Manabu Sakamoto

Dinosaurs and the Cretaceous Terrestrial Revolution

The observed diversity of dinosaurs reached its highest peak during the mid- and Late Cretaceous, the 50 Myr that preceded their extinction, and yet this explosion of dinosaur diversity may be explained largely by sampling bias. It has long been debated whether dinosaurs were part of the Cretaceous Terrestrial Revolution (KTR), from 125–80 Myr ago, when flowering plants, herbivorous and social insects, squamates, birds and mammals all underwent a rapid expansion. Although an apparent explosion of dinosaur diversity occurred in the mid-Cretaceous, coinciding with the emergence of new groups (e.g. neoceratopsians, ankylosaurid ankylosaurs, hadrosaurids and pachycephalosaurs), results from the first quantitative study of diversification applied to a new supertree of dinosaurs show that this apparent burst in dinosaurian diversity in the last 18 Myr of the Cretaceous is a sampling artefact. Indeed, major diversification shifts occurred largely in the first one-third of the groups history. Despite the appearance of new clades of medium to large herbivores and carnivores later in dinosaur history, these new originations do not correspond to significant diversification shifts. Instead, the overall geometry of the Cretaceous part of the dinosaur tree does not depart from the null hypothesis of an equal rates model of lineage branching. Furthermore, we conclude that dinosaurs did not experience a progressive decline at the end of the Cretaceous, nor was their evolution driven directly by the KTR.

The Cranial Osteology and Feeding Ecology of the Metriorhynchid Crocodylomorph Genera Dakosaurus and Plesiosuchus from the Late Jurassic of Europe

Background Dakosaurus and Plesiosuchus are characteristic genera of aquatic, large-bodied, macrophagous metriorhynchid crocodylomorphs. Recent studies show that these genera were apex predators in marine ecosystems during the latter part of the Late Jurassic, with robust skulls and strong bite forces optimized for feeding on large prey. Methodology/Principal Findings Here we present comprehensive osteological descriptions and systematic revisions of the type species of both genera, and in doing so we resurrect the genus Plesiosuchus for the species Dakosaurus manselii. Both species are diagnosed with numerous autapomorphies. Dakosaurus maximus has premaxillary ‘lateral plates’; strongly ornamented maxillae; macroziphodont dentition; tightly fitting tooth-to-tooth occlusion; and extensive macrowear on the mesial and distal margins. Plesiosuchus manselii is distinct in having: non-amblygnathous rostrum; long mandibular symphysis; microziphodont teeth; tooth-crown apices that lack spalled surfaces or breaks; and no evidence for occlusal wear facets. Our phylogenetic analysis finds Dakosaurus maximus to be the sister taxon of the South American Dakosaurus andiniensis, and Plesiosuchus manselii in a polytomy at the base of Geosaurini (the subclade of macrophagous metriorhynchids that includes Dakosaurus, Geosaurus and Torvoneustes). Conclusions/Significance The sympatry of Dakosaurus and Plesiosuchus is curiously similar to North Atlantic killer whales, which have one larger ‘type’ that lacks tooth-crown breakage being sympatric with a smaller ‘type’ that has extensive crown breakage. Assuming this morphofunctional complex is indicative of diet, then Plesiosuchus would be a specialist feeding on other marine reptiles while Dakosaurus would be a generalist and possible suction-feeder. This hypothesis is supported by Plesiosuchus manselii having a very large optimum gape (gape at which multiple teeth come into contact with a prey-item), while Dakosaurus maximus possesses craniomandibular characteristics observed in extant suction-feeding odontocetes: shortened tooth-row, amblygnathous rostrum and a very short mandibular symphysis. We hypothesise that trophic specialisation enabled these two large-bodied species to coexist in the same ecosystem.

The oldest known metriorhynchid super-predator: a new genus and species from the Middle Jurassic of England, with implications for serration and mandibular evolution in predacious clades

The Oxford Clay Formation of England has yielded numerous sympatric species of metriorhynchid crocodylomorphs, although disagreement has persisted regarding the number of valid species. For over 140 years teeth reminiscent of the genus Dakosaurus have been known from the Oxford Clay Formation but these have never been properly described and their taxonomy and systematic affinity remain contentious. Furthermore, an enigmatic mandible and associated postcranial skeleton discovered by Alfred Leeds in the Fletton brick pits near Peterborough also remains undescribed. We show that this specimen, and several isolated teeth, represents the oldest known remains of a large-bodied predatory metriorhynchid. This material is described herein and referred to Tyrannoneustes lythrodectikos gen. et sp. nov. This species has a unique occlusal pattern: the dentition was arranged so that the posterior maxillodentary teeth interlock in the same plane and occlude mesiodistally. It is the first described crocodylomorph with microscopic denticles that are not contiguous along the carinae (forming short series of up to 10 denticles) and do not noticeably alter the height of the keel. Additionally, the dorsally expanded and curved posterior region of the mandible ventrally displaced the dentary tooth row relative to the jaw joint facilitating the enlargement of the dentition and increasing optimum gape. Therefore, Tyrannoneustes would have been a large-bodied marine predator that was well-suited to feed on larger prey than other contemporaneous metriorhynchids. A new phylogenetic analysis finds Tyrannoneustes to be the sister taxon to the subclade Geosaurini. An isolated tooth, humerus, and well-preserved mandible suggest a second species of metriorhynchid super-predator may also have lived in the Oxford Clay sea. Finally, we revise the diagnoses and descriptions of the other Oxford Clay metriorhynchid species, providing a guide for differentiating the many contemporaneous taxa from this exceptional fossil assemblage. http://zoobank.org/urn:lsid:zoobank.org:pub:C6222858-EC36-430D-8E28-1F636A6697CA

The evolution of cranial form and function in theropod dinosaurs: insights from geometric morphometrics.

Abstract Theropod dinosaurs, an iconic clade of fossil species including Tyrannosaurus and Velociraptor, developed a great diversity of body size, skull form and feeding habits over their 160+ million year evolutionary history. Here, we utilize geometric morphometrics to study broad patterns in theropod skull shape variation and compare the distribution of taxa in cranial morphospace (form) to both phylogeny and quantitative metrics of biting behaviour (function). We find that theropod skulls primarily differ in relative anteroposterior length and snout depth and to a lesser extent in orbit size and depth of the cheek region, and oviraptorosaurs deviate most strongly from the “typical” and ancestral theropod morphologies. Noncarnivorous taxa generally fall out in distinct regions of morphospace and exhibit greater overall disparity than carnivorous taxa, whereas large‐bodied carnivores independently converge on the same region of morphospace. The distribution of taxa in morphospace is strongly correlated with phylogeny but only weakly correlated with functional biting behaviour. These results imply that phylogeny, not biting function, was the major determinant of theropod skull shape.

Convergence and Divergence in the Evolution of Cat Skulls: Temporal and Spatial Patterns of Morphological Diversity

Background Studies of biological shape evolution are greatly enhanced when framed in a phylogenetic perspective. Inclusion of fossils amplifies the scope of macroevolutionary research, offers a deep-time perspective on tempo and mode of radiations, and elucidates life-trait changes. We explore the evolution of skull shape in felids (cats) through morphometric analyses of linear variables, phylogenetic comparative methods, and a new cladistic study of saber-toothed cats. Methodology/Principal Findings A new phylogenetic analysis supports the monophyly of saber-toothed cats (Machairodontinae) exclusive of Felinae and some basal felids, but does not support the monophyly of various saber-toothed tribes and genera. We quantified skull shape variation in 34 extant and 18 extinct species using size-adjusted linear variables. These distinguish taxonomic group membership with high accuracy. Patterns of morphospace occupation are consistent with previous analyses, for example, in showing a size gradient along the primary axis of shape variation and a separation between large and small-medium cats. By combining the new phylogeny with a molecular tree of extant Felinae, we built a chronophylomorphospace (a phylogeny superimposed onto a two-dimensional morphospace through time). The evolutionary history of cats was characterized by two major episodes of morphological divergence, one marking the separation between saber-toothed and modern cats, the other marking the split between large and small-medium cats. Conclusions/Significance Ancestors of large cats in the ‘Panthera’ lineage tend to occupy, at a much later stage, morphospace regions previously occupied by saber-toothed cats. The latter radiated out into new morphospace regions peripheral to those of extant large cats. The separation between large and small-medium cats was marked by considerable morphologically divergent trajectories early in feline evolution. A chronophylomorphospace has wider applications in reconstructing temporal transitions across two-dimensional trait spaces, can be used in ecophenotypical and functional diversity studies, and may reveal novel patterns of morphospace occupation.

Phylogenetically structured variance in felid bite force: the role of phylogeny in the evolution of biting performance.

A key question in evolution is the degree to which morphofunctional complexes are constrained by phylogeny. We investigated the role of phylogeny in the evolution of biting performance, quantified as bite forces, using phylogenetic eigenvector regression. Results indicate that there are strong phylogenetic signals in both absolute and size‐adjusted bite forces, although it is weaker in the latter. This indicates that elimination of size influences reduces the level of phylogenetic inertia and that the majority of the phylogenetic constraint is a result of size. Tracing the evolution of bite force through phylogeny by character optimization also supports this notion, in that relative bite force is randomly distributed across phylogeny whereas absolute bite force diverges according to clade. The nonphylogenetically structured variance in bite force could not be sufficiently explained by species‐unique morphology or by ecology. This study demonstrates the difficulties in identifying causes of nonphylogenetically structured variance in morphofunctional character complexes.

Dinosaurs in decline tens of millions of years before their final extinction

Significance Whether dinosaurs were in decline before their final extinction 66 Mya has been debated for decades with no clear resolution. This dispute has not been resolved because of inappropriate data and methods. Here, for the first time to our knowledge, we apply a statistical approach that models changes in speciation and extinction through time. We find overwhelming support for a long-term decline across all dinosaurs and within all three major dinosaur groups. Our results highlight that dinosaurs showed a marked reduction in their ability to replace extinct species with new ones, making them vulnerable to extinction and unable to respond quickly to and recover from the final catastrophic event 66 Mya. Whether dinosaurs were in a long-term decline or whether they were reigning strong right up to their final disappearance at the Cretaceous–Paleogene (K-Pg) mass extinction event 66 Mya has been debated for decades with no clear resolution. The dispute has continued unresolved because of a lack of statistical rigor and appropriate evolutionary framework. Here, for the first time to our knowledge, we apply a Bayesian phylogenetic approach to model the evolutionary dynamics of speciation and extinction through time in Mesozoic dinosaurs, properly taking account of previously ignored statistical violations. We find overwhelming support for a long-term decline across all dinosaurs and within all three dinosaurian subclades (Ornithischia, Sauropodomorpha, and Theropoda), where speciation rate slowed down through time and was ultimately exceeded by extinction rate tens of millions of years before the K-Pg boundary. The only exceptions to this general pattern are the morphologically specialized herbivores, the Hadrosauriformes and Ceratopsidae, which show rapid species proliferations throughout the Late Cretaceous instead. Our results highlight that, despite some heterogeneity in speciation dynamics, dinosaurs showed a marked reduction in their ability to replace extinct species with new ones, making them vulnerable to extinction and unable to respond quickly to and recover from the final catastrophic event.

‘Residual diversity estimates’ do not correct for sampling bias in palaeodiversity data

Summary It is widely accepted that the fossil record suffers from various sampling biases – diversity signals through time may partly or largely reflect the rock record – and many methods have been devised to deal with this problem. One widely used method, the ‘residual diversity’ method, uses residuals from a modelled relationship between palaeodiversity and sampling (sampling-driven diversity model) as ‘corrected’ diversity estimates, but the unorthodox way in which these residuals are generated presents serious statistical problems; the response and predictor variables are decoupled through independent sorting, rendering the new bivariate relationship meaningless. Here, we use simple simulations to demonstrate the detrimental consequences of independent sorting, through assessing error rates and biases in regression model coefficients. Regression models based on independently sorted data result in unacceptably high rates of incorrect and systematically, directionally biased estimates, when the true parameter values are known. The large number of recent papers that used the method are likely to have produced misleading results and their implications should be reassessed. We note that the ‘residuals’ approach based on the sampling-driven diversity model cannot be used to ‘correct’ for sampling bias, and instead advocate the use of phylogenetic multiple regression models that can include various confounding factors, including sampling bias, while simultaneously accounting for statistical non-independence owing to shared ancestry. Evolutionary dynamics such as speciation are inherently a phylogenetic process, and only an explicitly phylogenetic approach will correctly model this process.

Phylogenetic eigenvectors and nonstationarity in the evolution of theropod dinosaur skulls.

Despite the long‐standing interest in nonstationarity of both phenotypic evolution and diversification rates, only recently have methods been developed to study this property. Here, we propose a methodological expansion of the phylogenetic signal‐representation (PSR) curve based on phylogenetic eigenvectors to test for nonstationarity. The PSR curve is built by plotting the coefficients of determination R2 from phylogenetic eigenvector regression (PVR) models increasing the number of phylogenetic eigenvectors against the accumulated eigenvalues. The PSR curve is linear under a stationary model of trait evolution (i.e. the Brownian motion model). Here we describe the distribution of shifts in the models R2 and used a randomization procedure to compare observed and simulated shifts along the PSR curve, which allowed detecting nonstationarity in trait evolution. As an applied example, we show that the main evolutionary pattern of variation in the theropod dinosaur skull was nonstationary, with a significant shift in evolutionary rates in derived oviraptorosaurs, an aberrant group of mostly toothless, crested, birdlike theropods. This result is also supported by a recently proposed Bayesian‐based method (AUTEUR). A significant deviation between Ceratosaurus and Limusaurus terminal branches was also detected. We purport that our new approach is a valuable tool for evolutionary biologists, owing to its simplicity, flexibility and comprehensiveness.

How long is a piece of Strix? Methods in measuring and measuring the measurers

An experiment to quantify intra- and interobserver error in anatomical measurements found that interobserver measurements can vary by over 14% of mean specimen length; disparity in measurement increases logarithmically with the number of contributors; instructions did not reduce variation or measurement disparity; scale of the specimen influenced the precision of measurement (relative error increasing with specimen size); different methods of taking a measurement yielded different results, although they did not differ in terms of precision, and topographical complexity of the elements being considered may potentially influence error (error increasing with complexity). These results highlight concerns about introduction of noise and potential bias that should be taken into account when compiling composite datasets and meta-analyses.