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The RCA cluster in mammalian genomes encodes several proteins that recognize antigens or pathogens in the innate immune response to infection. However, in rodents and primates there is evidence that two different RCA genes (called Zp3r in mice, C4BPA in humans) are expressed in sperm and bind proteins expressed in the egg coat at fertilization. We will use codon models to characterize the rate of adaptive molecular evolution (the response to positive selection) for each gene in Glires (rodents, rabbits + pikas) and in Primates (lemurs + lorises, tarsiers, monkeys, and humans + other apes). By comparing among genes and between taxa, we can test the prediction that sexual selection associated with sperm competition (among males) or conflicts of interest (between mates) leads to higher rates of adaptive evolution in rodent Zp3r and in primate C4BPA, compared to other genes in the RCA cluster (or compared to the orthologous gene in the other taxon) under natural selection associated with pathogen defense.

The acquisition of UCP1-mediated non-shivering thermogenesis (NST) was an important event during the evolution of mammals. Here, we assessed the thermogenic neofunctionalization that occurred in the mammalian UCP1, by performing detailed comparative evolutionary genomics analyses (including phylogenetic and selection analyses) of the UCP family members across all major vertebrate classes. Heterogeneously distributed positive selection signatures were found in several UCPs, being preferably located in the mitochondrial matrix domains. Additionally, comparisons with non-mammalian orthologs showed increased evolutionary rates of the mammalian UCP1, not observable in the phylogenetically related UCP2 and UCP3 paralogs. Also, parallel signatures of episodic positive selection (ω > 1) were found in the ancestral branches of both Glires (rodents and lagomorphs) and Afroinsectivores (afrosoricids and macroscelids), underlining the importance of the UCP1 thermogenic activity in these mammalian groups. Finally, we hypothesize that the independent positive selection events that occurred in these two lineages resulted in two UCP1-mediated NST approaches, namely the cold acute response in the Glires and the reproduction success enhancement in the Afroinsectivores.

Comparisons of wild and domestic populations have established brain reduction as one of the most consistent patterns correlated with domestication. Over a century of scholarly work has been devoted to this subject, and yet, new data continue to foster its debate. Current arguments, both for and against the validity of brain reduction occurring in domestic taxa, have repeatedly cited a small set of reviews on this subject. The original works, their sampling, methodological details, and nuances of results that would be key to establishing validity, particularly in light of new data, have not been investigated. To facilitate and encourage a more informed discussion, we present a comprehensive review of original brain reduction literature for four mammalian clades: Artiodactyla, Perissodactyla, Carnivora, and Glires. Among these are studies that generated the most cited brain reduction values in modern domestication literature. In doing so, we provide a fairer stage for the critique of traits associated with domestication. We conclude that while brain reduction magnitudes may contain error, empirical data collectively support the reduction in brain size and cranial capacity for domestic forms.

Diverse morphological evidence from both living and fossil taxa suggests several higher-level groupings of the Recent orders of eutherian mammals. The strongest hypotheses closely relate rodents and lagomorphs within Glires, proboscideans and sirenians within Tethytheria, hyracoids and tethytheres within Paenungulata, chiropterans and dermopterans, and pholidotans and edentates. Somewhat weaker evidence supports groupings of Glires with macroscelideans, primates and tree-shrews with bats and flying lemurs (Archonta), and all Eutheria excluding pangolins and edentates (Epitheria). There is some tenuous evidence for the monophyly of all modern ungulate orders (including cetaceans), and for the division between artiodactyls and other ungulates. Rather than providing only a confusing and unresolved picture of higher eutherian relationships, comparative morphology and paleontology offer some compelling hypotheses that comprise a framework for studies of macromolecular traits.

The position of some taxa on the Tree of Life remains controversial despite the increase in genomic data used to infer phylogenies. While analyzing large datasets alleviates stochastic errors, it does not prevent systematic errors in inference, caused by both biological (e.g., incomplete lineage sorting, hybridization) and methodological (e.g., incorrect modeling, erroneous orthology assessments) factors. In our study, we systematically investigated factors that could result in these controversies, using the treeshrew (Scandentia, Mammalia) as a study case. Recent studies have narrowed the phylogenetic position of treeshrews to three competing hypotheses: sister to primates and flying lemurs (Primatomorpha), sister to rodents and lagomorphs (Glires), or sister to a clade comprising all of these. We sampled 50 mammal species including three treeshrews, a selection of taxa from the potential sister groups, and outgroups. Using a large diverse set of loci, we assessed support for the alternative phylogenetic position of treeshrews. A plurality of loci support treeshrews as sister to rodents and lagomorphs; however, only a few loci exhibit strong support for any hypothesis. Surprisingly, we found that a subset of loci that strongly support the monophyly of Primates, support treeshrews as sister to primates and flying lemurs. The overall small magnitude of differences in phylogenetic signal among the alternative hypotheses suggests that these three groups diversified nearly simultaneously. However, with our large dataset and approach to examining support, we provide evidence for the hypothesis of treeshrews as sister to rodents and lagomorphs, while demonstrating why support for alternate hypotheses has been seen in prior work. We also suggest that locus selection can unwittingly bias results.

My thesis explores how the information content of fossil Glires (rodents + rabbits) effects phylogenetic reconstruction and the implications for downstream analysis and interpretation. The first two chapters take a detailed look at the phylogenetic signal contained within fossil Glires, while the third and fourth chapters put interpretation of fossils into practice through analyses of phylogeny, biogeographic history, anatomy and geometric morphometrics. In the final chapter, I discuss the importance of my biogeographic, anatomical and phylogenetic results within the context of Glires evolution. I also recommend the inclusion of fossil data in total-evidence approaches where possible and give suggestions for future work., Whitten Studentship

The middle Eocene in Nei Mongol (China) was an interval of profound faunal changes as regards the basal Glires and gliriform mammals in general. A major diversification of rodent lineages (ctenodactyloids) and more modern small-sized lagomorphs was accompanied by a decline of mimotonids (Gomphos and Mimolagus) and anagalids. The latter was an enigmatic group of basal Euarchontoglires endemic to China and Mongolia. Here, we describe the first anagalid tooth (a P4) from the Huheboerhe classic site in the Erlian Basin. The tooth, characterized by its unique morphology intermediate between mimotonids and anagalids is semihypsodont, has a single buccal root typical of mimotonids, a large paracone located anteriorly, and a nascent hypocone, characteristic of advanced anagalids. The new finding of neither an abundant nor speciose group suggests a greater diversity of anagalids in the Eocene of China. This discovery is important because it demonstrates the convergent adaptations in anagalids, possibly of ecological significance.

From darkness to Enlightenment, and vice versa: rediscovery of the skull of Procavia capensis (Pallas, 1766) (Hyracoidea, Mammalia) described in 1767 by Daubenton in the Histoire naturelle.A skull of Procavia capensis (Pallas, 1766) (Hyracoidea, Mammalia), currently on display in the Galerie de Paleontologie et d'Anatomie comparee (Paleontology and comparative Anatomy Gallery) of the Museum national d'Histoire naturelle, Paris, is here identified as the one Daubenton described in 1767 in the catalog of the viviparous quadruped collections of the King's Cabinet he wrote for Buffon's Histoire naturelle (Natural History). While Daubenton clearly recognized in this skull from Sidon, Lebanon, the most remarkable characters of hyracoids, especially the teeth, he could not identify the animal, since the first precise description of the species was published by Pallas at the same time (at the end of 1766). In subsequent volumes of the Histoire naturelle, Buffon repeatedly dealt with the hyrax, on the basis of new data, but he failed to assign the skull of Sidon to this species, although Pallas recognized the nature of this skull as early as 1776. In a volume of the Histoire naturelle published in 1789, after Buffon's death, this skull was illustrated on a plate and considered as belonging to a primate, the Bengal slow loris (Nycticebus bengalensis (Lacepede, 1800)). Fifteen years later, it was one of the specimens which enabled Cuvier to remove the hyrax from the order Glires or Rodents, in which it was generally placed since Pallas, to assign it to the Pachydermes.

A new genus and species of eurymylid (Mammalia, Glires) from the upper Paleocene of Xinjiang, northwestern China, is reported. Eurymylids are a group of basal Glires, containing stem taxa to rodents. The new taxon is based on an anterior part of a skull with poorly preserved dentition. The preserved dental morphologies are sufficient to show that the new taxon has important differences from other basal Glires. The enamel microstructure of the new taxon is simple, which has prisms with variable sizes and distinct seams, and probably primitive for Glires. The new taxon adds to the species diversity and morphology of the basal Glires in Asia. It further supports the notion that Asia was the origin center for Glires. The temporal distributions of the Asian eurymylids, mimotonids, and alagomyids are exclusively Paleogene and suggest potential competing relationships between them and rodents and lagomorphs during the transition from the Late Paleocene to Eocene. As an important group of the Paleogene mammals, the Glires evolution may also be affected by regional and global environmental changes that have shaped faunal turnover patterns of central Asia.

The rhinarium, a specialized nose-tip characterized by an area of naked and wet skin around the nostrils, is a typical mammalian structure. The type and amount of innervation suggests a sensory role and morphological diversity implies so far unidentified species-specific functional specializations. Rhinaria also vary in temperature and this may be related to the functions of these sensory organs. We performed a comparative study on rhinarium temperature in order to learn more about possible correlations with phylogeny and ecology. We have concentrated on terrestrial carnivorans and large herbivores, but also investigated a number of other species, some of them lacking typical rhinaria. We used infrared (IR) thermography to determine nose skin temperatures from safe distances and without interfering with the animals’ behavior. In all groups studied, the temperature of the rhinarium/nose-tip decreased with decreasing ambient temperature. At all ambient temperatures, rhinarium temperature was lower, by 9–17 °C, in carnivorans compared to herbivores. Glires (rodents and lagomorphs), haplorrhine primates, and omnivorous Perisso- and Artiodactyla were intermediate. In strepsirrhine primates, rhinarium temperature was similar to ambient temperature. Our findings in Strepsirrhini are consistent with the hypothesis that their rhinaria have an indirect role in chemical communication. Warm rhinaria in herbivores suggest a tactile function, while the low skin temperatures on carnivoran rhinaria may make the skin particularly sensitive to warming.

Glires, the most speciose clade of placental mammals nowadays includes the conservative, uniformly shaped lagomorphs and widely diversified rodents. Both groups are recognized in the fossil record since the early Paleogene, but Rodentia appeared slightly earlier (the late Paleocene) than lagomorphs of modern aspect (the early Eocene). The earliest Glires currently recognized come from Asia (East China), where they were scarce and relatively poorly diversified. They are basal taxa of neither rodent nor lagomorph clear affiliations, although probably ancestral for both. In contrast, the earliest record of North American Glires consists of scarce Rodentiaformes (known also from the late Paleocene of Asia) and the primitive basal rodents Ischyromyidae, the latter a widely diversified and abundant group. Ischyromyid rodents differ from other basal Glires lineages in generally large size, approximately that of ground squirrels or marmots. Ischyromyids are an important example of “the Paleocene Paradox” in the fossil record, which is a discrepancy between the fact that the earliest fossil rodents are known from North America while it is widely presumed that the Rodentia originated in Asia from earlier gliroid mammals. Here, I provide a brief review of the early diversification of Glires both in Asia and North America, and discuss the earliest morphologies in this group. Two related important points in the beginning of the evolutionary history of Glires are the skull structure as a whole and the dentition.

Quantification of skeletal remains in faunal assemblages is often central to the study of human behavior at archaeological sites. Recently, we introduced the Number of Distinct Elements (NDE) as a simpler, experimentally robust alternative to the Minimum Number of Elements (MNE). The MNE is a widely used counting method that has been shown to inflate the representation of rare elements and is affected by the issue of aggregation, among other problems (Morin et al., 2017, Journal of Archaeological Method and Theory 24, 938–973). The NDE approach avoids both of these issues because it focuses on a specific suite of constant landmarks, which means that counts are independent of sample size. The present paper discusses how the NDE differs from MNE and zone-based recording methods and expands its use to equids, suiformes, camelids, tapirids, proboscideans, rhinocerotids and carnivores. A list of NDE landmarks is also presented for typically smaller animals, such as glires (rodents and lagomorphs), birds and turtles/tortoises.

The blood concentrations of leukocytes and the major classes of leukocytes were compared across over 200 species of birds and over 300 species of mammals based on phylogenic relations, body weight and diet. The concentration of leukocytes was markedly higher in birds than mammals reflecting elevated concentrations of all major classes but particularly those of lymphocytes, monocytes, eosinophils and basophils. Overall, there were no differences between blood leukocyte concentrations in placental and marsupial mammals. There were differences between leukocytes concentrations within the placental mammals, for instance being lower in mammalian species within the taxa Glires than in Laurasiatheria and Primatomorpha which in turn are lower than in Afrotheria and Xenarthra. There were also differences in leukocyte concentrations in birds being higher in species with the taxa Afroaves than in Australaves. There were phylogenic differences in the percentages of the leukocyte classes. For instance, in placental compared marsupial mammals, the percentage neutrophils is elevated, the percentage lymphocytes is depressed and neutrophil to lymphocyte (N:L) ratio was much higher. Moreover, the percentage heterophils is high, the percentage lymphocytes is low and heterophil to lymphocyte (H:L) ratio is greater in birds from the taxa Paleognathae than the Neognathae. There was a positive relationship between concentrations of leukocytes or neutrophils and log body weight

Early lagomorphs are central to our understanding of how the brain evolved in Glires (rodents, lagomorphs and their kin) from basal members of Euarchontoglires (Glires + Euarchonta, the latter grouping primates, treeshrews, and colugos). Here, we report the first virtual endocast of the fossil lagomorphMegalagus turgidus, from the Orella Member of the Brule Formation, early Oligocene, Nebraska, USA. The specimen represents one of the oldest nearly complete lagomorph skulls known. Primitive aspects of the endocranial morphology inMegalagusinclude large olfactory bulbs, exposure of the midbrain, a small neocortex and a relatively low encephalization quotient. Overall, this suggests a brain morphology closer to that of other basal members of Euarchontoglires (e.g. plesiadapiforms and ischyromyid rodents) than to that of living lagomorphs. However, the well-developed petrosal lobules inMegalagus, comparable to the condition in modern lagomorphs, suggest early specialization in that order for the stabilization of eye movements necessary for accurate visual tracking. Our study sheds new light on the reconstructed morphology of the ancestral brain in Euarchontoglires and fills a critical gap in the understanding of palaeoneuroanatomy of this major group of placental mammals.

Anagalidae are extinct primitive Euarchontoglires from Asia, regarded as relatively closely related to basal Glires. So far, the group has been reported only from China and stratigraphically spans from the early Paleocene to the latest Eocene/earliest Oligocene. Anagalids are characterized by a relatively full dental formula featuring slightly enlarged semi-procumbent incisors, prominent canines, and tall cheek teeth with usually heavily worn crowns, indicative of an abrasive diet. Here we report a new genus and species from the late Eocene Ergilin Dzo Formation in southern Mongolia. The first non-Chinese anagalid is also the northernmost record of the family. Zofiagale ergilinensis gen. and sp.nov. is remarkable for its relatively small size (comparable only to the Paleocene genera Huaiyangale and Stenanagale), lack of P1, and molariform teeth showing almost no wear, suggesting a different diet than most Anagalidae. Furthermore, its molars display a strong buccal cingulum, a character in anagalids shared only with Wanogale. Our phylogenetic analysis of representatives of all anagalid genera based on 82 dental characters places Anagale and Anaptogale as the most basal lineages and clusters Zofiagale gen. nov. together with Qipania and Hsiuannania. These results suggest three independent northward dispersal events within the family in the late Eocene.

Hepatitis C virus (HCV) belongs to the Hepacivirus genus and is genetically heterogeneous, with seven major genotypes further divided into several recognized subtypes. HCV origin was previously dated in a range between ∼200 and 1000 years ago. Hepaciviruses have been identified in several domestic and wild mammals, the largest viral diversity being observed in bats and rodents. The closest relatives of HCV were found in horses/donkeys (equine hepaciviruses, EHV). However, the origin of HCV as a human pathogen is still an unsolved puzzle. Using a selection-informed evolutionary model, we show that the common ancestor of extant HCV genotypes existed at least 3000 years ago (CI: 3192–5221 years ago), with the oldest genotypes being endemic to Asia. EHV originated around 1100 CE (CI: 291–1640 CE). These time estimates exclude that EHV transmission was mainly sustained by widespread veterinary practices and suggest that HCV originated from a single zoonotic event with subsequent diversification in human populations. We also describe a number of biologically important sites in the major HCV genotypes that have been positively selected and indicate that drug resistance-associated variants are significantly enriched at positively selected sites. HCV exploits several cell-surface molecules for cell entry, but only two of these (CD81 and OCLN) determine the species-specificity of infection. Herein evolutionary analyses do not support a long-standing association between primates and hepaciviruses, and signals of positive selection at CD81 were only observed in Chiroptera. No evidence of selection was detected for OCLN in any mammalian order. These results shed light on the origin of HCV and provide a catalog of candidate genetic modulators of HCV phenotypic diversity.

Phylogenetic inference artifacts can occur when sequence evolution deviates from assumptions made by the models used to analyze them. The combination of strong model assumption violations and highly heterogeneous lineage evolutionary rates can become problematic in phylogenetic inference, and lead to the well-described long-branch attraction (LBA) artifact. Here, we define an objective criterion for assessing lineage evolutionary rate heterogeneity among predefined lineages: the result of a likelihood ratio test between a model in which the lineages evolve at the same rate (homogeneous model) and a model in which different lineage rates are allowed (heterogeneous model). We implement this criterion in the algorithm Locus Specific Sequence Subsampling (LS³), aimed at reducing the effects of LBA in multi-gene datasets. For each gene, LS³ sequentially removes the fastest-evolving taxon of the ingroup and tests for lineage rate homogeneity until all lineages have uniform evolutionary rates. The sequences excluded from the homogeneously evolving taxon subset are flagged as potentially problematic. The software implementation provides the user with the possibility to remove the flagged sequences for generating a new concatenated alignment. We tested LS³ with simulations and two real datasets containing LBA artifacts: a nucleotide dataset regarding the position of Glires within mammals and an amino-acid dataset concerning the position of nematodes within bilaterians. The initially incorrect phylogenies were corrected in all cases upon removing data flagged by LS³.

The present study describes the organization of the nuclei of the cholinergic, catecholaminergic, serotonergic and orexinergic systems in the brains of two members of Euarchontoglires, Lepus capensis and Tupaia belangeri. The aim of the present study was to investigate the nuclear complement of these neural systems in comparison to previous studies on Euarchontoglires and generally with other mammalian species. Brains were coronally sectioned and immunohistochemically stained with antibodies against choline acetyltransferase, tyrosine hydroxylase, serotonin and orexin-A. The majority of nuclei revealed in the current study were similar between the species investigated and to mammals generally, but certain differences in the nuclear complement highlight potential phylogenetic interrelationships within the Euarchontoglires and across mammals. In the northern tree shrew the nucleus of the trapezoid body contained neurons immunoreactive to the choline acetyltransferase antibody with some of these neurons extending into the lamellae within the superior olivary nuclear complex (SON). The cholinergic nature of the neurons of this nucleus, and the extension of cholinergic neurons into the SON, has not been noted in any mammal studied to date. In addition, cholinergic neurons forming the medullary tegmental field were also present in the northern tree shrew. Regarding the catecholaminergic system, the cape hare presented with the rodent specific rostral dorsal midline medullary nucleus (C3), and the northern tree shrew lacked both the ventral and dorsal divisions of the anterior hypothalamic group (A15v and A15d). Both species were lacking the primate/megachiropteran specific compact portion of the locus coeruleus complex (A6c). The nuclei of the serotonergic and orexinergic systems of both species were similar to those seen across most Eutherian mammals. Our results lend support to the monophyly of the Glires, and more broadly suggest that the megachiropterans are more closely related to the primates than are any other members of Euarchontoglires studied to date.

Glires (lagomorphs, rodents, and their kin), based on molecular and morphological evidence, form a monophyletic clade nested within Euarchontoglires, a large clade including also primates, tree shrews (Scandentia), and flying lemurs (Dermoptera). The earliest currently known Glires are represented by duplicidentate lineage (closer to lagomorphs than to rodents), which appeared shortly after the K/Pg boundary in Asia. Evolution of Glires is interspersed with instances of convergence between its two main branches: Duplicidentata and Simplicidentata (rodents, eurymylids, and their relatives), and also convergences on basal Euarchontoglires (Pseudictopidae), Anagalidae, or even some ungulate lineages. Within more closely related basal lines, parallel evolution is frequent. Homoplastic characters manifest themselves mainly in the teeth and appendicular skeleton. An important example of convergent evolution within Glires (and broader within Euarchontoglires) is the structure of the tarsal joint, and the calcaneal morphology in particular. Lagomorphs, similar to ungulates and elephant shrews (and several fossil taxa), have two articulation facets at the eminence of the calcaneus. The calcaneoastragalar facet is typical of all mammals, while the calcaneofibular one is characteristic of all true lagomorphs and probably Mimotona, the earliest duplicidentate, but is absent in Gomphos and Mimolagus. Further, it is known in Rhombomylus, a Paleogene Asian eurymylid (basal simplicidentate), and in Paleocene Pseudictops, a basal Euarchontoglires. The calcaneofibular facet stabilizes the tarsal joint, thus contributing to increased cursoriality. Overall, this chapter focuses on convergence and parallelism observed in the dental and pedal characters of the early Glires, with emphasis on the duplicidentates.

Background Phylogenetic relationships between Lagomorpha, Rodentia and Primates and their allies (Euarchontoglires) have long been debated. While it is now generally agreed that Rodentia constitutes a monophyletic sister-group of Lagomorpha and that this clade (Glires) is sister to Primates and Dermoptera, higher-level relationships within Rodentia remain contentious. Results We have sequenced and performed extensive evolutionary analyses on the mitochondrial genome of the scaly-tailed flying squirrel Anomalurus sp., an enigmatic rodent whose phylogenetic affinities have been obscure and extensively debated. Our phylogenetic analyses of the coding regions of available complete mitochondrial genome sequences from Euarchontoglires suggest that Anomalurus is a sister taxon to the Hystricognathi, and that this clade represents the most basal divergence among sampled Rodentia. Bayesian dating methods incorporating a relaxed molecular clock provide divergence-time estimates which are consistently in agreement with the fossil record and which indicate a rapid radiation within Glires around 60 million years ago. Conclusion Taken together, the data presented provide a working hypothesis as to the phylogenetic placement of Anomalurus, underline the utility of mitochondrial sequences in the resolution of even relatively deep divergences and go some way to explaining the difficulty of conclusively resolving higher-level relationships within Glires with available data and methodologies.

Understanding the pattern of brain evolution in early rodents is central to reconstructing the ancestral condition for Glires, and for other members of Euarchontoglires including Primates. We describe the oldest virtual endocasts known for fossil rodents, which pertain toParamys copei(Early Eocene) andParamys delicatus(Middle Eocene). Both specimens ofParamyshave larger olfactory bulbs and smaller paraflocculi relative to total endocranial volume than later occurring rodents, which may be primitive traits for Rodentia. The encephalization quotients (EQs) ofPa. copeiandPa. delicatusare higher than that of later occurring (Oligocene)Ischyromys typus, which contradicts the hypothesis that EQ increases through time in all mammalian orders. However, both species ofParamyshave a lower relative neocortical surface area than later rodents, suggesting neocorticalization occurred through time in this Order, although to a lesser degree than in Primates.Paramyshas a higher EQ but a lower neocortical ratio than any stem primate. This result contrasts with the idea that primates were always exceptional in their degree of overall encephalization and shows that relative brain size and neocortical surface area do not necessarily covary through time. As such, these data contradict assumptions made about the pattern of brain evolution in Euarchontoglires.

Comparative studies amongst extant species are one of the pillars of evolutionary neurobiology. In the 20th century, most comparative studies remained restricted to analyses of brain structure volume and surface areas, besides estimates of neuronal density largely limited to the cerebral cortex. Over the last 10 years, we have amassed data on the numbers of neurons and other cells that compose the entirety of the brain (subdivided into cerebral cortex, cerebellum, and rest of brain) of 39 mammalian species spread over 6 clades, as well as their densities. Here we provide that entire dataset in a format that is readily useful to researchers of any area of interest in the hope that it will foster the advancement of evolutionary and comparative studies well beyond the scope of neuroscience itself. We also reexamine the relationship between numbers of neurons, neuronal densities and body mass, and find that in the rest of brain, but not in the cerebral cortex or cerebellum, there is a single scaling rule that applies to average neuronal cell size, which increases with the linear dimension of the body, even though there is no single scaling rule that relates the number of neurons in the rest of brain to body mass. Thus, larger bodies do not uniformly come with more neurons - but they do fairly uniformly come with larger neurons in the rest of brain, which contains a number of structures directly connected to sources or targets in the body.