Mitogenomic analysis of a late Pleistocene jaguar from North America.

The jaguar (Panthera onca) is the largest living cat species native to the Americas and one of few large American carnivorans to have survived into the Holocene. However, the extent to which jaguar diversity declined during the end-Pleistocene extinction event remains unclear. For example, Pleistocene jaguar fossils from North America are notably larger than the average extant jaguar, leading to hypotheses that jaguars from this continent represent a now-extinct subspecies (Panthera onca augusta) or species (Panthera augusta). Here, we used a hybridization capture approach to recover an ancient mitochondrial genome from a large, late Pleistocene jaguar from Kingston Saltpeter Cave, Georgia, United States, which we sequenced to 26-fold coverage. We then estimated the evolutionary relationship between the ancient jaguar mitogenome and those from other extinct and living large felids, including multiple jaguars sampled across the species' current range. The ancient mitogenome falls within the diversity of living jaguars. All sampled jaguar mitogenomes share a common mitochondrial ancestor ~400 thousand years ago, indicating that the lineage represented by the ancient specimen dispersed into North America from the south at least once during the late Pleistocene. While genomic data from additional and older specimens will continue to improve understanding of Pleistocene jaguar diversity in the Americas, our results suggest that this specimen falls within the variation of extant jaguars despite the relatively larger size and geographic location and does not represent a distinct taxon.

Dire wolves were the last of an ancient New World canid lineage.

Dire wolves are considered to be one of the most common and widespread large carnivores in Pleistocene America1, yet relatively little is known about their evolution or extinction. Here, to reconstruct the evolutionary history of dire wolves, we sequenced five genomes from sub-fossil remains dating from 13,000 to more than 50,000 years ago. Our results indicate that although they were similar morphologically to the extant grey wolf, dire wolves were a highly divergent lineage that split from living canids around 5.7 million years ago. In contrast to numerous examples of hybridization across Canidae2,3, there is no evidence for gene flow between dire wolves and either North American grey wolves or coyotes. This suggests that dire wolves evolved in isolation from the Pleistocene ancestors of these species. Our results also support an early New World origin of dire wolves, while the ancestors of grey wolves, coyotes and dholes evolved in Eurasia and colonized North America only relatively recently.

American mastodon mitochondrial genomes suggest multiple dispersal events in response to Pleistocene climate oscillations.

Pleistocene glacial-interglacial cycles are correlated with dramatic temperature oscillations. Examining how species responded to these natural fluctuations can provide valuable insights into the impacts of present-day anthropogenic climate change. Here we present a phylogeographic study of the extinct American mastodon (Mammut americanum), based on 35 complete mitochondrial genomes. These data reveal the presence of multiple lineages within this species, including two distinct clades from eastern Beringia. Our molecular date estimates suggest that these clades arose at different times, supporting a pattern of repeated northern expansion and local extirpation in response to glacial cycling. Consistent with this hypothesis, we also note lower levels of genetic diversity among northern mastodons than in endemic clades south of the continental ice sheets. The results of our study highlight the complex relationships between population dispersals and climate change, and can provide testable hypotheses for extant species expected to experience substantial biogeographic impacts from rising temperatures.

Clarifying relationships between cranial form and function in tapirs, with implications for the dietary ecology of early hominins.

Paleontologists and paleoanthropologists have long debated relationships between cranial morphology and diet in a broad diversity of organisms. While the presence of larger temporalis muscle attachment area (via the presence of sagittal crests) in carnivorans is correlated with durophagy (i.e. hard-object feeding), many primates with similar morphologies consume an array of tough and hard foods-complicating dietary inferences of early hominins. We posit that tapirs, large herbivorous mammals showing variable sagittal crest development across species, are ideal models for examining correlations between textural properties of food and sagittal crest morphology. Here, we integrate dietary data, dental microwear texture analysis, and finite element analysis to clarify the functional significance of the sagittal crest in tapirs. Most notably, pronounced sagittal crests are negatively correlated with hard-object feeding in extant, and several extinct, tapirs and can actually increase stress and strain energy. Collectively, these data suggest that musculature associated with pronounced sagittal crests-and accompanied increases in muscle volume-assists with the processing of tough food items in tapirs and may yield similar benefits in other mammals including early hominins.

Seasonal denning behavior and population dynamics of the late Pleistocene peccary Platygonus compressus (Artiodactyla: Tayassuidae) from Bat Cave, Missouri.

The late Pleistocene faunal assemblage from Bat Cave, central Ozarks, Missouri provides an opportunity to assess specific aspects of behavior, ecology, and ontogeny of the Rancholabrean species Platygonus compressus. All identifiable elements referable to this taxon were catalogued and examined, and a minimum number of individuals of 73 was determined for the sample. Evidence of seasonal behavioral patterns are reported for the first time in a fossil peccary. Maturation of individuals was assessed using the tooth eruption sequence and occlusal wear patterns for all tooth-bearing mandibular elements and isolated lower dentition. Approximate ages were established through comparison with the extant collared peccary. The presence of distinct, developmentally non-overlapping age groups suggests that P. compressus was seasonally present at the Bat Cave locality, with the cave functioning as seasonal shelter in which individuals would occasionally die. The study also suggests the peccaries engaged in synchronous, seasonal breeding behaviors. Demographic assessment of the Bat Cave peccary population suggests that younger individuals formed the bulk of the population at a given time with progressively older individuals becoming scarcer until the age of about 10 years, which matches the typical demographic patterns and life expectancy of extant peccaries.

Yucatán carnivorans shed light on the Great American Biotic Interchange.

The Great American Biotic Interchange is considered to be a punctuated process, primarily occurring during four major pulses that began approximately 2.5 Ma. Central America and southeastern Mexico have a poor fossil record of this dynamic faunal history due to tropical climates. Exploration of submerged caves in the Yucatán, particularly the natural trap Hoyo Negro, is exposing a rich and remarkably well-preserved late Pleistocene fauna. Radiometric dates on megafauna range from approximately 38 400-12 850 cal BP, and extinct species include the ursid Arctotherium wingei and canid Protocyon troglodytes. Both genera were previously thought to be indigenous to and confined to South America and appear to represent an instance of large placental mammals, descended from North American progenitors, migrating back north across the Panama Isthmus. This discovery expands the distribution of these carnivorans greater than 2000 km outside South America. Their presence along with a diverse sloth assemblage suggests a more complex history of these organisms in Middle America. We suggest that landscape and ecological changes caused by latest Pleistocene glaciation supported an interchange pulse that included A. wingei, P. troglodytes and Homo sapiens.

First occurrence of the enigmatic peccaries Mylohyus elmorei and Prosthennops serus from the Appalachians: latest Hemphillian to Early Blancan of Gray Fossil Site, Tennessee.

Two peccary species, Mylohyus elmorei and Prosthennops serus are described from the medium-bodied fauna of the Gray Fossil Site (GFS) of northeastern Tennessee. This site, recognized as an oak-hickory forest, is latest Hemphillian or earliest Blancan based on mammalian biochronology, with an estimated age of 4.9-4.5 Ma. The GFS represents the only site outside the Palmetto Fauna of Florida with M. elmorei, greatly expanding the species range north over 920 km, well into the Appalachian region. This is also the first Appalachian occurrence of the relatively widespread P. serus. Our understanding of intraspecific variation for both M. elmorei and P. serus is expanded due to morphological and proportional differences found in cranial and dental material from the GFS, Tyner Farm locality, Palmetto Fauna, and within the literature. The GFS M. elmorei material represents the most complete mandible and second cranium for the species, and preserve intraspecific variation in the length of the diastema, dental proportions, and the complexity of the cuspules of the hypoconulid complex. Similarly, mandibular material from the GFS for P. serus exhibited larger dentitions and a greater degree of robustness than currently recognized for the species.

Dental caries in the fossil record: a window to the evolution of dietary plasticity in an extinct bear.

During the late Pleistocene of North America (≈36,000 to 10,000 years ago), saber-toothed cats, American lions, dire wolves, and coyotes competed for prey resources at Rancho La Brea (RLB). Despite the fact that the giant short-faced bear (Arctodus simus) was the largest land carnivoran present in the fauna, there is no evidence that it competed with these other carnivores for prey at the site. Here, for the first time, we report carious lesions preserved in specimens of A. simus, recovered from RLB. Our results suggest that the population of A. simus from RLB was more omnivorous than the highly carnivorous populations from the Northwest. This dietary variation may be a consequence of different competitive pressures.

Anatomical study of the auditory region of Arctotherium tarijense (Ursidae, Tremarctinae), an extinct short-faced bear from the Pleistocene of South America.

Here we present the most detailed morphological study of the auditory region of a tremarctinae bear, Arctotherium tarijense Ameghino. In addition, we provide new anatomical information of the Tremarctinae inner ear, such as coplanarity and deviation from orthogonality of the semicircular canals, as an approach to infer the head movements which encountered the extinct forms in locomotion. Based on morphological comparisons, A. tarijense exhibits the following particular features: the cavum tympani presents the highest relative volume compared with other ursids; the processus paraoccipitalis has a foramen that is absent in other tremarctines; there is only one (ventral) recess in the anterior region of the cavum tympani; and the recessus epytimpanicus is the smallest for all ursids studied. In relation to the inner ear, A. tarijense shows the lowest values of orthogonality deviation and highest scores of locomotor agility. Based on this, is possible to make a preliminary proposal that this species had a relative high vestibular sensibility and therefore a better ability to explore different kind of habitats. However, this hypothesis might be contrasted among bears taking into account the orientation of each semicircular canal in a phylogenetic framework.

Ancient mitochondrial DNA reveals convergent evolution of giant short-faced bears (Tremarctinae) in North and South America.

The Tremarctinae are a subfamily of bears endemic to the New World, including two of the largest terrestrial mammalian carnivores that have ever lived: the giant, short-faced bears Arctodus simus from North America and Arctotherium angustidens from South America (greater than or equal to 1000 kg). Arctotherium angustidens became extinct during the Early Pleistocene, whereas Arctodus simus went extinct at the very end of the Pleistocene. The only living tremarctine is the spectacled bear (Tremarctos ornatus), a largely herbivorous bear that is today only found in South America. The relationships among the spectacled bears (Tremarctos), South American short-faced bears (Arctotherium) and North American short-faced bears (Arctodus) remain uncertain. In this study, we sequenced a mitochondrial genome from an Arctotherium femur preserved in a Chilean cave. Our molecular phylogenetic analyses revealed that the South American short-faced bears were more closely related to the extant South American spectacled bear than to the North American short-faced bears. This result suggests striking convergent evolution of giant forms in the two groups of short-faced bears (Arctodus and Arctotherium), potentially as an adaptation to dominate competition for megafaunal carcasses.

Was the giant short-faced bear a hyper-scavenger? A new approach to the dietary study of ursids using dental microwear textures.

Dramatic environmental changes associated with global cooling since the late Miocene, and the onset of glacial-interglacial cycles in the Pleistocene served as a backdrop to the evolutionary radiation of modern bears (family Ursidae). These environmental changes likely prompted changes in food availability, and triggered dietary adaptations that served as motive forces in ursid evolution. Here, we assess correspondence of dental microwear textures of first and second lower molars with diet in extant ursids. We use the resulting baseline data to evaluate the hypothesis that the Pleistocene giant short-faced bear, Arctodus simus, was a bone consumer and hyper-scavenger at Rancho La Brea, California, USA. Significant variation along the tooth row is consistent with functional differentiation, with the second molar serving as a better dietary recorder than the first. Results evince significant variation among species: carnivorous and omnivorous ursids (Ursus maritimus, U. americanus) have significantly higher and more variable complexity (Asfc) than more herbivorous ones (Ailuropoda melanoleuca, Tremarctos ornatus, U. malayanus), and A. melanoleuca is differentiated from U. maritimus and U. americanus by significantly higher and more variable anisotropy (epLsar) values. Arctodus simus from Rancho La Brea exhibits wear attributes most comparable to its closest living relative (T. ornatus), which is inconsistent with hard-object (e.g., bone) consumption, and the hypothesis that short-faced bears were bone consuming hyper-scavengers across their range.

Direct comparisons of 2D and 3D dental microwear proxies in extant herbivorous and carnivorous mammals.

The analysis of dental microwear is commonly used by paleontologists and anthropologists to clarify the diets of extinct species, including herbivorous and carnivorous mammals. Currently, there are numerous methods employed to quantify dental microwear, varying in the types of microscopes used, magnifications, and the characterization of wear in both two dimensions and three dimensions. Results from dental microwear studies utilizing different methods are not directly comparable and human quantification of wear features (e.g., pits and scratches) introduces interobserver error, with higher error being produced by less experienced individuals. Dental microwear texture analysis (DMTA), which analyzes microwear features in three dimensions, alleviates some of the problems surrounding two-dimensional microwear methods by reducing observer bias. Here, we assess the accuracy and comparability within and between 2D and 3D dental microwear analyses in herbivorous and carnivorous mammals at the same magnification. Specifically, we compare observer-generated 2D microwear data from photosimulations of the identical scanned areas of DMTA in extant African bovids and carnivorans using a scanning white light confocal microscope at 100x magnification. Using this magnification, dental microwear features quantified in 2D were able to separate grazing and frugivorous bovids using scratch frequency; however, DMTA variables were better able to discriminate between disparate dietary niches in both carnivorous and herbivorous mammals. Further, results demonstrate significant interobserver differences in 2D microwear data, with the microwear index remaining the least variable between experienced observers, consistent with prior research. Overall, our results highlight the importance of reducing observer error and analyzing dental microwear in three dimensions in order to consistently interpret diets accurately.

Implications of diet for the extinction of saber-toothed cats and American lions.

The saber-toothed cat, Smilodon fatalis, and American lion, Panthera atrox, were among the largest terrestrial carnivores that lived during the Pleistocene, going extinct along with other megafauna ∼12,000 years ago. Previous work suggests that times were difficult at La Brea (California) during the late Pleistocene, as nearly all carnivores have greater incidences of tooth breakage (used to infer greater carcass utilization) compared to today. As Dental Microwear Texture Analysis (DMTA) can differentiate between levels of bone consumption in extant carnivores, we use DMTA to clarify the dietary niches of extinct carnivorans from La Brea. Specifically, we test the hypothesis that times were tough at La Brea with carnivorous taxa utilizing more of the carcasses. Our results show no evidence of bone crushing by P. atrox, with DMTA attributes most similar to the extant cheetah, Acinonyx jubatus, which actively avoids bone. In contrast, S. fatalis has DMTA attributes most similar to the African lion Panthera leo, implying that S. fatalis did not avoid bone to the extent previously suggested by SEM microwear data. DMTA characters most indicative of bone consumption (i.e., complexity and textural fill volume) suggest that carcass utilization by the extinct carnivorans was not necessarily more complete during the Pleistocene at La Brea; thus, times may not have been "tougher" than the present. Additionally, minor to no significant differences in DMTA attributes from older (∼30-35 Ka) to younger (∼11.5 Ka) deposits offer little evidence that declining prey resources were a primary cause of extinction for these large cats.

Extinction implications of a chenopod browse diet for a giant Pleistocene kangaroo.

Kangaroos are the world's most diverse group of herbivorous marsupials. Following late-Miocene intensification of aridity and seasonality, they radiated across Australia, becoming the continent's ecological equivalents of the artiodactyl ungulates elsewhere. Their diversity peaked during the Pleistocene, but by approximately 45,000 years ago, 90% of larger kangaroos were extinct, along with a range of other giant species. Resolving whether climate change or human arrival was the principal extinction cause remains highly contentious. Here we combine craniodental morphology, stable-isotopic, and dental microwear data to reveal that the largest-ever kangaroo, Procoptodon goliah, was a chenopod browse specialist, which may have had a preference for Atriplex (saltbushes), one of a few dicots using the C(4) photosynthetic pathway. Furthermore, oxygen isotope signatures of P. goliah tooth enamel show that it drank more in low-rainfall areas than its grazing contemporaries, similar to modern saltbush feeders. Saltbushes and chenopod shrublands in general are poorly flammable, so landscape burning by humans is unlikely to have caused a reduction in fodder driving the species to extinction. Aridity is discounted as a primary cause because P. goliah evolved in response to increased aridity and disappeared during an interval wetter than many it survived earlier. Hunting by humans, who were also bound to water, may have been a more decisive factor in the extinction of this giant marsupial.