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6 results for “terrestrial tetrapods”
Equilibrium Dynamics Shape Diversity Patterns Across Terrestrial Tetrapod Clades
<p>This repository contains all scripts, data, and documentation supporting the analyses in our study. The materials are organized into folders corresponding to specific steps of the workflow. This README provides a detailed guide to the structure, contents, and usage of each folder.</p> <h2>Folder Structure and Contents</h2> <h3>1. Environmental Variables (<code>Grid_level_environment</code>)</h3> <ul> <li> <p>Contains grid-cell level environmental variables in <code>environmental_data.rds</code>.</p> <ul> <li> <p>Includes <strong>temperature</strong> (°C), <strong>precipitation</strong> (mm), and <strong>net primary productivity (NPP)</strong>.</p> </li> <li> <p>Includes <strong>grid cell IDs</strong> and <strong>latitude/longitude coordinates</strong>.</p> </li> </ul> </li> </ul> <h3>2. Evolutionary Rates Across Species and Grid Cells (<code>Grid_level_speciation</code>)</h3> <ul> <li> <p>Contains present-day <strong>speciation rate estimates</strong> for each species.</p> <ul> <li> <p>Includes <strong>DR</strong>, <strong>BAMM</strong>, and <strong>ClaDS</strong> estimates.</p> </li> <li> <p>Maps each species’ speciation rate to its corresponding grid cells.</p> </li> </ul> </li> </ul> <h3>3. Evolutionary Time Across Grid Cells (<code>Grid_level_assemblage_age</code>)</h3> <ul> <li> <p>Contains files used for <strong>BioGeoBEARS DEC model integration</strong> at the grid-cell level for each tetrapod clade (amphibians, reptiles, birds, mammals).</p> </li> <li> <p>Each clade is organized in a separate folder with the following files:</p> <ul> <li> <p><strong>Assemblage age:</strong> <code>arrival_time_clade*.csv</code></p> </li> <li> <p><strong>Most likely biogeographic areas per grid cell:</strong> <code>clade*_biogeo_area.csv</code></p> </li> <li> <p><strong>Presence/absence matrix:</strong> <code>clade*_PAM.csv</code></p> </li> <li> <p><strong>Clade phylogenetic tree:</strong> <code>clade*_tree.tre</code></p> </li> <li> <p><strong>DEC area file:</strong> <code>geo_area_clade*.data</code></p> </li> <li> <p><strong>DEC outputs:</strong> <code>results_DEC_clade*.Rdata</code></p> </li> <li> <p><strong>Estimated geographic area plots across the phylogeny:</strong> <code>DEC_plot_clade*.pdf</code></p> </li> </ul> </li> </ul> <h3>4. Path Analysis Example (<code>Path_model</code>)</h3> <ul> <li> <p>Contains an example R script: <code>path_analysis_clades.R</code>.</p> <ul> <li> <p>Illustrates <strong>path models</strong> applied to tetrapod clades.</p> </li> <li> <p>Example uses <strong>mammalian clades</strong>; replace the dataset to run on other clades.</p> </li> </ul> </li> </ul> <h3>5. Path Analysis Outputs (<code>Path_outputs_&_clade_traits</code>)</h3> <ul> <li> <p>Contains outputs from <strong>path analyses</strong> for each tetrapod clade.</p> <ul> <li> <p><code>Path_all_effects.csv</code> consolidates all path outputs and includes <strong>clade-level traits</strong> (see Methods in the main paper).</p> </li> <li> <p>Other files include:</p> <ul> <li> <p><code>Path_direct_effects.csv</code> – direct effects across clades</p> </li> <li> <p><code>Path_indirect_via_productivity.csv</code> – indirect effects via productivity</p> </li> <li> <p><code>Path_indirect_via_speciation.csv</code> – indirect effects via speciation</p> </li> <li> <p><code>Path_indirect_via_time.csv</code> – indirect effects via evolutionary time</p> </li> </ul> </li> </ul> </li> </ul> <h3>6. Path Output Figures (<code>Path_outputs_figures</code>)</h3> <ul> <li> <p>Contains R scripts to <strong>visualize path model outputs</strong> across tetrapod clades:</p> <ul> <li> <p>Direct effects: <code>Path_direct_effects.R</code></p> </li> <li> <p>Indirect effects: <code>Path_indirect_via_productivity.R</code>, <code>Path_indirect_via_speciation.R</code>, <code>Path_indirect_via_time.R</code></p> </li> <li> <p>Total effects: <code>Path_total_effects.R</code></p> </li> </ul> </li> </ul> <h3>7. Clade-Level Trait Effects on Richness (<code>Clade_level_effects.R</code>)</h3> <ul> <li> <p>Contains the R script <code>Clade_level_effects.R</code>.</p> </li> <li> <p>Explores whether <strong>the effects of the tested predictors on species richness depend on clade-level traits</strong>, including:</p> <ul> <li> <p><strong>Physiological traits:</strong> endothermy vs ectothermy</p> </li> <li> <p><strong>Spatial–historical traits:</strong> climate origin, range size, centroid displacement, displacement rate</p> </li> <li> <p><strong>Temporal/size-related traits:</strong> clade age, species richness</p> </li> </ul> </li> </ul>
Figure 1. Structural changes between fish and tetrapods. A in Thermal physiology and the origin of terrestriality in vertebrates
Figure 1. Structural changes between fish and tetrapods. A, Eusthenopteron, the most thoroughly known Upper Devonian choanate sarcopterygian (from Andrews & Westoll, 1970). B, Panderichthys, an Upper Devonian fish intermediate between Eusthenopteron and the Upper Devonian amphibians (from Vorobyeva & Schultze, 1991). C, the Upper Devonian amphibian Acanthostega (Coates & Clack, 1995). D, the Upper Devonian amphibian Ichthyostega (from Coates & Clack, 1995). More details of the forelimb have since been discovered (Clack, Blom & Ahlberg, 2003). Animals are reproduced at approximately equal head/trunk lengths.
Data from: Diversity dynamics of Phanerozoic terrestrial tetrapods at the local-community scale
The fossil record provides one of the strongest tests of the hypothesis that diversity within local communities is constrained over geological timescales. Constraints to diversity are particularly controversial in modern terrestrial ecosystems, yet long-term patterns are poorly understood. Here we document patterns of local richness in Phanerozoic terrestrial tetrapods using a global data set comprising 145,332 taxon occurrences from 27,531 collections. We show that the local richness of non-flying terrestrial tetrapods has risen asymptotically since their initial colonization of land, increasing at most threefold over the last 300 million years. Statistical comparisons support phase-shift models, with most increases in local richness occurring: (1) during the colonization of land by vertebrates, concluding by the late Carboniferous; and (2) across the Cretaceous/Paleogene boundary. Individual groups, such as mammals, lepidosaurs and dinosaurs also experienced early increases followed by periods of stasis often lasting tens of millions of years. Mammal local richness abruptly tripled across the Cretaceous/Paleogene boundary, but did not increase over the next 66 million years. These patterns are consistent with the hypothesis that diversity is constrained at the local-community scale.
Data from: Diversity dynamics of Phanerozoic terrestrial tetrapods at the local-community scale
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Data from: Biogeographical network analysis of cretaceous terrestrial tetrapods: a phylogeny-based approach
Network methods are widely used to represent and analyse biogeography. It is difficult, however, to convert occurrence data of fossil vertebrates to a biogeographical network, as most species were known from a single locality. A new method for creating a biogeographical network that can incorporate phylogenetic information is proposed in this study, which increases the number of edges in the network of fossil vertebrates and enables the application of various network methods. Using ancestral state reconstruction via maximum parsimony, the method first estimates the biogeographical regions of all internal nodes of a given phylogeny using biogeographical information on the terminal taxa. Then, each internal node in the phylogenetic tree is converted to an edge in the biogeographical network that connects the region(s), if unambiguously estimated, of its two descendants. The new method was applied to phylogenetic trees generated by a birth-death model. Under all conditions tested, an average of >70% of the internal nodes in phylogenetic trees were converted into edges. Three network indices—link density, average link weight, and endemism index—were evaluated for their usefulness in comparing different biogeographical networks. The endemism index reflects the rate of dispersal; the other indices reflect nonbiogeographical parameters, the number of taxa and regions, which highlights the importance of evaluating network indices before applying them to biogeographical studies. Multiple Cretaceous biogeographical networks were constructed from the phylogenies of five tetrapod taxa: terrestrial crocodyliforms, terrestrial turtles, non-avian dinosaurs, avians, and pterosaurs. The networks of avians and pterosaurs showed similar topologies and a strong correlation, and unexpectedly high endemism indices. These similarities were probably a result of shared taphonomic biases (i.e., the Lagerstätten effect) for volant taxa with fragile skeletons. The crocodyliform network was partitioned into the Gondwanan and Laurasian continents. The dinosaur network was partitioned into three groups of continents: (1) North America, Asia, and Australia; (2) Europe and Africa; (3) India, Madagascar, and South America. When Early and Late Cretaceous dinosaurs were analysed separately, the dinosaur networks were divided into (1) North America, Asia, and Australia; and (2) Europe, Africa, India, and South America for the Early Cretaceous and (1) North America, Asia, and Europe; (2) India, Madagascar, and South America for the Late Cretaceous. This partitioning of dinosaur and crocodyliform networks corroborates the results of previous biogeographical studies and indicates that the method introduced here can retrieve biogeographical signals from a source phylogeny when sufficient data are available for most targeted biogeographical regions.
Data from: Biogeographical network analysis of cretaceous terrestrial tetrapods: a phylogeny-based approach
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