Ancestral State Estimation with Phylogenetic Ridge Regression

Evolutionary patterns of cat-like carnivorans unveil drivers of the sabertooth morphology

The sabertooth morphology stands as a classic case of convergence, manifesting recurrently across various vertebrate groups, prominently within two carnivorans clades: felids and nimravids. Nonetheless, the evolutionary mechanisms driving these recurring phenotypes remain insufficiently understood, lacking a robust phylogenetic and spatiotemporal framework. We reconstruct the tempo and mode of craniomandibular evolution of Felidae and Nimravidae and evaluate the strength of the dichotomy between conical and saber-toothed species, as well as within saber-toothed morphotypes. To do so, we investigate morphological variation, convergence, phenotypic integration, and evolutionary rates, employing a comprehensive dataset of nearly 200 3D models encompassing mandibles and crania from both extinct and extant feline-like carnivorans, spanning their entire evolutionary timeline. Our results reject the hypothesis of a distinctive sabertooth morphology, revealing instead a continuous spectrum of feline-like phenotypes in both the cranium and mandible, with sporadic instances of unequivocal convergence. Disparity peaked at the end of the Miocene and is usually higher in clades containing taxa with extreme sabertoothed adaptations. We show that taxa with saberteeth exhibit a lower degree of craniomandibular integration, allowing to exhibit a greater range of phenotypes. Those same groups usually show a burst of morphological evolutionary rate at the beginning of their evolutionary history. Consequently, we propose that a reduced degree of integration coupled with rapid evolutionary rates emerge as key components in the development of a sabertooth morphology in multiple clades.

Evolutionary history of hominin brain size and phylogenetic comparative methods

An absolutely and relatively large brain has traditionally been viewed as a distinctive characteristic of the Homo genus, with anatomically modern humans presented at the apex of a long line of progressive increases in encephalization. Many studies continue to focus attention on increasing brain size in the Homo genus, while excluding measures of absolute and relative brain size of more geologically recent, smaller brained, hominins such as Homo floresiensis, and Homo naledi and smaller brained Homo erectus specimens. This review discusses the benefits of using phylogenetic comparative methods to trace the diverse changes in hominin brain evolution and the drawbacks of not doing so.

Trapped in the morphospace: The relationship between morphological integration and functional performance

The evolution of complex morphological structures can be characterized by the interplay between different anatomical regions evolving under functional integration in response to shared selective pressures. Using the highly derived humeral morphology of talpid moles as a model, here we test whether functional performance is linked to increased levels of evolutionary integration between humerus subunits and, if so, what the strength is of the relationship. Combining two-dimensional geometric morphometrics, phylogenetic comparative methods, and functional landscape modeling, we demonstrate that the high biomechanical performance of subterranean moles' humeri is coupled with elevated levels of integration, whereas taxa with low-performance values show intermediate or low integration. Theoretical morphs occurring in high-performance areas of the functional landscape are not occupied by any species, and show a marked drop in covariation levels, suggesting the existence of a strong relationship between integration and performance in the evolution of talpid moles' humeri. We argue that the relative temporal invariance of the subterranean environment may have contributed to stabilize humeral morphology, trapping subterranean moles in a narrow region of the landscape and impeding any attempt to reposition on a new ascending slope.

New giant carnivorous dinosaur reveals convergent evolutionary trends in theropod arm reduction

Giant carnivorous dinosaurs such as Tyrannosaurus rex and abelisaurids are characterized by highly reduced forelimbs that stand in contrast to their huge dimensions, massive skulls, and obligate bipedalism.^1,2 Another group that follows this pattern, yet is still poorly known, is the Carcharodontosauridae: dominant predators that inhabited most continents during the Early Cretaceous^3-5 and reached their largest sizes in Aptian-Cenomanian times.^6-10 Despite many discoveries over the last three decades, aspects of their anatomy, especially with regard to the skull, forearm, and feet, remain poorly known. Here we report a new carcharodontosaurid, Meraxes gigas, gen. et sp. nov., based on a specimen recovered from the Upper Cretaceous Huincul Formation of northern Patagonia, Argentina. Phylogenetic analysis places Meraxes among derived Carcharodontosauridae, in a clade with other massive South American species. Meraxes preserves novel anatomical information for derived carcharodontosaurids, including an almost complete forelimb that provides evidence for convergent allometric trends in forelimb reduction among three lineages of large-bodied, megapredatory non-avian theropods, including a remarkable degree of parallelism between the latest-diverging tyrannosaurids and carcharodontosaurids. This trend, coupled with a likely lower bound on forelimb reduction, hypothesized to be about 0.4 forelimb/femur length, combined to produce this short-armed pattern in theropods. The almost complete cranium of Meraxes permits new estimates of skull length in Giganotosaurus, which is among the longest for theropods. Meraxes also provides further evidence that carchardontosaurids reached peak diversity shortly before their extinction with high rates of trait evolution in facial ornamentation possibly linked to a social signaling role.

Modeling Pulsed Evolution and Time-independent Variation Improves the Confidence Level of Ancestral and Hidden State Predictions

Ancestral state reconstruction is not only a fundamental tool for studying trait evolution, but also very useful for predicting the unknown trait values (hidden states) of extant species. A well-known problem in ancestral and hidden state predictions is that the uncertainty associated with predictions can be so large that predictions themselves are of little use. Therefore, for meaningful interpretation of predicted traits and hypothesis testing, it is prudent to accurately assess the uncertainty of the predictions. Commonly used constant-rate Brownian motion (BM) model fails to capture the complexity of tempo and mode of trait evolution in nature, making predictions under the BM model vulnerable to lack-of-fit errors from model misspecification. Using empirical data (mammalian body size and bacterial genome size), we show that the distribution of residual Z-scores under the BM model is neither homoscedastic nor normal as expected. Consequently, the 95% confidence intervals (CIs) of predicted traits are so unreliable that the actual coverage probability ranges from 33% (strongly permissive) to 100% (strongly conservative). Alternative methods such as BayesTraits and StableTraits that allow variable rates in evolution improve the predictions but are computationally expensive. Here we develop RasperGade, a method of ancestral and hidden state prediction that uses the Levy process to explicitly model gradual evolution, pulsed evolution and time-independent variation. Using the same empirical data, we show that RasperGade outperforms both BayesTraits and StableTraits in providing reliable confidence estimates and is orders-of-magnitude faster. Our results suggest that, when predicting the ancestral and hidden states of continuous traits, the rate variation should always be assessed and the quality of confidence estimates should always be examined.

The link between avian brachial index, flight capability and the neornithine evolutionary radiation

In dictating the relative distances between the elbow, shoulder and wrist, avian brachial index (BI = humerus/radius-ulna length) likely influences wing kinematics and, therefore, might predict extinct avian flight capability. This underpins the hypothesis that non-neornithine Mesozoic avialans with relatively low BIs (associated with improved flight capabilities) restricted neornithine diversification until after the Cretaceous-Paleogene boundary. Here, correlations between flight metrics (wingbeat frequency (f), stroke angle (θ), wing loading (Q) and aspect ratio) and BI were investigated and vice versa. Additionally, the evolutionary model best describing the phylogenetic distribution of BI, and the temporal patterns in BI, flight metrics, body mass (M_b ), and size-corrected humerus (L_h ) and radius-ulna (L_ru ) length were determined. BI was best described by Ornstein-Uhlenbeck processes, with low α values indicating a gradual shift towards a future theoretical optimum. BI also decreased overall through evolutionary time with the flight metrics mirroring temporal patterns of change in BI. M_b , L_h and L_ru overall decreased apart from increases in L_h and L_ru following the middle-late Miocene (also leading to BI increasing) due to diversifications of the Anatinae and Sphenisciformes. L_h overall decreased further than L_ru. Consequently, decreasing L_h mainly contributed to decreasing BI through evolutionary time, implying flight performance increased through neornithine evolution. However, the timings of radiations in these variables implies an Eocene radiation of neornthine flight ecology rather than a rapid expansion into niches vacated by non-neornithine Mesozoic avialians following the Cretaceous-Paleogene boundary. Multiple regressions showed f, θ and Q explained 60% of variation in BI. However, unequivocally evaluating whether BI is related to wing movement (and flight capability) requires direct measures of wing movement for many species, which are currently unavailable. Finally, the findings here and previously observed clade-specificity in BI, suggest flight ecology may also be clade-specific. Hence, the utility of phylogeny in predicting flight ecology requires exploration.

Arothron: An R package for geometric morphometric methods and virtual anthropology applications

OBJECTIVES

The statistical analysis of fossil remains is essential to understand the evolution of the genus Homo. Unfortunately, the human fossil record is straight away scarce and plagued with severe loss of information caused by taphonomic processes. The recently developed field of Virtual Anthropology helps to ameliorate this situation by using digital techniques to restore damaged and incomplete fossils.

MATERIALS AND METHODS

We present the package Arothron, an R software suite meant to process and analyze digital models of skeletal elements. Arothron includes tools to digitally extract virtual cavities such as cranial endocasts, to statistically align disarticulated or broken bony elements, and to visualize local variations between surface meshes and landmark configurations.

RESULTS

We describe the main functionalities of Arothron and illustrate their usage through reproducible case studies. We describe a tool for segmentation of skeletal cavities by showing its application on a malleus bone, a Neanderthal tooth, and a modern human cranium, reproducing their shape and calculating their volume. We illustrate how to digitally align a disarticulated model of a modern human cranium, and how to combine piecemeal shape information on individual specimens into one. In addition, we present useful visualization tools by comparing the morphological differences between the right hemisphere of the Neanderthal and the modern human brain.

CONCLUSIONS

The Arothron R package is designed to study digital models of fossil specimens. By using Arothron, scientists can handle digital models with ease, investigate the inner morphology of 3D skeletal models, gain a full representation of the original shapes of damaged specimens, and compare shapes across specimens.

Divergence-time estimates for hominins provide insight into encephalization and body mass trends in human evolution

Quantifying speciation times during human evolution is fundamental as it provides a timescale to test for the correlation between key evolutionary transitions and extrinsic factors such as climatic or environmental change. Here, we applied a total evidence dating approach to a hominin phylogeny to estimate divergence times under different topological hypotheses. The time-scaled phylogenies were subsequently used to perform ancestral state reconstructions of body mass and phylogenetic encephalization quotient (PEQ). Our divergence-time estimates are consistent with other recent studies that analysed extant species. We show that the origin of the genus Homo probably occurred between 4.30 and 2.56 million years ago. The ancestral state reconstructions show a general trend towards a smaller body mass before the emergence of Homo, followed by a trend towards a greater body mass. PEQ estimations display a general trend of gradual but accelerating encephalization evolution. The obtained results provide a rigorous temporal framework for human evolution.