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.

Sub-zero temperatures and large-scale weather patterns induce tooth damage in Icelandic arctic foxes.

Tooth damage in carnivores can reflect shifts in both diet and feeding habits, and in large carnivores, it is associated with increased bone consumption. Variation in tooth condition in Icelandic arctic foxes, a mesocarnivore, was recorded from 854 individual foxes spanning 29 years. We hypothesized that annual climatic variations, which can influence food abundance and accessibility, will influence tooth condition by causing dietary shifts toward less edible prey. We examined tooth condition in relation to four climatic predictors: mean annual winter temperature, indices of both the El Niño anomaly and North Atlantic subpolar gyre (SPG), and the number of rain-on-snow days (ROS). We found unequivocal evidence for a strong effect of annual climate on tooth condition. Teeth of Icelandic foxes were in better condition when winter temperatures were higher, when the SPG was more positive, and when the number of ROS was low. We also found a substantial subregional effect with foxes from northeastern Iceland having lower tooth damage than those from two western sites. Contradicting our original hypothesis that foxes from northeastern Iceland, where foxes are known to scavenge on large mammal remains (e.g., sheep and horses), would show the highest tooth damage, we suggest that western coastal sites exhibited greater tooth damage because cold winter temperatures lowered the availability of seabirds, causing a shift in diet toward abrasive marine subsidies (e.g., bivalves) and frozen beach wrack. Our study shows that monitoring tooth breakage and wear can be a useful tool for evaluating the impact of climate on carnivore populations and that climate change may influence the condition and fitness of carnivores in complex and potentially conflicting ways.

Teaching Dynamics to Biology Undergraduates: the UCLA Experience.

There is a growing realization that traditional "Calculus for Life Sciences" courses do not show their applicability to the Life Sciences and discourage student interest. There have been calls from the AAAS, the Howard Hughes Medical Institute, the NSF, and the American Association of Medical Colleges for a new kind of math course for biology students, that would focus on dynamics and modeling, to understand positive and negative feedback relations, in the context of important biological applications, not incidental "examples." We designed a new course, LS 30, based on the idea of modeling biological relations as dynamical systems, and then visualizing the dynamical system as a vector field, assigning "change vectors" to every point in a state space. The resulting course, now being given to approximately 1400 students/year at UCLA, has greatly improved student perceptions toward math in biology, reduced minority performance gaps, and increased students' subsequent grades in physics and chemistry courses. This new course can be customized easily for a broad range of institutions. All course materials, including lecture plans, labs, homeworks and exams, are available from the authors; supporting videos are posted online.

The impact of large terrestrial carnivores on Pleistocene ecosystems.

Large mammalian terrestrial herbivores, such as elephants, have dramatic effects on the ecosystems they inhabit and at high population densities their environmental impacts can be devastating. Pleistocene terrestrial ecosystems included a much greater diversity of megaherbivores (e.g., mammoths, mastodons, giant ground sloths) and thus a greater potential for widespread habitat degradation if population sizes were not limited. Nevertheless, based on modern observations, it is generally believed that populations of megaherbivores (>800 kg) are largely immune to the effects of predation and this perception has been extended into the Pleistocene. However, as shown here, the species richness of big carnivores was greater in the Pleistocene and many of them were significantly larger than their modern counterparts. Fossil evidence suggests that interspecific competition among carnivores was relatively intense and reveals that some individuals specialized in consuming megaherbivores. To estimate the potential impact of Pleistocene large carnivores, we use both historic and modern data on predator-prey body mass relationships to predict size ranges of their typical and maximum prey when hunting as individuals and in groups. These prey size ranges are then compared with estimates of juvenile and subadult proboscidean body sizes derived from extant elephant growth data. Young proboscideans at their most vulnerable age fall within the predicted prey size ranges of many of the Pleistocene carnivores. Predation on juveniles can have a greater impact on megaherbivores because of their long interbirth intervals, and consequently, we argue that Pleistocene carnivores had the capacity to, and likely did, limit megaherbivore population sizes.

Olfaction written in bone: cribriform plate size parallels olfactory receptor gene repertoires in Mammalia.

The evolution of mammalian olfaction is manifested in a remarkable diversity of gene repertoires, neuroanatomy and skull morphology across living species. Olfactory receptor genes (ORGs), which initiate the conversion of odorant molecules into odour perceptions and help an animal resolve the olfactory world, range in number from a mere handful to several thousand genes across species. Within the snout, each of these ORGs is exclusively expressed by a discrete population of olfactory sensory neurons (OSNs), suggesting that newly evolved ORGs may be coupled with new OSN populations in the nasal epithelium. Because OSN axon bundles leave high-fidelity perforations (foramina) in the bone as they traverse the cribriform plate (CP) to reach the brain, we predicted that taxa with larger ORG repertoires would have proportionately expanded footprints in the CP foramina. Previous work found a correlation between ORG number and absolute CP size that disappeared after accounting for body size. Using updated, digital measurement data from high-resolution CT scans and re-examining the relationship between CP and body size, we report a striking linear correlation between relative CP area and number of functional ORGs across species from all mammalian superorders. This correlation suggests strong developmental links in the olfactory pathway between genes, neurons and skull morphology. Furthermore, because ORG number is linked to olfactory discriminatory function, this correlation supports relative CP size as a viable metric for inferring olfactory capacity across modern and extinct species. By quantifying CP area from a fossil sabertooth cat (Smilodon fatalis), we predicted a likely ORG repertoire for this extinct felid.

The Influence of Sniffing on Airflow and Odorant Deposition in the Canine Nasal Cavity.

Nasal airflow plays a critical role in olfaction by transporting odorant from the environment to the olfactory epithelium, where chemical detection occurs. Most studies of olfaction neglect the unsteadiness of sniffing and assume that nasal airflow and odorant transport are "quasi-steady," wherein reality most mammals "sniff." Here, we perform computational fluid dynamics simulations of airflow and odorant deposition in an anatomically accurate model of the coyote (Canis latrans) nasal cavity during quiet breathing, a notional quasi-steady sniff, and unsteady sniffing to: quantify the influence of unsteady sniffing, assess the validity of the quasi-steady assumption, and investigate the functional advantages of sniffing compared to breathing. Our results reveal that flow unsteadiness during sniffing does not appreciably influence qualitative (gross airflow and odorant deposition patterns) or quantitative (time-averaged olfactory flow rate and odorant uptake) measures of olfactory function. A quasi-steady approximation is, therefore, justified for simulating time-averaged olfactory function in the canine nose. Simulations of sniffing versus quiet breathing demonstrate that sniffing delivers about 2.5 times more air to the olfactory recess and results in 2.5-3 times more uptake of highly- and moderately-soluble odorants in the sensory region per unit time, suggesting one reason why dogs actively sniff. Simulations also reveal significantly different deposition patterns in the olfactory region during inspiration for different odorants, and that during expiration there is little retronasal odorant deposition in the sensory region. These results significantly improve our understanding of canine olfaction, and have several practical implications regarding computer simulation of olfactory function.

The influence of nasal airflow on respiratory and olfactory epithelial distribution in felids.

The surface area of the maxilloturbinals and fronto-ethmoturbinals is commonly used as an osteological proxy for the respiratory and the olfactory epithelium, respectively. However, this assumption does not fully account for animals with short snouts in which these two turbinal structures significantly overlap, potentially placing fronto-ethmoturbinals in the path of respiratory airflow. In these species, it is possible that anterior fronto-ethmoturbinals are covered with non-sensory (respiratory) epithelium instead of olfactory epithelium. In this study, we analyzed the distribution of olfactory and non-sensory, respiratory epithelia on the turbinals of two domestic cats (Felis catus) and a bobcat (Lynx rufus). We also conducted a computational fluid dynamics simulation of nasal airflow in the bobcat to explore the relationship between epithelial distribution and airflow patterns. The results showed that a substantial amount of respiratory airflow passes over the anterior fronto-ethmoturbinals, and that contrary to what has been observed in caniform carnivorans, much of the anterior ethmoturbinals are covered by non-sensory epithelium. This confirms that in short-snouted felids, portions of the fronto-ethmoturbinals have been recruited for respiration, and that estimates of olfactory epithelial coverage based purely on fronto-ethmoturbinal surface area will be exaggerated. The correlation between the shape of the anterior fronto-ethmoturbinals and the direction of respiratory airflow suggests that in short-snouted species, CT data alone are useful in assessing airflow patterns and epithelium distribution on the turbinals.

Respiratory and olfactory turbinal size in canid and arctoid carnivorans.

Within the nasal cavity of mammals is a complex scaffold of paper-thin bones that function in respiration and olfaction. Known as turbinals, the bones greatly enlarge the surface area available for conditioning inspired air, reducing water loss, and improving olfaction. Given their functional significance, the relative development of turbinal bones might be expected to differ among species with distinct olfactory, thermoregulatory and/or water conservation requirements. Here we explore the surface area of olfactory and respiratory turbinals relative to latitude and diet in terrestrial Caniformia, a group that includes the canid and arctoid carnivorans (mustelids, ursids, procyonids, mephitids, ailurids). Using high-resolution computed tomography x-ray scans, we estimated respiratory and olfactory turbinal surface area and nasal chamber volume from three-dimensional virtual models of skulls. Across the Caniformia, respiratory surface area scaled isometrically with estimates of body size and there was no significant association with climate, as estimated by latitude. Nevertheless, one-on-one comparisons of sister taxa suggest that arctic species may have expanded respiratory turbinals. Olfactory surface area scaled isometrically among arctoids, but showed positive allometry in canids, reflecting the fact that larger canids, all of which are carnivorous, had relatively greater olfactory surface areas. In addition, among the arctoids, large carnivorous species such as the polar bear (Ursus maritimus) and wolverine (Gulo gulo) also displayed enlarged olfactory turbinals. More omnivorous caniform species that feed on substantial quantities of non-vertebrate foods had less expansive olfactory turbinals. Because large carnivorous species hunt widely dispersed prey, an expanded olfactory turbinal surface area may improve a carnivore's ability to detect prey over great distances using olfactory cues.

Aquatic adaptations in the nose of carnivorans: evidence from the turbinates.

Inside the mammalian nose lies a labyrinth of bony plates covered in epithelium collectively known as turbinates. Respiratory turbinates lie anteriorly and aid in heat and water conservation, while more posterior olfactory turbinates function in olfaction. Previous observations on a few carnivorans revealed that aquatic species have relatively large, complex respiratory turbinates and greatly reduced olfactory turbinates compared with terrestrial species. Body heat is lost more quickly in water than air and increased respiratory surface area likely evolved to minimize heat loss. At the same time, olfactory surface area probably diminished due to a decreased reliance on olfaction when foraging under water. To explore how widespread these adaptations are, we documented scaling of respiratory and olfactory turbinate surface area with body size in a variety of terrestrial, freshwater, and marine carnivorans, including pinnipeds, mustelids, ursids, and procyonids. Surface areas were estimated from high-resolution CT scans of dry skulls, a novel approach that enabled a greater sampling of taxa than is practical with fresh heads. Total turbinate, respiratory, and olfactory surface areas correlate well with body size (r(2) ≥0.7), and are relatively smaller in larger species. Relative to body mass or skull length, aquatic species have significantly less olfactory surface area than terrestrial species. Furthermore, the ratio of olfactory to respiratory surface area is associated with habitat. Using phylogenetic comparative methods, we found strong support for convergence on 1:3 proportions in aquatic taxa and near the inverse in terrestrial taxa, indicating that aquatic mustelids and pinnipeds independently acquired similar proportions of olfactory to respiratory turbinates. Constraints on turbinate surface area in the nasal chamber may result in a trade-off between respiratory and olfactory function in aquatic mammals.

Naturally-occurring tooth wear, tooth fracture, and cranial injuries in large carnivores from Zambia.

Determining the incidence and causes of craniodental damage in wild carnivores is often constrained by limited access to specimens with associated ecological data, such as prey type and abundance. We assessed dental condition and cranial injuries in lion, leopard, and spotted hyena in relation to prey and predator populations in Zambia's Luangwa Valley, where large prey are more abundant and lion and leopard more numerous, and the Greater Kafue Ecosystem, where smaller prey species are more prevalent and lion and leopard less common. In Luangwa, lions had significantly higher rates of tooth fracture, and blunt trauma injuries attributable to prey-handling, compared to Kafue lions. In contrast, leopards in both regions had similar rates of tooth wear and breakage. Overall, lions showed a significantly higher tooth fracture rate than leopards on a per tooth basis. Spotted hyenas had the highest rates of tooth wear and fracture among all three carnivores, and greatly exceeded previously recorded rates based on historical samples. Despite larger numbers of lion and leopard in Luangwa, there was no difference in incidence of intraspecific injuries between regions. These results are consistent with a greater abundance of large prey species, especially buffalo, in the diets of Luangwa lions, and previous work showing a reliance on smaller prey species in Kafue throughout the large carnivore guild.

The dog-human connection.

This special issue of The Anatomical Record is the end result of a rare convergence of researchers scattered around the globe who came together to explore the mystery of the dog-human connection. Many of the discussions at the 12th International Congress of Vertebrate Morphology in Prague (July 23, 2019) are echoed within this issue. The enigmatic origins of dog domestication (as well as feralized descendants such as the dingo) are discussed, including phases of domestication that we might infer, and our historical knowledge of dog breeding. Emphasized by the morphological and genetic data are the forces of selection, both unintentional and intentional. In our modern life with dogs, we enjoy their companionship and benefit from the utility of many breeds, but we encounter unintended health care issues that are often breed-specific. Dogs are so different in their sensory specializations (especially olfaction), but have uniquely (among other domestic mammals) developed highly sophisticated means of interspecific communication with humans. In sum, the manuscripts within this issue discuss anatomical, paleontological, genetic, and behavioral evidence bearing on the antiquity of the domestic dog, the process of domestication, and the many ways in which dogs continue to affect human life.

The impact of extreme skull morphology in domestic dogs on cribriform plate shape.

Dog owners are often impressed by their dog's sense of smell. Many of these dogs, however, have skulls that are quite altered from those of their closest canid relatives. Housed within these skulls are essential olfactory structures like the cribriform plate that play a role in olfaction and the transmission of olfactory nerve impulses to the olfactory bulb of the brain. With improvements in CT technology and accessibility, we are now able to digitally reconstruct in 3D cribriform plate morphology and study its variation within and among species. In this study, we CT scanned the skulls of 95 dog specimens from 45 different domestic dog breeds and 12 species of wild canid and compared the shape of the cribriform plate among three main groups: domestic dog breeds, wolf-like canids, and fox-like canids. Despite only recent selective pressure for extreme skull morphology, domestic dogs display much more variation in cribriform plate shape than wild canids, indicating that cribriform plate shape is plastic and linked to skull shape. Intense artificial selection on domestic dog skull phenotype in the last 200 years has clear effects on secondary features of the domestic dog skull, implying that selection for overt phenotypes also can impact other anatomical features associated with the skull, like the cribriform plate.

"Mucosal maps" of the canine nasal cavity: Micro-computed tomography and histology.

Nasal turbinals, delicate and complex bones of the nasal cavity that support respiratory or olfactory mucosa (OM), are now easily studied using high resolution micro-computed tomography (µ-CT). Standard µ-CT currently lacks the capacity to identify OM or other mucosa types without additional radio-opaque staining techniques. However, even unstained mucosa is more radio-opaque than air, and thus mucosal thickness can be discerned. Here, we assess mucosal thickness of the nasal fossa using the cranium of a cadaveric adult dog that was µ-CT scanned with an isotropic resolution of 30 µm, and subsequently histologically sectioned and stained. After co-alignment of µ-CT slice planes to that of histology, mucosal thickness was estimated at four locations. Results based on either µ-CT or histology indicate olfactory mucosa is thicker on average compared with non-olfactory mucosa (non-OM). In addition, olfactory mucosa has a lesser degree of variability than the non-OM. Variability in the latter appears to relate mostly to the varying degree of vascularity of the lamina propria. Because of this, in structures with both specialized vascular respiratory mucosa and OM, such as the first ethmoturbinal (ET I), the range of thickness of OM and non-OM may overlap. Future work should assess the utility of diffusible iodine-based contrast enhanced CT techniques, which can differentiate epithelium from the lamina propria, to enhance our ability to differentiate mucosa types on more rostral ethmoturbinals. This is especially critical for structures such as ET I, which have mixed functional roles in many mammals.

Domesticating olfaction: Dog breeds, including scent hounds, have reduced cribriform plate morphology relative to wolves.

The domestic dog is assumed by nearly everyone to be the consummate smeller. Within the species Canis familiaris individual breeds, such as the bloodhound or beagle, are known as olfactory stars. These are "scent breeds," a grouping variably defined as a genetic clade or breed class commonly used for scent detection tasks. Previous work suggests that the dog has a more robust olfactory anatomy than many mammal species. Now we undertake a closer investigation of the dog's olfactory system, both in relationship to its closest wild relatives, the wolf and coyote, and across individual breeds. First, we seek to resolve whether the dog has lost olfactory capacity through its domestication from the wolf lineage. Second, we test the inertial lore that among dogs, "scent breeds," have a superior olfactory facility. As a measure of relative olfactory capacity, we look to the cribriform plate (CP), a bony cup in the posterior nasal cavity perforated by passageways for all olfactory nerve bundles streaming from the periphery to the brain. Using high-resolution computed tomography (CT) scans and digital quantification, we compare relative CP size in 46 dog breeds, the coyote and gray wolf. Results show the dog has a reduced CP surface area relative to the wolf and coyote. Moreover, we found no significant differences between CP size of "scent" and "non-scent" breeds. Our study suggests that the dog lost olfactory capacity as a result of domestication and this loss was not recovered in particular breed groupings through directed artificial selection for increased olfactory facility.

Reimagining the Introductory Math Curriculum for Life Sciences Students.

Calculus is typically one of the first college courses encountered by science, technology, engineering, and mathematics (STEM) majors. Calculus often presents major challenges affecting STEM student persistence, particularly for students from groups historically underrepresented in STEM. For life sciences majors, calculus courses may not offer content that is relevant to biological systems or connect with students' interests in biology. We developed a transformative approach to teaching college-level math, using a dynamical systems perspective that focuses first on demonstrating why students need math to understand living systems, followed by providing quantitative and computational skills, including concepts from calculus, that students need to build and analyze mathematical models representing these systems. We found that students who complete these new math courses perform better in subsequent science courses than their counterparts who take traditional calculus courses. We also provide evidence that the new math curriculum positively impacts students' academic performance, with data that show narrowing of the achievement gap, based on students' math grades, between student subgroups in the new math courses. Moreover, our results indicate that students' interest in the concepts and skills critical to the quantitative preparation of 21st-century life sciences majors increases after completing the new contextualized math curriculum.

Megafaunal extinctions and the disappearance of a specialized wolf ecomorph.

The gray wolf (Canis lupus) is one of the few large predators to survive the Late Pleistocene megafaunal extinctions [1]. Nevertheless, wolves disappeared from northern North America in the Late Pleistocene, suggesting they were affected by factors that eliminated other species. Using skeletal material collected from Pleistocene permafrost deposits of eastern Beringia, we present a comprehensive analysis of an extinct vertebrate by exploring genetic (mtDNA), morphologic, and isotopic (delta(13)C, delta(15)N) data to reveal the evolutionary relationships, as well as diet and feeding behavior, of ancient wolves. Remarkably, the Late Pleistocene wolves are genetically unique and morphologically distinct. None of the 16 mtDNA haplotypes recovered from a sample of 20 Pleistocene eastern-Beringian wolves was shared with any modern wolf, and instead they appear most closely related to Late Pleistocene wolves of Eurasia. Moreover, skull shape, tooth wear, and isotopic data suggest that eastern-Beringian wolves were specialized hunters and scavengers of extinct megafauna. Thus, a previously unrecognized, uniquely adapted, and genetically distinct wolf ecomorph suffered extinction in the Late Pleistocene, along with other megafauna. Consequently, the survival of the species in North America depended on the presence of more generalized forms elsewhere.

Iterative evolution of large-bodied hypercarnivory in canids benefits species but not clades.

Ecological specialization has costs and benefits at various scales: traits benefitting an individual may disadvantage its population, species or clade. In particular, large body size and hypercarnivory (diet over 70% meat) have evolved repeatedly in mammals; yet large hypercarnivores are thought to be trapped in a macroevolutionary "ratchet", marching unilaterally toward decline. Here, we weigh the impact of this specialization on extinction risk using the rich fossil record of North American canids (dogs). In two of three canid subfamilies over the past 40 million years, diversification of large-bodied hypercarnivores appears constrained at the clade level, biasing specialized lineages to extinction. However, despite shorter species durations, extinction rates of large hypercarnivores have been mostly similar to those of all other canids. Extinction was size- and carnivory-selective only at the end of the Pleistocene epoch 11,000 years ago, suggesting that large hypercarnivores were not disadvantaged at the species level before anthropogenic influence.

Problems with inferring a lack of competition between Rancho La Brea dire wolves and sabertooth cats based on dental enamel.

Van Valkenburgh et al. challenge the conclusions of a recent study by DeSantis et al. that claimed that sabertooth cats and dire wolves did not compete for similar prey.