year 2020 to work with completed years only. We used the subject areas assigned by WOS to provide an overview of the fields of science in which A. aquaticus has been most studied. Each paper had between one and ten subject areas assigned by WOS (2845 assignments to 1235 papers, meaning 2.3 assignments per paper, on average). To represent these multiple assignments in relation to the actual number of papers per year, we calculated "fractional assignments" by adding up all assignments to a field per year, divided by the total number of assignments in that year, and then multiplied by the number of papers. For example, if there were 12 assignments to "toxicology" in 1993, and 133 assignments in 1993, but only 21 papers published, "toxicology" would get a score of 1.9 papers in 1993 (as calculated by = (12/133)*21). In Figure 1, we represent these "fractional assignments" in the top panel, and the total number of assignments in the lower panel.</p> <p><strong>Caption for figure (1) in publication:</strong></p> <p>FIGURE 1 | Over 150 years of research on and with Asellus aquaticus. The figure summarizes published scientific literature on A. aquaticus. We conducted a quantitative literature survey with the search tools of Web of Science (WOS; Clarivate analytics) by searching for the term "asellus aquaticus" in six databases (i.e., BIOSIS, CABI, FSTA, Medline, WOS Core Collection, and Zoological Records). We found 1235 records, published between 1867 and 2020. (A) The graph shows the number of publications per year within a given subject area, as designated by WOS. (B) The graph shows the total number of publications assigned to a specific subject area. The top 10 fields account for 72.58% of all publications, and are indicated by color coding in A and B (multiple assignments are possible, summing up to 2845 assignments). The inset in B shows a wordcloud with the 100 most used keywords from all A. aquaticus’ publications. Furthermore, we compiled all records with relevant information (e.g., title, keywords, research areas, and abstract) to a single file which is available online. More details can be found in the Supplementary Material.</p>
Novel integrative modeling of molecules and morphology across evolutionary timescales
<p>Evolutionary models account for either population or species-level processes, but usually not both. We introduce a new model, the FBD-MSC, which makes it possible for the first time to integrate both the genealogical and fossilization phenomena, by means of the multispecies coalescent (MSC) and the fossilized birth-death (FBD) processes. Using this model, we reconstruct the phylogeny representing all extant and many fossil Caninae, recovering both the relative and absolute time of speciation events. We quantify known inaccuracy issues with divergence time estimates using the popular strategy of concatenating molecular alignments, and show that the FBD-MSC solves them. Our new integrative method and empirical results advance the paradigm and practice of probabilistic total evidence analyses in evolutionary biology.</p>
Figure 7 in Phylogenetic biome conservatism as a key concept for an integrative understanding of evolutionary history: Galliformes and Falconiformes as study cases
Figure 7. Biome transitions in Falconiformes. The number of recent species is indicated inside the circles. Arrow thickness is proportional to the number of colonizations. The dashed lines indicate only one colonization event. The number of transitions that did not imply colonization (niche conservatism) is indicated as different areas of the circles, classified in four categories. For more details about absolute scores, see Table 3.
Figure 5 in Phylogenetic biome conservatism as a key concept for an integrative understanding of evolutionary history: Galliformes and Falconiformes as study cases
Figure 5. Ancestral biome reconstruction for Falconiformes. Coloured circles represent the ten different biomes implemented in the model (Walter, 1970; Hernández Fernández, 2001); those at the nodes represent the inferred ancestral biome(s); those at the tips correspond to the recent biome distribution of species. Along the time scale, geological and climatic histories are shown, in addition to intercontinental biotic interchanges. Abbreviations: Af, Africa; Au, Australia; EAs, Eurasia; LB, land bridge; NA, North America; SA, South America.
Figure 6 in Phylogenetic biome conservatism as a key concept for an integrative understanding of evolutionary history: Galliformes and Falconiformes as study cases
Figure 6. Colonization dynamics of Falconiformes. Each graph represents the rate of colonization by new lineages for each biome throughout the Cenozoic.
Figure 4 in Phylogenetic biome conservatism as a key concept for an integrative understanding of evolutionary history: Galliformes and Falconiformes as study cases
Figure 4. Biome transitions in Galliformes. The number of recent species is indicated inside the circles. Arrow thickness is proportional to the number of colonizations. The dashed lines indicate only one colonization event. The number of transitions that did not imply colonization (niche conservatism) is indicated as different areas of the circles, classified in five categories. For more details about absolute scores, see Table 2.
Figure 2 in Phylogenetic biome conservatism as a key concept for an integrative understanding of evolutionary history: Galliformes and Falconiformes as study cases
Figure 2. Ancestral biome reconstruction for Galliformes. Coloured circles represent the ten different biomes implemented in the model (Walter, 1970; Hernández Fernández, 2001); those at the nodes represent the inferred ancestral biome(s) occupancy; those at the tips correspond to the recent biome distribution of species. Along the time scale, geological and climatic histories are shown, in addition to intercontinental biotic interchanges. Abbreviations: Af, Africa; Au, Australia; EAs, Eurasia; LB, land bridge; NA, North America; SA, South America.
Figure 3 in Phylogenetic biome conservatism as a key concept for an integrative understanding of evolutionary history: Galliformes and Falconiformes as study cases
Figure 3. Colonization dynamics of Galliformes. Each graph represents the rate of colonization by new lineages for each biome throughout the Cenozoic.
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.
Data from: Evolutionary and demographic history of the Californian scrub white oak species complex: an integrative approach
Open the record for dataset details and reuse information.
Novel integrative modeling of molecules and morphology across evolutionary timescales
Open the record for dataset details and reuse information.
Data from: Pan-evolutionary and regulatory genome architecture delineated by integrated macro- and microsynteny approach
<p>Based on the published algorithms or tools developed by our and other groups, we introduce a detailed protocol for the most comprehensive and up-to-date genome synteny pipeline (called PanSyn) and provides step-by-step instructions as well as application examples for demonstrating how to use it. PanSyn pipeline includes three major modules (microsynteny analysis, macrosynteny analysis, and integrated micro & macro analysis). PanSyn not only fills a gap of lacking a user-friendly, highly-customized tool for genome macrosynteny analysis but also allows for integrated pan-evolutionary and regulatory analysis of genome microsyntenty and macrosynteny which are not yet available in any public synteny software or tools. PanSyn has been tested under Linux system. PanSyn has multiple subroutines. Users only need to simply modify the configuration file and corresponding command parameters to execute them. Outputs include vector diagrams that are suitable for custom modification. <br> </p>
Evolutionary modularity, integration and disparity in an accretionary skeleton: Analysis of venerid Bivalvia
<p><span><span><span><span><span><span><span><span><span><span><span>Modular evolution, the relatively independent evolution of body parts, may promote high morphological disparity in a clade. Conversely, integrated evolution via the stronger covariation of parts may limit disparity. However, integration can also promote high disparity by channeling morphological evolution along lines of least resistance—a process that may be particularly important in the accumulation of disparity among organisms with accretionary growth, as in many invertebrate systems. We use a time-calibrated phylogenetic hypothesis and high-density, 3D semilandmarking to analyze the relationship between modularity, integration, and disparity in the most diverse extant bivalve family: the Veneridae. In general, venerids have a simple, two-module parcellation of body features that is divided into features of the calcium carbonate shell and features of the internal soft anatomy. This division falls more along developmental than functional lines when placed in the context of bivalve evolutionary-development and biomechanics. While the venerid body is tightly integrated in absolute terms, increasing modularity strength among subclades and ecologies appears to correlate with increasing disparity, indicating that shifts towards more mosaic evolution beget higher morphologic variance in this speciose family.</span></span></span></span></span></span></span></span></span></span></span></p>
A quantitative assessment of the patterns of integration in the mandible of bovids and their relationships with trophic ecology, phylogeny, and evolutionary rates
<p>Dataset and R script supporting the findings of the study "A quantitative assessment of the patterns of integration in the mandible of bovids and their relationships with trophic ecology, phylogeny, and evolutionary rates". </p>
Unraveling the evolutionary history of the snakefly family Inocelliidae (Insecta: Raphidioptera) through integrative phylogenetics
<p>Inocelliidae is one of the two extant families of the holometabolan order Raphidioptera (snakeflies), with the modern fauna represented by seven genera and 44 species. The evolutionary history of the family is little known. Here we present the first phylogenetic and biogeographic analyses based on a worldwide sampling of taxa and datasets combined with morphological characters and mitochondrial genomes, aiming to investigate the intergeneric phylogeny and historical biogeography of Inocelliidae. The phylogenetic inference from the combined analysis of morphological and molecular data recovered the sister-group relationship between a clade of (<em>Negha</em> + <em>Indianoinocellia</em>) + <em>Sininocellia</em> and a clade of <em>Fibla</em> + the <em>Inocellia</em> clade (interiorly nested by <em>Amurinocellia</em> and <em>Parainocellia</em>). <em>Amurinocellia</em> <strong>stat. rev.</strong> and <em>Parainocellia</em><strong> stat. rev. et emend. nov.</strong> are relegated to subgeneric status within Inocellia, while a newly erected subgenus of <em>Inocellia</em>, <em>Epinocellia</em> <strong>subgen. nov.</strong>, accommodates the former <em>Parainocellia</em> <em>burmana</em> (U. Aspöck and H. Aspöck, 1968) plus a new species <em>Inocellia</em> (<em>Epinocellia</em>) weii sp. nov. Further, the <em>Inocellia</em> crassicornis group constitutes the nominate subgenus <em>Inocellia</em> <strong>stat. nov</strong>., but the <em>Inocellia</em> <em>fulvostigmata</em> group is paraphyletic. Diversification within Inocelliidae is distinguished by an Eocene divergence leading to extant genera and a Miocene radiation of species. A biogeographic scenario depicts how the diverse inocelliid fauna from East Asia could have originated from western North America via dispersal across the Beringia during the early Tertiary, and how the Miocene ancestors of <em>Inocellia</em> could have accomplished long-distance dispersals via the Tibet‐Himalayan corridor or eastern Palaearctic to western Palaearctic. Our results shed new light specifically on the evolution of Inocelliidae and, in general, the Raphidioptera.</p>
Genetic admixture and evolutionary history of Han Chinese in the Shandong Peninsula inferred from integrative modern and ancient genomic resources
<p>The allele frequency data of 264 individuals from Shandong Province and supplementary table.</p>
Data from: Morphological integration during postnatal ontogeny: Implications for evolutionary biology
<p>How covariance patterns of phenotypes change during development is fundamental for a broader understanding of evolution. There is compelling evidence that mammalian cranium covariance patterns change during ontogeny. However, it is unclear to what extent variation in covariance patterns during ontogeny can impact the response to selection. To tackle this question we explored: i) the extent to which covariance patterns change during postnatal ontogeny; ii) in which ontogenetic stages covariance patterns differ the most, and iii) the extent to which the phenotypic covariance pattern at different ontogenetic stages can be explained by the same processes determining additive genetic covariance. We sampled postnatal ontogenetic series for both marsupials, and placentals. Within each ontogenetic series, we compared covariance matrices (<strong>P</strong>-matrices) at different ontogenetic stages. Furthermore, we compared these <strong>P</strong>-matrices to two target matrices [adult <strong>P</strong>-matrix and an additive genetic covariance matrix (<strong>G</strong>-matrix)]. Our results show that for all ontogenetic series, covariance patterns from weaning onward are conserved and probably shaped by the same processes determining the <strong>G</strong>-matrix. We conclude that irrespective of eventual differences in how selection operates during most of postnatal ontogeny, the net response to such pressures will probably not be affected by ontogenetic differences in the covariance pattern.</p>
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Allen Brain Atlas
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International Brain Laboratory public data
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OpenNeuro
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