Evolution in the sabre-tooth cat, Smilodon fatalis, in response to Pleistocene climate change

Unexpectedly uneven distribution of functional trade-offs explains cranial morphological diversity in carnivores

Functional trade-offs can affect patterns of morphological and ecological evolution as well as the magnitude of morphological changes through evolutionary time. Using morpho-functional landscape modelling on the cranium of 132 carnivore species, we focused on the macroevolutionary effects of the trade-off between bite force and bite velocity. Here, we show that rates of evolution in form (morphology) are decoupled from rates of evolution in function. Further, we found theoretical morphologies optimising for velocity to be more diverse, while a much smaller phenotypic space was occupied by shapes optimising force. This pattern of differential representation of different functions in theoretical morphological space was highly correlated with patterns of actual morphological disparity. We hypothesise that many-to-one mapping of cranium shape on function may prevent the detection of direct relationships between form and function. As comparatively only few morphologies optimise bite force, species optimising this function may be less abundant because they are less likely to evolve. This, in turn, may explain why certain clades are less variable than others. Given the ubiquity of functional trade-offs in biological systems, these patterns may be general and may help to explain the unevenness of morphological and functional diversity across the tree of life.

On Information Rank Deficiency in Phenotypic Covariance Matrices

This paper investigates a form of rank deficiency in phenotypic covariance matrices derived from geometric morphometric data, and its impact on measures of phenotypic integration. We first define a type of rank deficiency based on information theory, then demonstrate that this deficiency impairs the performance of phenotypic integration metrics in a model system. Lastly, we propose methods to treat for this information rank deficiency. Our first goal is to establish how the rank of a typical geometric morphometric covariance matrix relates to the information entropy of its eigenvalue spectrum. This requires clear definitions of matrix rank, of which we define three: the full matrix rank (equal to the number of input variables), the mathematical rank (the number of non-zero eigenvalues), and the information rank or 'effective rank' (equal to the number of non-redundant eigenvalues). We demonstrate that effective rank deficiency arises from a combination of methodological factors - Generalized Procrustes analysis, use of the correlation matrix, and insufficient sample size - as well as phenotypic covariance. Secondly, we use dire wolf jaws to document how differences in effective rank deficiency bias two metrics used to measure phenotypic integration. The eigenvalue variance characterizes the integration change incorrectly, and the standardized generalized variance lacks the sensitivity needed to detect subtle changes in integration. Both metrics are impacted by the inclusion of many small, but non-zero, eigenvalues arising from a lack of information in the covariance matrix, a problem that usually becomes more pronounced as the number of landmarks increases. We propose a new metric for phenotypic integration that combines the standardized generalized variance with information entropy. This metric is equivalent to the standardized generalized variance, but calculated only from those eigenvalues that carry non-redundant information. It is the standardized generalized variance scaled to the effective rank of the eigenvalue spectrum. We demonstrate that this metric successfully detects the shift of integration in our dire wolf sample. Our third goal is to generalize the new metric to compare data sets with different sample sizes and numbers of variables. We develop a standardization for matrix information based on data permutation, then demonstrate that Smilodon jaws are more integrated than dire wolf jaws. Finally, we describe how our information entropy-based measure allows phenotypic integration to be compared in dense semilandmark data sets without bias, allowing characterization of the information content of any given shape, a quantity we term 'latent dispersion'.

Computed tomography reveals hip dysplasia in the extinct Pleistocene saber-tooth cat Smilodon

Reconstructing the behavior of extinct species is challenging, particularly for those with no living analogues. However, damage preserved as paleopathologies on bone can record how an animal moved in life, potentially reflecting behavioral patterns. Here, we assess hypothesized etiologies of pathology in a pelvis and associated right femur of a Smilodon fatalis saber-toothed cat, one of the best-studied species from the Pleistocene-age Rancho La Brea asphalt seeps, California, USA, using visualization by computed tomography (CT). The pelvis exhibits massive destruction of the right hip socket that was interpreted, for nearly a century, to have developed from trauma and infection. CT imaging reveals instead that the pathological distortions characterize chronic remodeling that began at birth and led to degeneration of the joint over the animal's life. These results suggest that this individual suffered from hip dysplasia, a congenital condition common in domestic dogs and cats. This individual reached adulthood but could not have hunted properly nor defended territory on its own, likely relying on a social group for feeding and protection. While extant social felids are rare, these fossils and others with similar pathologies are consistent with a spectrum of social strategies in Smilodon supported by a predominance of previous studies.

Variation in the sacroiliac joint in Felidae

Felidae species show a great diversity in their diet, foraging and hunting strategies, from small to large prey. Whether they belong to solitary or group hunters, the behavior of cats to subdue resisting small or large prey presents crucial differences. It is assumed that pack hunting reduces the per capita risk of each individual. We hypothesize that the sacroiliac articulation plays a key role in stabilizing the predator while subduing and killing prey. Using CT-scan from 59 felid coxal bones, we calculated the angle between both iliac articular surfaces. Correlation of this inter-iliac angle with body size was calculated and ecological stressors were evaluated on inter-iliac angle. Body size significantly influences inter-iliac angle with small cats having a wider angle than big cats. Arboreal species have a significantly larger angle compared to cursorial felids with the smallest value, and to scansorial and terrestrial species with intermediate angles. Felids hunting large prey have a smaller angle than felids hunting small and mixed prey. Within the Panthera lineage, pack hunters (lions) have a larger angle than all other species using solitary hunting strategy. According to the inter-iliac angle, two main groups of felids are determined: (i) predators with an angle of around 40° include small cats (i.e., Felis silvestris, Leopardus wiedii, Leptailurus serval, Lynx Canadensis, L. rufus; median = 43.45°), the only pack-hunting species (i.e., Panthera leo; median = 37.90°), and arboreal cats (i.e., L. wiedii, Neofelis nebulosa; median = 49.05°), (ii) predators with an angle of around 30° include solitary-hunting big cats (i.e., Acinonyx jubatus, P. onca, P. pardus, P. tigris, P. uncia; median = 31.80°). We suggest different pressures of selection to interpret these results. The tightening of the iliac wings around the sacrum probably enhances big cats’ ability for high speed and large prey control. In contrast, pack hunting in lions reduced the selective pressure for large prey.

Measures of Relative Dentary Strength in Rancho La Brea Smilodon fatalis over Time

The late Pleistocene megafaunal extinction of approximately 12,000 years ago, included the demise of Smilodon fatalis, a hypercarnivore from the Rancho La Brea deposits, which has been studied across time by looking at different deposits or pits to determine morphological size and shape changes and trends during this time. To better understand functional aspects of these changes, this study focused on a measure of jaw strength over time, which can give an indication of morphological changes within the jaw that cannot be seen using surface morphometrics. By radiographing dentaries, cortical bone can be seen, which provides an estimate of resistance to bending forces while biting, and can be measured and used as an indicator of jaw strength. Measurements were taken at repeatable locations on the dentary of the depth of the cortical bone, and of a standardized measure of cortical bone, which allows for the comparison between different individuals. Specimens included those of five different pits ranging from about 37 Kybp to 13 Kybp (just before the extinction of S. fatalis). No significant difference was found in the depth of jaws at any of the measurement points from any of the pits. However, significant differences were found in both the actual thickness of cortical bone, and the standardized thickness of cortical bone at the lower P4 between pit 13 (which had the lowest amount of bone) and pit 61/67 (which had the highest). These conclusions support other studies that have shown that individuals in pit 13 were under physiological and perhaps dietary stress, which may be reflected in the deposition of cortical bone, while the opposite trend is seen in the individuals in pit 61/67. Our results further support findings suggesting Smilodon did not appear to be morphologically most vulnerable right before its extinction.

First records of Canis dirus and Smilodon fatalis from the late Pleistocene Tule Springs local fauna, upper Las Vegas Wash, Nevada

Late Pleistocene groundwater discharge deposits (paleowetlands) in the upper Las Vegas Wash north of Las Vegas, Nevada, have yielded an abundant and diverse vertebrate fossil assemblage, the Tule Springs local fauna (TSLF). The TSLF is the largest open-site vertebrate fossil assemblage dating to the Rancholabrean North American Land Mammal Age in the southern Great Basin and Mojave Desert. Over 600 discrete body fossil localities have been recorded from the wash, including an area that now encompasses Tule Springs Fossil Beds National Monument (TUSK). Paleowetland sediments exposed in TUSK named the Las Vegas Formation span the last 250 ka, with fossiliferous sediments spanning ∼100–13 ka. The recovered fauna is dominated by remains of Camelopsand Mammuthus, and also includes relatively common remains of extinct Equusand Bisonas well as abundant vertebrate microfaunal fossils. Large carnivorans are rare, with only Puma concolor and Panthera atrox documented previously. Postcranial remains assigned to the species Canis dirus (dire wolf) and Smilodon fatalis (sabre-toothed cat) represent the first confirmed records of these species from the TSLF, as well as the first documentation of Canis dirus in Nevada and the only known occurrence of Smilodonin southern Nevada. The size of the recovered canid fossil precludes assignment to other Pleistocene species of Canis. The morphology of the felid elements differentiates them from other large predators such as Panthera, Homotherium, and Xenosmilus, and the size of the fossils prevents assignment to other species of Smilodon. The confirmed presence of S. fatalis in the TSLF is of particular interest, indicating that this species inhabited open habitats. In turn, this suggests that the presumed preference of S. fatalis for closed-habitat environments hunting requires further elucidation.

Extinct Beringian wolf morphotype found in the continental U.S. has implications for wolf migration and evolution

Pleistocene diversity was much higher than today, for example there were three distinct wolf morphotypes (dire, gray, Beringian) in North America versus one today (gray). Previous fossil evidence suggested that these three groups overlapped ecologically, but split the landscape geographically. The Natural Trap Cave (NTC) fossil site in Wyoming, USA is an ideally placed late Pleistocene site to study the geographical movement of species from northern to middle North America before, during, and after the last glacial maximum. Until now, it has been unclear what type of wolf was present at NTC. We analyzed morphometrics of three wolf groups (dire, extant North American gray, Alaskan Beringian) to determine which wolves were present at NTC and what this indicates about wolf diversity and migration in Pleistocene North America. Results show NTC wolves group with Alaskan Beringian wolves. This provides the first morphological evidence for Beringian wolves in mid‐continental North America. Their location at NTC and their radiocarbon ages suggest that they followed a temporary channel through the glaciers. Results suggest high levels of competition and diversity in Pleistocene North American wolves. The presence of mid‐continental Beringian morphotypes adds important data for untangling the history of immigration and evolution of Canis in North America.

The scaling of postcranial muscles in cats (Felidae) I: forelimb, cervical, and thoracic muscles

The body masses of cats (Mammalia, Carnivora, Felidae) span a ~300-fold range from the smallest to largest species. Despite this range, felid musculoskeletal anatomy remains remarkably conservative, including the maintenance of a crouched limb posture at unusually large sizes. The forelimbs in felids are important for body support and other aspects of locomotion, as well as climbing and prey capture, with the assistance of the vertebral (and hindlimb) muscles. Here, we examine the scaling of the anterior postcranial musculature across felids to assess scaling patterns between different species spanning the range of felid body sizes. The muscle architecture (lengths and masses of the muscle-tendon unit components) for the forelimb, cervical and thoracic muscles was quantified to analyse how the muscles scale with body mass. Our results demonstrate that physiological cross-sectional areas of the forelimb muscles scale positively with increasing body mass (i.e. becoming relatively larger). Many significantly allometric variables pertain to shoulder support, whereas the rest of the limb muscles become relatively weaker in larger felid species. However, when phylogenetic relationships were corrected for, most of these significant relationships disappeared, leaving no significantly allometric muscle metrics. The majority of cervical and thoracic muscle metrics are not significantly allometric, despite there being many allometric skeletal elements in these regions. When forelimb muscle data were considered in isolation or in combination with those of the vertebral muscles in principal components analyses and MANOVAs, there was no significant discrimination among species by either size or locomotory mode. Our results support the inference that larger felid species have relatively weaker anterior postcranial musculature compared with smaller species, due to an absence of significant positive allometry of forelimb or vertebral muscle architecture. This difference in strength is consistent with behavioural changes in larger felids, such as a reduction of maximal speed and other aspects of locomotor abilities.

Big cat, small cat: reconstructing body size evolution in living and extinct Felidae

The evolution of body mass is a fundamental topic in evolutionary biology, because it is closely linked to manifold life history and ecological traits and is readily estimable for many extinct taxa. In this study, we examine patterns of body mass evolution in Felidae (Placentalia, Carnivora) to assess the effects of phylogeny, mode of evolution, and the relationship between body mass and prey choice in this charismatic mammalian clade. Our data set includes 39 extant and 26 extinct taxa, with published body mass data supplemented by estimates based on condylobasal length. These data were run through 'SURFACE' and 'bayou' to test for patterns of body mass evolution and convergence between taxa. Body masses of felids are significantly different among prey choice groupings (small, mixed and large). We find that body mass evolution in cats is strongly influenced by phylogeny, but different patterns emerged depending on inclusion of extinct taxa and assumptions about branch lengths. A single Ornstein-Uhlenbeck optimum best explains the distribution of body masses when first-occurrence data were used for the fossil taxa. However, when mean occurrence dates or last known occurrence dates were used, two selective optima for felid body mass were recovered in most analyses: a small optimum around 5 kg and a large one around 100 kg. Across living and extinct cats, we infer repeated evolutionary convergences towards both of these optima, but, likely due to biased extinction of large taxa, our results shift to supporting a Brownian motion model when only extant taxa are included in analyses.

The fossil record of phenotypic integration and modularity: A deep-time perspective on developmental and evolutionary dynamics

Variation is the raw material for natural selection, but the factors shaping variation are still poorly understood. Genetic and developmental interactions can direct variation, but there has been little synthesis of these effects with the extrinsic factors that can shape biodiversity over large scales. The study of phenotypic integration and modularity has the capacity to unify these aspects of evolutionary study by estimating genetic and developmental interactions through the quantitative analysis of morphology, allowing for combined assessment of intrinsic and extrinsic effects. Data from the fossil record in particular are central to our understanding of phenotypic integration and modularity because they provide the only information on deep-time developmental and evolutionary dynamics, including trends in trait relationships and their role in shaping organismal diversity. Here, we demonstrate the important perspective on phenotypic integration provided by the fossil record with a study of Smilodon fatalis (saber-toothed cats) and Canis dirus (dire wolves). We quantified temporal trends in size, variance, phenotypic integration, and direct developmental integration (fluctuating asymmetry) through 27,000 y of Late Pleistocene climate change. Both S. fatalis and C. dirus showed a gradual decrease in magnitude of phenotypic integration and an increase in variance and the correlation between fluctuating asymmetry and overall integration through time, suggesting that developmental integration mediated morphological response to environmental change in the later populations of these species. These results are consistent with experimental studies and represent, to our knowledge, the first deep-time validation of the importance of developmental integration in stabilizing morphological evolution through periods of environmental change.

Ecological changes in Coyotes (Canis latrans) in response to the ice age megafaunal extinctions

Coyotes (Canis latrans) are an important species in human-inhabited areas. They control pests and are the apex predators in many ecosystems. Because of their importance it is imperative to understand how environmental change will affect this species. The end of the Pleistocene Ice Age brought with it many ecological changes for coyotes and here we statistically determine the changes that occurred in coyotes, when these changes occurred, and what the ecological consequences were of these changes. We examined the mandibles of three coyote populations: Pleistocene Rancho La Brean (13-29 Ka), earliest Holocene Rancho La Brean (8-10 Ka), and Recent from North America, using 2D geometric morphometrics to determine the morphological differences among them. Our results show that these three populations were morphologically distinct. The Pleistocene coyotes had an overall robust mandible with an increased shearing arcade and a decreased grinding arcade, adapted for carnivory and killing larger prey; whereas the modern populations show a gracile morphology with a tendency toward omnivory or grinding. The earliest Holocene populations are intermediate in morphology and smallest in size. These findings indicate that a niche shift occurred in coyotes at the Pleistocene/Holocene boundary - from a hunter of large prey to a small prey/more omnivorous animal. Species interactions between Canis were the most likely cause of this transition. This study shows that the Pleistocene extinction event affected species that did not go extinct as well as those that did.