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Apodemus peninsulae, a dominant rodent species in temperature forests of northeastern China, is a model animal to explore the ecological functions of reciprocal coevolution of animals and plants. From August to October 2016, 24 infra-red cameras were installed to study the feeding behavior and activity patterns of A. peninsulae in its natural environment. By analyzing 5618 video records, we found that feeding behavior, followed by motor and sentinel behaviors, was their main activity. In the behavior spectra, motor behavior (creep, walk, and skip), feeding behavior (forage, feeding, transport, hoarding, and clean), and sentinel behavior (alert, flee, banishment, and coexistence) accounted for 57.96%, 40.36%, and 1.68% of their behavior, respectively. The peak of feeding behavior occurred between 18:00 and 23:00, and feeding behavior frequency, duration, and activity rhythms differ among August to October. Furthermore, activity was the greatest after sunset and before sunrise, indicating a nocturnal lifestyle; however, from August to October, the start time of the activity was earlier, and the end time was later than usual. On average, mice spent 21.6 ± 11.6 times/night feeding, with a duration of 63.58 ± 98.36 s; while they spent less time in foraging, 39.05 ± 51.63 s. We found a significant difference in feeding and foraging frequency, with mice spending on average 10.84 ± 9.85 times/night and 9.23 ± 11.17 times/night, respectively. Our results show that feeding and foraging behavior is also influenced by light intensity, suggesting a preference for crepuscular periods of the day. Infra-red cameras are very useful in detecting activity patterns of animals that are not easily observable; these cameras are able to capture a large amount of valuable information for research into ecological functions.

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.

Background Tamquammys has been considered one of the basal ctenodactyloid rodents, which has been documented in the earliest to middle Eocene (~ 56.0–48.5 Ma) in China. It was the most abundant and widespread rodent genus in the Erlian Basin (Nei Mongol, China) and dominated Arshantan small-mammal faunas of that region. Here for the first time we describe the morphology of the astragalocalcaneal complex in Tamquammys robustus (larger) and T. wilsoni, and interpret it against the background of locomotor adaptations of basal Euarchontoglires (rodents, lagomorphs, tree shrews, and primates). Results The comparative morphology of the tarsal elements in Tamquammys robustus and T. wilsoni shows overall slenderness of the bones and their similarity to the tarsal elements of Rattus, a generalist species, and those of small rock squirrels (e.g. Sciurotamias). The two species differ slightly in their cursorial ability; smaller T. wilsoni shows some adaptations to climbing. The results of principal component analysis of the calcaneus and astragalus support this observation and place T. robustus in-between Rattus and ground/rock squirrel morphospace, and T. wilsoni closer to euarchontans, Tupaia and Purgatorius. Conclusions The morphology of the tarsal elements in Tamquammys indicates a generalist rodent morphotype with no particular adaptations to arboreality. We suggest that Tamquammys as a basal ctenodactyloid is closer to the ancestral astragalocalcaneal morphology of rodents than that of more derived North American paramyines of similar age. Overall similarity in Tamquammys tarsal elements structure to Purgatorius, a basal primate, may point to the antiquity of the tarsal structure in Tamquammys and a generally unspecialized foot structure in early Euarchontoglires. Electronic supplementary material The online version of this article (10.1186/s12862-018-1259-1) contains supplementary material, which is available to authorized users.

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.

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.

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

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.

Previous phylogenetic analyses have led to incongruent evolutionary relationships between tree shrews and other suborders of Euarchontoglires. What caused the incongruence remains elusive. In this study, we identified 6845 orthologous genes between seventeen placental mammals. Tree shrews and Primates were monophyletic in the phylogenetic trees derived from the first or/and second codon positions whereas tree shrews and Glires formed a monophyly in the trees derived from the third or all codon positions. The same topology was obtained in the phylogeny inference using the slowly and fast evolving genes, respectively. This incongruence was likely attributed to the fast substitution rate in tree shrews and Glires. Notably, sequence GC content only was not informative to resolve the controversial phylogenetic relationships between tree shrews, Glires, and Primates. Finally, estimation in the confidence of the tree selection strongly supported the phylogenetic affiliation of tree shrews to Primates as a monophyly.

Tree shrew (Tupaia belangeri) is currently placed in Order Scandentia and has a wide distribution in Southeast Asia and Southwest China. Due to its unique characteristics, such as small body size, high brain-to-body mass ratio, short reproductive cycle and life span, and low-cost of maintenance, tree shrew has been proposed to be an alternative experimental animal to primates in biomedical research. However, there are some debates regarding the exact phylogenetic affinity of tree shrew to primates. In this study, we determined the mtDNA entire genomes of three Chinese tree shrews (T. belangeri chinensis) and one Malayan flying lemur (Galeopterus variegatus). Combined with the published data for species in Euarchonta, we intended to discern the phylogenetic relationship among representative species of Dermoptera, Scandentia and Primates. The mtDNA genomes of Chinese tree shrews and Malayan flying lemur shared similar gene organization and structure with those of other mammals. Phylogenetic analysis based on 12 concatenated mitochondrial protein-encoding genes revealed a closer relationship between species of Scandentia and Glires, whereas species of Dermoptera were clustered with Primates. This pattern was consistent with previously reported phylogeny based on mtDNA data, but differed from the one reconstructed on the basis of nuclear genes. Our result suggested that the matrilineal affinity of tree shrew to primates may not be as close as we had thought. The ongoing project for sequencing the entire genome of Chinese tree shrew will provide more information to clarify this important issue.

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.

The molecular relationship of placental mammals has attracted great interest in recent years. However, 2 crucial and conflicting hypotheses remain, one with respect to the position of the root of the eutherian tree and the other the relationship between the orders Rodentia, Lagomorpha (rabbits, hares), and Primates. Although most mitochondrial (mt) analyses have suggested that rodents have a basal position in the eutherian tree, some nuclear data in combination with mt-rRNA genes have placed the root on the so-called African clade or on a branch that includes this clade and the Xenarthra (e.g., anteater and armadillo). In order to generate a new and independent set of molecular data for phylogenetic analysis, we have established cDNA sequences from different tissues of various mammalian species. With this in mind, we have identified and sequenced 8 housekeeping genes with moderately fast rate of evolution from 22 placental mammals, representing 11 orders. In order to determine the root of the eutherian tree, the same genes were also sequenced for 3 marsupial species, which were used as outgroup. Inconsistent with the analyses of nuclear + mt-rRNA gene data, the current data set did not favor a basal position of the African clade or Xenarthra in the eutherian tree. Similarly, by joining rodents and lagomorphs on the same basal branch (Glires hypothesis), the data set is also inconsistent with the tree commonly favored in mtDNA analyses. The analyses of the currently established sequences have helped examination of problematic parts in the eutherian tree at the same time as they caution against suggestions that have claimed that basal eutherian relationships have been conclusively settled.

Phylogenetic analyses based on morphological data support monophyly of Glires, but not a link between Glires and zalambdalestids. Glires are more closely related to several Tertiary taxa, including primates, leptictids, pseudictopids, anagalids, and macroscelideans. Phylogenetically constrained distributions of Glires support the conventional view for a post K-T boundary radiation of modern orders of placental mammals and disagree with conclusions of some molecular studies that divergence of Rodentia and Lagomorpha at infraordinal, ordinal, and certain supraordinal levels occurred in the Cretaceous. Current hypotheses employed to explain the discrepancy between the fossil record and the molecular clock hypothesis are not supported by phylogenetic and distributional evidence of Glires. There is no compelling evidence that close relatives of Glires were present in the Cretaceous.

It is postulated widely that changes in developmental timing (i.e., heterochrony) represent a major mechanism of evolutionary change. However, it is only with recent methodological advances that changes in the order in which development proceeds (sequence heterochrony) can be identified and quantified. We apply these techniques to examine whether heterochrony in the early embryonic (organogenetic) period has played an important role in the diversification of mammals. Although we find clear instances of sequence heterochrony in mammals, particularly between eutherians and marsupials, the majority of mammalian lineages that we could examine (those within the major clades Euarchontoglires and Laurasiatheria) show few or no heterochronic changes in the 116 events examined (e.g., Artiodactyla, Euarchonta, Fereuungulata, Glires, Primates, Rodentia). This is in contrast with the timing shifts reported between and within other tetrapod clades. Our results suggest that sequence heterochrony in embryonic stages has not been a major feature of mammalian evolution. This might be because mammals, and perhaps amniotes in general, develop for an extended time in a protected environment, which could shield the embryos from strong diversifying selection. Our results are also consistent with the view that mammal embryos are subject to special developmental constraints. Therefore, other mechanisms explaining the diversity of extant mammals must be sought.

The so-called Glires hypothesis postulates a sister-group relationship between Rodentia (e.g., rat and mouse) and Lagomorpha (e.g., rabbit). Recent molecular phylogenetic analyses have yielded incongruent results, and either supported or refuted the Glires grouping. In order to study this inconsistency we have reconstructed phylogenetic trees based on data sets of 20 orthologous nuclear protein coding genes (6441 aa, sites) and 12 mitochondrial protein coding genes (3559 aa sites). The size of the nuclear data set is considerably larger than any comparable data set hitherto used to study the Glires concept. Analysis of the nuclear data strongly supported the phylogenetic tree (frog, chicken, ((rat, mouse), (rabbit, (human, (cattle, dog))))), while the mt data could not conclusively resolve the position of rabbit relative to that of human. This result was supported by all methods. Thus, the Glires hypothesis was rejected by this study.

Complete mitochondrial genomes are reported for a pika (Ochotona collaris) and a vole (Volemys kikuchii) then analysed together with 35 other mitochondrial genomes from mammals. With standard phylogenetic methods the pika joins with the other lagomorph (rabbit) and the vole with the other murid rodents (rat and mouse). In addition, with hedgehog excluded, the seven rodent genomes consistently form a homogeneous group in the unrooted placental tree. Except for uncertainty of the position of tree shrew, the clade Glires (monophyletic rodents plus lagomorphs) is consistently found. The unrooted tree obtained by ProtML (Protein Maximum Likelihood, a program in MOLPHY) is compatible with a reclassification of mammals [Syst. Biol. 48, 1‐5 (1999)] which is also supported by other recent studies. However, when this tree is rooted with marsupials plus platypus, the outgroup often joins the lineage leading to the three murid rodents, so the rodents are no longer monophyletic. Apart from misplacing the root, the presence of the outgroups also distorts other parts of the unrooted tree. Either constraining the tree to maintain rodents monophyletic, or omitting murids, maintains the ingroup tree and sees the outgroup join on the edge to Xenarthra, to Afrotheria, or to these two groups together. This emphasises the importance of carrying out both an unrooted and a rooted analysis. It is known from cancer research that murid rodents have reduced activity in some DNA repair mechanisms and this alters their substitution pattern ‐ this may be the case for mitochnodrial DNA as well. Comparing nucleotide compositions may identify taxa that differ in aspects of their DNA repair mechanisms. q 2002 Elsevier Science B.V. All rights reserved.

The well-accepted Euarchonta grandorder is a pruned version of Archonta nested within the Euarchontoglires (or Supraprimates) clade. At present, it includes tree shrews (Scandentia), flying lemurs (Dermoptera) and primates (Primates). Here, a phylogenomic dataset containing 1912 exons from 22 representative mammals was compiled to investigate the phylogenetic relationships within this group. Phylogenetic analyses and hypothesis testing suggested that tree shrews can be classified as a sister group to Primates or to Glires or even as a basal clade within Euarchontoglires. Further analyses of both modified and original previously published datasets found that the phylogenetic position of tree shrews is unstable. We also found that two of three exonic indels reported as synapomorphies of Euarchonta in a previous study do not unambiguously support the monophyly of such a clade. Therefore, the monophyly of both Euarchonta and Sundatheria (Dermoptera + Scandentia) are suspect. Molecular dating and divergence rate analyses suggested that the ancestor of Euarchontoglires experienced a rapid divergence, which may cause the unresolved position of tree shrews even using the whole genomic data.

We provide the first full description of the rodentiaform Tribosphenomys minutus from the late Paleocene Bayan Ulan locality of Inner Mongolia, China. All material presently referable to the taxon is treated, including the holotype plus more recently discovered teeth, jaws, and postcranial elements. To elucidate the phylogenetic placement of Tribosphenomys, a suite of 82 osteological characters across 36 terminal taxa was sampled and analyzed. A data matrix was generated and subjected to phylogenetic analyses using parsimony. The results of the analyses confirm the outgroup placement of Tribosphenomys relative to Rodentia (in the crown-clade restricted sense of that name). Other results include a sister-group pairing of lagomorphs and rodents (Glires), with various extinct taxa interposed as sequential outgroups to each of these crown clades. The phylogenetic definitions of names attaching to major clades of gliroid mammals are reviewed, with new ones being proposed.

Higher level relationships among placental mammals, as well as the historical biogeography and morphological diversification of this group, remain unclear1,2,3. Here we analyse independent molecular data sets, having aligned lengths of DNA of 5,708 and 2,947 base pairs, respectively, for all orders of placental mammals. Phylogenetic analyses resolve placental orders into four groups: Xenarthra, Afrotheria, Laurasiatheria, and Euarchonta plus Glires. The first three groups are consistently monophyletic with different methods of analysis. Euarchonta plus Glires is monophyletic or paraphyletic depending on the phylogenetic method. A unique nine-base-pair deletion in exon 11 of the BRCA1 gene provides additional support for the monophyly of Afrotheria, which includes proboscideans, sirenians, hyracoids, tubulidentates, macroscelideans, chrysochlorids and tenrecids. Laurasiatheria contains cetartiodactyls, perissodactyls, carnivores, pangolins, bats and eulipotyphlan insectivores. Parallel adaptive radiations have occurred within Laurasiatheria and Afrotheria. In each group, there are aquatic, ungulate and insectivore-like forms.

Most of us have seen movies where, with the single beam of a gunlike device, a mad scientist in a white lab coat shrinks large-bodied animals to the size of an ant. Were elephants and elephant shrews victims of such a fantastic fate? From the time of their first description in 1800, elephant shrews (Macroscelidea) were considered related to shrews and other insectivores along with tenrecs (Tenrecidae) and golden moles (Chrysochloridae), whereas elephants (Proboscidea) were originally placed more or less close to ungulates such as hippos and rhinos (the now obsolete Pachydermata). Since then, paleontologists have unearthed numerous fossil relatives that have shed new light on the study of both taxa. Thanks to these fossil discoveries, and to the progress of comparative anatomy and phylogenetic methods, the relationships of both elephants and elephant shrews were eventually reconsidered (Fig. 1A). For instance, elephants were securely placed close to sirenians (dugongs and manatees) and hyracoids (dassies) in Paenungulata, whereas elephant shrews showed affinities with Glires (rabbits and rodents). These morphological analyses also recognized Cetacea (whales and dolphins) as the sister taxon of artiodactyls (cows, pigs, etc.) and that carnivorans shared a common ancestor with pangolins (Pholidota). On the verge of the new millennium, more than 250 years after Linnaeus's foundation of taxonomy, 18 living orders of placental mammals were recognized, but several of their proposed relationships were …

The interordinal relationships of eutherian (placental) mammals were evaluated by a phylogenetic analysis of four published data sets (three sequences and one morphological). The nature and degree of support and coneict for particular groups were assessed by separate boot- strap and homogeneity tests, which were followed by combined analyses of the sequence and morphological data. Between orders, strong support (i.e., $ 95% bootstrap scores) was found for a paraphyletic Artiodactyla (relative to Cetacea) and a monophyletic Cetartiodactyla (Artiodactyla and Cetacea) and Paenungulata(Hyracoidea,Proboscidea, and Sirenia).In turn, somereasonableto strong evidence ($ 85%) was obtained for Hyracoidea with Sirenia, Dermoptera with Scandentia, Glires (Lagomorpha with Rodentia), and Afrotheria (Amblysomus, Macroscelidea, Paenungulata, and Tubulidentata). Otherwise, no other interordinal clades were supported at these reasonable to strong levels. This overall lack of resolution for eutherian interordinal clusters agrees with other studies that suggest further progress will continue to be slow and difecult. Further resolution will require the integration of more recently published data, the continued sampling of taxa and char- acters, and the use of more powerful methods of data analysis. (Congruence; eutherian mammals; gene sequences; morphology; phylogeny.)

The gut microbial communities of animals play key roles in host evolution. However, the possible relationship between gut microbiota and host divergence time remains unknown. Here, we investigated the gut microbiota of eight Glires species (four lagomorph species and four rodent species) distributed throughout the Qinghai-Tibet plateau and Inner Mongolia grassland. Lagomorphs and rodents had distinct gut microbial compositions. Three out of four lagomorph species were dominated by Firmicutes, while rodents were dominated by Bacteroidetes in general. The alpha diversity values (Shannon diversity and evenness) exhibited significant differences between any two species within the lagomorphs, whereas there were no significant differences among rodents. The structure of the gut microbiota showed significant differences between lagomorphs and rodents. In addition, we calculated host phylogeny and divergence times, and used a phylogenetic approach to reconstruct how the animal gut microbiota has diverged from their ancestral species. Some core bacterial genera (e.g. Prevotella and Clostridium) shared by more than nine-tenths of all the Glires individuals associated with plant polysaccharide degradation showed marked changes within lagomorphs. Differences in Glires gut microbiota (based on weighted UniFrac and Bray-Curtis dissimilarity metrics) were positively correlated with host divergence time. Our results thus suggest the gut microbial composition is associated with host phylogeny, and further suggest that dissimilarity of animal gut microbiota may predict host divergence time.

Glires represent a eutherian clade consisting of rodents and lagomorphs (hares, rabbits, and pikas). Chromosome evolution of Glires is known to have variable rates in different groups: from slowly evolving lagomorphs and squirrels to extremely rapidly evolving muroids. Previous interordinal homology maps between slowly evolving Glires were based on comparison with humans. Here, we used sets of chromosome-specific probes from Tamias sibiricus (Sciuridae), Castor fiber (Castoridae) and humans to study karyotypes of six ground squirrels (genera Marmota and Spermophilus) and one tree squirrel (genus Sciurus), mountain hare (genus Lepus), and rabbit (genus Oryctolagus). These data supplemented with GTG banding comparisons allowed us to build comparative chromosome maps. Our data showed the absence of previously found squirrel associations HSA 1/8 and 2/17 in the Eurasian ground squirrels--sousliks and woodchucks, and disruptions of squirrel HSA 10/13 and HSA 8/4/8/12/22 syntenies in the four Spermophilus species studied here. We found that the karyotypes of Sciuridae and Leporidae are highly conserved and close to the Rodentia ancestral karyotype, while Castoridae chromosomes underwent many more changes. We suggest that Lagomorpha and Sciuridae (in contrast to all other rodent families) should be considered as core Glires lineages, characterized by cytogenetically conserved karyotypes which contain chromosomal elements inherent to karyotype of common Glires ancestor. Our data allowed us to further refine the putative ancestral karyotypes of Rodentia. We also describe here the putative ancestral karyotypes of Glires and lagomorphs.

Recent analyses of amino acid sequence data from selected proteins inCavia, Rattus, Homo, Bos, Sus, and a few additional rodents and other eutherians suggested that Rodentia is not a monophyletic taxon and thatCavia and other hystricognaths may have branched off earlier than the separation between Muroidea and Primates during mammalian evolution. Because this hypothesis of polyphyly is contrary to the otherwise unanimous recognition of rodent monophyly, we have reevaluated the morphological and developmental evidence from the cranium, dentition, postcranial skeleton, and fetal membranes for the taxa Hystricognathi, Muroidea, other Rodentia, Primates, Artiodactyla, and Lagomorpha, as well as for the eutherian morphotype. Our character analyses provide strong corroboration for the traditional hypothesis of rodent monophyly and lend additional support to the suggestion that Lagomorpha is the sister taxon of Rodentia. Our survey of published molecular data furnishes little or no support for the proposed hypothesis of rodent polyphyly. We conclude that this hypothesis is the result of poor sampling of sequence data from rodents and other eutherians, rather than any inherent difficulties in the use of molecular evidence for the assessment of mammalian evolution. The available molecular data suggest thatCavia differs considerably from other hystricognaths in many proteins, but the reasons for this remain to be investigated.

Rodents represent the largest order of living mammals. It comprises 5 sub-orders, among which Sciuromorpha (Sciuridae, Gliridae and Aplodontiidae) are assumed to occupy a basal position in rodent evolution. Banded karyotypes of some representatives of the Sciuridae family have been compared to each other, and comparisons with man were performed using chromosome paintings. Sciuridae karyotypes have conserved several eutherian ancestral syntenies. Like Sciuridae, Gliridae possess some chromosomes easily comparable with those of Primates. Comparisons of Gliridae and Sciuridae chromosomes with those of the presumed eutherian ancestor provide information about their chromosomal evolution and their position among Rodentia. Although both Sciuridae and Gliridae karyotypes are relatively conserved, they display many differences, indicating their early divergence. The reconstruction of their chromosomal evolution allowed us to propose the composition of their presumed ancestral karyotypes, with 2n = 48 and 2n = 38 for Gliridae and Sciuridae, respectively. Since rodent emergence, a single rearrangement is common to these 2 families. It formed a chromosome with fragments homologous to human chromosomes 4-8p-4-12-22, not detected in other rodents, and thus characteristic for the Sciuromorpha. This allowed us to reassess the chromosomal signatures of Rodentia. Finally, we show that the speed of chromosomal evolution in Gliridae is intermediate between that of Sciuridae (low) and Muridae (high).

The evolutionary relationships of the various orders of placental mammals remain an issue of uncertainty and controversy. Molecular studies of mammalian phylogeny at the DNA level that include more than just a few orders are still relatively meager. Here we report results on mammalian phylogeny deduced from the coding sequence of the single-copy nuclear gene for the interphotoreceptor retinoid binding protein (IRBP). Analysis of 13 species representing eight eutherian orders and one marsupial yielded results that falsify the hypothesis that megachiropteran bats are "flying primates," only convergently resembling microchiropteran bats. Instead, in agreement with more traditional views, as well as those from other recent molecular studies, the results strongly support a monophyletic Chiroptera (micro- and megabats grouped together). The IRBP results also offer some rare molecular support for the Glires concept, in which rodents and lagomorphs form a superordinal grouping. Also in congruence with other recent molecular evidence, IRBP sequences do not support the view of a superorder Archonta that includes Chiroptera along with Dermoptera (flying lemur), Scandentia (tree shrew), and Primates. IRBP was not however, without its shortcomings as a molecular phylogenetic system: high levels of homoplasy, evident in the marsupial outgroup, did not allow us to properly root the tree, and several of the higher level eutherian clades were only weakly supported (e.g., a Carnivora/Chiroptera clade and an Artiodactyla/Carnivora/Chiroptera clade). We suggest that these shortcomings may be diminished as the phylogenetic density of the data set is increased.

THE guinea-pig (Caviaporcellus), traditionally classified as a New World hystricomorph rodent, often shows anomalous morphological and molecular features in comparison with other eutherian mammals1–14. For example, its insulin differs from that of other mammals in anabolic and growth-promoting activities and in its capability to form hexamers5,6. Indeed, the literature about the molecular evolution of guinea-pigs abounds in references to 'convergent evolution', 'extremely rapid rates of substitution', and 'unique evolutionary mechanisms'. These claims are based on the assumption that the guinea-pig is a rodent. Our phylogenetic analyses of amino-acid sequence data, however, imply that the guinea-pig diverged before the separation of the primates and the artiodactyls from the myomorph rodents (rats and mice). If true, then the myomorphs and the caviomorphs do not constitute a natural clade, and the Caviomorpha (or the Histricomorpha) should be elevated in taxonomical rank and regarded as a separate mammalian order distinct from the Rodentia. If, as suggested by recent data15,16, the myomorphs branched off before the divergence among the carnivores, lagomorphs, artiodactyls and primates, then the new order would represent an early divergence in eutherian radiation.

We describe several fossils referable to Gomphos elkema from deposits close to the Paleocene-Eocene boundary at Tsagan Khushu, Mongolia. Gomphos shares a suite of cranioskeletal characters with extant rabbits, hares, and pikas but retains a primitive dentition and jaw compared to its modern relatives. Phylogenetic analysis supports the position of Gomphos as a stem lagomorph and excludes Cretaceous taxa from the crown radiation of placental mammals. Our results support the hypothesis that rodents and lagomorphs radiated during the Cenozoic and diverged from other placental mammals close to the Cretaceous-Tertiary boundary.

With complete sets of chromosome-specific painting probes derived from flow-sorted chromosomes of human and grey squirrel (Sciurus carolinensis), the whole genome homologies between human and representatives of tree squirrels (Sciurus carolinensis, Callosciurus erythraeus), flying squirrels (Petaurista albiventer) and chipmunks (Tamias sibiricus) have been defined by cross-species chromosome painting. The results show that, unlike the highly rearranged karyotypes of mouse and rat, the karyotypes of squirrels are highly conserved. Two methods have been used to reconstruct the genome phylogeny of squirrels with the laboratory rabbit (Oryctolagus cuniculus) as the out-group: (1) phylogenetic analysis by parsimony using chromosomal characters identified by comparative cytogenetic approaches; (2) mapping the genome rearrangements onto recently published sequence-based molecular trees. Our chromosome painting results, in combination with molecular data, show that flying squirrels are phylogenetically close to New World tree squirrels. Chromosome painting and G-banding comparisons place chipmunks (Tamias sibiricus ), with a derived karyotype, outside the clade comprising tree and flying squirrels. The superorder Glires (orde Rodentia + order Lagomorpha) is firmly supported by two conserved syntenic associations between human chromosomes 1 and 10p homologues, and between 9 and 11 homologues.

Rhombomylus is a gliroid mammal endemic to several early Eocene localities of central and eastern Asia. It is best represented by a collection of numerous jaws and teeth, dozens of juvenile and adult skulls, and associated postcranial specimens from the early Eocene Yuhuangding Formation at the Dajian village, Junxian County, Hubei Province, China. These specimens are the best preserved material of early nonrodent, nonlagomorph Glires known to date, and they provide a unique opportunity for us to understand anatomy, intraspecies variation, postnatal ontogeny, phylogeny, and evolution of basal gliroid mammals. This study opens with an introduction to the current knowledge of the phylogeny of gliroid mammals, a brief review of the research history of Rhombomylus, and a description of the locality where the specimens were collected. The core of the study consists of a taxonomic revision of the genus, a detailed description of the osteological morphology, extensive analyses on morphological character...

Rodentia is the largest order of placental mammals, with approximately 2,050 species divided into 28 families. It is also one of the most controversial with respect to its monophyly, relationships between families, and divergence dates. Here, we have analyzed and compared the performance of three nuclear genes (von Willebrand Factor, interphotoreceptor retinoid-binding protein, and Alpha 2B adrenergic receptor) for a large taxonomic sampling, covering the whole rodent and placental diversity. The phylogenetic results significantly support rodent monophyly, the association of Rodentia with Lagomorpha (the Glires clade), and a Glires + Euarchonta (Primates, Dermoptera, and Scandentia) clade. The resolution of relationships among rodents is also greatly improved. The currently recognized families are divided here into seven well-defined clades (Anomaluromorpha, Castoridae, Ctenohystrica, Geomyoidea, Gliridae, Myodonta, and Sciuroidea) that can be grouped into three major clades: Ctenohystrica, Gliridae + Sciuroidea, and a mouse-related clade (Anomaluromorpha, Castoridae + Geomyoidea, and Myodonta). Molecular datings based on these three genes suggest that the rodent radiation took place at the transition between Paleocene and Eocene. The divergence between rodents and lagomorphs is placed just at the K-T boundary and the first splits among placentals in the Late Cretaceous. Our results thus tend to reconcile molecular and morphological-paleontological insights.

The complete mitochondrial genome of an African cane rat, Thryonomys swinderianus (Rodentia, Hystricognathi), was included in a phylogenetic analysis along with 4 rodents, 14 additional eutherians, and 3 noneutherian outgroups. Monophyly of the suborder Hystricognathi, represented by the cane rat and the South American guinea pig, Cavia porcellus, was strongly supported by maximum-parsimony, neighbor-joining, and maximum-likelihood methods. The molecular-based estimate of the divergence time of Old and New World Hystricognathi (approximately 85 million years before present, MYBP) is consistent with an hypothesis of vicariance divergence due to the rifting of the African and South American continents 86-100 MYBP. Monophyly of Rodentia or the superordinal clade Glires (Rodentia and Lagomorpha) were not supported.

Phylogenetic relationships of 25 mammalian species representing 17 of the 18 eutherian orders were examined using DNA sequences from a 1.2-kb region of the 5′ end of exon 1 of the single-copy nuclear gene known as interphotoreceptor retinoid binding protein (IRBP). A wide variety of methods of analysis of the DNA sequence, and of the translated products, all supported a five-order clade consisting of elephant shrew (Macroscelidea)/aardvark (Tubulidentata)/and the paenungulates (hyracoids, sirenians, and elephants), with bootstrap support in all cases of 100%. The Paenungulata was also strongly supported by these IRBP data. In the majority of analyses this monophyletic five-order grouping was the first branch off the tree after the Edentata. These results are highly congruent with two other recent sources of molecular data. Another superordinal grouping, with similar 100% bootstrap support in all of the same wide-ranging types of analyses, was Artiodactyla/Cetacea. Other superordinal affinities, suggested by the analyses, but with less convincing support, included a Perissodactyla/Artiodactyla/Cetacea clade, an Insectivora/Chiroptera clade, and Glires (an association of rodents and lagomorphs).

EVER since they have been classified as ruminants in the Old Testament (Leviticus 11:6, Deuteronomy 14:7) and equated with hyraxes in the vulgate Latin translation, rabbits and their relatives (order Lagomorpha) have frequently experienced radical changes in taxonomic rank. By using 91 orthologous protein sequences, we have attempted to answer the classical question "What, if anything, is a rabbit?"1. Here we show that Lagomorpha is significantly more closely related to Primates and Scandentia (tree shrews) than it is to rodents. This newly determined phylogenetic position invalidates the superordinal taxon Glires (Lagomorpha + Rodentia), and indicates that the morphological 'synapomorphies' previously used to cluster rodents and lagomorphs into Glires2,3, may actually represent symplesiomorphies or homoplasies that are of no phylogenetic value. This raises the possibility that the ancestral eutherian morphotype may have possessed many rodent-like morphological characters.

Based on the number of tissues separating maternal from fetal blood, placentas are classified as epitheliochorial, endotheliochorial or hemochorial. We review the occurrence of these placental types in the various orders of eutherian mammals within the framework of the four superorders identified by the techniques of molecular phylogenetics. The superorder Afrotheria diversified in ancient Africa and its living representatives include elephants, sea cows, hyraxes, aardvark, elephant shrews and tenrecs. Xenarthra, comprising armadillos, anteaters and sloths, diversified in South America. All placentas examined from members of these two oldest superorders are either endotheliochorial or hemochorial. The superorder Euarchontoglires includes two sister groups, Glires and Euarchonta. The former comprises rodents and lagomorphs, which typically have hemochorial placentas. The most primitive members of Euarchonta, the tree shrews, have endotheliochorial placentation. Flying lemurs and all higher primates have hemochorial placentas. However, the lemurs and lorises are exceptional among primates in having epitheliochorial placentation. Laurasiatheria, the last superorder to arise, includes several orders with epitheliochorial placentation. These comprise whales, camels, pigs, ruminants, horses and pangolins. In contrast, nearly all carnivores have endotheliochorial placentation, whilst bats have endotheliochorial or hemochorial placentas. Also included in Laurasiatheria are a number of insectivores that have many conserved morphological characters; none of these has epitheliochorial placentation. Consideration of placental type in relation to the findings of molecular phylogenetics suggests that the likely path of evolution in Afrotheria was from endotheliochorial to hemochorial placentation. This is also a likely scenario for Xenarthra and the bats. We argue that a definitive epitheliochorial placenta is a secondary specialization and that it evolved twice, once in the Laurasiatheria and once in the lemurs and lorises.

Although the two major groups of gliriform mammals, the rodents and lagomorphs, are frequently grouped together by nonspecialists, the opinion of both paleontologists and neomammalogists has long been that the two orders are not closely related. Now, new evidence on this question has come from recent fossil discoveries in China and from reevaluation of other evidence, especially developmental. After a review of the past interpretations and new evidence, we return to the view that the Lagomorpha and Rodentia can be traced to a common ancestral group and that the Cohort Glires is a valid taxonomic unit.

International audience; Phylogenetic analysis of DNA sequences from primates, rodents, lagomorphs, artiodactyls, carnivores, and birds strongly suggests that the order Rodentia is an outgroup to the other four mammalian orders and that Artiodactyla and Carnivora belong to a superordinal clade. Further, there is strong evidence against the Glires concept, which unites Lagomorpha and Rodentia. The radiation among Lagomorpha, Primates, and Artiodactyla--Carnivora is very bush-like, but there is some evidence that Lagomorpha has branched off first. Thus, the branching sequence for these five orders of mammals seems to be Rodentia, Lagomorpha, Primates, Artiodactyla, and Carnivora. The branching date for Rodentia could be as early as 100 million years ago. The rate of nucleotide substitution in the rodent lineage is shown to be at least 1.5 times higher than those in the other four mammalian lineages.