The genomic natural history of the aurochs.

Now extinct, the aurochs (Bos primigenius) was a keystone species in prehistoric Eurasian and North African ecosystems, and the progenitor of cattle (Bos taurus), domesticates that have provided people with food and labour for millennia1. Here we analysed 38 ancient genomes and found 4 distinct population ancestries in the aurochs-European, Southwest Asian, North Asian and South Asian-each of which has dynamic trajectories that have responded to changes in climate and human influence. Similarly to Homo heidelbergensis, aurochsen first entered Europe around 650 thousand years ago2, but early populations left only trace ancestry, with both North Asian and European B. primigenius genomes coalescing during the most recent glaciation. North Asian and European populations then appear separated until mixing after the climate amelioration of the early Holocene. European aurochsen endured the more severe bottleneck during the Last Glacial Maximum, retreating to southern refugia before recolonizing from Iberia. Domestication involved the capture of a small number of individuals from the Southwest Asian aurochs population, followed by early and pervasive male-mediated admixture involving each ancestral strain of aurochs after domestic stocks dispersed beyond their cradle of origin.

The genome of the black-footed cat: Revealing a rich natural history and urgent conservation priorities for small felids.

Habitat degradation and loss of genetic diversity are common threats faced by almost all of today's wild cats. Big cats, such as tigers and lions, are of great concern and have received considerable conservation attention through policies and international actions. However, knowledge of and conservation actions for small wild cats are lagging considerably behind. The black-footed cat, Felis nigripes, one of the smallest felid species, is experiencing increasing threats with a rapid reduction in population size. However, there is a lack of genetic information to assist in developing effective conservation actions. A de novo assembly of a high-quality chromosome-level reference genome of the black-footed cat was made, and comparative genomics and population genomics analyses were carried out. These analyses revealed that the most significant genetic changes in the evolution of the black-footed cat are the rapid evolution of sensory and metabolic-related genes, reflecting genetic adaptations to its characteristic nocturnal hunting and a high metabolic rate. Genomes of the black-footed cat exhibit a high level of inbreeding, especially for signals of recent inbreeding events, which suggest that they may have experienced severe genetic isolation caused by habitat fragmentation. More importantly, inbreeding associated with two deleterious mutated genes may exacerbate the risk of amyloidosis, the dominant disease that causes mortality of about 70% of captive individuals. Our research provides comprehensive documentation of the evolutionary history of the black-footed cat and suggests that there is an urgent need to investigate genomic variations of small felids worldwide to support effective conservation actions.

Complex Evolutionary History With Extensive Ancestral Gene Flow in an African Primate Radiation.

Understanding the drivers of speciation is fundamental in evolutionary biology, and recent studies highlight hybridization as an important evolutionary force. Using whole-genome sequencing data from 22 species of guenons (tribe Cercopithecini), one of the world's largest primate radiations, we show that rampant gene flow characterizes their evolutionary history and identify ancient hybridization across deeply divergent lineages that differ in ecology, morphology, and karyotypes. Some hybridization events resulted in mitochondrial introgression between distant lineages, likely facilitated by cointrogression of coadapted nuclear variants. Although the genomic landscapes of introgression were largely lineage specific, we found that genes with immune functions were overrepresented in introgressing regions, in line with adaptive introgression, whereas genes involved in pigmentation and morphology may contribute to reproductive isolation. In line with reports from other systems that hybridization might facilitate diversification, we find that some of the most species-rich guenon clades are of admixed origin. This study provides important insights into the prevalence, role, and outcomes of ancestral hybridization in a large mammalian radiation.

Describing the musculature of mystacial pads in harbour seals (Phoca vitulina) using diceCT.

Pinnipeds have long, sensitive, moveable mystacial vibrissae. In other mammals, intrinsic muscles contribute to protracting the vibrissae. However, the mystacial muscles of pinnipeds have not yet been systematically described. Using traditional histological methods provides us with two-dimensional muscle images, but having the ability to visualise these structures in three dimensions would allow for a more comprehensive understanding of pinniped vibrissal anatomy, especially given the challenges posed by their large and extremely curved mystacial pad. We predicted that harbour seals would have large, regular intrinsic muscles due to their well-organised, moveable vibrissae. We adopted diffusible iodine contrast-enhanced computer tomography (diceCT) to describe, for the first time, the three-dimensional architecture of the mystacial vibrissal muscles found in harbour seals. Our observations show that their vibrissae are organised into grids within the mystacial pad. We identified both sling-shaped and oblique intrinsic muscles that connect one vibrissae to the next in the same row. We also identified extrinsic muscles, including the m. nasolabialis, m. maxillolabialis, m. levator nasolabialis and m. orbicularis oris. Contrary to our prediction, the intrinsic muscles were not very large, although they were regularly distributed throughout the pad. Rather, the extrinsic muscles, particularly the m. nasolabialis and m. maxillolabialis were large, deep and well-defined, running throughout the length of the mystacial pad. Therefore, we suggest that these extrinsic muscles, the m. nasolabialis and m. maxillolabialis, are responsible for driving vibrissal protraction underwater. These findings demonstrate the importance of three-dimensional visualisation techniques in advancing our understanding of mystacial anatomy and function in pinnipeds.

Rapid evolution of the primate larynx?

Tissue vibrations in the larynx produce most sounds that comprise vocal communication in mammals. Larynx morphology is thus predicted to be a key target for selection, particularly in species with highly developed vocal communication systems. Here, we present a novel database of digitally modeled scanned larynges from 55 different mammalian species, representing a wide range of body sizes in the primate and carnivoran orders. Using phylogenetic comparative methods, we demonstrate that the primate larynx has evolved more rapidly than the carnivoran larynx, resulting in a pattern of larger size and increased deviation from expected allometry with body size. These results imply fundamental differences between primates and carnivorans in the balance of selective forces that constrain larynx size and highlight an evolutionary flexibility in primates that may help explain why we have developed complex and diverse uses of the vocal organ for communication.

Abnormal (Hydroxy)proline Deuterium Content Redefines Hydrogen Chemical Mass.

Analyzing the δ2H values in individual amino acids of proteins extracted from vertebrates, we unexpectedly found in some samples, notably bone collagen from seals, more than twice as much deuterium in proline and hydroxyproline residues than in seawater. This corresponds to at least 4 times higher δ2H than in any previously reported biogenic sample. We ruled out diet as a plausible mechanism for such anomalous enrichment. This finding puts into question the old adage that "you are what you eat".

On the use of genome-wide data to model and date the time of anthropogenic hybridisation: An example from the Scottish wildcat.

While hybridisation has long been recognised as an important natural phenomenon in evolution, the conservation of taxa subject to introgressive hybridisation from domesticated forms is a subject of intense debate. Hybridisation of Scottish wildcats and domestic cats is a good example in this regard. Here, we developed a modelling framework to determine the timescale of introgression using approximate Bayesian computation (ABC). Applying the model to ddRAD-seq data from 129 individuals, genotyped at 6546 loci, we show that a population of wildcats genetically distant from domestic cats is still present in Scotland. These individuals were found almost exclusively within the captive breeding programme. Most wild-living cats sampled were introgressed to some extent. The demographic model predicts high levels of gene-flow between domestic cats and Scottish wildcats (13% migrants per generation) over a short timeframe, the posterior mean for the onset of hybridisation (T1 ) was 3.3 generations (~10 years) before present. Although the model had limited power to detect signals of ancient admixture, we found evidence that significant recent hybridisation may have occurred subsequent to the founding of the captive breeding population (T2 ). The model consistently predicts T1 after T2 , estimated here to be 19.3 generations (~60 years) ago, highlighting the importance of this population as a resource for conservation management. Additionally, we evaluate the effectiveness of current methods to classify hybrids. We show that an optimised 35 SNP panel is a better predictor of the ddRAD-based hybrid score in comparison with a morphological method.

Variation in predicted COVID-19 risk among lemurs and lorises.

The novel coronavirus SARS-CoV-2, which in humans leads to the disease COVID-19, has caused global disruption and more than 2 million fatalities since it first emerged in late 2019. As we write, infection rates are at their highest point globally and are rising extremely rapidly in some areas due to more infectious variants. The primary target of SARS-CoV-2 is the cellular receptor angiotensin-converting enzyme-2 (ACE2). Recent sequence analyses of the ACE2 gene predict that many nonhuman primates are also likely to be highly susceptible to infection. However, the anticipated risk is not equal across the Order. Furthermore, some taxonomic groups show high ACE2 amino acid conservation, while others exhibit high variability at this locus. As an example of the latter, analyses of strepsirrhine primate ACE2 sequences to date indicate large variation among lemurs and lorises compared to other primate clades despite low sampling effort. Here, we report ACE2 gene and protein sequences for 71 individual strepsirrhines, spanning 51 species and 19 genera. Our study reinforces previous results while finding additional variability in other strepsirrhine species, and suggests several clades of lemurs have high potential susceptibility to SARS-CoV-2 infection. Troublingly, some species, including the rare and endangered aye-aye (Daubentonia madagascariensis), as well as those in the genera Avahi and Propithecus, may be at high risk. Given that lemurs are endemic to Madagascar and among the primates at highest risk of extinction globally, further understanding of the potential threat of COVID-19 to their health should be a conservation priority. All feasible actions should be taken to limit their exposure to SARS-CoV-2.

IMPROVED DIAGNOSIS OF FOOT OSTEOARTHRITIS IN ELEPHANTS (ELEPHAS MAXIMUS, LOXODONTA AFRICANA) USING STEREORADIOGRAPHY.

Diagnosis of foot disease in elephants is challenging. Owing to their large size, the available diagnostic tools and the expense of imaging are diagnostically limiting. Stereoradiography is the preparation of paired radiographs that form a three-dimensional (3D) image when viewed stereoscopically. Clinicians and veterinary students graded osteoarthritis in the feet of African (Loxodonta africana) and Asian (Elephas maximus) elephants taken postmortem with standard 2D radiographs, as well as 3D stereoradiographs. These gradings were compared with the actual gross pathology identified in the specimens. Although veterinary students diagnoses were no better than chance from 2D radiographs, 83.6% of the students could correctly differentiate severity between joints on stereoradiography; this is an absolute improvement of 30.1% (95% confidence interval [CI] = 19.6%-40.6%). Overall, participants were 27.4% (95% CI = 18.4%-36.3%) more successful at diagnosing pathology on stereoradiographs. Half of participants were shown standard 2D radiographs first, the others stereoradiographs first, but the difference in gradings between the two groups was not statistically significant. Stereoradiography appears to hold the potential to improve diagnosis of osteoarthritis in elephant feet, particularly by less experienced clinicians, and the technique is low-cost and applicable under field conditions.

A mitochondrial genetic divergence proxy predicts the reproductive compatibility of mammalian hybrids.

Numerous pairs of evolutionarily divergent mammalian species have been shown to produce hybrid offspring. In some cases, F1 hybrids are able to produce F2s through matings with F1s. In other instances, the hybrids are only able to produce offspring themselves through backcrosses with a parent species owing to unisexual sterility (Haldane's Rule). Here, we explicitly tested whether genetic distance, computed from mitochondrial and nuclear genes, can be used as a proxy to predict the relative fertility of the hybrid offspring resulting from matings between species of terrestrial mammals. We assessed the proxy's predictive power using a well-characterized felid hybrid system, and applied it to modern and ancient hominins. Our results revealed a small overlap in mitochondrial genetic distance values that distinguish species pairs whose calculated distances fall within two categories: those whose hybrid offspring follow Haldane's Rule, and those whose hybrid F1 offspring can produce F2s. The strong correlation between genetic distance and hybrid fertility demonstrated here suggests that this proxy can be employed to predict whether the hybrid offspring of two mammalian species will follow Haldane's Rule.

DIFFUSE IDIOPATHIC SKELETAL HYPEROSTOSIS IN CAPTIVE GORILLAS (GORILLA SPP.): APPEARANCES AND DIAGNOSIS.

Diffuse idiopathic skeletal hyperostosis (DISH) is a disorder of unknown cause, in which new bone forms in soft tissues attached to the skeleton. Originally described in humans, in whom it is quite common, it is usually asymptomatic. New bone may completely bridge across joints, especially in the spine. However, it can be difficult to distinguish from diseases such as spondyloarthritis and spondylosis. With safer and increased use of radiography in diagnosis, the unfamiliar skeletal changes of asymptomatic DISH may now be coincidentally revealed during investigation of other disorders and result in misdiagnosis and unnecessary treatment. There have been case reports of its occurrence in great apes, but this is the first study to illustrate its appearances in a series of 11 skeletons of western and eastern lowland gorillas (Gorilla gorilla gorilla and Gorilla beringei graueri) from zoos in Europe and the United States. The study combines a review of available clinical and postmortem records with examination of the skeletons and radiologic investigation, such as computed tomography (CT). The results indicate that the disorder is probably common in older (>30 yr) captive gorillas, but that it is asymptomatic. It was not symptomatic during life in any of these animals. Several cases had unexpected features, such as extensive involvement of the thorax and extra-articular sacroiliac and tibiofibular joint fusions that are not typical in humans. By illustrating these skeletons, the study should aid differentiation of DISH from spondylosis (syn spondylosis deformans) and spondyloarhritis. It illustrates those features that are atypical of human DISH. CT scanning is valuable in such cases for examining diagnostically important areas such as sacroiliac joints. Increased awareness of DISH should help with understanding its cause, both in gorillas and humans.

Gross intestinal morphometry and allometry in primates.

Although it is generally assumed that among mammals and within mammal groups, those species that rely on diets consisting of greater amounts of plant fiber have larger gastrointestinal tracts (GIT), statistical evidence for this simple claim is largely lacking. We compiled a dataset on the length of the small intestine, caecum, and colon in 42 strepsirrhine, platyrrhine, and catarrhine primate species, using specimens with known body mass (BM). We tested the scaling of intestine length with BM, and whether dietary proxies (percentage of leaves and a diet quality index) were significant covariates in these scaling relationships, using two sets of models: one that did not account for the phylogenetic structure of the data, and one that did. Intestine length mainly scaled geometrically at exponents that included 0.33 in the confidence interval; Strepsirrhini exhibited particularly long caeca, while those of Catarrhini were comparatively short. Diet proxies were only significant for the colon and the total large intestine (but not for the small intestine or the caecum), and only in conventional statistics (but not when accounting for phylogeny), indicating the pattern occurred across but not within clades. Compared to terrestrial Carnivora, primates have similar small intestine lengths, but longer large intestines. The data on intestine lengths presented here corroborate recent results on GIT complexity, suggesting that diet, as currently described, does not exhaustively explain GIT anatomy within primate clades.

Testing hypotheses for the function of the carnivoran baculum using finite-element analysis.

The baculum (os penis) is a mineralized bone within the glans of the mammalian penis and is one of the most morphologically diverse structures in the mammal skeleton. Recent experimental work provides compelling evidence for sexual selection shaping the baculum, yet the functional mechanism by which this occurs remains unknown. Previous studies have tested biomechanical hypotheses for the role of the baculum based on simple metrics such as length and diameter, ignoring the wealth of additional shape complexity present. For the first time, to our knowledge, we apply a computational simulation approach (finite-element analysis; FEA) to quantify the three-dimensional biomechanical performance of carnivoran bacula (n = 74) based upon high-resolution micro-computed tomography scans. We find a marginally significant positive correlation between sexual size dimorphism and baculum stress under compressive loading, counter to the 'vaginal friction' hypothesis of bacula becoming more robust to overcome resistance during initial intromission. However, a highly significant negative relationship exists between intromission duration and baculum stress under dorsoventral bending. Furthermore, additional FEA simulations confirm that the presence of a ventral groove would reduce deformation of the urethra. We take this as evidence in support of the 'prolonged intromission' hypothesis, suggesting the carnivoran baculum has evolved in response to pressures on the duration of copulation and protection of the urethra.

Synchronous diversification of Sulawesi's iconic artiodactyls driven by recent geological events.

The high degree of endemism on Sulawesi has previously been suggested to have vicariant origins, dating back to 40 Ma. Recent studies, however, suggest that much of Sulawesi's fauna assembled over the last 15 Myr. Here, we test the hypothesis that more recent uplift of previously submerged portions of land on Sulawesi promoted diversification and that much of its faunal assemblage is much younger than the island itself. To do so, we combined palaeogeographical reconstructions with genetic and morphometric datasets derived from Sulawesi's three largest mammals: the babirusa, anoa and Sulawesi warty pig. Our results indicate that although these species most likely colonized the area that is now Sulawesi at different times (14 Ma to 2-3 Ma), they experienced an almost synchronous expansion from the central part of the island. Geological reconstructions indicate that this area was above sea level for most of the last 4 Myr, unlike most parts of the island. We conclude that emergence of land on Sulawesi (approx. 1-2 Myr) may have allowed species to expand synchronously. Altogether, our results indicate that the establishment of the highly endemic faunal assemblage on Sulawesi was driven by geological events over the last few million years.

A fossil protein chimera; difficulties in discriminating dinosaur peptide sequences from modern cross-contamination.

A decade ago, reports that organic-rich soft tissue survived from dinosaur fossils were apparently supported by proteomics-derived sequence information of exceptionally well-preserved bone. This initial claim to the sequencing of endogenous collagen peptides from an approximately 68 Myr Tyrannosaurus rex fossil was highly controversial, largely on the grounds of potential contamination from either bacterial biofilms or from laboratory practice. In a subsequent study, collagen peptide sequences from an approximately 78 Myr Brachylophosaurus canadensis fossil were reported that have remained largely unchallenged. However, the endogeneity of these sequences relies heavily on a single peptide sequence, apparently unique to both dinosaurs. Given the potential for cross-contamination from modern bone analysed by the same team, here we extract collagen from bone samples of three individuals of ostrich, Struthio camelus The resulting LC-MS/MS data were found to match all of the proposed sequences for both the original Tyrannosaurus and Brachylophosaurus studies. Regardless of the true nature of the dinosaur peptides, our finding highlights the difficulty of differentiating such sequences with confidence. Our results not only imply that cross-contamination cannot be ruled out, but that appropriate measures to test for endogeneity should be further evaluated.

LAPAROSCOPIC-ASSISTED INSERTION OF A VENTRICULOPERITONEAL SHUNT IN A RESCUED ASIATIC BLACK BEAR (URSUS THIBETANUS) IN LAOS.

A 3-yr-old Asiatic black bear (Ursus thibetanus), weighing 68 kg, underwent a laparoscopic-assisted placement of a ventriculoperitoneal shunt for hydrocephalus in the Lao People's Democratic Republic. Rescued as a young cub with a notably domed head, the bear's condition had deteriorated with age, but euthanasia was not a viable option because of cultural issues. Surgery was attempted as a palliative measure. The bear had ventrally orientated crossed eyes (abducens nerve palsy and dorsal midbrain syndrome), papilledema, severe rhinorrhea, depressed mentation, lethargy, a very poor appetite, and was stunted. Hydrocephalus was confirmed via intraoperative 2.0-5.0 MHz head ultrasound, as no magnetic resonance imaging was available in the country. Surgery was planned via 3D modeling of museum skulls and brain cavity, and ultrasound examination of formalin-preserved brains of other carnivores with hydrocephalus. The bear demonstrated a notable improvement in mentation, appetite, and behavior, maintained for 4 yr following surgery.

The scaling of postcranial muscles in cats (Felidae) II: hindlimb and lumbosacral muscles.

In quadrupeds the musculature of the hindlimbs is expected to be responsible for generating most of the propulsive locomotory forces, as well as contributing to body support by generating vertical forces. In supporting the body, postural changes from crouched to upright limbs are often associated with an increase of body mass in terrestrial tetrapods. However, felids do not change their crouched limb posture despite undergoing a 300-fold size increase between the smallest and largest extant species. Here, we test how changes in the muscle architecture (masses and lengths of components of the muscle-tendon units) of the hindlimbs and lumbosacral region are related to body mass, to assess whether there are muscular compensations for the maintenance of a crouched limb posture at larger body sizes. We use regression and principal component analyses to detect allometries in muscle architecture, with and without phylogenetic correction. Of the muscle lengths that scale allometrically, all scale with negative allometry (i.e. relative shortening with increasing body mass), whereas all tendon lengths scale isometrically. Only two muscles' belly masses and two tendons' masses scale with positive allometry (i.e. relatively more massive with increasing body mass). Of the muscles that scale allometrically for physiological cross-sectional area, all scale positively (i.e. relatively greater area with increasing body mass). These muscles are mostly linked to control of hip and thigh movements. When the architecture data are phylogenetically corrected, there are few significant results, and only the strongest signals remain. None of the vertebral muscles scaled significantly differently from isometry. Principal component analysis and manovas showed that neither body size nor locomotor mode separate the felid species in morphospace. Our results support the inference that, despite some positively allometric trends in muscle areas related to thigh movement, larger cats have relatively weaker hindlimb and lumbosacral muscles in general. This decrease in power may be reflected in relative decreases in running speeds and is consistent with prevailing evidence that behavioural changes may be the primary mode of compensation for a consistently crouched limb posture in larger cats.

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.

A Computed Tomographic Study of the Molar Teeth of Babyrousa spp.

A photographic and computed tomography (CT) scanning study was carried out on 295 molar teeth of 18 adult male Babyrousa babyrussa skulls and 8 skulls of Babyrousa celebensis including seven adult males and one adult female. The occlusal morphology of the permanent maxillary and mandibular molar teeth of B. babyrussa was very similar to that of B. celebensis. Most B. babyrussa maxillary molar teeth had six roots, with small numbers of teeth having four, five or seven roots. A similar pattern was suggested in B. celebensis. Mandibular molar teeth had between four and eight roots. Tooth roots of maxillary and mandibular first and second molar teeth were largely tapering, rod-like structures. The roots of the right and left maxillary third molar teeth had a more complex arrangement; some were inserted almost vertically into the maxilla; others were orientated in a more distal direction. The mesial and distal roots were splayed in appearance. The right and left mandibular third molar tooth roots retained elements of the open 'C' shape and were generally orientated distally. The pulp chambers were arched to fit under the main cusps in all molar teeth. Pulp canals were variable in number.

Skull morphology analysis suggests the extinct Cape lion, Panthera leo melanochaita (Smith, 1842), is not distinctive.

The lion (Panthera leo) was extirpated from the Cape region of South Africa during the mid-nineteenth century. Whilst historically classified as a distinct subspecies known as the Cape lion (P. l. melanochaita), recent molecular studies challenge the distinctiveness of this population, suggesting that it represents the southernmost population of the species' Southern Clade. The Cape lion is often cited as having a distinctive skull morphology, which has justified its subspecific classification, but only a limited number of specimens have been available for examination, so that the Cape lion's skull morphology has not been satisfactorily understood. In this study we collected morphometric data from a greatly enlarged sample of 22 Cape lion skulls, including 12 adults, constituting the largest sample size analysed for this possible subspecies. The results suggest that (1) morphological characteristics of the skull previously thought to distinguish the Cape lion are not diagnostic, and (2) nor is the skull morphology of male and female Cape lions distinct from that of males and females of other southern African lions. Our results independently support those based on molecular investigations, which suggest that the Cape lion was not distinct from other lions within the Southern Clade.