Morphological Species Delimitation in The Western Pond Turtle (Actinemys): Can Machine Learning Methods Aid in Cryptic Species Identification?

As the discovery of cryptic species has increased in frequency, there has been an interest in whether geometric morphometric data can detect fine-scale patterns of variation that can be used to morphologically diagnose such species. We used a combination of geometric morphometric data and an ensemble of five supervised machine learning methods (MLMs) to investigate whether plastron shape can differentiate two putative cryptic turtle species, Actinemys marmorata and Actinemys pallida. Actinemys has been the focus of considerable research due to its biogeographic distribution and conservation status. Despite this work, reliable morphological diagnoses for its two species are still lacking. We validated our approach on two datasets, one consisting of eight morphologically disparate emydid species, the other consisting of two subspecies of Trachemys (T. scripta scripta, T. scripta elegans). The validation tests returned near-perfect classification rates, demonstrating that plastron shape is an effective means for distinguishing taxonomic groups of emydids via MLMs. In contrast, the same methods did not return high classification rates for a set of alternative phylogeographic and morphological binning schemes in Actinemys. All classification hypotheses performed poorly relative to the validation datasets and no single hypothesis was unequivocally supported for Actinemys. Two hypotheses had machine learning performance that was marginally better than our remaining hypotheses. In both cases, those hypotheses favored a two-species split between A. marmorata and A. pallida specimens, lending tentative morphological support to the hypothesis of two Actinemys species. However, the machine learning results also underscore that Actinemys as a whole has lower levels of plastral variation than other turtles within Emydidae, but the reason for this morphological conservatism is unclear.

Small skeletons show size-specific scaling: an exploration of allometry in the mammalian lumbar spine.

Studies of vertebrate bone biomechanics often focus on skeletal adaptations at upper extremes of body mass, disregarding the importance of skeletal adaptations at lower extremes. Yet mammals are ancestrally small and most modern species have masses under 5 kg, so the evolution of morphology and function at small size should be prioritized for understanding how mammals subsist. We examined allometric scaling of lumbar vertebrae in the small-bodied Philippine endemic rodents known as cloud rats, which vary in mass across two orders of magnitude (15.5 g-2700 g). External vertebral dimensions scale with isometry or positive allometry, likely relating to body size and nuances in quadrupedal posture. In contrast to most mammalian trabecular bone studies, bone volume fraction and trabecular thickness scale with positive allometry and isometry, respectively. It is physiologically impossible for these trends to continue to the upper extremes of mammalian body size, and we demonstrate a fundamental difference in trabecular bone allometry between large- and small-bodied mammals. These findings have important implications for the biomechanical capabilities of mammalian bone at small body size; for the selective pressures that govern skeletal evolution in small mammals; and for the way we define 'small' and 'large' in the context of vertebrate skeletons.

From Fairies to Giants: Untangling the Effect of Body Size, Phylogeny, and Ecology on Vertebral Bone Microstructure of Xenarthran Mammals.

Trabecular bone is a spongy bone tissue that serves as a scaffolding-like support inside many skeletal elements. Previous research found allometric variation in some aspects of trabecular bone architecture (TBA) and bone microstructure, whereas others scale isometrically. However, most of these studies examined very wide size and phylogenetic ranges or focused exclusively on primates or lab mice. We examined the impact of body size on TBA across a smaller size range in the mammalian clade Xenarthra (sloths, armadillos, and anteaters). We µCT-scanned the last six presacral vertebrae of 23 xenarthran specimens (body mass 120 g-35 kg). We collected ten gross-morphology measurements and seven TBA metrics and analyzed them using phylogenetic and nonphylogenetic methods. Most metrics had similar allometries to previous work. However, because ecology and phylogeny align closely in Xenarthra, the phylogenetic methods likely removed some covariance due to ecology; clarifying the impact of ecology on TBA in xenarthrans requires further work. Regressions for Folivora had high P-values and low R-squared values, indicating that the extant sloth sample either is too limited to determine patterns or that the unique way sloths load their vertebral columns causes unusually high TBA variation. The southern three-banded armadillo sits far below the regression lines, which may be related to its ability to roll into a ball. Body size, phylogeny, and ecology impact xenarthran TBA, but parsing these effects is highly complex.

The evolution of the synapsid tusk: insights from dicynodont therapsid tusk histology.

The mammalian tusk is a unique and extreme morphotype among modern vertebrate dentitions. Tusks-defined here as ever-growing incisors or canines composed of dentine-evolved independently multiple times within mammals yet have not evolved in other extant vertebrates. This suggests that there is a feature specific to mammals that facilitates the evolution of this specialized dentition. To investigate what may underpin the evolution of tusks, we histologically sampled the tusks of dicynodont therapsids: the earliest iteration of tusk evolution and the only non-mammalian synapsid clade to have acquired such a dentition. We studied the tissue composition, attachment tissues, development and replacement in 10 dicynodont taxa and show multiple developmental pathways for the adult dentitions of dicynodont tusks and tusk-like caniniforms. In a phylogenetic context, these developmental pathways reveal an evolutionary scenario for the acquisition of an ever-growing tusk-an event that occurred convergently, but only in derived members of our sample. We propose that the evolution of an ever-growing dentition, such as a tusk, is predicated on the evolution of significantly reduced tooth replacement and a permanent soft-tissue attachment. Both of these features are fixed in the dentitions of crown-group mammals, which helps to explain why tusks are restricted to this clade among extant vertebrates.

Fossils reveal the complex evolutionary history of the mammalian regionalized spine.

A unique characteristic of mammals is a vertebral column with anatomically distinct regions, but when and how this trait evolved remains unknown. We reconstructed vertebral regions and their morphological disparity in the extinct forerunners of mammals, the nonmammalian synapsids, to elucidate the evolution of mammalian axial differentiation. Mapping patterns of regionalization and disparity (heterogeneity) across amniotes reveals that both traits increased during synapsid evolution. However, the onset of regionalization predates increased heterogeneity. On the basis of inferred homology patterns, we propose a "pectoral-first" hypothesis for region acquisition, whereby evolutionary shifts in forelimb function in nonmammalian therapsids drove increasing vertebral modularity prior to differentiation of the vertebral column for specialized functions in mammals.

Predator-prey interactions amongst Permo-Triassic terrestrial vertebrates as a deterministic factor influencing faunal collapse and turnover.

Unlike modern mammalian communities, terrestrial Paleozoic and Mesozoic vertebrate systems were characterized by carnivore faunas that were as diverse as their herbivore faunas. The comparatively narrow food base available to carnivores in these paleosystems raises the possibility that predator-prey interactions contributed to unstable ecosystems by driving populations to extinction. Here, we develop a model of predator-prey interactions based on diversity, abundance and body size patterns observed in the Permo-Triassic vertebrate fossil record of the Karoo Basin, South Africa. Our simulations reflect empirical evidence that despite relatively high carnivore: herbivore species ratios, herbivore abundances were sufficient for carnivores to maintain required intake levels through most of the Karoo sequence. However, high mortality rates amongst herbivore populations, even accounting for birth rates of different-sized species, are predicted for assemblages immediately preceding the end-Guadalupian and end-Permian mass extinctions, as well as in the Middle Triassic when archosaurs replaced therapsids as the dominant terrestrial fauna. These results suggest that high rates of herbivore mortality could have played an important role in biodiversity declines leading up to each of these turnover events. Such declines would have made the systems especially vulnerable to subsequent stochastic events and environmental perturbations, culminating in large-scale extinctions.

Nocturnality in synapsids predates the origin of mammals by over 100 million years.

Nocturnality is widespread among extant mammals and often considered the ancestral behavioural pattern for all mammals. However, mammals are nested within a larger clade, Synapsida, and non-mammalian synapsids comprise a rich phylogenetic, morphological and ecological diversity. Even though non-mammalian synapsids potentially could elucidate the early evolution of diel activity patterns and enrich the understanding of synapsid palaeobiology, data on their diel activity are currently unavailable. Using scleral ring and orbit dimensions, we demonstrate that nocturnal activity was not an innovation unique to mammals but a character that appeared much earlier in synapsid history, possibly several times independently. The 24 Carboniferous to Jurassic non-mammalian synapsid species in our sample featured eye morphologies consistent with all major diel activity patterns, with examples of nocturnality as old as the Late Carboniferous (ca 300 Ma). Carnivores such as Sphenacodon ferox and Dimetrodon milleri, but also the herbivorous cynodont Tritylodon longaevus were likely nocturnal, whereas most of the anomodont herbivores are reconstructed as diurnal. Recognizing the complexity of diel activity patterns in non-mammalian synapsids is an important step towards a more nuanced picture of the evolutionary history of behaviour in the synapsid clade.

Shape and mechanics in thalattosuchian (Crocodylomorpha) skulls: implications for feeding behaviour and niche partitioning.

Variation in modern crocodilian and extinct thalattosuchian crocodylomorph skull morphology is only weakly correlated with phylogeny, implying that factors other than evolutionary proximity play important roles in determining crocodile skull shape. To further explore factors potentially influencing morphological differentiation within the Thalattosuchia, we examine teleosaurid and metriorhynchid skull shape variation within a mechanical and dietary context using a combination of finite element modelling and multivariate statistics. Patterns of stress distribution through the skull were found to be very similar in teleosaurid and metriorhynchid species, with stress peaking at the posterior constriction of the snout and around the enlarged supratemporal fenestrae. However, the magnitudes of stresses differ, with metriorhynchids having generally stronger skulls. As with modern crocodilians, a strong linear relationship between skull length and skull strength exists, with short-snouted morphotypes experiencing less stress through the skull than long-snouted morphotypes under equivalent loads. Selection on snout shape related to dietary preference was found to work in orthogonal directions in the two families: diet is associated with snout length in teleosaurids and with snout width in metriorhynchids, suggesting that teleosaurid skulls were adapted for speed of attack and metriorhynchid skulls for force production. Evidence also indicates that morphological and functional differentiation of the skull occurred as a result of dietary preference, allowing closely related sympatric species to exploit a limited environment. Comparisons of the mechanical performance of the thalattosuchian skull with extant crocodilians show that teleosaurids and long-snouted metriorhynchids exhibit stress magnitudes similar to or greater than those of long-snouted modern forms, whereas short-snouted metriorhynchids display stress magnitudes converging on those found in short-snouted modern species. As a result, teleosaurids and long-snouted metriorhynchids were probably restricted to lateral attacks of the head and neck, but short-snouted metriorhynchids may have been able to employ the grasp and shake and/or 'death roll' feeding and foraging behaviours.