Assessing bite force estimates in extinct mammals and archosaurs using phylogenetic predictions

Bite force is an ecologically important biomechanical performance measure that is informative in inferring the ecology of extinct taxa. However, biomechanical modelling to estimate bite force is associated with some level of uncertainty. Here, I assess the accuracy of bite force estimates in extinct taxa using a Bayesian phylogenetic prediction model. I first fitted a phylogenetic regression model on a training set comprising extant data. The model predicts bite force from body mass and skull width while accounting for differences owing to biting position. The posterior predictive model has a 93% prediction accuracy as evaluated using leave-one-out cross-validation. I then predicted bite force in 37 species of extinct mammals and archosaurs from the posterior distribution of predictive models, generating posterior predictive distributions of null expectations given body mass, skull width and phylogenetic position. Biomechanically estimated bite forces from the literature fall within the posterior predictive distributions for all except four species of extinct taxa and are thus as accurate as predicted from body size and skull width, given the variation inherent in extant taxa and the amount of time available for variance to accrue. Biomechanical modelling remains a valuable means to estimate bite force in extinct taxa and should be reliably informative of functional performances and serve to provide insights into past ecologies

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, APhys) in extinct archosaurs from skull width (WSk) 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 APhys 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

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

1 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. 2. Here, we use simple simulations to demonstrate the detrimental consequences of independent sorting, through assessing error rates and biases in regression model coefficients. 3. 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. 4. 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

Synthesis and photochemical reactivity of caged glutamates with a π-​extended coumarin chromophore as a photolabile protecting group

International audience'Caging' and 'uncaging' bioactive substrates are key techniques in studying a wide variety of biological processes. In the present study, two-types of novel caged glutamates with a two-photon absorption (TPA) core, that is, π-extended coumarin, were synthesized and their photochemical release of glutamate was analyzed. The high yields of glutamate (>92%) were observed in the photolysis of compounds 1 and 10, respectively

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

Epidemiology of ASD in Preschool-age Children in Japan

In recent years, it has been reported that the prevalence of autism spectrum disorder (ASD) is increasing, but there are few research reports in Asia equivalent to those in Europe and the United States. Since large-scale epidemiological studies of neurodevelopmental disorders (NDDs) have not been conducted in Japan, the delay in early detection is conspicuous compared to other countries. Therefore, we started epidemiological studies in a medium-sized city (Hirosaki City) in northern Japan from 2013 to elucidate the prevalence of ASD and have been conducting a 9-year community cohort survey. In 2020, we published an adjusted prevalence of ASD of 3.2% at the age of 5 years, no change in 4-year incidence, and comorbidity of ASD. Since then, we have focused on sleep problems at the age of 5 years and have been studying the estimation of the prevalence of sleep disorders and the relationship with neurological development disorders. In this chapter, in addition to our research results since 2013, we will introduce the screening and support system in the community in Japan

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 whether rates are non-independent throughout the evolutionary history of each tree. 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 account for the undesired effects of shared ancestry

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. USA113, 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