Rodent Phylogeny Research Articles

Phylogeny, Ecology, and Gene Families Covariation Shaped the Olfactory Subgenome of Rodents.

Olfactory receptor (OR) genes represent the largest multigenic family in mammalian genomes and encode proteins that bind environmental odorant molecules. The OR repertoire is extremely variable among species and is subject to many gene duplications and losses, which have been linked to ecological adaptations in mammals. Although they have been studied on a broad taxonomic scale (i.e., placental), finer sampling has rarely been explored in order to better capture the mechanisms that drove the evolution of the OR repertoire. Among placental mammals, rodents are well-suited for this task, as they exhibit diverse life history traits, and genomic data are available for most major families and a diverse array of lifestyles. In this study, 53 rodent published genomes were mined for their OR subgenomes. We retrieved more than 85,000 functional and pseudogene OR sequences that were subsequently classified into phylogenetic clusters. Copy number variation among rodents is similar to that of other mammals. Using our OR counts along with comparative phylogenetic approaches, we demonstrated that ecological niches such as diet, period of activity, and a fossorial lifestyle strongly impacted the proportion of OR pseudogenes. Within the OR subgenome, phylogenetic inertia was the main factor explaining the relative variations of the 13 OR gene families. However, a striking exception was a convergent 10-fold expansion of the OR family 14 among the phylogenetically divergent subterranean mole-rat lineages belonging to Bathyergidae and Spalacidae families. This study illustrates how the diversity of the OR repertoire has evolved among rodents, both shaped by selective forces stemming from species life history traits and neutral evolution along the rodent phylogeny.

Virus isolation data improve host predictions for New World rodent orthohantaviruses.

Identifying reservoir host species is crucial for understanding the ecology of multi-host pathogens and predicting risks of pathogen spillover from wildlife to people. Predictive models are increasingly used for identifying ecological traits and prioritizing surveillance of likely zoonotic reservoirs, but these often employ different types of evidence for establishing host associations. Comparisons between models with different infection evidence are necessary to guide inferences about the trait profiles of likely hosts and identify which hosts and geographical regions are likely sources of spillover. Here, we use New World rodent-orthohantavirus associations to explore differences in the performance and predictions of models trained on two types of evidence for infection and onward transmission: RT-PCR and live virus isolation data, representing active infections versus host competence, respectively. Orthohantaviruses are primarily carried by muroid rodents and cause the diseases haemorrhagic fever with renal syndrome (HFRS) and hantavirus cardiopulmonary syndrome (HCPS) in humans. We show that although boosted regression tree (BRT) models trained on RT-PCR and live virus isolation data both performed well and capture generally similar trait profiles, rodent phylogeny influenced previously collected RT-PCR data, and BRTs using virus isolation data displayed a narrower list of predicted reservoirs than those using RT-PCR data. BRT models trained on RT-PCR data identified 138 undiscovered hosts and virus isolation models identified 92 undiscovered hosts, with 27 undiscovered hosts identified by both models. Distributions of predicted hosts were concentrated in several different regions for each model, with large discrepancies between evidence types. As a form of validation, virus isolation models independently predicted several orthohantavirus-rodent host associations that had been previously identified through empirical research using RT-PCR. Our model predictions provide a priority list of species and locations for future orthohantavirus sampling. More broadly, these results demonstrate the value of multiple data types for predicting zoonotic pathogen hosts. These methods can be applied across a range of systems to improve our understanding of pathogen maintenance and increase efficiency of pathogen surveillance.

Rodent Suborders

Abstract For two hundred years the status of rodent suborders has been unstable. What are the natural groupings of extant rodent families? The formal recognition of rodent suborders has remained challenging and consensus has been elusive. Classically conceived rodent suborders are widely viewed as artificial, but no universally accepted classification has emerged to reflect the major features of rodent evolution. Over the last two decades molecular studies have established that extant rodents comprise three monophyletic clades. We review the molecular basis for these groups and recognize them as taxonomic units: Suborder Ctenohystrica Huchon et al., 2000, Suborder Supramyomorpha D’Elía et al., 2019, and a group of families clustered with Sciuridae. The latter differs from Sciuromorpha as traditionally conceived because the suborder includes Aplodontiidae but excludes Castoridae. We review morphological character complexes that are distributed broadly within these three clades, name the third group Eusciurida, new suborder, and find this three-fold division of extant Rodentia to reflect well the major features of rodent phylogeny. That some morphological features do not characterize all families within suborders, or are not unique to individual suborders, indicates major parallel innovations and reversals in rodent evolution. These incongruent morphologies invite future study.

Rodent systematics in an age of discovery: recent advances and prospects

With almost 2,600 species, Rodentia is the most diverse order of mammals. Here, we provide an overview of changes in our understanding of the systematics of living rodents, including species recognition and delimitation, phylogenetics, and classification, with emphasis on the last three decades. Roughly, this corresponds to the DNA sequencing era of rodent systematics, but the field is undergoing a transition into the genomic era. At least 248 species were newly described in the period 2000–2017, including novelties such as the first living member of Diatomyidae and a murid species without molars (Paucidentomys vermidax), thus highlighting the fact that our understanding of rodent diversity is going through an age of discovery. Mito-nuclear discordance (including that resulting from mitochondrial introgression) has been detected in some of the few taxonomic studies that have assessed variation of two or more unlinked loci. As studies incorporate more loci, incomplete lineage sorting and introgression are likely to gain recognition as widespread phenomena in the near future. Molecular phylogenetics has had a major impact in rodent phylogeny and allowed the identification of three major rodent clades, here recognized as suborders: 1) the Hystricomorpha (sometimes referred as the Ctenohystrica) and including two infraorders, Hystricognathi and Ctenodactylomorphi; 2) the Sciuromorpha; and 3) the Supramyomorpha, a new suborder that comprises the infraorders Castorimorphi, Anomalurimorphi, and Myomorphi. In spite of the greater understanding and ensuing stability of rodent phylogeny gained during the last three decades, several major areas of the rodent tree remain unresolved or poorly supported. We expect that the analysis of genomic-scale data will help resolve those areas of the radiation of Rodentia that still remain poorly understood.

Mammalian Comparative Genomics Reveals Genetic and Epigenetic Features Associated with Genome Reshuffling in Rodentia.

Understanding how mammalian genomes have been reshuffled through structural changes is fundamental to the dynamics of its composition, evolutionary relationships between species and, in the long run, speciation. In this work, we reveal the evolutionary genomic landscape in Rodentia, the most diverse and speciose mammalian order, by whole-genome comparisons of six rodent species and six representative outgroup mammalian species. The reconstruction of the evolutionary breakpoint regions across rodent phylogeny shows an increased rate of genome reshuffling that is approximately two orders of magnitude greater than in other mammalian species here considered. We identified novel lineage and clade-specific breakpoint regions within Rodentia and analyzed their gene content, recombination rates and their relationship with constitutive lamina genomic associated domains, DNase I hypersensitivity sites and chromatin modifications. We detected an accumulation of protein-coding genes in evolutionary breakpoint regions, especially genes implicated in reproduction and pheromone detection and mating. Moreover, we found an association of the evolutionary breakpoint regions with active chromatin state landscapes, most probably related to gene enrichment. Our results have two important implications for understanding the mechanisms that govern and constrain mammalian genome evolution. The first is that the presence of genes related to species-specific phenotypes in evolutionary breakpoint regions reinforces the adaptive value of genome reshuffling. Second, that chromatin conformation, an aspect that has been often overlooked in comparative genomic studies, might play a role in modeling the genomic distribution of evolutionary breakpoints.

The early evolutionary history of anomaluroid rodents in Africa: new dental remains of a zegdoumyid (Zegdoumyidae, Anomaluroidea) from the Eocene of Tunisia

The Late Early‐to‐Early Middle Eocene Zegdoumyidae are the oldest representatives of the order Rodentia to be known in Africa thus far. Despite the fragmentary nature of their fossil record, these early African rodents have been central in discussions surrounding the early evolutionary history of the Anomaluroidea clade (the living forms of which are the ‘scaly‐tailed squirrels’, i.e. Anomaluridae). Here, we describe new dental remains attributable to Zegdoumys sbeitlai, a zegdoumyid from Tunisia (Djebel Chambi, CBI‐1) dated at ca 50–45 Ma. The original material referred to this taxon was limited to four teeth documenting few dental loci. The new gathered material comprises practically all dental loci (except P4), thereby allowing a better description and characterization of this taxon. This Tunisian species is clearly distinct from its roughly coeval Algerian counterpart (Z. lavocati) or from the younger species recorded from Namibia (Z. namibiensis). We investigated the phylogenetic positions of Z. sbeitlai and the Zegdoumyidae in a high‐level rodent phylogeny with a cladistic assessment of the dental evidence. Our results show that zegdoumyids represent the earliest offshoots (pectinately arranged) of a large clade that also encompasses the more advanced Eocene anomaluroids (here named Nementchamyidae), the Miocene Nonanomaluridae, and the stem and crown Anomaluridae. In this phylogenetic context, the species of Zegdoumys are the basalmost members of this large Anomaluroidea clade. Zegdoumyid taxa are therefore the oldest stem anomaluroid candidates, a statement which strengthens support for the hypothesis of the great antiquity of the Anomaluroidea clade in Africa. From a historical biogeography perspective, this assumption suggests that anomaluroids invaded Asia from Afro‐Arabia sometime during the Middle Eocene, a dispersal event which was likely concomitant but opposite to the dispersals envisaged for the hystricognathous rodents and anthropoid primates from Asia to Afro‐Arabia.

Gross, Histological and Ultrastructural Features of the Bulbourethral Gland in the Greater Cane Rat (Thryonomys swinderianus)

The present study examines the structure and ultrastructure of the bulbourethral glands in 10 sexually matured male greater cane rats raised in captivity. Following anaesthesia, the rats were perfusion-fixed transcardially and the bulbourethral glands dissected out. Upon morphologic and morphometric analysis, the Cowper's glands were observed to have an average volume of 0.24±0.08 ml, a diameter of 6.3±0.6 mm and weighs 0.199±0.06 g. The paired, gourd-shaped tubuloalveolar glands were surrounded by dense connective tissues and separated into lobules by capsular septae. Each lobule consists of endpiece/secretory units and excretory ducts lined by simple glandular epithelium and pseudo-stratified epithelium, respectively. The round end pieces consisted of 8-10 pyramidal to columnar epithelial cells with flattened, basally located nuclei and granule-filled cytoplasm that bounded a narrow glandular lumen. The striking ultrastructural features of these secretory cells were the presence of some granules with uniform electron density and those with regions of lesser density as well as the absence of secretory vacuoles. Another unique characteristic of these secretory granules is the presence of electron dense strands radiating from their surfaces. The apical surfaces of the cells were also studded with abundant microvilli. From the findings, the structure of bulbourethral glands in the greater cane rat shows more resemblances to that of humans than to its rodent phylogeny. These findings serve as additional knowledge in the structural interpretation of the bulbourethral gland and its secretory products.

Jumping and gliding rodents: Mitogenomic affinities of Pedetidae and Anomaluridae deduced from an RNA-Seq approach

An RNA-Seq strategy was used to obtain the complete set of protein-coding mitochondrial genes from two rodent taxa. Thanks to the next generation sequencing (NGS) 454 approach, we determined the complete mitochondrial DNA genome from Graphiurus kelleni (Mammalia: Rodentia: Gliridae) and partial mitogenome from Pedetes capensis (Pedetidae), and compared them with published rodent and outgroup mitogenomes. We finished the mitogenome sequencing by a series of amplicons using conserved PCR primers to fill the gaps corresponding to tRNA, rRNA and control regions. Phylogenetic analyses of the mitogenomes suggest a well-supported rodent phylogeny in agreement with nuclear gene trees. Pedetes groups with Anomalurus into the clade Anomaluromorpha, while Graphiurus branches within the squirrel-related clade. Moreover, Pedetes+Anomalurus branch with Castor into the mouse-related clade. Our study demonstrates the utility of NGS for obtaining new mitochondrial genomes as well as the importance of choosing adequate models of sequence evolution to infer the phylogeny of rodents.

Complex patterns of host switching in New World arenaviruses

We empirically tested the long-standing hypothesis of codivergence of New World arenaviruses (NWA) with their hosts. We constructed phylogenies for NWA and all known hosts and used them in reconciliation analyses. We also constructed a phylogenetic tree of all Sigmodontinae and Neotominae rodents and tested whether viral-host associations were phylogenetically clustered. We determined host geographical overlap to determine to what extent opportunity to switch hosts was limited by host relatedness or physical proximity. With the exception of viruses from North America, no phylogenetically codivergent pattern between NWA and their hosts was found. We found that different virus clades were clustered differently and that Clade B with members pathogenic to humans was randomly distributed across the rodent phylogeny. Furthermore, viral relatedness within Clade B was significantly explained by the geographic overlap of their hosts' ranges rather than host relatedness, indicating that they are capable of host switching opportunistically. This has important bearings on their potential to become panzootic. Together, these analyses suggest that NWA have not codiverged with their hosts and instead have evolved predominantly via host switching.

Zegdoumyidae (Rodentia, Mammalia), stem anomaluroid rodents from the Early to Middle Eocene of Algeria (Gour Lazib, Western Sahara): new dental evidence

The Palaeogene fossil record of rodents in Africa is very poor compared to that of North America or Eurasia. Despite this, Africa has long appeared to be a centre of adaptive radiation for two distinct groups of Rodentia: Hystricognathi and Anomaluroidea. The >45-million-year-old enigmatic Zegdoumyidae is the oldest and only rodent family known of this age from Africa (Algeria and Tunisia). Zegdoumyids have been tentatively regarded as a possible early African stem group for Anomaluridae, a link that has never been clearly established because of the highly fragmentary nature of zegdoumyid fossils, as well as the major temporal and morphological gaps between zegdoumyids and the first true anomaluroids from the Late Eocene. About 200 rodent teeth have been sorted after acid treatment of indurated sediments from several new localities in the Gour Lazib of western Algeria dating from the late Early or early Middle Eocene. These new fossils allow us to better describe the morphology of the Zegdoumyidae (especially Glibia and Zegdoumys) and to identify a new taxon, Lazibemys zegdouensis gen. et sp. nov. With this material, we investigated the phylogenetic position of the Zegdoumyidae in a high-level rodent phylogeny with cladistic assessment of the dental evidence. Our analyses have yielded six equally most-parsimonious trees in which zegdoumyids represent the earliest offshoots (pectinately arranged) of a large clade that embraces Eocene anomaluroids plus stem and crown Anomaluridae. This phylogenetic assumption underscores the great antiquity of the Anomaluroidea clade in Africa, as expected given the high morphological divergence of the Late Eocene African anomaluroids. Zegdoumyids exhibit a variety of dental morphologies and provide some suggestions on evolutionary trends within the Anomaluroidea (early stages of pentalophodonty, incisor enamel microstructure transitional from the pauciserial to the uniserial condition). The source of Zegdoumyidae is still unclear inasmuch as there is no well-identified sister group among early Palaeogene rodents. Zegdoumyids seem to share a common ancestry with both stem Myodonta and North American Sciuravidae. Given the high degree of dental specialization of zegdoumyids, we cannot exclude the possibility that zegdoumyids are rooted in a more primitive, as yet unknown, African rodent lineage older than the Early-Middle Eocene.

Similarity in ectoparasite faunas of Palaearctic rodents as a function of host phylogenetic, geographic or environmental distances: Which matters the most?

Different host species harbour parasite faunas that are anywhere from very similar to very different in species composition. A priori, the similarity in the parasite faunas of any two host species should decrease with increases in either the phylogenetic distance, the distinctness of the environments occupied or the geographical distance between these hosts. We tested these predictions using extensive data on the faunas of fleas (Insecta: Siphonaptera) and gamasid mites (Acari: Parasitiformes) parasitic on rodents across the Palaearctic. For each pair of host species, we computed the similarity in parasite faunas based on both species composition as well as the phylogenetic and/or taxonomic distinctness of parasite species. Phylogenetic distances between hosts were based on patristic distances through a rodent phylogeny, geographic distances were computed from geographic range data, and environmental dissimilarity was measured from the average climatic and vegetation scores of each host range. Using multiple regressions on distance matrices to assess the separate explanatory power of each of the three dependent variables, environmental dissimilarity between the ranges of host species emerged as the best predictor of dissimilarity between parasite faunas, especially for fleas; in the case of mites, phylogenetic distance between host species was also important. A closer look at the data indicates that the flea and mite faunas of two hosts inhabiting different environments are always different, whilst hosts living in similar environments can have either very similar or dissimilar parasite faunas. Additional tests showed that dissimilarity in flea or mite faunas between host geographic ranges was best explained by dissimilarity in vegetation, followed by dissimilarity in climatic conditions. Thus, external environmental factors may play greater roles than commonly thought in the evolution of host–parasite associations.

Rodent phylogeny revised: analysis of six nuclear genes from all major rodent clades.

BackgroundRodentia is the most diverse order of placental mammals, with extant rodent species representing about half of all placental diversity. In spite of many morphological and molecular studies, the family-level relationships among rodents and the location of the rodent root are still debated. Although various datasets have already been analyzed to solve rodent phylogeny at the family level, these are difficult to combine because they involve different taxa and genes.ResultsWe present here the largest protein-coding dataset used to study rodent relationships. It comprises six nuclear genes, 41 rodent species, and eight outgroups. Our phylogenetic reconstructions strongly support the division of Rodentia into three clades: (1) a "squirrel-related clade", (2) a "mouse-related clade", and (3) Ctenohystrica. Almost all evolutionary relationships within these clades are also highly supported. The primary remaining uncertainty is the position of the root. The application of various models and techniques aimed to remove non-phylogenetic signal was unable to solve the basal rodent trifurcation.ConclusionSequencing and analyzing a large sequence dataset enabled us to resolve most of the evolutionary relationships among Rodentia. Our findings suggest that the uncertainty regarding the position of the rodent root reflects the rapid rodent radiation that occurred in the Paleocene rather than the presence of conflicting phylogenetic and non-phylogenetic signals in the dataset.

The chorda tympani and its significance for rodent phylogeny

The topographical relationship of the chorda tympani to the tensor tympani muscle in the middle ear region of rodents was recorded, finding that this character provides new phylogenetic information. For this purpose we examined histological serial sections of 63 rodent species representing most families. Two lagomorph species were used as an outgroup. Computed 3D models of middle ear structures of several rodent taxa were prepared for the first time. We observed two different character states concerning the topography of the chorda tympani and the insertion tendon of the tensor tympani muscle: hypotensoric and epitensoric; the latter displays three subtypes. We assume that the shift from a plesiomorphic hypotensoric chorda tympani to an apomorphic epitensoric condition occurred at least six times independently in rodent phylogeny; however, this derived state is bound to higher taxonomic levels. The anomalurids under study show an epitensoric course of the chorda tympani through a mallear channel above the insertion of the tendon – just as in Pedetes capensis. Therefore, we suggest a new synapomorphy for these two taxa, confirming other new evidence as to their monophyly. The principal quality of the character used in this study is discussed.

Suprafamilial relationships among Rodentia and the phylogenetic effect of removing fast-evolving nucleotides in mitochondrial, exon and intron fragments.

BackgroundThe number of rodent clades identified above the family level is contentious, and to date, no consensus has been reached on the basal evolutionary relationships among all rodent families. Rodent suprafamilial phylogenetic relationships are investigated in the present study using ~7600 nucleotide characters derived from two mitochondrial genes (Cytochrome b and 12S rRNA), two nuclear exons (IRBP and vWF) and four nuclear introns (MGF, PRKC, SPTBN, THY). Because increasing the number of nucleotides does not necessarily increase phylogenetic signal (especially if the data is saturated), we assess the potential impact of saturation for each dataset by removing the fastest-evolving positions that have been recognized as sources of inconsistencies in phylogenetics.ResultsTaxonomic sampling included multiple representatives of all five rodent suborders described. Fast-evolving positions for each dataset were identified individually using a discrete gamma rate category and sites belonging to the most rapidly evolving eighth gamma category were removed. Phylogenetic tree reconstructions were performed on individual and combined datasets using Parsimony, Bayesian, and partitioned Maximum Likelihood criteria. Removal of fast-evolving positions enhanced the phylogenetic signal to noise ratio but the improvement in resolution was not consistent across different data types. The results suggested that elimination of fastest sites only improved the support for nodes moderately affected by homoplasy (the deepest nodes for introns and more recent nodes for exons and mitochondrial genes).ConclusionThe present study based on eight DNA fragments supports a fully resolved higher level rodent phylogeny with moderate to significant nodal support. Two inter-suprafamilial associations emerged. The first comprised a monophyletic assemblage containing the Anomaluromorpha (Anomaluridae + Pedetidae) + Myomorpha (Muridae + Dipodidae) as sister clade to the Castorimorpha (Castoridae + Geomyoidea). The second suprafamilial clustering identified a novel association between the Sciuromorpha (Gliridae + (Sciuridae + Aplodontidae)) and the Hystricomorpha (Ctenodactylidae + Hystricognathi) which together represents the earliest dichotomy among Rodentia. Molecular time estimates using a relaxed Bayesian molecular clock dates the appearance of the five suborders nearly contemporaniously at the KT boundary and this is congruent with suggestions of an early explosion of rodent diversity. Based on these newly proposed phylogenetic relationships, the evolution of the zygomasseteric pattern that has been used for a long time in rodent systematics is evaluated.

Middle ear morphology in dormice (Rodentia: Gliridae)

Dormouse middle ears have been examined from the points of view of comparative anatomy (Doran 1878; Bondy 1907; Hinchcliffe and Pye 1969), function in relation to ecology (Simkin 1965), and phylogenetic systematics (e.g. Ognev 1947; Lavocat and Parent 1971; Parent 1980, 1983; Wahlert et al. 1993; Potapova 2001), in most cases being considered only as small parts of much wider studies. Perhaps surprisingly, the anatomical descriptions of the ear region of dormice have not been entirely congruent. One group has stated that the stapedius muscle is missing in Glis glis (Hinchcliffe and Pye 1969; Pye and Hinchcliffe 1976), whereas another group described this muscle in dormice (Lavocat and Parent 1971; Parent 1976, 1980). While Hinchcliffe and Pye (1969) referred to ‘‘slight trabeculation’’ in the tympanic cavity of Glis, Simkin (1965) and Potapova (2001) described a chambered middle ear cavity. The conducting apparatus of dormice has been largely ignored, although there are brief descriptions of the ossicles in Doran (1878) and Ognev (1947). Rodent phylogeny is in a state of flux (Huchon et al. 2002), the clades and the names given to them often differing by study. The term ‘‘myomorph’’ is used here informally to denote the clade to which the Muridae belongs, which probably also contains the Spalacidae (considered to be a separate family by Norris et al. 2004), Dipodidae, Geomyidae and Heteromyidae. The

Molecular Systematics of Sciurognathi (Rodentia): The Mitochondrial Cytochrome b and 12S rRNA Genes Support the Anomaluroidea (Pedetidae and Anomaluridae)

Nucleotide sequence data from the mitochondrial 12S rRNA and cytochrome b genes were used to analyze phylogenetic relationships among sciurognath rodents. Our sample taxa included representatives of 11 sciurognath and 3 hystricognath families with two marsupial species, Didelphis virginiana and Macropus robustus, as outgroups. The dataset was analyzed using both maximum-parsimony (weighted and unweighted) and likelihood methods. Three suprafamilial groupings are strongly supported: Geomyidae + Heteromyidae (Geomyoidea), Sciuridae + Aplodontidae (Sciuroidea), and Pedetidae + Anomaluridae (Anomaluroidea). Although moderately supported, two sister group relationships were identified between Gliridae and Sciuroidea and between Castor and Geomyoidea. In contrast to previous nuclear DNA evidence, the evolutionary affinities between Ctenodactylidae and Hystricognathi (Ctenohystrica) and between Muridae and Dipodidae (Myodonta) are not supported by the mitochondrial data. Molecular divergence dates based on the combined data were estimated for suprafamilial groupings and are discussed in the light of current morphological and paleontological interpretations of rodent phylogeny.

Long-branch attraction phenomenon and the impact of among-site rate variation on rodent phylogeny

The phylogenetic relationships among major lineages of rodents is one of the issues most debated by both paleontologists and molecular biologists. In the present study, we have analyzed all complete mammalian mitochondrial genomes available in the databases, including five rodent species (rat, mouse, dormouse, squirrel and guinea-pig). Phylogenetic analyses were performed on H-strand amino acid sequences by means of maximum-likelihood and on H-strand protein-coding and ribosomal genes by means of distance methods. Also, log-likelihood ratio tests were applied to different tree topologies under the assumption of rodent monophyly, paraphyly or polyphyly. The analyses significantly rejected rodent monophyly and showed the existence of two differentiated clades, one containing non-murids (dormouse, squirrel and guinea-pig) and the other containing murids (rat and mouse). Long-branch attraction between murids and the outgroups could not be responsible for the existence of two different rodent clades, as no significant differences in evolutionary rate have been observed, except in the case of the squirrel, which shows a lower rate. The impact of among-site rate variation models on the phylogeny of rodents has been evaluated using the gamma distribution model. Results have shown that relationships among rodents remained unchanged, and the general topology of the tree was not affected, even though some branches were not properly resolved, most likely due to a lack of fit between estimated and real rate heterogeneity parameters.

Hantaviruses.

Since the recognition of the hantavirus pulmonary syndrome (HPS) in the USA in 1993, interest in hantavirus diseases has intensified worldwide. It is clear that hantaviruses have been historically responsible for a variety of human illnesses. Hantaviruses form a separate genus within the Bunyaviridae family. There are currently >20 recognised sero/genotypes and many others are under investigation. Each hantavirus type appears to be specific to a different rodent host. Virus phylogeny very closely reflects rodent phylogeny. The different hantavirus types are associated with different types of disease both in terms of target organs and disease severity. Two major diseases are recognised: haemorrhagic fever with renal syndrome (HFRS) and HPS. HFRS is primarily a disease of the old world while HPS is only recognised in the Americas. Over the past few decades the understanding and recognition of hantavirus disease throughout the world have greatly expanded. The number of recognised virus types continues to grow, as does the spectrum of hantavirus disease. There is evidence of hantavirus causing human disease in the British Isles, but at present it remains a largely uncharacterised disease.

Molecular evolution of the nuclear von Willebrand factor gene in mammals and the phylogeny of rodents.

Nucleotide sequences of exon 28 of the von Willebrand Factor (vWF) were analyzed for a representative sampling of rodent families and eutherian orders, with one marsupial sequence as outgroup. The aim of this study was to test if inclusion of an increased taxonomic diversity in molecular analyses would shed light on three uncertainties concerning rodent phylogeny: (1) relationships between rodent families, (2) Rodentia monophyly, and (3) the sister group relationship of rodents and lagomorphs. The results did not give evidence of any particular rodent pattern of molecular evolution relative to a general eutherian pattern. Base compositions and rates of evolution of vWF sequences of rodents were in the range of placental variation. The 10 rodent families studied here cluster in five clades: Hystricognathi, Sciuridae and Aplodontidae (Sciuroidea), Muridae, Dipodidae, and Gliridae. Among hystricognaths, the following conclusions are drawn: a single colonization event in South America by Caviomorpha, a paraphyly of Old World and New World porcupines, and an African origin for Old World porcupines. Despite a broader taxonomic sampling diversity, we did not obtain a robust answer to the question of Rodentia monophyly, but in the absence of any other alternative, we cannot reject the hypothesis of a single origin of rodents. Moreover, the phylogenetic position of Lagomorpha remains totally unsettled.

Substitution rate variation in closely related rodent species.

The existence of evolutionary rate variation has previously been demonstrated between different orders, different species and even between different regions of the same gene. To examine rate variation between closely related species of rodents we have sequenced the adenine phosphorybosyltransferase (APRT) gene from Mus spicilegus, Mus pahari, Mastomys hildebrandtii, Stochomys longicaudatus and Gerbillus campestris and compared these sequences with the previously published Mus musculus, Rattus norvegicus and Mesocricetus auratus APRT sequences. The alignment of these eight rodent APRT sequences reveals two large insertions within the introns: an insertion with sequence similar to a B1 repetitive element is found within Mastomys and an insertion with sequence similar to a B2 repetitive element is found within M. pahari. A phylogeny for the rodent APRTs agrees with the previously published rodent phylogeny based on other molecular and morphological data. The relative rate test which is often used to test for variation in rates of evolution in different lineages is shown here to be sensitive to the choice of outgroup and therefore should be used with great caution. This sensitivity is detectable only with closely related species and results from the prevalence of homoplastic substitutions. Rate variation is demonstrated within the APRT exons and introns and between the rodent species (with the most significant difference being a rate difference in M. spicilegus). In addition, some third codon positions are shown to be more prone to substitution than others. This clearly demonstrates that even between very closely related species there is ample evidence of major differences in rates of evolution among species, among regions of the gene and among different positions within the gene. We also demonstrate that standard methods of analysis might not detect this variation.