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35 results for “phylogenetic comparative method”
Challenges of sampling and how phylogenetic comparative methods help: Supplementary data
<p>Supplementary data and results files for the paper:</p> <p>Macklin-Cordes, Jayden L. & Erich R. Round (2022). Challenges of sampling and how phylogenetic comparative methods help: With a case study of the Pama-Nyungan laminal contrast. <em>Linguistic Typology</em> (advance online publication). <a href="https://doi.org/10.1515/lingty-2021-0025">https://doi.org/10.1515/lingty-2021-0025</a></p>
Supplementary material: How should functional relationships be evaluated using phylogenetic comparative methods? A case study using metabolic rate and body temperature
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Data from: Pollinator shifts, contingent evolution, and evolutionary constraint drive floral disparity in Salvia (Lamiaceae): evidence from morphometrics and phylogenetic comparative methods
Switches in pollinators have been argued to be key drivers of floral evolution in angiosperms. However, few studies have tested the relationship between floral shape evolution and switches in pollination in large clades. In concert with a dated phylogeny, we present a morphometric analysis of corolla, anther connective, and style shape across 44% of nearly 1,000 species of Salvia (Lamiaceae) and test four hypotheses of floral evolution. We demonstrate that floral morphospace of New World (NW) Salvia is largely distinct from that of Old World (OW) Salvia and that these differences are pollinator driven; that shifts in floral morphology sometimes mirror shifts in pollinators; that anther connectives (key constituents of the Salvia staminal lever) and styles co-evolved from curved to linear shapes following shifts from bee to bird pollination; and that morphological differences between NW and OW bee flowers are partly the legacy of constraints imposed by an earlier shift to bird pollination in the NW. The distinctive staminal lever in Salvia is a morphologically diverse structure that has evolved in concert with both the corolla and style, under different pollinator pressures, and in contingent fashion.
Data from: Phylogenetic comparative methods on phylogenetic networks with reticulations
The goal of Phylogenetic Comparative Methods (PCMs) is to study the distribution of quantitative traits among related species. The observed traits are often seen as the result of a Brownian Motion (BM) along the branches of a phylogenetic tree. Reticulation events such as hybridization, gene flow or horizontal gene transfer, can substantially affect a species' traits, but are not modeled by a tree. Phylogenetic networks have been designed to represent reticulate evolution. As they become available for downstream analyses, new models of trait evolution are needed, applicable to networks. One natural extension of the BM is to use a weighted average model for the trait of a hybrid, at a reticulation point. We develop here an efficient recursive algorithm to compute the phylogenetic variance matrix of a trait on a network, in only one preorder traversal of the network. We then extend the standard PCM tools to this new framework, including phylogenetic regression with covariates (or phylogenetic ANOVA), ancestral trait reconstruction, and Pagel's λ test of phylogenetic signal. The trait of a hybrid is sometimes outside of the range of its two parents, for instance because of hybrid vigor or hybrid depression. These two phenomena are rather commonly observed in present-day hybrids. Transgressive evolution can be modeled as a shift in the trait value following a reticulation point. We develop a general framework to handle such shifts, and take advantage of the phylogenetic regression view of the problem to design statistical tests for ancestral transgressive evolution in the evolutionary history of a group of species. We study the power of these tests in several scenarios, and show that recent events have indeed the strongest impact on the trait distribution of present-day taxa. We apply those methods to a dataset of Xiphophorus fishes, to confirm and complete previous analysis in this group. All the methods developed here are available in the Julia package PhyloNetworks.
Analyzing disparity and rates of morphological evolution with model-based phylogenetic comparative methods
<p>Understanding variation in rates of evolution and morphological disparity is a goal of macroevolutionary research. In a phylogenetic comparative methods framework, we present three explicit models for linking the rate of evolution of a trait to the state of another evolving trait. This allows testing hypotheses about causal influences on rates of phenotypic evolution with phylogenetic comparative data. We develop a statistical framework for fitting the models with generalized least-squares regression, and use this to discuss issues and limitations in the study of rates of evolution more generally. We show that the power to detect effects on rates of evolution is low in that even strong causal effects are unlikely to explain more than a few percent of observed variance in disparity. We illustrate the models and issues by testing if rates of beak-shape evolution in birds are influenced by brain size, as may be predicted from a Baldwin effect in which presumptively more behaviorally flexible large-brained species generate more novel selection on themselves leading to higher rates of evolution. From an analysis of morphometric data for 645 species we find evidence that both macro- and microevolution of the beak are faster in birds with larger brains, but with the caveat that there are no consistent effects of relative brain size.</p>
Data and code for: Feeding, mating, and animal wellbeing: New insights from Phylogenetic Comparative Methods
<p class="MsoNormal">Some species tend to thrive in captivity, while others risk health and reproductive problems. This enables the use of P<span>hylogenetic Comparative Methods (PCMs) </span>to identify aspects of natural biology that predispose species to faring poorly or well. Risk factors can then suggest new ways to improve animal care. A steady trickle of studies has applied PCMs to animal welfare over the last two decades, Lewis et al. (1) <span>providing the latest. Here we contextualise this new work and suggest further research it might inspire.</span></p> <p class="MsoNormal"><span>Provided here are the data and R code for Figure 1 provided in a commentary on: (1) Lewis, K., M.O. Parker, L. Proops, and S.D. McBride, <em>Risk factors for stereotypic behaviour in captive ungulates</em>. Proceedings of the Royal Society B: Biological Sciences, 2022. 289(1983): p. 20221311.</span></p>
Analyzing disparity and rates of morphological evolution with model-based phylogenetic comparative methods
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Data from: Analysing Thalattosuchia paleobiodiversity under the prism of phylogenetic comparative methods
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Data from: Phylogenetic comparative methods on phylogenetic networks with reticulations
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Data from: Pollinator shifts, contingent evolution, and evolutionary constraint drive floral disparity in Salvia (Lamiaceae): evidence from morphometrics and phylogenetic comparative methods
Open the record for dataset details and reuse information.
Data and code for: Feeding, mating, and animal wellbeing: New insights from Phylogenetic Comparative Methods
Open the record for dataset details and reuse information.
Phylogenetic comparative methods are problematic when applied to gene trees with speciation and duplication nodes: correcting for biases in testing the ortholog conjecture
<p>This repository contains “manuscript_dunn.RData” file, which is reproduced by using the files and scripts of Dunn et al. (Dunn CW, Zapata F, Munro C, Siebert S, Hejnol A (2018) Pairwise comparisons across species are problematic when analyzing functional genomic data. Proc Natl Acad Sci U S A 115: E409–E417. <a href="http://dx.doi.org/10.1073/pnas.1707515115">doi:10.1073/pnas.1707515115</a>).</p> <p>In this repository, we also supplied “Data_TMRR_latest.rda” file, containing the results generated by using our own scripts. Our scripts are available on GitHub: <a href="https://github.com/tbegum/Testing_the_ortholog_conjecture">https://github.com/tbegum/Testing_the_ortholog_conjecture</a>.</p> <p> </p>
FIGURE 10 in Comparative morphology of the eggs from the eight species in the genus Agathemera Stål (Insecta: Phasmatodea), through phylogenetic comparative method approach
FIGURE 10. Phylogenetic hypothesis based on the morphological characters from the Agathemera eggs. a. Unrooted tree considering all the Agathemera species' eggs. b. rooted tree considering just the species in clade 1 (sensu Vera et al. 2012) and A. grylloidea as outgroup. c. Rooted tree considering only the species in clade 2 (sensu Vera et al. 2012) and A. luteola as outgroup. Black circles and their respective numbers indicate synapomorphies. Jacknife/Bootstrap values are shown for each node.
FIGURE 6 in Comparative morphology of the eggs from the eight species in the genus Agathemera Stål (Insecta: Phasmatodea), through phylogenetic comparative method approach
FIGURE 6. External morphology of the eggs from clade 2 and their respective operculum. a1-c1, dorsal view; a2-c2 operculum. The order of the eggs and operculum from right to left is A. grylloidea, A. elegans, A. mesoauriculae (escale = 1mm).
FIGURE 7 in Comparative morphology of the eggs from the eight species in the genus Agathemera Stål (Insecta: Phasmatodea), through phylogenetic comparative method approach
FIGURE 7. Ultrastructure surface of the micropylar plate of the eggs from clade 1 and their respective operculum. A1-E1, micropylar plate ultrastructure; A2-E2 ultrastructure surface of the operculum. The order of the micropylar plates and operculum from top to bottom is A. luteola, A. maculafulgens, A. crassa. A. millepunctata, A. claraziana.
FIGURE 8 in Comparative morphology of the eggs from the eight species in the genus Agathemera Stål (Insecta: Phasmatodea), through phylogenetic comparative method approach
FIGURE 8. Ultrastructure surface of the micropylar plate of the eggs from clade 2 and their respective operculum. A1-C1, micropylar plate ultrastructure; A2-C2 ultrastructure surface of the operculum. The order of the micropylar plates and operculum from top to botom is A. grylloidea, A. elegans, A. mesoauriculae.
FIGURE 9 in Comparative morphology of the eggs from the eight species in the genus Agathemera Stål (Insecta: Phasmatodea), through phylogenetic comparative method approach
FIGURE 9. Character states reconstruction by maximum parsimony over the molecular phylogeny (sensu Vera et al. 2012). The character states for both the ancestral nodes A-G and actual species (H-O) are represented by color-coded boxes, where numbers indicate the character and colors the state. Besides, examples of the micropylar plate open (A. maculafulgens) and closed (A. elegans) are shown. Note: character numbers are consistent with those throughout the text.
FIGURE 5 in Comparative morphology of the eggs from the eight species in the genus Agathemera Stål (Insecta: Phasmatodea), through phylogenetic comparative method approach
FIGURE 5. External morphology of the eggs from clade 1 and their respective operculum. a1-e1, dorsal view; a2-e2 operculum. The order of the eggs and operculum from right to left is A. luteola, A. maculafulgens, A. crassa. A. millepunctata, A. claraziana (escale = 1mm).
FIGURE 3 in Comparative morphology of the eggs from the eight species in the genus Agathemera Stål (Insecta: Phasmatodea), through phylogenetic comparative method approach
FIGURE 3. Principal component analysis for the Agathemera eggs. The percentage of the variance explained by each principal component plotted is in parentheses. Every line connects a data point with its corresponding centroid. a. PCA for the eight Agathemera species; b. PCA for the species from clade 1; c. PCA for species from clade 2.
FIGURE 2 in Comparative morphology of the eggs from the eight species in the genus Agathemera Stål (Insecta: Phasmatodea), through phylogenetic comparative method approach
FIGURE 2. Distribution of the nine morphometric variables measured. the species are ordered following the phylogenetic relationships. Boxes represent the values between the 25 and 75 percentiles respectively, the horizontal line is the median and the point within each box is the mean and the whiskers indicate the sample range. Light grey boxplots correspond to species from clade 1 and dark grey boxplots correspond to species from clade 2. a. Capsule width; b. Capsule length; c. Capsule height; d. Micropylar plate length; e. Micropylar plate width; f. Operculum length; g. Operculum width; h. Operculum height; i. Opercular angle.
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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
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International Brain Laboratory public data
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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.