Tiago R. Simões
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View article: Evolutionary Rate Incongruences in Squamates Reveal Contrasting Patterns of Evolutionary Novelties and Innovation
Evolutionary Rate Incongruences in Squamates Reveal Contrasting Patterns of Evolutionary Novelties and Innovation Open
Understanding the rate of phenotypic evolution can reveal fundamental aspects of organismal evolutionary trajectories. Hence, several studies have attempted to detect the tempo of evolution for multiple organisms, although based on differe…
View article: Origin and Early Evolution of Squamates and Their Kin: From Fossils to Genomes
Origin and Early Evolution of Squamates and Their Kin: From Fossils to Genomes Open
Squamates (lizards, including snakes) are the most diverse group of terrestrial vertebrates on Earth today and have an evolutionary history dating back to at least the Middle Triassic (ca. 242 Mya). Despite their vast taxonomic, morphologi…
View article: Cryptovaranoides is not a squamate
Cryptovaranoides is not a squamate Open
Accurate reconstruction of the timescale of organismal evolution requires knowledge of the placement of extinct representatives among living branches. The fossil record has the capacity to reframe hypotheses of organismal evolution by prod…
View article: †Cryptovaranoides is not a squamate
†Cryptovaranoides is not a squamate Open
Accurate reconstruction of the timescale of organismal evolution requires placement of extinct representatives among living branches. In this way, the fossil record has the capacity to revise hypotheses of organismal evolution by producing…
View article: Evolutionary rate incongruences in squamates reveal contrasting patterns of evolutionary novelties and innovation
Evolutionary rate incongruences in squamates reveal contrasting patterns of evolutionary novelties and innovation Open
Understanding the rate of phenotypic evolution can reveal fundamental aspects of organismal evolutionary trajectories. Hence, several studies have attempted to detect the tempo of evolution for multiple organisms, although based on radical…
View article: † <i>Cryptovaranoides</i> is not a squamate
† <i>Cryptovaranoides</i> is not a squamate Open
Accurate reconstruction of the timescale of organismal evolution requires placement of extinct representatives among living branches. In this way, the fossil record has the capacity to revise hypotheses of organismal evolution by producing…
View article: Early–middle Permian Mediterranean gorgonopsian suggests an equatorial origin of therapsids
Early–middle Permian Mediterranean gorgonopsian suggests an equatorial origin of therapsids Open
View article: Bayesian tip-dated timeline for diversification and major biogeographic events in Muroidea (Rodentia), the largest mammalian radiation
Bayesian tip-dated timeline for diversification and major biogeographic events in Muroidea (Rodentia), the largest mammalian radiation Open
View article: The affinities of the Late Triassic <i>Cryptovaranoides</i> and the age of crown squamates
The affinities of the Late Triassic <i>Cryptovaranoides</i> and the age of crown squamates Open
Most living reptile diversity is concentrated in Squamata (lizards, including snakes), which have poorly known origins in space and time. Recently, † Cryptovaranoides microlanius from the Late Triassic of the United Kingdom was described a…
View article: E<scp>vo</scp>P<scp>hylo</scp>: An <scp>r</scp> package for pre‐ and postprocessing of morphological data from relaxed clock Bayesian phylogenetics
E<span>vo</span>P<span>hylo</span>: An <span>r</span> package for pre‐ and postprocessing of morphological data from relaxed clock Bayesian phylogenetics Open
Relaxed clock Bayesian evolutionary inference (BEI) enables the co‐estimation of phylogenetic trees and evolutionary parameters associated with models of character and lineage evolution. Fast advances in new model developments over the pas…
View article: Ankylosaurian body armor function and evolution with insights from osteohistology and morphometrics of new specimens from the Late Cretaceous of Antarctica
Ankylosaurian body armor function and evolution with insights from osteohistology and morphometrics of new specimens from the Late Cretaceous of Antarctica Open
The body armor of ankylosaurians is a unique morphological feature among dinosaurs. While ankylosaurian body armor has been studied for decades, paleohistological analyses have only started to uncover the details of its function. Yet there…
View article: Handling Logical Character Dependency in Phylogenetic Inference: Extensive Performance Testing of Assumptions and Solutions Using Simulated and Empirical Data
Handling Logical Character Dependency in Phylogenetic Inference: Extensive Performance Testing of Assumptions and Solutions Using Simulated and Empirical Data Open
Logical character dependency is a major conceptual and methodological problem in phylogenetic inference of morphological data sets, as it violates the assumption of character independence that is common to all phylogenetic methods. It is m…
View article: Successive climate crises in the deep past drove the early evolution and radiation of reptiles
Successive climate crises in the deep past drove the early evolution and radiation of reptiles Open
Climate change–induced mass extinctions provide unique opportunities to explore the impacts of global environmental disturbances on organismal evolution. However, their influence on terrestrial ecosystems remains poorly understood. Here, w…
View article: Integrative Phylogenetics: Tools for Palaeontologists to Explore the Tree of Life
Integrative Phylogenetics: Tools for Palaeontologists to Explore the Tree of Life Open
The modern era of analytical and quantitative palaeobiology has only just begun, integrating methods such as morphological and molecular phylogenetics and divergence time estimation, as well as phenotypic and molecular rates of evolution. …
View article: An exceptionally preserved Sphenodon-like sphenodontian reveals deep time conservation of the tuatara skeleton and ontogeny
An exceptionally preserved Sphenodon-like sphenodontian reveals deep time conservation of the tuatara skeleton and ontogeny Open
Sphenodontian reptiles are an extremely old evolutionary lineage forming the closest relatives to squamates (lizards and snakes) and were globally distributed and more diverse than squamates during the first half of their evolutionary hist…
View article: Supplementary Data S1-S5 for "Successive climate crises in the deep past drove the early evolution and radiation of reptiles"
Supplementary Data S1-S5 for "Successive climate crises in the deep past drove the early evolution and radiation of reptiles" Open
Supplementary Data S1-S5, including raw data, descriptor files, input and output files, and codes for all analyses conducted
View article: Supplementary Data for "An exceptionally preserved Sphenodon-like sphenodontian reveals deep time conservation of the tuatara skeleton and ontogeny"
Supplementary Data for "An exceptionally preserved Sphenodon-like sphenodontian reveals deep time conservation of the tuatara skeleton and ontogeny" Open
Supplementary data including morphological data matrix for phylogenetic and morphospace analyses; all outputs from all phylogenetic analyses (log files, tree files, etc.); R scripts for morphospace analysis.
View article: Supplementary Data for "Tetrapodophis amplectus is not a snake: Reassessment of the osteology, phylogeny and functional morphology of an Early Cretaceous dolichosaurid lizard."
Supplementary Data for "Tetrapodophis amplectus is not a snake: Reassessment of the osteology, phylogeny and functional morphology of an Early Cretaceous dolichosaurid lizard." Open
Supplementary data files including datasets, input, and output files for the two datasets used for phylogenetic analyses. Data folders include raw morphological and molecular datasets provided as Nexus files. It combined morphological and …
View article: <i>Tetrapodophis amplectus</i>is not a snake: re-assessment of the osteology, phylogeny and functional morphology of an Early Cretaceous dolichosaurid lizard
<i>Tetrapodophis amplectus</i>is not a snake: re-assessment of the osteology, phylogeny and functional morphology of an Early Cretaceous dolichosaurid lizard Open
The origin of snakes remains one of the most contentious evolutionary transitions in vertebrate evolution. The discovery of snake fossils with well-formed hind limbs provided new insights into the phylogenetic and ecological origin of snak…
View article: Supplementary Data for "A Triassic stem lepidosaur illuminates the origin of lizard-like reptiles"
Supplementary Data for "A Triassic stem lepidosaur illuminates the origin of lizard-like reptiles" Open
Supplementary Data 1-3, three files that include dataset files (Datasets 1-2) and codes for replicating the analysis: Dataset 1 (Mr. Bayes codes within folders for each analysis conducted) and Dataset 3 (containing R scripts for morphospac…
View article: Author Correction: A New Clevosaurid from the Triassic (Carnian) of Brazil and the Rise of Sphenodontians in Gondwana
Author Correction: A New Clevosaurid from the Triassic (Carnian) of Brazil and the Rise of Sphenodontians in Gondwana Open
An amendment to this paper has been published and can be accessed via a link at the top of the paper.
View article: THE SQUAMATE TREE OF LIFE
THE SQUAMATE TREE OF LIFE Open
Squamates (lizards, snakes, and their kin such as amphisbaenians, or "worm lizards") represent the world's most diverse clade of terrestrial vertebrates with ∼11,000 described extant species, representing key components in many of the worl…
View article: Supplementary Data 1-4 for "Sustained High Rates of Morphological Evolution During the Rise of Tetrapods"
Supplementary Data 1-4 for "Sustained High Rates of Morphological Evolution During the Rise of Tetrapods" Open
Supplementary Data 1-4 including modified morphological dataset; updated character list; tables and input data for statistical analysis; R scripts used for all analyses
View article: Sphenodontian phylogeny and the impact of model choice in Bayesian morphological clock estimates of divergence times and evolutionary rates
Sphenodontian phylogeny and the impact of model choice in Bayesian morphological clock estimates of divergence times and evolutionary rates Open
View article: Megaevolutionary dynamics and the timing of evolutionary innovation in reptiles
Megaevolutionary dynamics and the timing of evolutionary innovation in reptiles Open
View article: Additional Files for Sphenodontian phylogeny and the Impact of Model Choice in Bayesian Morphological Clock Estimates of Divergence Times and Evolutionary Rates
Additional Files for Sphenodontian phylogeny and the Impact of Model Choice in Bayesian Morphological Clock Estimates of Divergence Times and Evolutionary Rates Open
Additional files 1-7 including all necessary data and coding to replicate the analyses: Additional File 1: Text document containing additional methodological information and supplementary figures. Additional File 2: Text document containin…
View article: Discovery of the oldest South American fossil lizard illustrates the cosmopolitanism of early South American squamates
Discovery of the oldest South American fossil lizard illustrates the cosmopolitanism of early South American squamates Open
Squamates have an extremely long evolutionary history with a fossil record that extends into the Middle Triassic. However, most of our knowledge of their early evolutionary history is derived from Laurasian records. Therefore, fundamental …
View article: Megaevolutionary dynamics in reptiles and the role of adaptive radiations in evolutionary innovation
Megaevolutionary dynamics in reptiles and the role of adaptive radiations in evolutionary innovation Open
Adaptive radiations are long believed to be responsible for the origin of phenotypic diversity and new body plans among higher clades in the fossil record. However, few studies have assessed rates of phenotypic evolution and disparity acro…
View article: Evaluating the Performance of Probabilistic Algorithms for Phylogenetic Analysis of Big Morphological Datasets: A Simulation Study
Evaluating the Performance of Probabilistic Algorithms for Phylogenetic Analysis of Big Morphological Datasets: A Simulation Study Open
Reconstructing the tree of life is an essential task in evolutionary biology. It demands accurate phylogenetic inference for both extant and extinct organisms, the latter being almost entirely dependent on morphological data. While parsimo…
View article: A tiny new Middle Triassic stem-lepidosauromorph from Germany: implications for the early evolution of lepidosauromorphs and the Vellberg fauna
A tiny new Middle Triassic stem-lepidosauromorph from Germany: implications for the early evolution of lepidosauromorphs and the Vellberg fauna Open