Using linear measurements to diagnose the ecological habitat of Spinosaurus.

Much of the ecological discourse surrounding the polarising theropod Spinosaurus has centred on qualitative discussions. Using a quantitative multivariate data analytical approach on size-adjusted linear measurements of the skull, we examine patterns in skull shape across a range of sauropsid clades and three ecological realms (terrestrial, semi-aquatic, and aquatic). We utilise cluster analyses to identify emergent properties of the data which associate properties of skull shape with ecological realm occupancy. Results revealed terrestrial ecologies to be significantly distinct from both semi- and fully aquatic ecologies, the latter two were not significantly different. Spinosaurids (including Spinosaurus) plotted away from theropods in morphospace and close to both marine taxa and wading birds. The position of nares and the degree of rostral elongation had the greatest effect on categorisation. Comparisons of supervised (k-means) and unsupervised clustering demonstrated categorising taxa into three groups (ecological realms) was inappropriate and suggested instead that cluster division is based on morphological adaptations to feeding on aquatic versus terrestrial food items. The relative position of the nares in longirostrine taxa is associated with which skull bones are elongated. Rostral elongation is observed by either elongating the maxilla and the premaxilla or by elongating the maxilla only. This results in the nares positioned towards the orbits or towards the anterior end of the rostrum respectively, with implications on available feeding methods. Spinosaurids, especially Spinosaurus, show elongation in the maxilla-premaxilla complex, achieving similar functional outcomes to elongation of the premaxilla seen in birds, particularly large-bodied piscivorous taxa. Such a skull construction would bolster "stand-and-wait" predation of aquatic prey to a greater extent than serving other proposed feeding methods.

Estimating bite force in extinct dinosaurs using phylogenetically predicted physiological cross-sectional areas of jaw adductor muscles.

I present a Bayesian phylogenetic predictive modelling (PPM) framework that allows the prediction of muscle parameters (physiological cross-sectional area, A Phys) in extinct archosaurs from skull width (W Sk) and phylogeny. This approach is robust to phylogenetic uncertainty and highly versatile given its ability to base predictions on simple, readily available predictor variables. The PPM presented here has high prediction accuracy (up to 95%), with downstream biomechanical modelling yielding bite force estimates that are in line with previous estimates based on muscle parameters from reconstructed muscles. This approach does not replace muscle reconstructions but one that provides a powerful means to predict A Phys from skull geometry and phylogeny to the same level of accuracy as that measured from reconstructed muscles in species for which soft tissue data are unavailable or difficult to obtain.

Strong support for a heterogeneous speciation decline model in Dinosauria: a response to claims made by Bonsor et al. (2020).

Through phylogenetic modelling, we previously presented strong support for diversification decline in the three major subclades of dinosaurs (Sakamoto et al. 2016 Proc. Natl Acad. Sci. USA 113, 5036-5040. (doi:10.1073/pnas.1521478113)). Recently, our support for this model has been criticized (Bonsor et al. 2020 R. Soc. Open Sci. 7, 201195. (doi:10.1098/rsos.201195)). Here, we highlight that these criticisms seem to largely stem from a misunderstanding of our study: contrary to Bonsor et al.'s claims, our model accounts for heterogeneity in diversification dynamics, was selected based on deviance information criterion (DIC) scores (not parameter significance), and intercepts were estimated to account for uncertainties in the root age of the phylogenetic tree. We also demonstrate that their new analyses are not comparable to our models: they fit simple, Dinosauria-wide models as a direct comparison to our group-wise models, and their additional trees are subclades that are limited in taxonomic coverage and temporal span, i.e. severely affected by incomplete sampling. We further present results of new analyses on larger, better-sampled trees (N = 961) of dinosaurs, showing support for the time-quadratic model. Disagreements in how we interpret modelled diversification dynamics are to be expected, but criticisms should be based on sound logic and understanding of the model under discussion.

The skull evolution of oviraptorosaurian dinosaurs: the role of niche partitioning in diversification.

Oviraptorosaurs are bird-like theropod dinosaurs that thrived in the final pre-extinction ecosystems during the latest Cretaceous, and the beaked, toothless skulls of derived species are regarded as some of the most peculiar among dinosaurs. Their aberrant morphologies are hypothesized to have been caused by rapid evolution triggered by an ecological/biological driver, but little is known about how their skull shapes and functional abilities diversified. Here, we use quantitative techniques to study oviraptorosaur skull form and mandibular function. We demonstrate that the snout is particularly variable, that mandibular form and upper/lower beak form are significantly correlated with phylogeny, and that there is a strong and significant correlation between mandibular function and mandible/lower beak shape, suggesting a form-function association. The form-function relationship and phylogenetic signals, along with a moderate allometric signal in lower beak form, indicate that similar mechanisms governed beak shape in oviraptorosaurs and extant birds. The two derived oviraptorosaur clades, oviraptorids and caenagnathids, are significantly separated in morphospace and functional space, indicating that they partitioned niches. Oviraptorids coexisting in the same ecosystem are also widely spread in morphological and functional space, suggesting that they finely partitioned feeding niches, whereas caenagnathids exhibit extreme disparity in beak size. The diversity of skull form and function was likely key to the diversification and evolutionary success of oviraptorosaurs in the latest Cretaceous.

Extreme and rapid bursts of functional adaptations shape bite force in amniotes.

Adaptation is the fundamental driver of functional and biomechanical evolution. Accordingly, the states of biomechanical traits (absolute or relative trait values) have long been used as proxies for adaptations in response to direct selection. However, ignoring evolutionary history, in particular ancestry, passage of time and the rate of evolution, can be misleading. Here, we apply a recently developed phylogenetic statistical approach using significant rate shifts to detect instances of exceptional rates of adaptive changes in bite force in a large group of terrestrial vertebrates, the amniotes. Our results show that bite force in amniotes evolved through multiple bursts of exceptional rates of adaptive changes, whereby whole groups-including Darwin's finches, maniraptoran dinosaurs (group of non-avian dinosaurs including birds), anthropoids and hominins (fossil and modern humans)-experienced significant rate increases compared to the background rate. However, in most parts of the amniote tree of life, we find no exceptional rate increases, indicating that coevolution with body size was primarily responsible for the patterns observed in bite force. Our approach represents a template for future studies in functional morphology and biomechanics, where exceptional rates of adaptive changes can be quantified and potentially linked to specific ecological factors underpinning major evolutionary radiations.

Transitions between foot postures are associated with elevated rates of body size evolution in mammals.

Terrestrial mammals have evolved various foot postures: flat-footed (plantigrady), tiptoed (digitigrady), and hooved (unguligrady) postures. Although the importance of foot posture on ecology and body size of mammalian species has been widely recognized, its evolutionary trajectory and influence on body size evolution across mammalian phylogeny remain untested. Taking a Bayesian phylogenetic approach combined with a comprehensive dataset of foot postures in 880 extant mammalian species, we investigated the evolutionary history of foot postures and rates of body size evolution, within the same posture and at transitions between postures. Our results show that the common ancestor of mammals was plantigrade, and transitions predominantly occurred only between plantigrady and digitigrady and between digitigrady and unguligrady. At the transitions between plantigrady and digitigrady and between digitigrady and unguligrady, rates of body size evolution are significantly elevated leading to the larger body masses of digitigrade species (∼1 kg) and unguligrade species (∼78 kg) compared with their respective ancestral postures [plantigrady (∼0.75 kg) and digitigrady]. Our results demonstrate the importance of foot postures on mammalian body size evolution and have implications for mammalian body size increase through time. In addition, we highlight a way forward for future studies that seek to integrate morphofunctional and macroevolutionary approaches.

Phylogenetic non-independence in rates of trait evolution.

Statistical non-independence of species' biological traits is recognized in most traits under selection. Yet, whether or not the evolutionary rates of such biological traits are statistically non-independent remains to be tested. Here, we test the hypothesis that phenotypic evolutionary rates are non-independent, i.e. contain phylogenetic signal, using empirical rates of evolution in three separate traits: body mass in mammals, beak shape in birds and bite force in amniotes. Specifically, we test if evolutionary rates are phylogenetically interdependent. We find evidence for phylogenetic signal in evolutionary rates in all three case studies. While phylogenetic signal diminishes deeper in time, this is reflective of statistical power owing to small sample and effect sizes. When effect size is large, e.g. owing to the presence of fossil tips, we detect high phylogenetic signals even in deeper time slices. Thus, we recommend that rates be treated as being non-independent throughout the evolutionary history of the group of organisms under study, and any summaries or analyses of rates through time-including associations of rates with traits-need to account for the undesired effects of shared ancestry.

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

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.

'Mystery big cats' in the Peruvian Amazon: morphometrics solve a cryptozoological mystery.

Two big cat skulls procured from hunters of Yanachaga National Park, Peru, were reported as those of cats informally dubbed the 'striped tiger' and 'anomalous jaguar'. Observations suggested that both skulls were distinct from those of jaguars, associated descriptions of integument did not conform to this species, and it has been implied that both represent members of one or two novel species. We sought to resolve the identity of the skulls using morphometrics. DNA could not be retrieved since both had been boiled as part of the defleshing process. We took 36 cranial and 13 mandibular measurements and added them to a database incorporating nearly 300 specimens of over 30 felid species. Linear discriminant analysis resolved both specimens as part of Panthera onca with high probabilities for cranial and mandibular datasets. Furthermore, the specimens exhibit characters typical of jaguars. If the descriptions of their patterning and pigmentation are accurate, we assume that both individuals were aberrant.

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.

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.

Jaw biomechanics and the evolution of biting performance in theropod dinosaurs.

Despite the great diversity in theropod craniomandibular morphology, the presence and distribution of biting function types across Theropoda has rarely been assessed. A novel method of biomechanical profiling using mechanical advantage computed for each biting position along the entirety of the tooth row was applied to 41 extinct theropod taxa. Multivariate ordination on the polynomial coefficients of the profiles reveals the distribution of theropod biting performance in function space. In particular, coelophysoids are found to occupy a unique region of function space, while tetanurans have a wide but continuous function space distribution. Further, the underlying phylogenetic structure and evolution of biting performance were investigated using phylogenetic comparative methods. There is a strong phylogenetic signal in theropod biomechanical profiles, indicating that evolution of biting performance does not depart from Brownian motion evolution. Reconstructions of ancestral function space occupation conform to this pattern, but phylogenetically unexpected major shifts in function space occupation can be observed at the origins of some clades. However, uncertainties surround ancestor estimates in some of these internal nodes, so inferences on the nature of these evolutionary changes must be viewed with caution.

Mass spectrometric imaging of ginsenosides localization in Panax ginseng root.

We performed mass spectrometric imaging (MSI) to localize ginsenosides (Rb(1), Rb(2) or Rc, and Rf) in cross-sections of the Panax ginseng root at a resolution of 100 microm using matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS). Tandem mass spectrometry (MS/MS) of alkali metal-adducted ginsenoside ions revealed structural information of the corresponding saccharides and aglycone. MALDI-MSI confirmed that ginsenosides were located more in the cortex and the periderm than that in the medulla of a lateral root. In addition, it revealed that localization of ginsenosides in a root tip (diameter, 2.7 mm) is higher than that in the center of the root (diameter, 7.3 mm). A quantitative difference was detected between localizations of protopanaxadiol-type ginsenoside (Rb(1), Rb(2), or Rc) and protopanaxatriol-type ginsenoside (Rf) in the root. This imaging approach is a promising technique for rapid evaluation and identification of medicinal saponins in plant tissues.

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 group's 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.

Alteration of phosphatidylinositol 3-kinase cascade in the multilobulated nuclear formation of adult T cell leukemia/lymphoma (ATLL).

Adult T cell leukemia/lymphoma (ATLL) has been characterized as one of the most aggressive human neoplasias and its incidence is thought to be caused by both genetic and epigenetic alterations to the host cellular genes of T cells infected with human T cell leukemia virus type I (HTLV-I). A multilobulated nuclear appearance is an important diagnostic marker of ATLL, and we have now identified that the molecular mechanisms underlying these formations occur through microtubule rearrangement via phosphatidylinositol 3-kinase (PI3-kinase) activation by AILIM/ICOS signaling. We also show that PTEN and/or SHIP-1, which are PIP3 inositol phosphatases that inhibit the activation of downstream effectors of the PI3-kinase cascade, are disrupted in both ATLL neoplasias and in multilobulated nuclei-forming Jurkat cells. This down-regulation of PTEN was found to be essential for the formation of ATLL-type nuclear lobules. Furthermore, PI3-kinase and PTEN activities were observed to be closely associated with cellular proliferation. Thus, our results suggest that alteration of PI3-kinase signaling cascades, as a result of the down-regulation of inositol phosphatases, induces ATLL-type multilobulated nuclear formation and is also associated with the cellular proliferation of malignant T cell leukemias/lymphomas.