Reassessment of the evolutionary history of the late Triassic and early Jurassic sauropodomorph dinosaurs through comparative cladistics and the supermatrix approach

Non-sauropod sauropodomorphs, also known as 'basal sauropodomorphs' or 'prosauropods', have been thoroughly studied in recent years. Several hypotheses on the interrelationships within this group have been proposed, ranging from a complete paraphyly, where the group represents a grade from basal saurischians to Sauropoda, to a group on its own. The grade-like hypothesis is the most accepted; however, the relationships between the different taxa are not consistent amongst the proposed scenarios. These inconsistencies have been attributed to missing data and unstable (i.e., poorly preserved) taxa, nevertheless, an extensive comparative cladistic analysis has found that these inconsistencies instead come from the character coding and character selection, plus the strategies on merging data sets. Furthermore, a detailed character analysis using information theory and mathematical topology as an approach for character delineation is explored here to operationalise characters and reduce the potential impact of missing data. This analysis also produced the largest and most comprehensive matrix after the reassessment and operationalisation of every character applied to this group far. Additionally, partition analyses performed on this data set have found consistencies in the interrelationships within non-sauropod Sauropodomorpha and has found strong support for smaller clades such as Plateosauridae, Riojasauridae, Anchisauridae, Massospondylinae and Lufengosarinae. The results of these analyses also highlight a different scenario on how quadrupedality evolved, independently originating twice within the group, and provide a better framework to understand the palaeo-biogeography and diversification rate of the first herbivore radiation of dinosaurs

Integrating genomics with the fossil record to explore the evolutionary history of Echinoidea

Echinoidea constitutes one of five major clades of living echinoderms, marine animals uniquely characterized by a pentaradial symmetry. Approximately 1,000 living and 10,000 extinct species have been described, including many commonly known as sea urchins, heart urchins and sand dollars. Today, echinoids are ubiquitous in benthic marine environments, where they strongly affect the functioning of biodiverse communities such as coral reefs and kelp forests. Given the quality of their fossil record, their remarkable morphological complexity and our thorough understanding of their development, echinoids provide unparalleled opportunities to explore evolutionary questions in deep-time, providing access to the developmental and morphological underpinnings of evolutionary innovation. These questions cannot be addressed without first resolving the phylogenetic relationships among living and extinct lineages. The goal of this dissertation is to advance our understanding of echinoid relationships and evolutionary history, as well as to explore more broadly the integration of phylogenomic, morphological and paleontological data in phylogenetic reconstruction and macroevolutionary inference.In Chapter 1, I report the results of the first phylogenomic analysis of echinoids based on the sequencing of 17 novel echinoid transcriptomes. Phylogenetic analyses of this data resolve the position of several clades—including the sand dollars—in disagreement with traditional morphological hypotheses. I demonstrate the presence of a strong phylogenetic signal for these novel resolutions, and explore scenarios to reconcile these findings with morphological evidence. In Chapter 7, I extend this approach with a more thorough taxon sampling, resulting in a robust topology with a near-complete sampling of major echinoid lineages. This effort reveals that apatopygids, a clade of three species with previously unclear affinities, represent the only living descendants of a once diverse Mesozoic clade. I also perform a thorough time calibration analysis, quantifying the relative effects of choosing among alternative models of molecular evolution, gene samples and clock priors. I introduce the concept of a chronospace and use it to reveal that only the last among the aforementioned choices affects significantly our understanding of echinoid diversification. Molecular clocks unambiguously support late Permian and late Cretaceous origins for crown group echinoids and sand dollars, respectively, implying long ghost ranges for both. Fossils have been shown to improve the accuracy of phylogenetic comparative methods, warranting their inclusion alongside extant terminals when exploring evolutionary processes across deep timescales. However, their impact on topological inference remains controversial. I explore this topic in Chapter 3 with the use of simulations, which show that morphological phylogenies are more accurate when fossil taxa are incorporated. I also show that tip-dated Bayesian inference, which takes stratigraphic information from fossils into account, outperforms uncalibrated methods. This approach is complemented in Chapter 2 with the analysis of empirical datasets, confirming that incorporating fossils reshapes phylogenies in a manner that is entirely distinct from increased sampling of extant taxa, a result largely attributable to the occurrence of distinctive character combinations among fossils. Even though phylogenomic and paleontological data are complementary resources for unraveling the relationships and divergence times of lineages, few studies have attempted to fully integrate them. Chapter 4 revisits the phylogeny of crown group Echinoidea using a total-evidence dating approach combining phylogenomic, morphological and stratigraphic information. To this end, I develop a method (genesortR) for subsampling molecular datasets that selects loci with high phylogenetic signal and low systematic biases. The results demonstrate that combining different data sources increases topological accuracy and helps resolve phylogenetic conflicts. Notably, I present a new hypothesis for the origin and early morphological evolution of the sand dollars and close allies. In Chapter 6, I compare the behavior of genesortR against alternative subsampling strategies across a sample of phylogenomic matrices. I find this method to systematically outperform random loci selection, unlike commonly-used approaches that target specific evolutionary rates or minimize sources of systematic error. I conclude that these methods should not be used indiscriminately, and that multivariate methods of phylogenomic subsampling should be favored. Finally, in Chapter 5, I explore the macroevolutionary dynamics of echinoid body size across 270 million years using data for more than 5,000 specimens in a phylogenetically explicit context. I also develop a method (extendedSurface) for parameterizing adaptive landscapes that overcomes issues with existing approaches and finds better fitting models. While echinoid body size has been largely constrained to evolve within a single adaptive peak, the disparity of the clade was generated by regime shifts driving the repeated evolution of miniaturized and gigantic forms. Most innovations occurred during the latter half of the Mesozoic, and were followed by a drastic slowdown in the aftermath of the Cretaceous-Paleogene mass extinction

Whole-body endothermy: ancient, homologous and widespread among the ancestors of mammals, birds and crocodylians

First published: 10 December 2021The whole-body (tachymetabolic) endothermy seen in modern birds and mammals is long held to have evolved independently in each group, a reasonable assumption when it was believed that its earliest appearances in birds and mammals arose many millions of years apart. That assumption is consistent with current acceptance that the non-shivering thermogenesis (NST) component of regulatory body heat originates differently in each group: from skeletal muscle in birds and from brown adipose tissue (BAT) in mammals. However, BAT is absent in monotremes, marsupials, and many eutherians, all whole-body endotherms. Indeed, recent research implies that BAT-driven NST originated more recently and that the biochemical processes driving muscle NST in birds, many modern mammals and the ancestors of both may be similar, deriving from controlled 'slippage' of Ca2+ from the sarcoplasmic reticulum Ca2+ -ATPase (SERCA) in skeletal muscle, similar to a process seen in some fishes. This similarity prompted our realisation that the capacity for whole-body endothermy could even have pre-dated the divergence of Amniota into Synapsida and Sauropsida, leading us to hypothesise the homology of whole-body endothermy in birds and mammals, in contrast to the current assumption of their independent (convergent) evolution. To explore the extent of similarity between muscle NST in mammals and birds we undertook a detailed review of these processes and their control in each group. We found considerable but not complete similarity between them: in extant mammals the 'slippage' is controlled by the protein sarcolipin (SLN), in birds the SLN is slightly different structurally and its role in NST is not yet proved. However, considering the multi-millions of years since the separation of synapsids and diapsids, we consider that the similarity between NST production in birds and mammals is consistent with their whole-body endothermy being homologous. If so, we should expect to find evidence for it much earlier and more widespread among extinct amniotes than is currently recognised. Accordingly, we conducted an extensive survey of the palaeontological literature using established proxies. Fossil bone histology reveals evidence of sustained rapid growth rates indicating tachymetabolism. Large body size and erect stature indicate high systemic arterial blood pressures and four-chambered hearts, characteristic of tachymetabolism. Large nutrient foramina in long bones are indicative of high bone perfusion for rapid somatic growth and for repair of microfractures caused by intense locomotion. Obligate bipedality appeared early and only in whole-body endotherms. Isotopic profiles of fossil material indicate endothermic levels of body temperature. These proxies led us to compelling evidence for the widespread occurrence of whole-body endothermy among numerous extinct synapsids and sauropsids, and very early in each clade's family tree. These results are consistent with and support our hypothesis that tachymetabolic endothermy is plesiomorphic in Amniota. A hypothetical structure for the heart of the earliest endothermic amniotes is proposed. We conclude that there is strong evidence for whole-body endothermy being ancient and widespread among amniotes and that the similarity of biochemical processes driving muscle NST in extant birds and mammals strengthens the case for its plesiomorphy.Gordon Grigg, Julia Nowack, José Eduardo Pereira Wilken Bicudo, Naresh Chandra Bal, Holly N. Woodward and Roger S. Seymou