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Interrelationships among Early Triassic faunas of Western Gondwana and Laurasia as illuminated by a new South American benthosuchid temnospondyl. Anat Rec (Hoboken) 2024; 307:726-743. [PMID: 38240478 DOI: 10.1002/ar.25384] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Revised: 12/29/2023] [Accepted: 12/30/2023] [Indexed: 03/16/2024]
Abstract
The End-Permian Mass Extinction marked a critical turning point in Earth's history, and the biological recovery that followed the crisis led to the emergence of several modern vertebrate and invertebrate taxa. Even considering the importance of the Early Triassic biotic recovery for the evolution of modern faunas and floras, our knowledge of this event is still hindered by the sparse sampling of crucial geological formations. This leaves our understanding of Early Triassic ecosystems fundamentally biased toward productive and historically well-explored geological units. Recent surveys in poorly known Gondwanan localities, such as those within the Sanga do Cabral Formation in southern Brazil, have unveiled insights into Early Triassic terrestrial ecosystems, shedding light on a diverse and previously unknown tetrapod fauna. Here, we report the discovery of a new temnospondyl genus and species in the Lower Triassic Sanga do Cabral Formation. The new taxon can be confidently assigned to the Benthosuchidae, a stereospondyl clade with a distribution previously restricted to the East European Platform. Phylogenetic analysis confirms the relationship of the new genus to the trematosaurian lineage, being closely related to the genus Benthosuchus. Our results raise questions about the biogeographical history of stereospondyls after the End-Permian Mass Extinction and suggest a potential connection between Russian and South American Early Triassic faunas. Further investigations are needed to thoroughly explore the potential dispersal routes that may explain this seemingly unusual biogeographical pattern.
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2
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The affinities of the Late Triassic Cryptovaranoides and the age of crown squamates. ROYAL SOCIETY OPEN SCIENCE 2023; 10:230968. [PMID: 37830017 PMCID: PMC10565374 DOI: 10.1098/rsos.230968] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Accepted: 09/18/2023] [Indexed: 10/14/2023]
Abstract
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 as the oldest crown squamate. If true, this result would push back the origin of all major lizard clades by 30-65 Myr and suggest that divergence times for reptile clades estimated using genomic and morphological data are grossly inaccurate. Here, we use computed tomography scans and expanded phylogenetic datasets to re-evaluate the phylogenetic affinities of †Cryptovaranoides and other putative early squamates. We robustly reject the crown squamate affinities of †Cryptovaranoides, and instead resolve †Cryptovaranoides as a potential member of the bird and crocodylian total clade, Archosauromorpha. Bayesian total evidence dating supports a Jurassic origin of crown squamates, not Triassic as recently suggested. We highlight how features traditionally linked to lepidosaurs are in fact widespread across Triassic reptiles. Our study reaffirms the importance of critically choosing and constructing morphological datasets and appropriate taxon sampling to test the phylogenetic affinities of problematic fossils and calibrate the Tree of Life.
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Handling Logical Character Dependency in Phylogenetic Inference: Extensive Performance Testing of Assumptions and Solutions Using Simulated and Empirical Data. Syst Biol 2023; 72:662-680. [PMID: 36773019 PMCID: PMC10276625 DOI: 10.1093/sysbio/syad006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Revised: 12/08/2022] [Accepted: 02/09/2023] [Indexed: 02/12/2023] Open
Abstract
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 more frequently observed in higher-level phylogenies or in data sets characterizing major evolutionary transitions, as these represent parts of the tree of life where (primary) anatomical characters either originate or disappear entirely. As a result, secondary traits related to these primary characters become "inapplicable" across all sampled taxa in which that character is absent. Various solutions have been explored over the last three decades to handle character dependency, such as alternative character coding schemes and, more recently, new algorithmic implementations. However, the accuracy of the proposed solutions, or the impact of character dependency across distinct optimality criteria, has never been directly tested using standard performance measures. Here, we utilize simple and complex simulated morphological data sets analyzed under different maximum parsimony optimization procedures and Bayesian inference to test the accuracy of various coding and algorithmic solutions to character dependency. This is complemented by empirical analyses using a recoded data set on palaeognathid birds. We find that in small, simulated data sets, absent coding performs better than other popular coding strategies available (contingent and multistate), whereas in more complex simulations (larger data sets controlled for different tree structure and character distribution models) contingent coding is favored more frequently. Under contingent coding, a recently proposed weighting algorithm produces the most accurate results for maximum parsimony. However, Bayesian inference outperforms all parsimony-based solutions to handle character dependency due to fundamental differences in their optimization procedures-a simple alternative that has been long overlooked. Yet, we show that the more primary characters bearing secondary (dependent) traits there are in a data set, the harder it is to estimate the true phylogenetic tree, regardless of the optimality criterion, owing to a considerable expansion of the tree parameter space. [Bayesian inference, character dependency, character coding, distance metrics, morphological phylogenetics, maximum parsimony, performance, phylogenetic accuracy.].
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Successive climate crises in the deep past drove the early evolution and radiation of reptiles. SCIENCE ADVANCES 2022; 8:eabq1898. [PMID: 35984885 PMCID: PMC9390993 DOI: 10.1126/sciadv.abq1898] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
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, we provide a new time tree for the early evolution of reptiles and their closest relatives to reconstruct how the Permian-Triassic climatic crises shaped their long-term evolutionary trajectory. By combining rates of phenotypic evolution, mode of selection, body size, and global temperature data, we reveal an intimate association between reptile evolutionary dynamics and climate change in the deep past. We show that the origin and phenotypic radiation of reptiles was not solely driven by ecological opportunity following the end-Permian extinction as previously thought but also the result of multiple adaptive responses to climatic shifts spanning 57 million years.
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Integrative Phylogenetics: Tools for Palaeontologists to Explore the Tree of Life. BIOLOGY 2022; 11:1185. [PMID: 36009812 PMCID: PMC9405010 DOI: 10.3390/biology11081185] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 07/27/2022] [Accepted: 08/03/2022] [Indexed: 11/17/2022]
Abstract
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. Calibrating the tree of life to geological time is at the nexus of many disparate disciplines, from palaeontology to molecular systematics and from geochronology to comparative genomics. Creating an evolutionary time scale of the major events that shaped biodiversity is key to all of these fields and draws from each of them. Different methodological approaches and data employed in various disciplines have traditionally made collaborative research efforts difficult among these disciplines. However, the development of new methods is bridging the historical gap between fields, providing a holistic perspective on organismal evolutionary history, integrating all of the available evidence from living and fossil species. Because phylogenies with only extant taxa do not contain enough information to either calibrate the tree of life or fully infer macroevolutionary dynamics, phylogenies should preferably include both extant and extinct taxa, which can only be achieved through the inclusion of phenotypic data. This integrative phylogenetic approach provides ample and novel opportunities for evolutionary biologists to benefit from palaeontological data to help establish an evolutionary time scale and to test core macroevolutionary hypotheses about the drivers of biological diversification across various dimensions of organisms.
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6
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The rise of mammals. Nat Ecol Evol 2021. [PMID: 34969988 DOI: 10.1038/s41559-021-01643-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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7
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Sustained high rates of morphological evolution during the rise of tetrapods. Nat Ecol Evol 2021; 5:1403-1414. [PMID: 34426679 DOI: 10.1038/s41559-021-01532-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Accepted: 07/09/2021] [Indexed: 11/09/2022]
Abstract
The fish-to-tetrapod transition is one of the most iconic events in vertebrate evolution, yet fundamental questions regarding the dynamics of this transition remain unresolved. Here, we use advances in Bayesian morphological clock modelling to reveal the evolutionary dynamics of early tetrapodomorphs (tetrapods and their closest fish relatives). We show that combining osteological and ichnological calibration data results in major shifts on the time of origin of all major groups of tetrapodomorphs (up to 25 million years) and that low rates of net diversification, not fossilization, explain long ghost lineages in the early tetrapodomorph fossil record. Further, our findings reveal extremely low rates of morphological change for most early tetrapodomorphs, indicating widespread stabilizing selection upon their 'fish' morphotype. This pattern was broken only by elpistostegalians (including early tetrapods), which underwent sustained high rates of morphological evolution for ~30 Myr during the deployment of the tetrapod body plan.
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Author Correction: A New Clevosaurid from the Triassic (Carnian) of Brazil and the Rise of Sphenodontians in Gondwana. Sci Rep 2021; 11:10090. [PMID: 33958637 PMCID: PMC8102482 DOI: 10.1038/s41598-021-88869-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
An amendment to this paper has been published and can be accessed via a link at the top of the paper.
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Sphenodontian phylogeny and the impact of model choice in Bayesian morphological clock estimates of divergence times and evolutionary rates. BMC Biol 2020; 18:191. [PMID: 33287835 PMCID: PMC7720557 DOI: 10.1186/s12915-020-00901-5] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Accepted: 10/16/2020] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND The vast majority of all life that ever existed on earth is now extinct and several aspects of their evolutionary history can only be assessed by using morphological data from the fossil record. Sphenodontian reptiles are a classic example, having an evolutionary history of at least 230 million years, but currently represented by a single living species (Sphenodon punctatus). Hence, it is imperative to improve the development and implementation of probabilistic models to estimate evolutionary trees from morphological data (e.g., morphological clocks), which has direct benefits to understanding relationships and evolutionary patterns for both fossil and living species. However, the impact of model choice on morphology-only datasets has been poorly explored. RESULTS Here, we investigate the impact of a wide array of model choices on the inference of evolutionary trees and macroevolutionary parameters (divergence times and evolutionary rates) using a new data matrix on sphenodontian reptiles. Specifically, we tested different clock models, clock partitioning, taxon sampling strategies, sampling for ancestors, and variations on the fossilized birth-death (FBD) tree model parameters through time. We find a strong impact on divergence times and background evolutionary rates when applying widely utilized approaches, such as allowing for ancestors in the tree and the inappropriate assumption of diversification parameters being constant through time. We compare those results with previous studies on the impact of model choice to molecular data analysis and provide suggestions for improving the implementation of morphological clocks. Optimal model combinations find the radiation of most major lineages of sphenodontians to be in the Triassic and a gradual but continuous drop in morphological rates of evolution across distinct regions of the phenotype throughout the history of the group. CONCLUSIONS We provide a new hypothesis of sphenodontian classification, along with detailed macroevolutionary patterns in the evolutionary history of the group. Importantly, we provide suggestions to avoid overestimated divergence times and biased parameter estimates using morphological clocks. Partitioning relaxed clocks offers methodological limitations, but those can be at least partially circumvented to reveal a detailed assessment of rates of evolution across the phenotype and tests of evolutionary mosaicism.
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Evaluating the Performance of Probabilistic Algorithms for Phylogenetic Analysis of Big Morphological Datasets: A Simulation Study. Syst Biol 2020; 69:1088-1105. [PMID: 32191335 DOI: 10.1093/sysbio/syaa020] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Revised: 02/26/2020] [Accepted: 03/15/2020] [Indexed: 01/31/2023] Open
Abstract
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 parsimony methods have traditionally dominated the field of morphological phylogenetics, a rapidly growing number of studies are now employing probabilistic methods (maximum likelihood and Bayesian inference). The present-day toolkit of probabilistic methods offers varied software with distinct algorithms and assumptions for reaching global optimality. However, benchmark performance assessments of different software packages for the analyses of morphological data, particularly in the era of big data, are still lacking. Here, we test the performance of four major probabilistic software under variable taxonomic sampling and missing data conditions: the Bayesian inference-based programs MrBayes and RevBayes, and the maximum likelihood-based IQ-TREE and RAxML. We evaluated software performance by calculating the distance between inferred and true trees using a variety of metrics, including Robinson-Foulds (RF), Matching Splits (MS), and Kuhner-Felsenstein (KF) distances. Our results show that increased taxonomic sampling improves accuracy, precision, and resolution of reconstructed topologies across all tested probabilistic software applications and all levels of missing data. Under the RF metric, Bayesian inference applications were the most consistent, accurate, and robust to variation in taxonomic sampling in all tested conditions, especially at high levels of missing data, with little difference in performance between the two tested programs. The MS metric favored more resolved topologies that were generally produced by IQ-TREE. Adding more taxa dramatically reduced performance disparities between programs. Importantly, our results suggest that the RF metric penalizes incorrectly resolved nodes (false positives) more severely than the MS metric, which instead tends to penalize polytomies. If false positives are to be avoided in systematics, Bayesian inference should be preferred over maximum likelihood for the analysis of morphological data.
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Megaevolutionary dynamics and the timing of evolutionary innovation in reptiles. Nat Commun 2020; 11:3322. [PMID: 32620878 PMCID: PMC7335191 DOI: 10.1038/s41467-020-17190-9] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2019] [Accepted: 06/17/2020] [Indexed: 11/18/2022] Open
Abstract
The origin of phenotypic diversity among higher clades is one of the most fundamental topics in evolutionary biology. However, due to methodological challenges, few studies have assessed rates of evolution and phenotypic disparity across broad scales of time to understand the evolutionary dynamics behind the origin and early evolution of new clades. Here, we provide a total-evidence dating approach to this problem in diapsid reptiles. We find major chronological gaps between periods of high evolutionary rates (phenotypic and molecular) and expansion in phenotypic disparity in reptile evolution. Importantly, many instances of accelerated phenotypic evolution are detected at the origin of major clades and body plans, but not concurrent with previously proposed periods of adaptive radiation. Furthermore, strongly heterogenic rates of evolution mark the acquisition of similarly adapted functional types, and the origin of snakes is marked by the highest rates of phenotypic evolution in diapsid history.
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12
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A tiny new Middle Triassic stem-lepidosauromorph from Germany: implications for the early evolution of lepidosauromorphs and the Vellberg fauna. Sci Rep 2020; 10:2273. [PMID: 32080209 PMCID: PMC7033234 DOI: 10.1038/s41598-020-58883-x] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Accepted: 01/22/2020] [Indexed: 11/10/2022] Open
Abstract
The Middle Triassic was a time of major changes in tetrapod faunas worldwide, but the fossil record for this interval is largely obscure for terrestrial faunas. This poses a severe limitation to our understanding on the earliest stages of diversification of lineages representing some of the most diverse faunas in the world today, such as lepidosauromorphs (e.g., lizards and tuataras). Here, we report a tiny new lepidosauromorph from the Middle Triassic from Vellberg (Germany), which combines a mosaic of features from both early evolving squamates and rhynchocephalians, such as the simultaneous occurrence of a splenial bone and partial development of acrodonty. Phylogenetic analyses applying different optimality criteria, and combined morphological and molecular data, consistently recover the new taxon as a stem-lepidosauromorph, implying stem-lepidosauromorph species coinhabited areas comprising today's central Europe at the same time as the earliest known rhynchocephalians and squamates. It further demonstrates a more complex evolutionary scenario for dental evolution in early lepidosauromorphs, with independent acquisitions of acrodonty early in their evolutionary history. The small size of most terrestrial vertebrates from Vellberg is conspicuous, contrasting to younger Triassic deposits worldwide, but comparable to Early Triassic faunas, suggesting a potential long-lasting Lilliput effect in this fauna.
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13
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New skulls and skeletons of the Cretaceous legged snake Najash, and the evolution of the modern snake body plan. SCIENCE ADVANCES 2019; 5:eaax5833. [PMID: 31799393 PMCID: PMC6867888 DOI: 10.1126/sciadv.aax5833] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Accepted: 09/25/2019] [Indexed: 06/10/2023]
Abstract
Snakes represent one of the most dramatic examples of the evolutionary versatility of the vertebrate body plan, including body elongation, limb loss, and skull kinesis. However, understanding the earliest steps toward the acquisition of these remarkable adaptations is hampered by the very limited fossil record of early snakes. Here, we shed light on the acquisition of the snake body plan using micro-computed tomography scans of the first three-dimensionally preserved skulls of the legged snake Najash and a new phylogenetic hypothesis. These findings elucidate the initial sequence of bone loss that gave origin to the modern snake skull. Morphological and molecular analyses including the new cranial data provide robust support for an extensive basal radiation of early snakes with hindlimbs and pelves, demonstrating that this intermediate morphology was not merely a transient phase between limbed and limbless body plans.
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Cranial ontogeny of Thamnophis radix (Serpentes: Colubroidea) with a re-evaluation of current paradigms of snake skull evolution. ROYAL SOCIETY OPEN SCIENCE 2019; 6:182228. [PMID: 31598225 PMCID: PMC6731736 DOI: 10.1098/rsos.182228] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Accepted: 07/17/2019] [Indexed: 06/10/2023]
Abstract
Accurate knowledge of skeletal ontogeny in extant organisms is crucial in understanding important morpho-functional systems and in enabling inferences of the ontogenetic stage of fossil specimens. However, detailed knowledge of skeletal ontogeny is lacking for most squamates, including snakes. Very few studies have discussed postnatal development in snakes, with none incorporating data from all three major ontogenetic stages-embryonic, juvenile and adult. Here, we provide the first analysis encompassing these three ontogenetic stages for any squamate, using the first complete micro-computed tomography (micro-CT)-based segmentations of any non-adult snake, based on fresh specimens of Thamnophis radix. The most significant ontogenetic changes involve the feeding apparatus, with major elongation of the tooth-bearing elements and jaw suspensorium causing a posterior shift in the jaw articulation. This shift enables macrostomy (large-gaped feeding in snakes) and occurs in T. radix via a different developmental trajectory than in most other macrostomatans, indicating that the evolution of macrostomy is more complex than previously thought. The braincase of T. radix is also evolutionarily unique among derived snakes in lacking a crista circumfenestralis, a phenomenon considered herein to represent paedomorphic retention of the embryonic condition. We thus present numerous important challenges to current paradigms regarding snake cranial evolution.
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The evolution of the axial skeleton intercentrum system in snakes revealed by new data from the Cretaceous snakes Dinilysia and Najash. Sci Rep 2019; 9:1276. [PMID: 30718525 PMCID: PMC6362196 DOI: 10.1038/s41598-018-36979-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Accepted: 11/12/2018] [Indexed: 11/09/2022] Open
Abstract
Snakes are an extremely modified and long-lived clade of lizards that have either lost or highly altered many of the synapomorphies that would clearly link them to their closest sister-group among squamates. We focus here on one postcranial morphological complex, the intercentrum system which in most non-ophidian squamates is limited to the cervical and caudal regions. The Cervical Intercentrum System (CeIS) is composed of a single intercentral element that sometimes articulates with a ventral projection (hypapophyses) of the centrum; the Caudal Intercentrum System (CaIS) is formed by an intercentral element, the haemal arch/chevron bone, and paired ventral projections of the centrum, the haemapophyses. In modern snakes, the intercentrum element of the CeIS is considered lost or fused to the hypaphophysis, and the chevron bone in CaIS is considered lost. Here, we describe new specimens of the early snake Dinilysia patagonica, and reinterpret previously known specimens of Dinilysia and Najash rionegrina, that do not show the expected snake morphology. The anatomy of these fossil taxa unambiguously shows that free cervical and caudal intercentra attached to distinct downgrowths (hypapophyses and haemapophyses) of the centra, are present in basal fossil snakes, and agrees with the proposed loss of post atlas-axis intercentra in later evolving snakes.
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Giant taxon-character matrices II: a response to Laing et al. (2017). Cladistics 2018; 34:702-707. [PMID: 34706486 DOI: 10.1111/cla.12231] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/10/2017] [Indexed: 11/28/2022] Open
Abstract
The trend towards big data analyses in evolutionary biology has been observed in phylogenetics via the assembly of giant datasets composed of genomic and phenotypic data. We recently (Simões et al., 2017. Giant taxon-character matrices: Quality of character constructions remains critical regardless of size. Cladistics 33, 198-219) presented a critique of the phylogenetic character concepts used in current morphological datasets, with the caution that giant datasets did not obviate the empirical requirement of rigor in character construction. Laing et al. (2017. Giant taxon-character matrices: The future of morphological systematics. Cladistics, https://doi.org/10.1111/cla.12197) have since argued that we had 'suggested' that large datasets inherently contain flawed characters, and that we had presented a substandard methodology of phylogenetic analysis. Laing et al. concluded by discussing their approach to phylogenetic signal, total evidence and the inevitability of large datasets. We here reply to Laing et al. by reviewing what we actually wrote regarding dataset size, characters and methodology. We show that Laing et al.'s. central premise is unsupported, thus characterizing a Straw Man argument, and deeply misrepresents our original study. In part two, we discuss total evidence and phylogenetic signal issues raised by Laing et al. that are of major consequence to the appropriate construction of large morphological datasets.
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17
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X-ray computed microtomography of Megachirella wachtleri. Sci Data 2018; 5:180244. [PMID: 30398474 PMCID: PMC6219415 DOI: 10.1038/sdata.2018.244] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2018] [Accepted: 09/19/2018] [Indexed: 11/09/2022] Open
Abstract
Understanding the origin and early evolution of squamates has been a considerable challenge given the extremely scarce fossil record of early squamates and their poor degree of preservation. In order to overcome those limitations, we conducted high-resolution X-ray computed tomography (CT) studies on the fossil reptile Megachirella wachtleri (Middle Triassic, northern Italy), which revealed an important set of features indicating this is the oldest known fossil squamate in the world, predating the previous oldest record by ca. 75 million years. We also compiled a new phylogenetic data set comprising a large sample of diapsid reptiles (including morphological and molecular data) to investigate the phylogenetic relationships of early squamates and other reptile groups along with the divergence time of those lineages. The re-description of Megachirella and a new phylogenetic hypothesis of diapsid relationships are presented in a separate study. Here we present the data descriptors for the tomographic scans of Megachirella, which holds fundamental information to our understanding on the early evolution of one of the largest vertebrate groups on Earth today.
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18
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New data on the Late Cretaceous lizard Dicothodon bajaensis (Squamata, Borioteiioidea) from Baja California, Mexico reveals an unusual tooth replacement pattern in squamates. AN ACAD BRAS CIENC 2018; 90:2781-2795. [PMID: 30043904 DOI: 10.1590/0001-3765201820170563] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2017] [Accepted: 12/18/2017] [Indexed: 11/22/2022] Open
Abstract
Borioteiioids comprise an extinct family of squamates that inhabited the Northern Hemisphere during the Cretaceous and were characterized by varying patterns of tooth replacement and dental morphology. Understanding the evolution of these tooth replacement patterns has, however, been largely hampered by an extremely fragmentary fossil record. Here we present new information on Dicothodon bajaensisfrom the Campanian of Baja California (Mexico), so far known only from isolated teeth and jaw fragments. Among abundant new materials there are ten maxillae and five dentaries belonging to distinct ontogenetic stages. Whereas juveniles display active tooth replacement, older specimens show no evidence of replacement. Dicothodon bajaensis is therefore inferred to have had arrested tooth replacement later in ontogeny. This provides the first evidence of cessation of tooth replacement during late ontogeny in lizards (living or extinct). This replacement type is also an evolutionary intermediate between the typical lizard replacement pattern, observed in some borioteiioids (e.g., Bicuspidon) and the complete absence of tooth replacement since early ontogeny as observed in other borioteiioids (e.g., Polyglyphanodon).
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19
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A mid-Cretaceous embryonic-to-neonate snake in amber from Myanmar. SCIENCE ADVANCES 2018; 4:eaat5042. [PMID: 30035227 PMCID: PMC6051735 DOI: 10.1126/sciadv.aat5042] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Accepted: 06/27/2018] [Indexed: 06/08/2023]
Abstract
We present the first known fossilized snake embryo/neonate preserved in early Late Cretaceous (Early Cenomanian) amber from Myanmar, which at the time, was an island arc including terranes from Austral Gondwana. This unique and very tiny snake fossil is an articulated postcranial skeleton, which includes posterior precloacal, cloacal, and caudal vertebrae, and details of squamation and body shape; a second specimen preserves a fragment of shed skin interpreted as a snake. Important details of skeletal ontogeny, including the stage at which snake zygosphene-zygantral joints began to form along with the neural arch lamina, are preserved. The vertebrae show similarities to those of fossil Gondwanan snakes, suggesting a dispersal route of Gondwanan faunas to Laurasia. Finally, the new species is the first Mesozoic snake to be found in a forested environment, indicating greater ecological diversity among early snakes than previously thought.
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Mosasauroid phylogeny under multiple phylogenetic methods provides new insights on the evolution of aquatic adaptations in the group. PLoS One 2017; 12:e0176773. [PMID: 28467456 PMCID: PMC5415187 DOI: 10.1371/journal.pone.0176773] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2017] [Accepted: 04/17/2017] [Indexed: 11/28/2022] Open
Abstract
Mosasauroids were a successful lineage of squamate reptiles (lizards and snakes) that radiated during the Late Cretaceous (95-66 million years ago). They can be considered one of the few lineages in the evolutionary history of tetrapods to have acquired a fully aquatic lifestyle, similarly to whales, ichthyosaurs and plesiosaurs. Despite a long history of research on this group, their phylogenetic relationships have only been tested so far using traditional (unweighted) maximum parsimony. However, hypotheses of mosasauroid relationships and the recently proposed multiple origins of aquatically adapted pelvic and pedal features in this group can be more thoroughly tested by methods that take into account variation in branch lengths and evolutionary rates. In this study, we present the first mosasauroid phylogenetic analysis performed under different analytical methods, including maximum likelihood, Bayesian inference, and implied weighting maximum parsimony. The results indicate a lack of congruence in the topological position of halisaurines and Dallasaurus. Additionally, the genus Prognathodon is paraphyletic under all hypotheses. Interestingly, a number of traditional mosasauroid clades become weakly supported, or unresolved, under Bayesian analyses. The reduced resolutions in some consensus trees create ambiguities concerning the evolution of fully aquatic pelvic/pedal conditions under many analyses. However, when enough resolution was obtained, reversals of the pelvic/pedal conditions were favoured by parsimony and likelihood ancestral state reconstructions instead of independent origins of aquatic features in mosasauroids. It is concluded that most of the observed discrepancies among the results can be associated with different analytical procedures, but also due to limited postcranial data on halisaurines, yaguarasaurines and Dallasaurus.
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Osteology, phylogeny, and functional morphology of two Jurassic lizard species and the early evolution of scansoriality in geckoes. Zool J Linn Soc 2016. [DOI: 10.1111/zoj.12487] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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The first iguanian lizard from the Mesozoic of Africa. ROYAL SOCIETY OPEN SCIENCE 2016; 3:160462. [PMID: 27703708 PMCID: PMC5043327 DOI: 10.1098/rsos.160462] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/28/2016] [Accepted: 08/22/2016] [Indexed: 06/06/2023]
Abstract
The fossil record shows that iguanian lizards were widely distributed during the Late Cretaceous. However, the biogeographic history and early evolution of one of its most diverse and peculiar clades (acrodontans) remain poorly known. Here, we present the first Mesozoic acrodontan from Africa, which also represents the oldest iguanian lizard from that continent. The new taxon comes from the Kem Kem Beds in Morocco (Cenomanian, Late Cretaceous) and is based on a partial lower jaw. The new taxon presents a number of features that are found only among acrodontan lizards and shares greatest similarities with uromastycines, specifically. In a combined evidence phylogenetic dataset comprehensive of all major acrodontan lineages using multiple tree inference methods (traditional and implied weighting maximum-parsimony, and Bayesian inference), we found support for the placement of the new species within uromastycines, along with Gueragama sulamericana (Late Cretaceous of Brazil). The new fossil supports the previously hypothesized widespread geographical distribution of acrodontans in Gondwana during the Mesozoic. Additionally, it provides the first fossil evidence of uromastycines in the Cretaceous, and the ancestry of acrodontan iguanians in Africa.
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Giant taxon-character matrices: quality of character constructions remains critical regardless of size. Cladistics 2016; 33:198-219. [DOI: 10.1111/cla.12163] [Citation(s) in RCA: 80] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/17/2016] [Indexed: 11/29/2022] Open
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A stem acrodontan lizard in the Cretaceous of Brazil revises early lizard evolution in Gondwana. Nat Commun 2015; 6:8149. [PMID: 26306778 PMCID: PMC4560825 DOI: 10.1038/ncomms9149] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2015] [Accepted: 07/23/2015] [Indexed: 12/03/2022] Open
Abstract
Iguanians are one of the most diverse groups of extant lizards (>1,700 species) with acrodontan iguanians dominating in the Old World, and non-acrodontans in the New World. A new lizard species presented herein is the first acrodontan from South America, indicating acrodontans radiated throughout Gondwana much earlier than previously thought, and that some of the first South American lizards were more closely related to their counterparts in Africa and Asia than to the modern fauna of South America. This suggests both groups of iguanians achieved a worldwide distribution before the final breakup of Pangaea. At some point, non-acrodontans replaced acrodontans and became the only iguanians in the Americas, contrary to what happened on most of the Old World. This discovery also expands the diversity of Cretaceous lizards in South America, which with recent findings, suggests sphenodontians were not the dominant lepidosaurs in that continent as previously hypothesized. Iguanians are a diverse group of lizards. Here, the authors report an acrodontan iguanian from the Late Cretaceous of Brazil, which suggests that this group achieved a global distribution during the Mesozoic but was replaced by non-acrodontans in the Americas.
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Redescription of Tijubina pontei, an Early Cretaceous lizard (Reptilia; Squamata) from the Crato Formation of Brazil. AN ACAD BRAS CIENC 2012; 84:79-94. [PMID: 22441597 DOI: 10.1590/s0001-37652012000100008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2011] [Accepted: 11/09/2011] [Indexed: 11/21/2022] Open
Abstract
The record of Gondwanan Mesozoic lizards is very poor. Among the few species described for this region there is Tijubina pontei, an Early Cretaceous lizard from the Crato Formation (late Aptian) of northeast Brazil. Its description is very brief and lacks most of its diagnostic characters and clear delimitation from other lizard species. Here, a full redescription of the holotype is provided. T. pontei is demonstrated to be a valid species and a new diagnosis is provided with reference to Olindalacerta brasiliensis, a contemporary species of the Crato Formation. It lacks the posteroventral and posterodorsal processes of the dentary; the tibial/fibular length equals the femoral length and its posterior dentary teeth are robust, cylindrically based, unsculptured and bear no cuspids. The systematic position of T. pontei still needs further clarification, but preliminary analyses indicate that it lies in a rather basal position among the Squamata, similarly to O. brasiliensis.
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Redescription of Tijubina pontei, an Early Cretaceous lizard (Reptilia; Squamata) from the Crato Formation of Brazil. AN ACAD BRAS CIENC 2012. [DOI: 10.1590/s0001-37652012005000001] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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