Relationships of Cetacea (Artiodactyla) among mammals: increased taxon sampling alters interpretations of key fossils and character evolution

Progress in the development and use of monoclonal antibodies to study the evolution and function of the immune systems in the extant lineages of ungulates

Details on the origin and function of the immune system are beginning to emerge from genomic studies tracing the origin of B and T cells and the major histocompatibility complex. This is being accomplished through identification of DNA sequences of ancestral genes present in the genomes of lineages of vertebrates that have evolved from a common primordial ancestor. Information on the evolution of the composition and function of the immune system is being obtained through development of monoclonal antibodies (mAbs) specific for the MHC class I and II molecules and differentially expressed on leukocytes differentiation molecules (LDM). The mAbs have provided the tools needed to compare the similarities and differences in the phenotype and function of immune systems that have evolved during speciation. The majority of information currently available on evolution of the composition and function of the immune system is derived from study of the immune systems in humans and mice. As described in the present review, further information is beginning to emerge from comparative studies of the immune systems in the extant lineages of species present in the two orders of ungulates, Perissodactyla and Artiodactyla. Methods have been developed to facilitate comparative research across species on pathogens affecting animal and human health.

Molecular Evidence for Relaxed Selection on the Enamel Genes of Toothed Whales (Odontoceti) with Degenerative Enamel Phenotypes

Different species of toothed whales (Odontoceti) exhibit a variety of tooth forms and enamel types. Some odontocetes have highly prismatic enamel with Hunter-Schreger bands, whereas enamel is vestigial or entirely lacking in other species. Different tooth forms and enamel types are associated with alternate feeding strategies that range from biting and grasping prey with teeth in most oceanic and river dolphins to the suction feeding of softer prey items without the use of teeth in many beaked whales. At the molecular level, previous studies have documented inactivating mutations in the enamel-specific genes of some odontocete species that lack complex enamel. At a broader scale, however, it is unclear whether enamel complexity across the full diversity of extant Odontoceti correlates with the relative strength of purifying selection on enamel-specific genes. Here, we employ sequence alignments for seven enamel-specific genes (ACP4, AMBN, AMELX, AMTN, ENAM, KLK4, MMP20) in 62 odontocete species that are representative of all extant families. The sequences for 33 odontocete species were obtained from databases, and sequences for the remaining 29 species were newly generated for this study. We screened these alignments for inactivating mutations (e.g., frameshift indels) and provide a comprehensive catalog of these mutations in species with one or more inactivated enamel genes. Inactivating mutations are rare in Delphinidae (oceanic dolphins) and Platanistidae/Inioidea (river dolphins) that have higher enamel complexity scores. By contrast, mutations are much more numerous in clades such as Monodontidae (narwhal, beluga), Ziphiidae (beaked whales), Physeteroidea (sperm whales), and Phocoenidae (porpoises) that are characterized by simpler enamel or even enamelless teeth. Further, several higher-level taxa (e.g., Hyperoodon, Kogiidae, Monodontidae) possess shared inactivating mutations in one or more enamel genes, which suggests loss of function of these genes in the common ancestor of each clade. We also performed selection (dN/dS) analyses on a concatenation of these genes and used linear regression and Spearman's rank-order correlation to test for correlations between enamel complexity and two different measures of selection intensity (# of inactivating mutations per million years, dN/dS values). Selection analyses revealed that relaxed purifying selection is especially prominent in physeteroids, monodontids, and phocoenids. Linear regressions and correlation analyses revealed a strong negative correlation between selective pressure (dN/dS values) and enamel complexity. Stronger purifying selection (low dN/dS) is found on branches with more complex enamel and weaker purifying selection (higher dN/dS) occurs on branches with less complex enamel or enamelless teeth. As odontocetes diversified into a variety of feeding modes, in particular, the suction capture of prey, a reduced reliance on the dentition for prey capture resulted in the relaxed selection of genes that are critical to enamel development.

DNA barcoding for the identification and authentication of medicinal deer (Cervus sp.) products in China

Deer products from sika deer (Cervus nippon) and red deer (C. elaphus) are considered genuine and used for Traditional Chinese Medicine (TCM) materials in China. Deer has a very high economic and ornamental value, resulting in the formation of a characteristic deer industry in the prescription preparation of traditional Chinese medicine, health food, cosmetics, and other areas of development and utilization. Due to the high demand for deer products, the products are expensive and have limited production, but the legal use of deer is limited to only two species of sika deer and red deer; other wild deer are prohibited from hunting, so there are numerous cases of mixing and adulteration of counterfeit products and so on. There have been many reports that other animal (pig, cow, sheep, etc.) tissues or organs are often used for adulteration and confusion, resulting in poor efficacy of deer traditional medicine and trade fraud in deer products. To authenticate the deer products in a rapid and effective manner, the analysis used 22 deer products (antler, meat, bone, fetus, penis, tail, skin, and wool) that were in the form of blind samples. Total DNA extraction using a modified protocol successfully yielded DNA from the blind samples that was useful for PCR. Three candidate DNA barcoding loci, cox1, Cyt b, and rrn12, were evaluated for their discrimination strength through BLAST and phylogenetic clustering analyses. For the BLAST analysis, the 22 blind samples obtained 100% match identity across the three gene loci tested. It was revealed that 12 blind samples were correctly labeled for their species of origin, while three blind samples that were thought to originate from red deer were identified as C. nippon, and seven blind samples that were thought to originate from sika deer were identified as C. elaphus, Dama dama, and Rangifer tarandus. DNA barcoding analysis showed that all three gene loci were able to distinguish the two Cervus species and to identify the presence of adulterant species. The DNA barcoding technique was able to provide a useful and sensitive approach in identifying the species of origin in deer products.

Exploring objective feature sets in constructing the evolution relationship of animal genome sequences

BACKGROUND

Exploring evolution regularities of genome sequences and constructing more objective species evolution relationships at the genomic level are high-profile topics. Based on the evolution mechanism of genome sequences proposed in our previous research, we found that only the 8-mers containing CG or TA dinucleotides correlate directly with the evolution of genome sequences, and the relative frequency rather than the actual frequency of these 8-mers is more suitable to characterize the evolution of genome sequences.

RESULT

Therefore, two types of feature sets were obtained, they are the relative frequency sets of CG1 + CG2 8-mers and TA1 + TA2 8-mers. The evolution relationships of mammals and reptiles were constructed by the relative frequency set of CG1 + CG2 8-mers, and two types of evolution relationships of insects were constructed by the relative frequency sets of CG1 + CG2 8-mers and TA1 + TA2 8-mers respectively. Through comparison and analysis, we found that evolution relationships are consistent with the known conclusions. According to the evolution mechanism, we considered that the evolution relationship constructed by CG1 + CG2 8-mers reflects the evolution state of genome sequences in current time, and the evolution relationship constructed by TA1 + TA2 8-mers reflects the evolution state in the early stage.

CONCLUSION

Our study provides objective feature sets in constructing evolution relationships at the genomic level.

Renewing Linnaean taxonomy: a proposal to restructure the highest levels of the Natural System

During the last century enormous progress has been made in the understanding of biological diversity, involving a dramatic shift from macroscopic to microscopic organisms. The question now arises as to whether the Natural System introduced by Carl Linnaeus, which has served as the central system for organizing biological diversity, can accommodate the great expansion of diversity that has been discovered. Important discoveries regarding biological diversity have not been fully integrated into a formal, coherent taxonomic system. In addition, because of taxonomic challenges and conflicts, various proposals have been made to abandon key aspects of the Linnaean system. We review the current status of taxonomy of the living world, focussing on groups at the taxonomic level of phylum and above. We summarize the main arguments against and in favour of abandoning aspects of the Linnaean system. Based on these considerations, we conclude that retaining the Linnaean Natural System provides important advantages. We propose a relatively small number of amendments for extending this system, particularly to include the named rank of world (Latin alternative mundis) formally to include non-cellular entities (viruses), and the named rank of empire (Latin alternative imperium) to accommodate the depth of diversity in (unicellular) eukaryotes that has been uncovered. We argue that in the case of both the eukaryotic domain and the viruses the cladistic approach intrinsically fails. However, the resulting semi-cladistic system provides a productive way forward that can help resolve taxonomic challenges. The amendments proposed allow us to: (i) retain named taxonomic levels and the three-domain system, (ii) improve understanding of the main eukaryotic lineages, and (iii) incorporate viruses into the Natural System. Of note, the proposal described herein is intended to serve as the starting point for a broad scientific discussion regarding the modernization of the Linnaean system.

Comparison of the Rostral Epidural Rete Mirabile and the Patterns of Its Blood Supply in Selected Suiformes and Hippopotamuses

The rostral epidural rete mirabile (rete mirabile epidurale rostrale) is built of considerable small arterial vessels that anastomose with each other. This structure is formed as a result of the division of a large arterial vessel into many small arteries. Furthermore, on the other side of the rete mirabile, these small arteries are joined together to form one large artery, through which blood flows out of the rete mirabile. This system participates in decreasing the temperature of the brain and thus protects the body from thermal stress. Moreover, it influences body-water balance and has a crucial role in the retrograde transfer of neuropeptides. The goal of this study was to describe the rostral epidural rete mirabile and pathways that provide blood to this structure as well as compare it in selected Suiformes and hippopotamuses. The study was performed on desert warthogs (Phacochoerus aethiopicus), Eurasian wild boars (Sus scrofa), collared peccaries (Pecari tajacu), pygmy hippopotamuses (Choeropsis liberiensis), and common hippopotamuses (Hippopotamus amphibius). Preparations were made using the latex method and corrosion cast. An elongated shape characterizes its anatomy with a much wider rostral part than caudal part in the Eurasian wild boars, desert warthogs, and collared peccaries. The main source of blood was the branch to the rostral epidural rete mirabile branched off from the internal carotid artery. Moreover, blood enters the rete by the caudal branch and rostral branch to the rostral epidural rete mirabile. In hippopotamuses, the major source of blood was the rostral branches to the rostral epidural rete mirabile.

Strategies of vascularization of the ethmoid labyrinth in selected even-toed ungulates (Artiodactyla) and carnivores (Carnivora)

The anatomy of the nasal cavity and its structures, as well as other elements building a scaffold for olfactory organs, differs significantly among various groups of mammals. Understanding anatomical conditions of quality of olfaction are being studied worldwide and is a complex problem. Among many studies regarding bone and epithelial structures of turbinates and connected anatomical structures, few studies describe the vascularization of turbinates. Ethmoid turbinates are above all covered in olfactory epithelium containing branched axons that receive olfactory stimuli and as olfactory nerves penetrate the cribriform lamina of the ethmoid bone conveying information from smell receptors to the brain. Differences in vascularization of the cribriform plate and turbinates may add crucial information complementing studies regarding the olfactory organ's bone and soft tissue structures. In the study, we describe the vascularization of the cribriform plate of the ethmoid bone of 54 Artiodactyla and Carnivora.

Bioinformatic analysis of the coding region of the melatonin receptor 1b gene as a reliable DNA marker to resolve interspecific mammal phylogenetic relationships

This research looks into the main DNA markers and the limits of their application in molecular phylogenetic analysis. Melatonin 1B (MTNR1B) receptor genes were analyzed from various biological sources. Based on the coding sequences of this gene, using the class Mammalia as example, phylogenetic reconstructions were made to study the potential of mtnr1b as a DNA marker for phylogenetic relationships investigating. The phylogenetic trees were constructed using NJ, ME and ML methods that establish the evolutionary relationships between different groups of mammals. The resulting topologies were generally in good agreement with topologies established on the basis of morphological and archaeological data as well as with other molecular markers. The present divergences provided a unique opportunity for evolutionary analysis. These results suggest that the coding sequence of the MTNR1B gene can be used as a marker to study the relationships of lower evolutionary levels (order, species) as well as to resolve deeper branches of the phylogenetic tree at the infraclass level.

Diet evolution of carnivorous and herbivorous mammals in Laurasiatheria

Background

Laurasiatheria contains taxa with diverse diets, while the molecular basis and evolutionary history underlying their dietary diversification are less clear.

Results

In this study, we used the recently developed molecular phyloecological approach to examine the adaptive evolution of digestive system-related genes across both carnivorous and herbivorous mammals within Laurasiatheria. Our results show an intensified selection of fat and/or protein utilization across all examined carnivorous lineages, which is consistent with their high-protein and high-fat diets. Intriguingly, for herbivorous lineages (ungulates), which have a high-carbohydrate diet, they show a similar selection pattern as that of carnivorous lineages. Our results suggest that for the ungulates, which have a specialized digestive system, the selection intensity of their digestive system-related genes does not necessarily reflect loads of the nutrient components in their diets but appears to be positively related to the loads of the nutrient components that are capable of being directly utilized by the herbivores themselves. Based on these findings, we reconstructed the dietary evolution within Laurasiatheria, and our results reveal the dominant carnivory during the early diversification of Laurasiatheria. In particular, our results suggest that the ancestral bats and the common ancestor of ruminants and cetaceans may be carnivorous as well. We also found evidence of the convergent evolution of one fat utilization-related gene, APOB, across carnivorous taxa.

Conclusions

Our molecular phyloecological results suggest that digestive system-related genes can be used to determine the molecular basis of diet differentiations and to reconstruct ancestral diets.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12862-022-02033-6.

Attenuated evolution of mammals through the Cenozoic

The Cenozoic diversification of placental mammals is the archetypal adaptive radiation. Yet, discrepancies between molecular divergence estimates and the fossil record fuel ongoing debate around the timing, tempo, and drivers of this radiation. Analysis of a three-dimensional skull dataset for living and extinct placental mammals demonstrates that evolutionary rates peak early and attenuate quickly. This long-term decline in tempo is punctuated by bursts of innovation that decreased in amplitude over the past 66 million years. Social, precocial, aquatic, and herbivorous species evolve fastest, especially whales, elephants, sirenians, and extinct ungulates. Slow rates in rodents and bats indicate dissociation of taxonomic and morphological diversification. Frustratingly, highly similar ancestral shape estimates for placental mammal superorders suggest that their earliest representatives may continue to elude unequivocal identification.

Comparative analysis of the specificity of monoclonal antibodies developed against the bottlenose dolphin, Tursiops truncatus, TNF-α, IL1-β, IL-6, IL-8, IL-10 with monoclonal antibodies made against ovine IFN-γ bovine IL-17A and IL-1β revealed they recognize epitopes conserved on dolphin and bovine orthologues

Opportunities to include Cetancodontamorpha in the study of the evolution of the immune system in the clades of Artiodactylamorpha, Ruminantiamorpha, Suinamorpha, and Camelidamorpha have increased with the use of the bottlenose dolphin, Tursiops truncatus, as a sentinel species to study the effects of environmental pollutants on the health of marine mammals. Efforts are currently underway to increase the number reagents needed for detailed studies. Thus far, screening of monoclonal antibodies (mAbs) made to leukocyte differentiation molecules (LDM) and the major histocompatibility (MHC) class I and class II molecules in Ruminantiamorpha have yielded some mAbs that recognize conserved epitopes expressed on orthologues in the bottlenose dolphin. More direct approaches are in progress to identify additional mAbs to bottlenose LDM and cytokines. As reported here, both direct and indirect approaches were used to identify mAbs specific for cytokines useful in monitoring the effects of environmental pollutants on the immune system. Immunization of mice with expressed bottlenose dolphin cytokines yielded mAbs specific for IFN-γ, TNF-α, IL-6, IL-8, IL-10, and IL-17A. Screening of previously developed mAbs used in livestock immunology research revealed mAbs developed against ovine IFN-γ and bovine IL-17 and IL-1β recognize conserved epitopes in bottlenose dolphin orthologues. The mAbs identified in the present study expand the reagents available to study the function of the immune system in bottlenose dolphins and cattle.

Differential MC5R loss in whales and manatees reveals convergent evolution to the marine environment

Melanocortin 5 receptor (MC5R), which is expressed in the terminally differentiated sebaceous gland, is a G protein-coupled receptor (GPCR). MC5R exists mostly in mammals but is completely lost in whales; only the relic of MC5R can be detected in manatees, and phenotypically, they have lost sebaceous glands. Interestingly, whales and manatees are both aquatic mammals but have no immediate common ancestors. The loss of MC5R and sebaceous glands in whales and manatees is likely to be a result of convergent evolution. Here, we find that MC5R in whales and manatees are lost by two different mechanisms. Homologous recombination of MC5R in manatees and the insertion of reverse transcriptase in whales lead to the gene loss, respectively. On one hand, in manatees, there are two "TTATC" sequences flanking MC5R, and homologous recombination of the segments between the two "TTATC" sequences resulted in the partial loss of the sequence of MC5R. On the other hand, in whales, reverse transcriptase inserts between MC2R and RNMT on the chromosome led to the loss of MC5R. Based on these two different mechanisms for gene loss in whales and manatees, we finally concluded that MC5R loss might be the result of convergent evolution to the marine environment, and we explored the impact on biological function that is significant to environmental adaptation.

Brawn before brains in placental mammals after the end-Cretaceous extinction

Mammals are the most encephalized vertebrates, with the largest brains relative to body size. Placental mammals have particularly enlarged brains, with expanded neocortices for sensory integration, the origins of which are unclear. We used computed tomography scans of newly discovered Paleocene fossils to show that contrary to the convention that mammal brains have steadily enlarged over time, early placentals initially decreased their relative brain sizes because body mass increased at a faster rate. Later in the Eocene, multiple crown lineages independently acquired highly encephalized brains through marked growth in sensory regions. We argue that the placental radiation initially emphasized increases in body size as extinction survivors filled vacant niches. Brains eventually became larger as ecosystems saturated and competition intensified.

Dietary niches of creodonts and carnivorans of the late Eocene Cypress Hills Formation

Modern North American carnivorous mammal assemblages consist of species from a single clade: the Carnivora. Carnivorans once coexisted with members of other meat-eating clades, including the creodonts (Hyaenodontida and Oxyaenida). Creodonts, however, went extinct in North America during the late Eocene and early Oligocene, potentially due to niche overlap and resource competition with contemporary carnivorans. In this study, we employ a community ecology approach to understand whether the dietary niches of coexisting creodonts and carnivorans overlapped during the late Eocene (Chadronian North American Land Mammal Age), a time when creodonts were dwindling and carnivorans were diversifying. We quantify niche overlap based on inferences of diet from carnassial tooth shape estimated using Orientation Patch Count, Dirichlet's Normal Surface Energy, and linear dental measurements as well as from body mass for all species in the Calf Creek Local Fauna of Cypress Hills, Saskatchewan (Treaty 4 land). Although creodonts and carnivorans shared characteristics of their carnassial tooth shape, suggesting similar chewing mechanics and feeding habits, we find that marked differences in body size likely facilitated niche partitioning, at least between the largest creodonts and carnivorans. Calculations of prey focus masses and prey mass spectra indicate that only the smallest creodont may have experienced significant competition for prey with the coeval carnivorans. We suggest that the ultimate extinction of creodonts from North America during the late Eocene and Oligocene was unlikely to have been driven by factors related to niche overlap with carnivorans.

Pronghorn (Antilocapra americana) enamel phosphate δ18O values reflect climate seasonality: Implications for paleoclimate reconstruction

Stable oxygen isotope (δ18O) compositions from vertebrate tooth enamel are widely used as biogeochemical proxies for paleoclimate. However, the utility of enamel oxygen isotope values for environmental reconstruction varies among species. Herein, we evaluate the use of stable oxygen isotope compositions from pronghorn (Antilocapra americana Gray, 1866) enamel for reconstructing paleoclimate seasonality, an elusive but important parameter for understanding past ecosystems. We serially sampled the lower third molars of recent adult pronghorn from Wyoming for δ18O in phosphate (δ18OPO4) and compared patterns to interpolated and measured yearly variation in environmental waters as well as from sagebrush leaves, lakes, and rivers (δ18Ow). As expected, the oxygen isotope compositions of phosphate from pronghorn enamel are enriched in 18O relative to environmental waters. For a more direct comparison, we converted δ18Ow values into expected δ18OPO4* values (δ18OW-PO4*). Pronghorn δ18OPO4 values from tooth enamel record nearly the full amplitude of seasonal variation from Wyoming δ18OW-PO4* values. Furthermore, pronghorn enamel δ18OPO4 values are more similar to modeled δ18OW-PO4* values from plant leaf waters than meteoric waters, suggesting that they obtain much of their water from evaporated plant waters. Collectively, our findings establish that seasonality in source water is reliably reflected in pronghorn enamel, providing the basis for exploring changes in the amplitude of seasonality of ancient climates. As a preliminary test, we sampled historical pronghorn specimens (1720 ± 100 AD), which show a mean decrease (a shift to lower values) of 1-2‰ in δ18OPO4 compared to the modern specimens. They also exhibit an increase in the δ18O amplitude, representing an increase in seasonality. We suggest that the cooler mean annual and summer temperatures typical of the 18th century, as well as enhanced periods of drought, drove differences among the modern and historical pronghorn, further establishing pronghorn enamel as excellent sources of paleoclimate proxy data.

Returning to the roots: resolution, reproducibility, and robusticity in the phylogenetic inference of Dissorophidae (Amphibia: Temnospondyli)

The phylogenetic relationships of most Paleozoic tetrapod clades remain poorly resolved, which is variably attributed to a lack of study, the limitations of inference from phenotypic data, and constant revision of best practices. While refinement of phylogenetic methods continues to be important, any phylogenetic analysis is inherently constrained by the underlying dataset that it analyzes. Therefore, it becomes equally important to assess the accuracy of these datasets, especially when a select few are repeatedly propagated. While repeat analyses of these datasets may appear to constitute a working consensus, they are not in fact independent, and it becomes especially important to evaluate the accuracy of these datasets in order to assess whether a seeming consensus is robust. Here I address the phylogeny of the Dissorophidae, a speciose clade of Paleozoic temnospondyls. This group is an ideal case study among temnospondyls for exploring phylogenetic methods and datasets because it has been extensively studied (eight phylogenetic studies to date) but with most (six studies) using a single matrix that has been propagated with very little modification. In spite of the conserved nature of the matrix, dissorophid studies have produced anything but a conserved topology. Therefore, I analyzed an independently designed matrix, which recovered less resolution and some disparate nodes compared to previous studies. In order to reconcile these differences, I carefully examined previous matrices and analyses. While some differences are a matter of personal preference (e.g., analytical software), others relate to discrepancies with respect to what are currently considered as best practices. The most concerning discovery was the identification of pervasive dubious scorings that extend back to the origins of the widely propagated matrix. These include scores for skeletal features that are entirely unknown in a given taxon (e.g., postcrania in Cacops woehri) and characters for which there appear to be unstated working assumptions to scoring that are incompatible with the character definitions (e.g., scoring of taxa with incomplete skulls for characters based on skull length). Correction of these scores and other pervasive errors recovered a distinctly less resolved topology than previous studies, more in agreement with my own matrix. This suggests that previous analyses may have been compromised, and that the only real consensus of dissorophid phylogeny is the lack of one.

Causes, Consequences, and Conservation of Ungulate Migration

Our understanding of ungulate migration is advancing rapidly due to innovations in modern animal tracking. Herein, we review and synthesize nearly seven decades of work on migration and other long-distance movements of wild ungulates. Although it has long been appreciated that ungulates migrate to enhance access to forage, recent contributions demonstrate that their movements are fine tuned to dynamic landscapes where forage, snow, and drought change seasonally. Researchers are beginning to understand how ungulates navigate migrations, with the emerging view that animals blend gradient tracking with spatial memory, some of which is socially learned. Although migration often promotes abundant populations—with broad effects on ecosystems—many migrations around the world have been lost or are currently threatened by habitat fragmentation, climate change, and barriers to movement. Fortunately, new efforts that use empirical tracking data to map migrations in detail are facilitating effective conservation measures to maintain ungulate migration.

The petrosal and basicranial morphology of Protoceras celer

Protoceratids are an extinct family of endemic North American artiodactyls. The phylogenetic position of protoceratids in relation to camelids and ruminants has been contentious for over a century. The petrosal morphology of basal (Leptotragulus) and derived (Syndyoceras) protoceratids has suggested that protoceratids are closely related to ruminants, whereas a prior description of a disarticulated intermediate protoceratid petrosal (Protoceras celer) indicated that protoceratids were closely related to camelids. This contradictory evidence implied that there were several character reversals within the protoceratid lineage and brought into question the utility of basicranial characters in artiodactyl phylogenetics. Here, we provide descriptions of an additional P. celer petrosal. The descriptions are based on data produced by computed tomography scans, which allowed us to image the petrosal in situ in the skull. Our results indicate that the petrosal morphology of P. celer is similar to that of other protoceratids, implying that, contrary to previous evidence, petrosal morphology is conserved within the Protoceratidae.

Protein Identification of Spermatozoa and Seminal Plasma in Bottlenose Dolphin (Tursiops truncatus)

Proteins play an important role in many reproductive functions such as sperm maturation, sperm transit in the female genital tract or sperm-oocyte interaction. However, in general, little information concerning reproductive features is available in the case of aquatic animals. The present study aims to characterize the proteome of both spermatozoa and seminal plasma of bottlenose dolphins (Tursiops truncatus) as a model organism for cetaceans. Ejaculate samples were obtained from two trained dolphins housed in an aquarium. Spermatozoa and seminal plasma were analyzed by means of proteomic analyses using an LC-MS/MS, and a list with the gene symbols corresponding to each protein was submitted to the DAVID database. Of the 419 proteins identified in spermatozoa and 303 in seminal plasma, 111 proteins were shared by both. Furthermore, 70 proteins were identified as involved in reproductive processes, 39 in spermatozoa, and 31 in seminal plasma. The five most abundant proteins were also identified in these samples: AKAP3, ODF2, TUBB, GSTM3, ROPN1 for spermatozoa and CST11, LTF, ALB, HSP90B1, PIGR for seminal plasma. In conclusion, this study provides the first characterization of the proteome in cetacean sperm and seminal plasma, opening the way to future research into new biomarkers, the analysis of conservation capacity or possible additional applications in the field of assisted reproductive technologies.

Genomic and anatomical comparisons of skin support independent adaptation to life in water by cetaceans and hippos

The macroevolutionary transition from terra firma to obligatory inhabitance of the marine hydrosphere has occurred twice in the history of Mammalia: Cetacea and Sirenia. In the case of Cetacea (whales, dolphins, and porpoises), molecular phylogenies provide unambiguous evidence that fully aquatic cetaceans and semiaquatic hippopotamids (hippos) are each other's closest living relatives. Ancestral reconstructions suggest that some adaptations to the aquatic realm evolved in the common ancestor of Cetancodonta (Cetacea + Hippopotamidae). An alternative hypothesis is that these adaptations evolved independently in cetaceans and hippos. Here, we focus on the integumentary system and evaluate these hypotheses by integrating new histological data for cetaceans and hippos, the first genome-scale data for pygmy hippopotamus, and comprehensive genomic screens and molecular evolutionary analyses for protein-coding genes that have been inactivated in hippos and cetaceans. We identified eight skin-related genes that are inactivated in both cetaceans and hippos, including genes that are related to sebaceous glands, hair follicles, and epidermal differentiation. However, none of these genes exhibit inactivating mutations that are shared by cetaceans and hippos. Mean dates for the inactivation of skin genes in these two clades serve as proxies for phenotypic changes and suggest that hair reduction/loss, the loss of sebaceous glands, and changes to the keratinization program occurred ∼16 Ma earlier in cetaceans (∼46.5 Ma) than in hippos (∼30.5 Ma). These results, together with histological differences in the integument and prior analyses of oxygen isotopes from stem hippopotamids ("anthracotheres"), support the hypothesis that aquatic skin adaptations evolved independently in hippos and cetaceans.

The evolution of mammalian brain size

Relative brain size has long been considered a reflection of cognitive capacities and has played a fundamental role in developing core theories in the life sciences. Yet, the notion that relative brain size validly represents selection on brain size relies on the untested assumptions that brain-body allometry is restrained to a stable scaling relationship across species and that any deviation from this slope is due to selection on brain size. Using the largest fossil and extant dataset yet assembled, we find that shifts in allometric slope underpin major transitions in mammalian evolution and are often primarily characterized by marked changes in body size. Our results reveal that the largest-brained mammals achieved large relative brain sizes by highly divergent paths. These findings prompt a reevaluation of the traditional paradigm of relative brain size and open new opportunities to improve our understanding of the genetic and developmental mechanisms that influence brain size.

Characters from the deciduous dentition and its interest for phylogenetic reconstruction in Hippopotamoidea (Cetartiodactyla: Mammalia)

Teeth are frequently used in phylogeny in order to better characterize the evolution of extinct mammal species. While most studies have focused on the adult dentition, the consideration of characters from the deciduous dentition could also contribute to reinforce phylogenetic assumptions or disentangle phylogenetic issues. We chose to investigate the characters of the deciduous dentition in cetartiodactyl taxa in relation to the disputed relationships within hippopotamoids, especially the position of Hippopotamidae. We describe the deciduous dentition of 51 species, among a dataset of 70 cetartiodactyls. We noticed that second and third deciduous premolars have a much lower degree of molarization, and are more suitable for coding than fourth deciduous premolars. Thirty-nine resulting characters were thus added to a previously published matrix, and parsimony and maximum-likelihood analyses were performed. Both analyses provided a better resolved topology for most taxa than without these characters, and with better support for most nodes in the parsimony analysis. Moreover, this analysis provides additional characters supporting the hypothesis of an emergence of hippopotamids within bothriodontine anthracotheres from the Palaeogene of Africa. The promising use of characters from the deciduous dentition in phylogeny should allow discussion of the underlying ontogenetic mechanisms at the origin of dental homology.

Ecomorphological variation in artiodactyl calcanei using 3D geometric morphometrics

Artiodactyl postcrania are commonly used as paleoecological indicators but these studies are usually limited to artiodactyls within a single family. Here, we use 3D geometric morphometrics to analyze the morphology of calcanei from five artiodactyl families (Antilocapridae, Bovidae, Cervidae, Giraffidae, and Tragulidae) and identify common ecological trends among these families using principal component analysis. Our results indicate that antilocaprid and some bovid calcanei show convergent evolution of cursorial morphology and that other bovids have independently evolved less cursorial morphology that is more similar to cervids. This study shows that parallel ecomorphological trends can be identified in multiple families of artiodactyls, as well as within artiodactyl groups. This further suggests that the calcaneus may be a good indicator of ecology and function in fossil groups that are taxonomically ambiguous or not closely related to living taxa.

Characterization of Cetacean Proline-Rich Antimicrobial Peptides Displaying Activity against ESKAPE Pathogens

Proline-rich antimicrobial peptides (PrAMPs) may be a valuable weapon against multi-drug resistant pathogens, combining potent antimicrobial activity with low cytotoxicity. We have identified novel PrAMPs from five cetacean species (cePrAMPs), and characterized their potency, mechanism of action and in vitro cytotoxicity. Despite the homology between the N-terminal of cePrAMPs and the bovine PrAMP Bac7, some differences emerged in their sequence, activity spectrum and mode of action. CePrAMPs with the highest similarity with the Bac7(1-35) fragment inhibited bacterial protein synthesis without membrane permeabilization, while a second subgroup of cePrAMPs was more membrane-active but less efficient at inhibiting bacterial translation. Such differences may be ascribable to differences in presence and positioning of Trp residues and of a conserved motif seemingly required for translation inhibition. Unlike Bac7(1-35), which requires the peptide transporter SbmA for its uptake, the activity of cePrAMPs was mostly independent of SbmA, regardless of their mechanism of action. Two peptides displayed a promisingly broad spectrum of activity, with minimal inhibiting concentration MIC ≤ 4 µM against several bacteria of the ESKAPE group, including Pseudomonas aeruginosa and Enterococcus faecium. Our approach has led us to discover several new peptides; correlating their sequences and mechanism of action will provide useful insights for designing optimized future peptide-based antibiotics.

Evolution of placentation in cattle and antelopes

Bovids have enjoyed great evolutionary success as evidenced by the large number of extant species. Several important domestic animals are from this family. They derive from both subfamilies: cattle and their kin belong to Bovinae and sheep and goats to Antilopinae. The premise of this review, therefore, is that evolution of reproduction and placentation is best understood in a context that includes antelope-like bovines and antelopes. Many key features of placentation, including hormone secretion, had evolved before bovids emerged as a distinct group. Variation nevertheless occurs. Most striking is the difference in fusion of the binucleate trophoblast cell with uterine epithelium that yields a transient trinucleate cell in bovines and many antelopes, but a more persistent syncytium in wildebeest, sheep and goat. There is considerable variation in placentome number and villus branching within the placentome. Many antelopes have right-sided implantation in a bicornuate uterus whilst others have a uterus duplex. Finally, there has been continued evolution of placental hormones with tandem duplication of PAG genes in cattle, differences in glycosylation of placental lactogen and the emergence of placental growth hormone in sheep and goats. The selection pressures driving this evolution are unknown though maternal-fetal competition for nutrients is an attractive hypothesis.

Death is on Our Side: Paleontological Data Drastically Modify Phylogenetic Hypotheses

Fossils are the only remaining evidence of the majority of species that have ever existed, providing a direct window into events in evolutionary history that shaped the diversification of life on Earth. Phylogenies underpin our ability to make sense of evolution but are routinely inferred using only data available from living organisms. Although extinct taxa have been shown to add crucial information for inferring macroevolutionary patterns and processes (such as ancestral states, paleobiogeography and diversification dynamics), the role fossils play in reconstructing phylogeny is controversial. Since the early years of phylogenetic systematics, different studies have dismissed the impact of fossils due to their incompleteness, championed their ability to overturn phylogenetic hypotheses or concluded that their behavior is indistinguishable from that of extant taxa. Based on taxon addition experiments on empirical data matrices, we show that the inclusion of paleontological data has a remarkable effect in phylogenetic inference. Incorporating fossils often (yet not always) induces stronger topological changes than increasing sampling of extant taxa. Fossils also produce unique topological rearrangements, allowing the exploration of regions of treespace that are never visited by analyses of only extant taxa. Previous studies have proposed a suite of explanations for the topological behavior of fossils, such as their retention of unique morphologies or their ability to break long branches. We develop predictive models that demonstrate that the possession of distinctive character state combinations is the primary predictor of the degree of induced topological change, and that the relative impact of taxa (fossil and extant) can be predicted to some extent before any phylogenetic analysis. Our results bolster the consensus of recent empirical studies by showing the unique role of paleontological data in phylogenetic inference, and provide the first quantitative assessment of its determinants, with broad consequences for the design of taxon sampling in both morphological and total-evidence analyses. [phylogeny, morphology, fossils, parsimony, Bayesian inference.]

Dental characters used in phylogenetic analyses of mammals show higher rates of evolution, but not reduced independence

Accurate reconstructions of phylogeny are essential for studying the evolution of a clade, and morphological characters are necessarily used for the reconstruction of the relationships of fossil organisms. However, variation in their evolutionary modes (for example rate variation and character non-independence) not accounted for in analyses may be leading to unreliable phylogenies. A recent study suggested that phylogenetic analyses of mammals may be suffering from a dominance of dental characters, which were shown to have lower phylogenetic signal than osteological characters and produced phylogenies less congruent with molecularly-derived benchmarks. Here we build on this previous work by testing five additional morphological partitions for phylogenetic signal and examining what aspects of dental and other character evolution may be affecting this, by fitting models of discrete character evolution to phylogenies inferred and time calibrated using molecular data. Results indicate that the phylogenetic signal of discrete characters correlate most strongly with rates of evolution, with increased rates driving increased homoplasy. In a dataset covering all Mammalia, dental characters have higher rates of evolution than other partitions. They do not, however, fit a model of independent character evolution any worse than other regions. Primates and marsupials show different patterns to other mammal clades, with dental characters evolving at slower rates and being more heavily integrated (less independent). While the dominance of dental characters in analyses of mammals could be leading to inaccurate phylogenies, the issue is not unique to dental characters and the results are not consistent across datasets. Molecular benchmarks (being entirely independent of the character data) provide a framework for examining each dataset individually to assess the evolution of the characters used.

Architectural instability, inverted skews and mitochondrial phylogenomics of Isopoda: outgroup choice affects the long-branch attraction artefacts

The majority strand of mitochondrial genomes of crustaceans usually exhibits negative GC skews. Most isopods exhibit an inversed strand asymmetry, believed to be a consequence of an inversion of the replication origin (ROI). Recently, we proposed that an additional ROI event in the common ancestor of Cymothoidae and Corallanidae families resulted in a double-inverted skew (negative GC), and that taxa with homoplastic skews cluster together in phylogenetic analyses (long-branch attraction, LBA). Herein, we further explore these hypotheses, for which we sequenced the mitogenome of Asotana magnifica (Cymothoidae), and tested whether our conclusions were biased by poor taxon sampling and inclusion of outgroups. (1) The new mitogenome also exhibits a double-inverted skew, which supports the hypothesis of an additional ROI event in the common ancestor of Cymothoidae and Corallanidae families. (2) It exhibits a unique gene order, which corroborates that isopods possess exceptionally destabilized mitogenomic architecture. (3) Improved taxonomic sampling failed to resolve skew-driven phylogenetic artefacts. (4) The use of a single outgroup exacerbated the LBA, whereas both the use of a large number of outgroups and complete exclusion of outgroups ameliorated it.

Fast speciations and slow genes: uncovering the root of living canids

Despite ongoing efforts relying on computationally intensive tree-building methods and large datasets, the deeper phylogenetic relationships between living canid genera remain controversial. We demonstrate that this issue arises fundamentally from the uncertainty of root placement as a consequence of the short length of the branch connecting the major canid clades, which probably resulted from a fast radiation during the early diversification of extant Canidae. Using both nuclear and mitochondrial genes, we investigate the position of the canid root and its consistency by using three rooting methods. We find that mitochondrial genomes consistently retrieve a root node separating the tribe Canini from the remaining canids, whereas nuclear data mostly recover a root that places the Urocyon foxes as the sister lineage of living canids. We demonstrate that, to resolve the canid root, the nuclear segments sequenced so far are significantly less informative than mitochondrial genomes. We also propose that short intervals between speciations obscure the place of the true root, because methods are susceptible to stochastic error in the presence of short internal branches near the root.

Inferring the mammal tree: Species-level sets of phylogenies for questions in ecology, evolution, and conservation

Big, time-scaled phylogenies are fundamental to connecting evolutionary processes to modern biodiversity patterns. Yet inferring reliable phylogenetic trees for thousands of species involves numerous trade-offs that have limited their utility to comparative biologists. To establish a robust evolutionary timescale for all approximately 6,000 living species of mammals, we developed credible sets of trees that capture root-to-tip uncertainty in topology and divergence times. Our "backbone-and-patch" approach to tree building applies a newly assembled 31-gene supermatrix to two levels of Bayesian inference: (1) backbone relationships and ages among major lineages, using fossil node or tip dating, and (2) species-level "patch" phylogenies with nonoverlapping in-groups that each correspond to one representative lineage in the backbone. Species unsampled for DNA are either excluded ("DNA-only" trees) or imputed within taxonomic constraints using branch lengths drawn from local birth-death models ("completed" trees). Joining time-scaled patches to backbones results in species-level trees of extant Mammalia with all branches estimated under the same modeling framework, thereby facilitating rate comparisons among lineages as disparate as marsupials and placentals. We compare our phylogenetic trees to previous estimates of mammal-wide phylogeny and divergence times, finding that (1) node ages are broadly concordant among studies, and (2) recent (tip-level) rates of speciation are estimated more accurately in our study than in previous "supertree" approaches, in which unresolved nodes led to branch-length artifacts. Credible sets of mammalian phylogenetic history are now available for download at http://vertlife.org/phylosubsets, enabling investigations of long-standing questions in comparative biology.

Large-scale ruminant genome sequencing provides insights into their evolution and distinct traits

The ruminants are one of the most successful mammalian lineages, exhibiting morphological and habitat diversity and containing several key livestock species. To better understand their evolution, we generated and analyzed de novo assembled genomes of 44 ruminant species, representing all six Ruminantia families. We used these genomes to create a time-calibrated phylogeny to resolve topological controversies, overcoming the challenges of incomplete lineage sorting. Population dynamic analyses show that population declines commenced between 100,000 and 50,000 years ago, which is concomitant with expansion in human populations. We also reveal genes and regulatory elements that possibly contribute to the evolution of the digestive system, cranial appendages, immune system, metabolism, body size, cursorial locomotion, and dentition of the ruminants.

Unexpected evolutionary patterns of dental ontogenetic traits in cetartiodactyl mammals

Studying ontogeny in both extant and extinct species can unravel the mechanisms underlying mammal diversification and specialization. Among mammalian clades, Cetartiodactyla encompass species with a wide range of adaptations, and ontogenetic evidence could clarify longstanding debates on the origins of modern specialized families. Here, we study the evolution of dental eruption patterns in early diverging cetartiodactyls to assess the ecological and biological significance of this character and shed new light on phylogenetic issues. After investigation of the ontogenetic dental series of 63 extinct genera, our parsimony reconstructions of eruption state evolution suggest that the eruption of molars before permanent premolars represents a plesiomorphic condition within Cetartiodactyla. This result substantially differs from a previous study based on modern species only. As a result, the presence of this pattern in most ruminants might represent an ancestral condition contributing to their specialized herbivory, rather than an original adaptation. In contrast, the late eruption of molars in hippopotamoids is more likely related to biological aspects, such as increases in body mass and slower pace of life. Our study mainly shows that eruption sequences reliably characterize higher level cetartiodactyl taxa and could represent a new source of phylogenetic characters, especially to disentangle the origin of hippopotamoids and cetaceans.

A Comparison of Common Hippopotamus (Artiodactyla) and Mysticete (Cetacea) Nostrils: An Open and Shut Case

Hippos are considered the closest living relatives to cetaceans and they have some similar adaptations for aquatic living, such as a modified respiratory tract. Behavioral observations of male and female common hippos (Hippopotamus amphibius) at Disney's Animal Kingdom® and the Adventure Aquarium were conducted to describe and examine movements of the nostrils during respiration (inspiration, expiration, and inter-breath interval). The hippo nostril is a crescent shaped opening with lateral and medial aspects that are mobile and can be adducted and abducted to regulate the nostril opening. Notably, the default (resting) position of the nostrils is closed during the inter-breath interval, even when hippos are resting in water and their heads are not submerged. Similar to cetaceans, this aquatic adaptation protects the respiratory tract from an accidental incursion of water that can occur even when the nostrils are above water. Dissection of a deceased captive common hippo suggests there are separate muscles that pull the medial and lateral aspects for abduction. The internal nasal passage has a nasal plug that is similar in shape but less pronounced than the nasal plugs of two baleen whale species studied (minke whale Balaenoptera acutorostrata, fin whale Balaenoptera physalus). Examination of the musculature suggests fibers attach from the premaxillae and extend caudally to retract the plug to open the nasal passage. We discuss similarities and differences of the nostrils/blowholes of fully aquatic, semi-aquatic, and terrestrial species to assess adaptations related to environmental conditions that may be convergent or derived from a common ancestor. Anat Rec, 2018. © 2018 Wiley Periodicals, Inc. Anat Rec, 302:693-702, 2019. © 2018 Wiley Periodicals, Inc.

Tracing whale myoglobin evolution by resurrecting ancient proteins

Extant cetaceans, such as sperm whale, acquired the great ability to dive into the ocean depths during the evolution from their terrestrial ancestor that lived about 50 million years ago. Myoglobin (Mb) is highly concentrated in the myocytes of diving animals, in comparison with those of land animals, and is thought to play a crucial role in their adaptation as the molecular aqualung. Here, we resurrected ancestral whale Mbs, which are from the common ancestor between toothed and baleen whales (Basilosaurus), and from a further common quadrupedal ancestor between whale and hippopotamus (Pakicetus). The experimental and theoretical analyses demonstrated that whale Mb adopted two distinguished strategies to increase the protein concentration in vivo along the evolutionary history of deep sea adaptation; gaining precipitant tolerance in the early phase of the evolution, and increase of folding stability in the late phase.

From Anomalous Arteries to Selective Brain Cooling: Parallel Evolution of the Artiodactyl Carotid Rete

Terrestrial artiodactyls (even-toed ungulates) inhabit some of the world's most extreme environments, including arid deserts and high elevations. As medium-to-large-bodied mammals, artiodactyls have a suite of specialized physiologies to facilitate occupation of regions unavailable to other large mammals. One such physiology is selective brain cooling, wherein reduction of brain temperature below core body temperature has been demonstrated to reduce evaporative water loss. This physiology is enabled by an arterial heat-exchanger called the carotid rete. The ubiquity of the carotid rete throughout the clade, as well as its evolutionary history, is currently uninvestigated. Here, I use osteological correlates to survey clade-wide presence and morphology of the carotid rete, prior to conducting a preliminary evolutionary analysis. Nearly all living artiodactyls possess a carotid rete and are capable of selective brain cooling; however, major arteries supplying the rete are derived from different embryonic aortic arches on a suborder-specific basis. Ancestral character estimation infers this pattern of variation to be the result of independent evolutionary processes, suggesting carotid rete homoplasy arising via parallelism. This is a surprising finding given the role this structure plays in driving a physiology that has been implicated in mitigating artiodactylan responses to extreme environmental conditions. Future studies should incorporate extinct species represented in the fossil record to better parse between parallel and convergent mechanisms, as well as to better understand the relationship between the carotid rete, selective brain cooling, and survivorship of climate perturbation. Anat Rec, 2018. © 2018 Wiley Periodicals, Inc. Anat Rec, 303:308-317, 2020. © 2018 American Association for Anatomy.

On the revolution of cetacean evolution

The order of Cetacea with 88 species including Odontoceti (or toothed whales) and Mysticeti (or baleen whales) is the most specialized and diversified group of mammals. The blue whale with a maximum recorded length of 29.9 m for 173 t of weight is the largest animal known to have ever existed, and any dolphin's brain is most powerful and complex than any other brain in the animal kingdom, second only to primate's. Nevertheless, Cetacea are mammals that re-entered the oceans only a little over 50 million years ago, a relatively short time on the evolutionary scale. During this time cetaceans and humans have developed marked morphological and behavioral differences, yet their genomes show a high level of similarity. This present review is focused on the description and significance of newly accessible cetacean genome tools and information, and their relevance in the study of the evolution of successful phenotypic adaptations associated to mammal's marine existence, and their applicability to the unresolved disease mechanisms in humans.

Prion Disease in Dromedary Camels, Algeria

Prions cause fatal and transmissible neurodegenerative diseases, including Creutzfeldt-Jakob disease in humans, scrapie in small ruminants, and bovine spongiform encephalopathy (BSE). After the BSE epidemic, and the associated human infections, began in 1996 in the United Kingdom, general concerns have been raised about animal prions. We detected a prion disease in dromedary camels (Camelus dromedarius) in Algeria. Symptoms suggesting prion disease occurred in 3.1% of dromedaries brought for slaughter to the Ouargla abattoir in 2015–2016. We confirmed diagnosis by detecting pathognomonic neurodegeneration and disease-specific prion protein (PrP^Sc) in brain tissues from 3 symptomatic animals. Prion detection in lymphoid tissues is suggestive of the infectious nature of the disease. PrP^Sc biochemical characterization showed differences with BSE and scrapie. Our identification of this prion disease in a geographically widespread livestock species requires urgent enforcement of surveillance and assessment of the potential risks to human and animal health.

The Dolphin Proline-Rich Antimicrobial Peptide Tur1A Inhibits Protein Synthesis by Targeting the Bacterial Ribosome

Proline-rich antimicrobial peptides (PrAMPs) internalize into susceptible bacteria using specific transporters and interfere with protein synthesis and folding. To date, mammalian PrAMPs have so far been identified only in artiodactyls. Since cetaceans are co-phyletic with artiodactyls, we mined the genome of the bottlenose dolphin Tursiops truncatus, leading to the identification of two PrAMPs, Tur1A and Tur1B. Tur1A, which is orthologous to the bovine PrAMP Bac7, is internalized into Escherichia coli, without damaging the membranes, using the inner membrane transporters SbmA and YjiL/MdM. Furthermore, like Bac7, Tur1A also inhibits bacterial protein synthesis by binding to the ribosome and blocking the transition from the initiation to the elongation phase. By contrast, Tur1B is a poor inhibitor of protein synthesis and may utilize another mechanism of action. An X-ray structure of Tur1A bound within the ribosomal exit tunnel provides a basis to develop these peptides as novel antimicrobial agents.

Evolution of the MC5R gene in placental mammals with evidence for its inactivation in multiple lineages that lack sebaceous glands

MC5R is one of five melanocortin receptor genes found in placental mammals. MC5R plays an important role in energy homeostasis and is also expressed in the terminal differentiation of sebaceous glands. Among placental mammals there are multiple lineages that either lack or have degenerative sebaceous glands including Cetacea (whales, dolphins, and porpoises), Hippopotamidae (hippopotamuses), Sirenia (manatees and dugongs), Proboscidea (elephants), Rhinocerotidae (rhinos), and Heterocephalus glaber (naked mole rat). Given the loss or diminution of sebaceous glands in these taxa, we procured MC5R sequences from publicly available genomes and transcriptomes, supplemented by a newly generated sequence for Choeropsis liberiensis (pygmy hippopotamus), to determine if this gene remains intact or is inactivated in association with loss/reduction of sebaceous glands. Our data set includes complete MC5R sequences for 114 placental mammal species including two individuals of Mammuthus primigenius (woolly mammoth) from Oimyakon and Wrangel Island. Complete loss or inactivation of the MC5R gene occurs in multiple placental lineages that have lost sebaceous glands (Cetacea, West Indian manatee, African elephant, white rhinoceros) or are characterized by unusual skin (pangolins, aardvarks). Both M. primigenius individuals share inactivating mutations with the African elephant even though sebaceous glands have been reported in the former. MC5R remains intact in hippopotamuses and the naked mole rat, although slightly elevated dN/dS ratios in these lineages allow for the possibility that the accumulation of inactivating mutations in MC5R may lag behind the relaxation of purifying selection. For Cetacea and Hippopotamidae, the absence of shared inactivating mutations in two different skin genes (MC5R, PSORS1C2) is consistent with the hypothesis that semi-aquatic lifestyles were acquired independently in these clades following divergence from a common ancestor.

Inferring 'weak spots' in phylogenetic trees: application to mosasauroid nomenclature

Mosasauroid squamates represented the apex predators within the Late Cretaceous marine and occasionally also freshwater ecosystems. Proper understanding of the origin of their ecological adaptations or paleobiogeographic dispersals requires adequate knowledge of their phylogeny. The studies assessing the position of mosasauroids on the squamate evolutionary tree and their origins have long given conflicting results. The phylogenetic relationships within Mosasauroidea, however, have experienced only little changes throughout the last decades. Considering the substantial improvements in the development of phylogenetic methodology that have undergone in recent years, resulting, among others, in numerous alterations in the phylogenetic hypotheses of other fossil amniotes, we test the robustness in our understanding of mosasauroid beginnings and their evolutionary history. We re-examined a data set that results from modifications assembled in the course of the last 20 years and performed multiple parsimony analyses and Bayesian tip-dating analysis. Following the inferred topologies and the 'weak spots' in the phylogeny of mosasauroids, we revise the nomenclature of the 'traditionally' recognized mosasauroid clades, to acknowledge the overall weakness among branches and the alternative topologies suggested previously, and discuss several factors that might have an impact on the differing phylogenetic hypotheses and their statistical support.

Dental Data Perform Relatively Poorly in Reconstructing Mammal Phylogenies: Morphological Partitions Evaluated with Molecular Benchmarks

Phylogenetic trees underpin reconstructions of evolutionary history and tests of evolutionary hypotheses. They are inferred from both molecular and morphological data, yet the relative value of morphology has been questioned in this context due to perceived homoplasy, developmental linkage, and nonindependence of characters. Nevertheless, fossil data are limited to incomplete subsets of preserved morphology, and different regions are treated as equivalent. Through meta-analysis of 40 data sets, we show here that the dental and osteological characters of mammals convey significantly different phylogenetic signals, and that osteological characters are significantly more compatible with molecular trees. Furthermore, the application of simplified paleontological filters (retaining only dental data) results in significantly greater loss of phylogenetic signal than random character ablation. Although the mammal fossil record is largely comprised of teeth, dental data alone are generally found to be less reliable for phylogenetic reconstruction given their incongruence with osteological and molecular data. These findings highlight the need for rigorous meta-analyses of distributions of homoplasy in morphological data. These tests, and consequent refinements to phylogenetic analyses that they permit, promise to improve the quality of all macroevolutionary studies that hinge on accurate trees. [Homoplasy; Mammalia; morphology; osteology; phylogeny; teeth.

Craniodental and humeral morphology of a new species of Masrasector (Teratodontinae, Hyaenodonta, Placentalia) from the late Eocene of Egypt and locomotor diversity in hyaenodonts

Hyaenodonta is a diverse clade of carnivorous mammals that were part of terrestrial faunas in the Paleogene of Eurasia and North America, but the oldest record for the group is Afro-Arabian, making the record there vital for understanding the evolution of this wide-spread group. Previous studies show an ancient split between two major clades of hyaenodonts that converged in hypercarnivory: Hyainailourinae and Hyaenodontinae. These clades are each supported by cranial characters. Phylogenetic analyses of hyaenodonts also support the monophyly of Teratodontinae, an Afro-Arabian clade of mesocarnivorous to hypercarnivorous hyaenodonts. Unfortunately, the cranial anatomy of teratodontines is poorly known, and aligning the clade with other lineages has been difficult. Here, a new species of the phylogenetically controversial teratodontine Masrasector is described from Locality 41 (latest Priabonian, late Eocene) from the Fayum Depression, Egypt. The hypodigm includes the most complete remains of a Paleogene teratodontine, including largely complete crania, multiple dentaries, and isolated humeri. Standard and "tip-dating" Bayesian analyses of a character-taxon matrix that samples cranial, postcranial, and dental characters support a monophyletic Masrasector within Teratodontinae, which is consistently placed as a close sister group of Hyainailouridae. The cranial morphology of Masrasector provides new support for an expanded Hyainailouroidea (Teratodontinae + Hyainailouridae), particularly characters of the nuchal crest, palate, and basicranium. A discriminant function analysis was performed using measurements of the distal humerus from a diverse sample of extant carnivorans to infer the locomotor habits of Masrasector. Masrasector was assigned to the "terrestrial" locomotor category, a result consistent with the well-defined medial trochlear ridges, and moderately developed supinator crests of the specimens. Masrasector appears to have been a fast-moving terrestrial form with a diverse diet. These specimens considerably improve our understanding of Teratodontinae, an ancient member of the Afro-Arabian mammalian fauna, and our understanding of hyaenodont diversity before the dispersal of Carnivora to the continent near the end of the Paleogene.