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opencc-zeroOct 2020View details →

Data from: Climatic drivers of latitudinal variation in Late Triassic tetrapod diversity

The latitudinal biodiversity gradient (LBG), the increase in biodiversity from the poles to the equator, is one of the most widely recognised global macroecological patterns, yet its deep time evolution and drivers remain uncertain. The Late Triassic (237–201 million years ago), a critical interval for the early evolution and radiation of modern tetrapod groups (e.g. crocodylomorphs, dinosaurs, mammaliamorphs), offers a unique opportunity to explore the palaeolatitudinal patterns of tetrapod diversity since it is extensively sampled spatially when compared with other pre-Cenozoic intervals, particularly at lower palaeolatitudes. Here, we explore palaeolatitudinal patterns of Late Triassic tetrapod diversity by applying sampling standardisation to comprehensive occurrence data from the Paleobiology Database. We then use palaeoclimatic model simulations to explore the palaeoclimatic ranges occupied by major tetrapod groups, allowing insight into the influence of palaeoclimate on the palaeolatitudinal distribution of these groups. Our results show that Late Triassic tetrapods generally do not conform to a modern-type LBG; instead, sampling-standardised species richness is highest at mid-palaeolatitudes. In contrast, the richness of pseudosuchians (crocodylians and their relatives) is highest at the palaeoequator, a pattern that is retained throughout their subsequent evolutionary history. Pseudosuchians generally occupied a more restricted range of palaeoclimatic conditions than other tetrapod groups, a condition analogous to modern day reptilian ectotherms, while avemetatarsalians (the archosaur group containing dinosaurs and pterosaurs) exhibit comparatively wider ranges, which is more similar to modern endotherms, such as birds and mammals, suggesting important implications for the evolution of thermal physiology in dinosaurs.

opencc-zeroApr 2020View details →

Data from: The smallest known Devonian tetrapod shows unexpectedly derived features, Part 2 of 2

A new genus and species of Devonian tetrapod, Brittagnathus minutus gen. et sp. nov., is described from a single complete right lower jaw ramus recovered from the Acanthostega mass-death deposit in the upper part of the Britta Dal Formation (upper Famennian) of Stensiö Bjerg, Gauss Peninsula, East Greenland. Visualisation by propagation phase contrast synchrotron microtomography (PPC-SRμCT) allows a complete digital dissection of the specimen. With a total jaw ramus length of 44.8 mm, Brittagnathus is by far the smallest Devonian tetrapod described to date. It differs from all previously knownDevonian tetrapods in having only a fang pair without a tooth row on the anterior coronoid, and a large posterior process on the posterior coronoid. The presence of an incipient surangular crest and a concave prearticular margin to the adductor fossa together cause the fossa to face somewhat mesially, reminiscent of the condition in Carboniferous tetrapods. A phylogenetic analysis places Brittagnathus crownward to other Devonian tetrapods, adjacent to the Tournaisian genus Pederpes. Together with other recent discoveries, it suggests that diversification of 'Carboniferous-grade' tetrapods had already begun before the end of the Devonian and that the group was not greatly affected by the end-Devonian mass extinction.

opencc-by-4.0Oct 2024View details →

Equilibrium Dynamics Shape Diversity Patterns Across Terrestrial Tetrapod Clades

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. <h2>Folder Structure and Contents</h2> <h3>1. Environmental Variables (<code>Grid_level_environment</code>)</h3> <ul> <li> Contains grid-cell level environmental variables in <code>environmental_data.rds</code>. <ul> <li> Includes temperature (°C), precipitation (mm), and net primary productivity (NPP). </li> <li> Includes grid cell IDs and latitude/longitude coordinates. </li> </ul> </li> </ul> <h3>2. Evolutionary Rates Across Species and Grid Cells (<code>Grid_level_speciation</code>)</h3> <ul> <li> Contains present-day speciation rate estimates for each species. <ul> <li> Includes DR, BAMM, and ClaDS estimates. </li> <li> Maps each species’ speciation rate to its corresponding grid cells. </li> </ul> </li> </ul> <h3>3. Evolutionary Time Across Grid Cells (<code>Grid_level_assemblage_age</code>)</h3> <ul> <li> Contains files used for BioGeoBEARS DEC model integration at the grid-cell level for each tetrapod clade (amphibians, reptiles, birds, mammals). </li> <li> Each clade is organized in a separate folder with the following files: <ul> <li> Assemblage age: <code>arrival_time_clade*.csv</code> </li> <li> Most likely biogeographic areas per grid cell: <code>clade*_biogeo_area.csv</code> </li> <li> Presence/absence matrix: <code>clade*_PAM.csv</code> </li> <li> Clade phylogenetic tree: <code>clade*_tree.tre</code> </li> <li> DEC area file: <code>geo_area_clade*.data</code> </li> <li> DEC outputs: <code>results_DEC_clade*.Rdata</code> </li> <li> Estimated geographic area plots across the phylogeny: <code>DEC_plot_clade*.pdf</code> </li> </ul> </li> </ul> <h3>4. Path Analysis Example (<code>Path_model</code>)</h3> <ul> <li> Contains an example R script: <code>path_analysis_clades.R</code>. <ul> <li> Illustrates path models applied to tetrapod clades. </li> <li> Example uses mammalian clades; replace the dataset to run on other clades. </li> </ul> </li> </ul> <h3>5. Path Analysis Outputs (<code>Path_outputs_&_clade_traits</code>)</h3> <ul> <li> Contains outputs from path analyses for each tetrapod clade. <ul> <li> <code>Path_all_effects.csv</code> consolidates all path outputs and includes clade-level traits (see Methods in the main paper). </li> <li> Other files include: <ul> <li> <code>Path_direct_effects.csv</code> – direct effects across clades </li> <li> <code>Path_indirect_via_productivity.csv</code> – indirect effects via productivity </li> <li> <code>Path_indirect_via_speciation.csv</code> – indirect effects via speciation </li> <li> <code>Path_indirect_via_time.csv</code> – indirect effects via evolutionary time </li> </ul> </li> </ul> </li> </ul> <h3>6. Path Output Figures (<code>Path_outputs_figures</code>)</h3> <ul> <li> Contains R scripts to visualize path model outputs across tetrapod clades: <ul> <li> Direct effects: <code>Path_direct_effects.R</code> </li> <li> Indirect effects: <code>Path_indirect_via_productivity.R</code>, <code>Path_indirect_via_speciation.R</code>, <code>Path_indirect_via_time.R</code> </li> <li> Total effects: <code>Path_total_effects.R</code> </li> </ul> </li> </ul> <h3>7. Clade-Level Trait Effects on Richness (<code>Clade_level_effects.R</code>)</h3> <ul> <li> Contains the R script <code>Clade_level_effects.R</code>. </li> <li> Explores whether the effects of the tested predictors on species richness depend on clade-level traits, including: <ul> <li> Physiological traits: endothermy vs ectothermy </li> <li> Spatial–historical traits: climate origin, range size, centroid displacement, displacement rate </li> <li> Temporal/size-related traits: clade age, species richness </li> </ul> </li> </ul>

opencc-zeroJan 2024View details →

What factors influence the rediscovery of lost tetrapod species? Appendix G: Variables tested for their influence on rediscovery

For the study associated with this dataset, we created a database of lost and rediscovered tetrapod species and identified patterns in their distribution and factors influencing rediscovery. This appendix provides a list of the lost and rediscovered species and all data used to calculate 11 variables (V): <ul> <li>V1: Taxonomic status - class, order, family, species name, common name;</li> <li>V2: Countries / islands occupied by each species;</li> <li>V3: The cumulative number of lost and rediscovered species - four columns, (i) last seen date, (ii) rediscovered date, (iii) for rediscovered species, the number of years lost, (iv) for lost species, the number of years lost;</li> <li>V4: Time lost (the number of years each species has been lost for);</li> <li>V5: Adult body mass (g) of each species;</li> <li>V6: Habitat breadth - the number of broad habitat types occupied by each species;</li> <li>V7: Habitat type - the broad habitat types occupied by each species;</li> <li>V8: Small island / mainland - whether a species occupies a small island (< 20,000 km2) or a mainland location (including islands > 20,000km2) (0 = mainland, 1 = small island);</li> <li>V9: Threats - the different threats associated with each species;</li> <li>V10: Human development - the highest level of human development across the range of each species, measured using the Human Development Index (HDI);</li> <li>V11: Survey effort - the level of effort invested in searching for each species (1 = low, 2 = medium, 3 = high, 4 = very high). See Supporting Information (Table S1) for the methods used to calculate this variable.</li> </ul>

opencc-zeroJan 2024View details →

What factors influence the rediscovery of lost tetrapod species? Appendix E: Lost and rediscovered species

opencc-zeroJan 2024View details →

What factors influence the rediscovery of lost tetrapod species? Appendix F: Excluded species

For the study associated with this dataset, we created a database of lost and rediscovered tetrapod species and identified patterns in their distribution and factors influencing rediscovery. Our lost species list included many of the species on another published list of lost species compiled by Re:wild (<a href="https://www.rewild.org/)">https://www.rewild.org/)</a> in collaboration with the International Union for Conservation of Nature (IUCN) (<a href="https://www.iucn.org/">https://www.iucn.org/</a>). However, we did not include some of the species included on the Re:wild/IUCN list. This appendix provides a list of those species. It includes the following information for each species: <ul> <li> taxonomy - class, order, scientific name, common name; </li> <li> threat status (as published on the IUCN Red List of Threatened Species); </li> <li> location - continent / island, range / country. </li> </ul>

opencc-zeroMar 2024View details →

Complex models of sequence evolution improve fit, but not gene tree discordance, for tetrapod mitogenomes

Variation in gene tree estimates is widely observed in empirical phylogenomic data and is often assumed to be the result of biological processes. However, a recent study using tetrapod mitochondrial genomes to control for biological sources of variation due to their haploid, uniparentally inherited, and non-recombining nature found that levels of discordance among mitochondrial gene trees were comparable to those found in studies that assume only biological sources of variation. Additionally, they found that several of the models of sequence evolution chosen to infer gene trees were doing an inadequate job of fitting the sequence data. These results indicated that significant amounts of gene tree discordance in empirical data may be due to poor fit of sequence evolution models and that more complex and biologically realistic models may be needed. To test how the fit of sequence evolution models relates to gene tree discordance, we analyzed the same mitochondrial datasets as the previous study using two additional, more complex models of sequence evolution that each model a different biologically realistic aspect of the evolutionary process: a covarion model to incorporate heterotachy, and a model partitioned model to incorporate variable evolutionary patterns by codon position. Our results show that both additional models fit the data better than the models used in the previous study, with the covarion being consistently and strongly preferred as tree size increases. However, even these more preferred models still inferred highly discordant mitochondrial gene trees, thus deepening the mystery around what we label the "Mito-Phylo Paradox" and leading us to ask whether the observed variation could be biological after all.

opencc-zeroSep 2022View details →

Temperature-dependent evolutionary speed shapes the evolution of biodiversity patterns across tetrapod radiations

Biodiversity varies predictably with environmental energy around the globe, but the underlying mechanisms remain incompletely understood. The evolutionary speed hypothesis predicts that environmental energy shapes variation in speciation rates through temperature- or life history-dependent rates of evolution. To test whether variation in evolutionary speed can explain the relationship between energy and biodiversity in birds, mammals, amphibians, and reptiles, we simulated diversification over 65 million years of geological and climatic change with a spatially explicit eco-evolutionary simulation model. We modeled four distinct evolutionary scenarios in which speciation-completion rates were dependent on temperature (M1), life history (M2), temperature and life history (M3), or were independent of temperature and life-history (M0). To assess the agreement between simulated and empirical data, we performed model selection by fitting supervised machine learning models to multidimensional biodiversity patterns. We show that a model with temperature-dependent rates of speciation (M1) consistently had the strongest support. In contrast to statistical inferences, which showed no general relationships between temperature and speciation rates in tetrapods, we demonstrate how process-based modeling can disentangle the causes behind empirical biodiversity patterns. Our study highlights how environmental energy has played a fundamental role in the evolution of biodiversity over deep time.

Fig. 6. Putative protorosaurid archosauromorph trace Paradoxichnium isp. A, B in Lopingian tetrapod footprints from the Venetian Prealps, Italy: New discoveries in a largely incomplete panorama

Fig. 6. Putative protorosaurid archosauromorph trace Paradoxichnium isp. A, B. Paradoxichnium isp. from Ulbe (Italy), Lopingian. A. MCV 10, right complete manus, note the proximally-positioned digits I and V and the triangular claw impressions. B. MCV 9, complete left manus impression. Note the proximally-positioned digits I and V, the parallel digits II–IV and the triangular claw impressions. C. Paradoxichnium problematicum Müller, 1959, holotype FG 20/1 from Culmitzch (Thuringia, Germany), Lopingian; right (C1) and left (C2) pes-manus couples; note the manual morphology similar to MCV 9. Convex hyporelief, spacing 0.5 mm. Photo (A1, B1), interpretive drawing (A2, B2), false-color depth map (A3, B3), contour lines (A4, B4). Scale bars 10 mm.

Fig. 5 in Lopingian tetrapod footprints from the Venetian Prealps, Italy: New discoveries in a largely incomplete panorama

Fig. 5. Pareiasaurian parareptile trace Pachypes isp. (MCV 3) from Ulbe (Italy), Lopingian. Left manual imprint showing digits I–IV, convex hyporelief. Photo (A), interpretive drawing (B), false-color depth map (C), contour lines (D). Scale bar 10 mm.

Fig. 2 in Lopingian tetrapod footprints from the Venetian Prealps, Italy: New discoveries in a largely incomplete panorama

Fig. 2. Sedimentary structures of Val Gardena Sandstone. Facies association a, fine-grained sandstone showing cross lamination (A) and parallel ripples B). Facies association b, reddish mudstone with paleosols (C), pedogenic veins and nodules in the mudstone (D). Note the gray dolostone strata on the top. Facies association c, gray dolostone strata interbedded in the reddish mudstone (E), invertebrate burrows in the dolostone (F). G. Bellerophon Formation, gray dolostone.

Fig. 8. A in Lopingian tetrapod footprints from the Venetian Prealps, Italy: New discoveries in a largely incomplete panorama

Fig. 8. A. Undetermined track (MCV 14/30) of therapsid synapsid from Cortiana (Italy), Lopingian. Incomplete right manual impression showing digits III–V and deep expulsion rims. Concave epirelief, spacing 1 mm. Photo (A1), interpretive drawing (A2), contour lines (A3), false-color depth map (A4). B. MGP 9/22, interpretive drawing of a complete left manual impression from the Bletterbach Gorge, Dolomites (Italy), Lopingian, after Conti et al. 1977). Scale bar 10 mm.

Fig. 1 in Lopingian tetrapod footprints from the Venetian Prealps, Italy: New discoveries in a largely incomplete panorama

Fig. 1. Geographic location and stratigraphy of the fossil sites (asterisked). Map showing location of the study area in North Italy (A) and Recoaro area (B). Simplified geological map (C). D. Synthetic stratigraphic log of the Permian of Venetian Prealps (a–c, facies associations). Location of Merendaore and Ulbe (E) and Cortiana (F) fossil sites. G, H. Photographs of the Ulbe outcrops, small scale transition between lithofacies (G) and large scale transition between formations (H), with indicated transition between red bed (Rb) and lagoon (Lg) lithofacies of the topmost strata of the Val Gardena Formation, immediately before the deposition of the Bellerophon Formation. BEL, Bellerophon Formation; GAR, Val Gardena Sandstone; Lg, lagoon lithofacies (dolostone); Ps, incipient paleosol with deep mudcracks; Rb, red bed lithofacies (laminated mudstone). Hammer for scale.

Fig. 3 in Lopingian tetrapod footprints from the Venetian Prealps, Italy: New discoveries in a largely incomplete panorama

Fig. 3. Putative parareptile trace cf. Capitosauroides isp. from Ulbe (Italy), Lopingian. A. MCV 7, left pes impression showing digits I–IV. B. MCV 11/05, right manual impression showing digits I–IV. Convex hyporelief, spacing 0.5 mm. Photo (A1, B1), interpretive drawing (A2, B2), false-color depth map (A3, B3), contour lines (A4, B4). Scale bars 10 mm.

Fig. 7 in Lopingian tetrapod footprints from the Venetian Prealps, Italy: New discoveries in a largely incomplete panorama

Fig. 7. Lacertoid neodiapsid eureptile trace Rhynchosauroides isp. (MCV 65) from Merendaore (Italy), Lopingian. Complete right manual impression. An incomplete track and a continuous tail are preserved on the same slab. Convex hyporelief (plaster cast), spacing 0.5 mm. Photo (A), interpretive drawing (B), contour lines (C), false-color depth map (D). Scale bar 10 mm.

opencc-by-4.0Aug 2009View details →

Fig. 4. Tetrapod Kinelia broomi Novikov 2002 in Alpha taxonomy of the Russian Permian procolophonoid reptiles

Fig. 4. Tetrapod Kinelia broomi Novikov 2002, Kutlukskaya Svita, uppermost Tatarian; PIN 4538/3 (holotype), partial right dentary. In medial (A) and lateral (B) views.

opencc-by-4.0Aug 2009View details →

Fig. 5. Tetrapod Kinelia broomi Novikov 2002 in Alpha taxonomy of the Russian Permian procolophonoid reptiles

Fig. 5. Tetrapod Kinelia broomi Novikov 2002, Kutlukskaya Svita, uppermost Tatarian; PIN 4538/3 (holotype), partial right dentary. In medial (A), occlusal (B), and lateral (C) views. D. Schematic representation of the four well−preserved tooth crowns of the dentary teeth from posterior view. Lingual to the right, not to scale.

opencc-by-4.0Dec 2005View details →

Fig. 10. Phylogenetic analysis. A, B in A new discosauriscid seymouriamorph tetrapod from the Lower Permian of Moravia, Czech Republic

Fig. 10. Phylogenetic analysis. A, B. Two of six most parsimonious trees recovered by PAUP* 40b10 from a heuristic search of 33 taxa and 150 characters. C. Bootstrap percentages on a 50% majority−rule consensus tree.