Evolutionary history of the most speciose mammals: molecular phylogeny of muroid rodents

Phylogenetic relationships between 32 species of rodents representing 14 subfamilies of Muridae and four subfamilies of Dipodidae were studied using sequences of the nuclear protein-coding genes Lecithin Cholesterol Acyl Transferase (LCAT) and von Willebrand Factor (vWF). An examination of some evolutionary properties of each data matrix indicates that the two genes are rather complementary, with lower rates of nonsynonymous substitutions for LCAT. Both markers exhibit a wide range of GC3 percentages (55%-89%), with several taxa above 70% GC3 for vWF, which indicates that those exonic regions might belong to the richest class of isochores. The primary sequence data apparently harbor few saturations, except for transitions on third codon positions for vWF, as indicated by comparisons of observed and expected pairwise values of substitutions. Phylogenetic trees based on 1,962 nucleotidic sites from the two genes indicate that the 14 Muridae subfamilies are organized into five major lineages. An early isolation leads to the clade uniting the fossorial Spalacinae and semifossorial Rhizomyinae with a strong robustness. The second lineage includes a series of African taxa representing nesomyines, dendromurines, cricetomyines, and the sole living member of mystromyines. The third one comprises only the mouselike hamster CALOMYSCUS: The fourth clade represents the cricetines, myospalacines, sigmodontines, and arvicolines, whereas the fifth one comprises four "traditional" subfamilies (Gerbillinae, Murinae, Otomyinae, and Acomyinae). Within these groups, we confirm the monophyly of almost all studied subfamilies, namely, Spalacinae, Rhizomyinae, Nesomyinae, Cricetomyinae, Arvicolinae, Sigmodontinae, Cricetinae, Gerbillinae, Acomyinae, and Murinae. Finally, we present evidence that the sister group of Acomyinae is Gerbillinae, and we confirm a nested position of Myospalacinae within Cricetinae and Otomyinae within Murinae. From a biogeographical point of view, the five main lineages spread and radiated from Asia with different degrees of success: the first three groups are now represented by a limited number of species and genera localized in some regions, whereas the last two groups radiated in a large variety of species and genera dispersed all over the world.     

Phylogeny of muroid rodents: relationships within and among major lineages as determined by IRBP gene sequences

The rodent family Muridae is the single most diverse family of mammals with over 1300 recognized species. We used DNA sequences from the first exon ( approximately 1200bp) of the IRBP gene to infer phylogenetic relationships within and among the major lineages of muroid rodents. We included sequences from every recognized muroid subfamily except Platacanthomyinae and from all genera within the endemic Malagasy subfamily Nesomyinae, all recognized tribes of Sigmodontinae, and a broad sample of genera in Murinae. Phylogenetic analysis of the IRBP data suggest that muroid rodents can be sorted into five major lineages: (1) a basal clade containing the fossorial rodents in the subfamilies Spalacinae, Myospalacinae, and Rhizomyinae, (2) a clade of African and Malagasy genera comprising the subfamilies Petromyscinae, Mystromyinae, Cricetomyinae, Nesomyinae, and core dendromurines, (3) a clade of Old World taxa belonging to Murinae, Otomyinae, Gerbillinae, Acomyinae, and Lophiomyinae, (4) a clade uniting the subfamilies Sigmodontinae, Arvicolinae, and Cricetinae, and (5) a unique lineage containing the monotypic Calomyscinae. Although relationships among the latter four clades cannot be resolved, several well-supported supergeneric groupings within each are identified. A preliminary examination of molar tooth morphology on the resulting phylogeny suggests the triserial murid molar pattern as conceived by evolved at least three times during the course of muroid evolution.     

Molecular Phylogeny of Rodents, with Special Emphasis on Murids: Evidence from Nuclear Gene LCAT

Phylogenetic relationships among 19 extant species of rodents, with special emphasis on rats, mice, and allied Muroidea, were studied using sequences of the nuclear protein-coding gene LCAT (lecithin:cholesterol acyltransferase), an enzyme of cholesterol metabolism. Analysis of 705 base pairs from the exonic regions of LCAT confirmed known groupings in and around Muroidea. Strong support was found for the families Sciuridae (squirrel and marmot) and Gliridae (dormice) and for suprafamilial taxa Muroidea and Caviomorpha (guinea pig and allies). Within Muroidea, the first branching leads to the fossorial mole rats Spalacinae and bamboo rats Rhizomyinae. The other Muroidea appear as a polytomy from which are issued Gerbillinae (gerbils), Murinae (rats and mice), Sigmodontinae (New World cricetids), Cricetinae (hamsters), and Arvicolinae (voles). Evidence from LCAT sequences agrees with that from a number of previous molecular and morphological studies, both concerning branching orders inside Muroidea and the bush-like radiation of rodent suprafamilial taxa (caviomorphs, sciurids, glirids, muroids), thus suggesting that this nuclear gene is an appropriate candidate for addressing questions of rodents relationships.     

The phylogenetic position of "Acomyinae" (Rodentia, Mammalia) as sister group of a Murinae + Gerbillinae clade: evidence from the nuclear ribonuclease gene.

The phylogenetic relationships of Acomys and Uranomys within Muridae were investigated using nuclear pancreatic ribonuclease A gene sequences. The various kinds of substitutions in the data matrix (15 taxa x 375 nucleotides) were examined for saturation, in order to apply a weighted parsimony approach. Phylogenies were derived by maximum parsimony (weighted and unweighted) and maximum likelihood procedures, using a dormouse (Gliridae) as outgroup. Maximum likelihood gave the most robust results. All analyses cluster some traditional taxa with a strong robustness, such as three species of the genus Mus, two South-East Asian rats, and two genera in each of the gerbil and vole families. When analyzed with those of other murid rodents representing Murinae, Gerbillinae, Arvicolinae, Cricetinae, and Sigmodontinae, sequences of the ribonuclease gene suggest that Acomys and Uranomys constitute a monophyletic clade at the subfamily level, denoted "Acomyinae." The relationships between the six subfamilies of Muridae appear poorly resolved, except for a clade uniting Murinae, Acomyinae, and Gerbillinae. Within this clade, the sister group of Acomyinae could not be identified, as the branch length defining a Gerbillinae + Murinae cluster is extremely short. The poor resolution of our phylogenetic inferences is probably the result of two confounding factors, namely the limited size of the pancreatic ribonuclease sequence and the probable short time intervals during the radiation of the six murid subfamilies involved in this study.     

Lung morphology in rodents (Mammalia, Rodentia) and its implications for systematics

A new nomenclature of the lung lobes and of the bronchial tree is presented, with which the lungs in 40 species of 11 rodent families are described. Whole, fixed lungs and silicone casts of the bronchial tree are tested for 23 characters, based on the distribution of lung lobes, the number and geometry of first order bronchi, the pulmonary blood supply, and lung symmetry. Ten lung morphotypes are recognized, seven of them representing one or more families: Castor type (Castoridae), Cryptomys type (Bathyergidae), Ctenodactylus type (Ctenodactylidae), Eliomys type (Gliridae), Myocastor type (Myocastoridae), Octodon type (Octodontidae and Echimyidae) and Rattus type (Sciuridae, Muridae pt. and Dipodidae). The Hydromys type is found only in Hydromys chrysogaster (Muridae), while Galea type A and B both appear in Galea musteloides (Caviidae). The data are phylogenetically analyzed by the program PAUP 4.0 using as outgroup Lagomorpha or Insectivora. On the species level, there are no well-resolved cladograms. On the family level, the cladograms do not contradict traditional rodent systematics with one exception: the Caviidae do not fall within Caviomorpha or even within the Hystricomorpha, but form a sister group to Dipodidae (Myomorpha). This appears to be a result of convergence. The lungs of Gliridae are more similar to those of Muridae than to those of Sciuridae. Included in the ingroup, Oryctolagus (Lagomorpha) forms a clade with Caviidae + Dipodidae. Thus, the "Glires hypothesis" is neither supported nor refuted.     

The phylogenetic position of the zokors (Myospalacinae) and comments on the families of muroids (Rodentia)

Recent molecular studies have concluded that the genus Myospalax evolved from within the rodent subfamily Cricetinae. This conclusion was tested using the complete sequences from the mitochondrial 12S rRNA and cytochrome b genes. Based on our analyses, Myospalax appears to be sister to a clade containing the subfamilies Spalacinae and Rhizomyinae, and all three of these lineages appear to be basal to the superfamily Muroidea. Based on the position of these three lineages, we suggest that they be placed in a distinct family, the Spalacidae, rather than subsumed as subfamilies in the family Muridae. Finally, our analyses suggest that the earlier placement of Myospalax as a member of the Cricetinae is the result of a single misidentified specimen, which was not a Myospalax.     

Phylogeny and divergence-date estimates of rapid radiations in muroid rodents based on multiple nuclear genes

The muroid rodents are the largest superfamily of mammals, containing nearly one third of all mammal species. We report on a phylogenetic study comprising 53 genera sequenced for four nuclear genes, GHR, BRCA1, RAG1, and c-myc, totaling up to 6400 nucleotides. Most relationships among the subfamilies are resolved. All four genes yield nearly identical phylogenies, differing only in five key regions, four of which may represent particularly rapid radiations. Support is very strong for a fundamental division of the mole rats of the subfamilies Spalacinae and Rhizomyinae from all other muroids. Among the other "core" muroids, a rapid radiation led to at least four distinct lineages: Asian Calomyscus, an African clade of at least four endemic subfamilies, including the diverse Nesomyinae of Madagascar, a hamster clade with maximum diversity in the New World, and an Old World clade including gerbils and the diverse Old World mice and rats (Murinae). The Deomyinae, recently removed from the Murinae, is well supported as the sister group to the gerbils (Gerbillinae). Four key regions appear to represent rapid radiations and, despite a large amount of sequence data, remain poorly resolved: the base of the "core" muroids, among the five cricetid (hamster) subfamilies, within a large clade of Sigmodontinae endemic to South America, and among major geographic lineages of Old World Murinae. Because of the detailed taxon sampling within the Murinae, we are able to refine the fossil calibration of a rate-smoothed molecular clock and apply this clock to date key events in muroid evolution. We calculate rate differences among the gene regions and relate those differences to relative contribution of each gene to the support for various nodes. The among-gene variance in support is greatest for the shortest branches. We present a revised classification for this largest but most unsettled mammalian superfamily.     

An Assessment of the Systematics of Arvicanthine Rodents Using Mitochondrial DNA Sequences: Evolutionary and Biogeographical Implications

Mitochondrial DNA sequences of cytochrome b (1140-bp), 12S (375-bp) and 16S (475-bp) ribosomal RNA gene fragments were used to investigate the phylogenetic relationships of a group of African rodents referred as the arvicanthines (Family Muridae, Subfamily Murinae). A total of 49 specimens including all seven genera and 15 of the 24 arvicanthine species currently recognized as well as outgroups from the subfamily Acomyinae, Arvicolinae, Gerbillinae, Murinae and Otomyinae were examined. Our molecular data support the monophyly of the African arvicanthine genera and their partition into three distinct lineages: one composed of Arvicanthis, Mylomys and Pelomys, one composed of Desmomys and Rhabdomys, and one represented by Lemniscomys. The Indian arvicanthine Golunda is external to this clade and is part of a larger clade, together with the African arvicanthines and other African Murinae such as Aethomys, Dasymys, Grammomys, and Hybomys, for which we propose the use of the tribal name Arvicanthini. The basal relationships within this set of species are poorly resolved, suggesting the possibility of a rapid radiation. Calibration based on the fossil record suggests that this radiative event would have taken place at about 8.0 Mya (Million years ago). The identification of the Otomyinae as the sister-taxon to Arvicanthini implies that the former are true murines and should therefore be given only tribal rank within the Murinae.     

Molecular evolutionary relationships of three genera of nesomyinae,endemic rodent taxa from madagascar

The relationships of Nesomyinae, a group of murid rodents endemic to the island of Madagascar, were investigated with two comparative molecular approaches. Compared to those of other muroid rodents representing Murinae, Cricetinae, Cricetomyinae. Arvicolinae, and Sigmodontinae, complete sequences of the 12S rRNA mitochondrial gene suggest that the Malagasy nesomyinesMacrotarsomys andNesomys are monophyletic and that their sister-group among the taxa analyzed isCricetomys. A limited series of DNA/DNA hybridization experiments extends these observations to a third nesomyine genus,Eliurus, and a second cricetomyine taxon,Saccostomus. By relating the amounts of overall genomic divergence with geological time as calibrated by theMus/Rattus dichotomy estimated at 12–14 My, the oldest within-Nesomyinae dichotomy is estimated to be 10.8 to 12.6 My. Thus, these three genera of Malagasy nesomyine rodents appear to be a rather ancient offshoot from African ancestors whose Recent relatives are Cricetomyinae. This preliminary observation should be confirmed by sampling additional genera of nesomyines and additional representatives for other subfamilies of African muroids.     

Interrelation between size of body and of digestive tract organs in some myomorpha: Isometry or allometry?

Using nonparametric tests, we analyzed the weights of the digestive tract organs of 198 rodent individuals belonging to 11 species of Arvicolinae (family Cricetidae) and Murinae (family Muridae), using both fresh and fixed material, the weight characteristics of which were identical. It has been shown that no unique dependence exists between the body weight and the entire digestive tract one in Arvicolinae rodents weighing 8–73 g. It was also shown that interspecific differences in the relative mass of such a dynamic system of organs as the digestive system cannot always be regarded as a function of the body size alone.     

On the role of phylogeny in determining activity patterns of rodents

Evolutionary plasticity is limited, to a certain extent, by phylogenetic constraints. We asked whether the diel activity patterns of animals reflect their phylogenies by analyzing daily activity patterns in the order Rodentia. We carried out a literature survey of activity patterns of 700 species, placing each in an activity time category: diurnal, nocturnal, or active at both periods (a-rhythmic). The proportion of rodents active at these categories in the entire order, was compared to the activity patterns of species of different families for which we had data for over ten species each: Dipodidae, Echimyidae, Geomyidae, Heteromyidae, Muridae, and Sciuridae. Activity times of rodents from different habitat types were also compared to the ordinal activity time pattern. We also calculated the probability that two random species (from a particular subgroup: family, habitat, etc.) will be active in the same period of the day and compared it to this probability with species drawn from the entire order. Activity patterns at the family level were significantly different from the ordinal pattern, emphasizing the strong relationship between intra-family taxonomic affiliation and daily activity patterns. Large families (Muridae and Sciuridae) analyzed by subfamilies and tribes showed a similar but stronger pattern than that of the family level. Thus it is clear that phylogeny constrains the evolution of activity patterns in rodents, and may limit their ability to use the time niche axis for ecological separation. Rodents living in cold habitats differed significantly from the ordinal pattern, showing more diurnal and a-rhythmic activity patterns, possibly due to physiological constraints. Ground-dwelling rodents differed significantly, showing a high tendency towards a-rhythmic activity, perhaps reflecting their specialized habitat. Electronic supplementary material Electronic supplementary material is available for this article at and accessible for authorised users.     

Parallel evolution of Myobiidae (Acari: Prostigmata) mites and jerboas (Rodentia: Dipodoidea)

The phenomenon of the parallel evolution is considered with the example of the myobiid mites (Acari: Prostigmata: Myobiidae) and the jerboas (Rodentia: Dipodoidea). According to recent phylogenetic studies of the superfamily Dipodoidea it is separated into 4 family: Allactagidae, Dipodidae, Zapodidae and Sminthidae (Shenbrot e. a., 1995). The myobiid mites of the subenus Dipodomyobia (11 species) of the genus Cryptomyobia are known as specific parasites associated with jerboas of the families Dipodidae and Allactagidae. One more species (Radfordia ewingi) considered as incertae sedis species within the genus Radfordia is found on the jerboas of the family Zapodidae. The myobiid mites are apparently absent on the members of the family Sminthidae. The reconstruction of phylogeny of the myobiid subgenus Dipodomyobia was carried out by the cladistic method (software PAUP 3.0 s). The analysis was based on 13 morphological characters. At the first step of analysis 42 parsimonious trees have been obtained. The strict consensus tree displays one distinct cluster, which incorporates mites of the allactaga species of group restricted to the jerboa family Allactagidae, and several plesions, species of which are usually refferred to as dipi species group and associated with the family Dipodidae (fig. 1). At the second step of analysis, two characters, which appeared as homoplasies at the first step of analysis were excluded, and one new characters (structure of male genital shield) was additionally included. Single cladogram obtained displays two general clusters and one plesion. The first cluster comprises the allactaga species group (parasites of Allactagidae). The second cluster incorporates the dipi species group, the parasites of subfamilies Dipodinae and Paradipodinae of Dipodidae). The plesion is represented by one species Cryptomyobia baranovae being a specific parasite of Salpingotus crassicauda (Cardiocraninae, Dipodidae). There is the high level congruence between the pattern of myobiid cladogram and jerboas phylogeny proposed by Shenbrot (1992) (fig. 2). The position of one species C. paradipi (the parasite of Paradipus ctenodactylus, single representative of subfam. Paradipodinae) does not fit to this phylogenetic system of the jerboas. This mite species belongs to the claster dipi. All others myobiid species of this group are the parasites of the subfamily Dipodinae. In the cladogram of jerboas, the subfam. Paradipodinae is a sister group of Cardiocraninae, but not of Dipodinae, as it is suggested by the parasitological data. If sinapomorphies in the node Paradipodinae--Cardiocraninae are not correct (as Shenbrot admitted), there would be a complete congruence between the phylogenetic pattern of myobiid and of jerboas. The general phylogeny of Dipodoidea based on citogenetical data was proposed by Vorontsov e. a. (1971). 3 families only were recognized within Dipodoidea: Zapodidae, Sminthidae and Dipodidae. The latter family included 3 subfamilies: Dipodinae, Cardiocraninae and Allactaginae. The version of the jerboa phylogeny proposed in the present paper based on parasitological data corresponds in general lines to the hypotesis of Vorontsov e. a. (1971). The myobiid mites are absent on Sminthidae, they are represented by one species incertae sedis on Zapodidae, and by the subgenus Dipodomyobia on others jerboas (Dipodidae sensu Vorontsov e. a.). According to the parasitological data, the subfamilies Dipodinae and Allactaginae are the sister groups, because the myobiid mites of the subgenus Dipodomyobia parazitise on the jerboas of these taxa only. The subfamily Paradipodinae (sensu Shenbrot) is a sister group for Dipodinae, as far as species C. paradipi is the sister species to other members of the dipi group. The subfamily Cardiocraninae is a sister group for the node Dipodinae-Paradipodinae and also should be included to Dipodidae, because the aberrant species C. baranovae is obviously related to the dipi species group.     

Species differences among various rodents in the conversion of 7alpha-hydroxycholesterol in liver microsomes

Our previous study demonstrated that there are species differences among vertebrates in their conversion of 7alpha-hydroxycholesterol (7HC) to 7-ketocholesterol (7KC). To examine this further, we investigated the differences in the products of 7alpha-hydroxycholesterol in various species of male muroid rodents. Adult male Syrian hamsters (Mesocricetus auratus), dwarf hamsters (Phodopus rovolovskii), Djungarian hamsters (Phodopus sungorus), Chinese hamsters (Cricetulus griseus), rat-like hamsters (Tscherskia triton), and hispid cotton rats (Sigmodon hispidus) were used. Microsomal fractions were prepared from their livers, and the activities of the enzymes that participate in the dehydrogenation of 7alpha-hydroxycholesterol were determined by measuring the products using high-performance liquid chromatography. 7alpha-hydroxycholesterol was converted to both 7alpha-hydroxy-4-cholesten-3-one (7HCO) and 7-ketocholesterol in all of the hamsters tested. However, in the rat-like hamster and the hispid cotton rat, 7alpha-hydroxycholesterol was converted mostly to 7alpha-hydroxy-4-cholesten-3-one, as also observed in the rat (Rattus norvegicus). The results suggest that microsomal enzyme activity in the conversion of 7alpha-hydroxycholesterol to 7-ketocholesterol varies considerably, even within the subfamily Cricetinae and the family Muridae.     

Aspekte zur Herkunft und Verbreitung der Muriden

Wenn es zutrifi, daf3 die typisch afrikanischen, friiher den Muridae zugestellten Gruppen Den- dromurinae, Petromyscinae und Cricetomyinae den Cricetiden viel naher stehen und dafl die bei den Muriden noch verbliebenen afrikanischen Otomyinae - wie hier dargelegt wird - den Muriden mindestens ebenso fern stehen wie die oben genannten, so bleiben von den echten Muriden in Afrika nur die Murinae iibrig. Diese aber sind hochstwahrscheinlich sudostasiati- schen Ursprungs und nach Afrika relativ spat eingewandert. Afrika scheint also keine autochthonen Muriden zu besitzen. Fossilienfunde und tiergeographische Tatsachen stiitzen diese Ansicht.

Summary

Aspects of the Origin and Distribution of the Muridae Importance of the Systematic Position of the Otominae
If it is right that the typical african groups of Dendromurinae, Petromyscinae and Cricetomyinae – formerly all considered as Muridae – are Cricetids and that the African Otomyinae – as stated here – are not Murids, the Murinae are the only remaining "true" Muridae of Africa. These, however are probably of Southeast Asian origin and are relative lately immigrated in Africa. Africa therefore seems to have no autochthonous Muridae. This opinion is supported by fossils and zoogeographical facts.     

Molecular phylogeny of the Praomys complex (Rodentia: Murinae): a study based on DNA/DNA hybridization experiments.

Within the Murinae (Muridae: Rodentia), the African rats of the Praomys group, whose systematics has been studied through different approaches, have raised numerous taxonomic problems. Different taxa related to Praomys have successively been described, among which Mastomys, Myomys and Hylomyscus were considered either as separate genera or subgenera of Praomys. In order to clarify the relationships within the Praomys group, we conducted a series of DNA/DNA hybridization experiments involving different species of Praomys, Mastomys, Myomys and Hylomyscus plus other Murinae and a Cricetomyinae. This study indicates that the Praomys complex is a monophyletic entity clearly separated from the other African and Asian Murinae. If Mastomys and Hylomyscus appeared to be independent genera, the taxonomic situation of Praomys and Myomys is more difficult to ascertain. Indeed, Praomys tullbergi appears more closely related to Myomys daltoni than to another species of Praomys , namely P. jacksoni , suggesting paraphyly for Praomys. Furthermore, P. jacksoni is as distant from P. tullbergi as from any species of Mastomys. Additional species of Praomys and, especially, of Myomys , are needed for reaching a definitive conclusion on these latter taxa. The Praomys group is more related to Mus than to Rattus. To calibrate our molecular distances with geological time, we used a dating of 10 Myr for the Musi Rattus dichotomy. The inferred rate of molecular evolution suggests a dating of c. 8 Myr for the separation of the Praomys group from the Mus lineage.     

Short Retroposons of the B2 Superfamily: Evolution and Application for the Study of Rodent Phylogeny

Short retroposons can be used as natural phylogenetic markers. By means of hybridization and PCR analysis, we demonstrate that B2 retroposon copies are present only in the three rodent families: Muridae, Cricetidae, and Spalacidae. This observation highlights the close phylogenetic relation between these families. Two novel B2-related retroposon families, named DIP and MEN elements, are described. DIP elements are found only in the genomes of jerboas (family Dipodidae) and birch mice (family Zapodidae), demonstrating the close relationship between these rodents. MEN element copies were isolated from the squirrel, Menetes berdmorei, but were not detected in three other species from the family Sciuridae. The MEN element has an unusual dimeric structure: the left and right monomers are B2- and B1-related sequences, respectively. Comparison of the B2, DIP, MEN, and 4.5S₁ RNA elements revealed an 80-bp core sequence located at the beginning of the B2 superfamily retroposons. This observation suggests that these retroposon families descended from a common progenitor. A likely candidate for this direct progenitor could be the ID retroposon. Received: 20 December 1996 / Accepted: 17 June 1997     

Confrontation of morphological and molecular data: the Praomys group (Rodentia, Murinae) as a case of adaptive convergences and morphological stasis

Phylogenetic relationships in a group of 21 African rodent species designated as the Praomys group (Murinae) were investigated using morphological characters and sequence data from the complete mitochondrial cytochrome b gene and nuclear IRBP gene fragment (840bp). The molecular results confirm the monophyly of the Praomys group, including the species Malacomys verschureni, while the other Malacomys species appear very divergent. The basal relationships within the Praomys group are poorly resolved, suggesting a rapid radiation at about 7-9 million years ago based on genetic divergence rates calibrated from the fossil record. Discrepancies between molecular and morphological results probably reflect of numerous convergences as well as variations in the rates of morphological evolution among lineages. Reconstructions of the ancestral character states suggest a savannah origin for the Praomys group, along with some morphological traits conserved by stasis in savannah taxa. At the same time, forest taxa seem to be characterized by an accelerated morphological evolution, with acquisition of convergent adaptive characters.     

Morphological diversity of Old World rats and mice (Rodentia, Muridae) mandible in relation with phylogeny and adaptation

The respective roles of the phylogenetic and ecological components in an adaptive radiation are tested on a sample of Old World rats and mice (Muridae, Murinae). Phylogeny was established on nuclear and mitochondrial genes and reconstructed by maximum likelihood and Bayesian methods. This phylogeny is congruent with previous larger scale ones recently published, but includes some new results: Bandicota and Nesokia are sister taxa and Micromys would be closely related to the Rattus group. The ecological diversification is investigated through one factor, the diet, and the mandible outline provides the morphological marker. Elliptic and radial Fourier transforms are used for quantifying size and shape differences among species. Univariate size and shape parameters indicate that phylogeny is more influential on size than diet, and the reverse occurs for shape and robust patterns are recognized by multivariate analyses of the data sets provided by the Fourier methods. Omnivorous and herbivorous groups are well separated despite some overlapping, as well as are other Murinae with a specialized diet (insects, seeds). Phylogeny is also influential as shown by the segregation of several groups (Praomys, Arvicanthini, Rattus, Apodemus). Allometric shape variation was investigated, and although present it does not overwhelm effects of either phylogeny or diet. Massive mandibles characterize herbivorous Murinae and slender mandibles, the insectivorous ones. A strong angular process relative to the coronoid process characterizes seedeaters, and the reverse characterized Murinae with a diet based largely on animal matter. Such changes in morphology are clearly in relation with the functioning of the mandible, and with the forces required by the nature of the food: the need of a stronger occlusal force in herbivorous species would explain massive mandibles, and an increase of the grasping and piercing function of incisors in insectivorous species would explain slender mandibles.     

Positive selection for indel substitutions in the rodent sperm protein catsper1

Catsper1 is a voltage-gated calcium channel located in the plasma membrane of the sperm tail and is necessary for sperm motility and fertility in mice. We here examine the evolutionary pattern of Catsper1 from nine species of the rodent subfamily Murinae of family Muridae. We show that the rate of insertion/deletion (indel) substitutions in exon 1 of the gene is 4-15 times that in introns or neutral genomic regions, suggesting the presence of strong positive selection that promotes fixations of indel mutations in exon 1. The number of indel polymorphisms within species appears higher than expected from interspecific comparisons, although there are too little data to provide a statistically significant conclusion. These results, together with an earlier report in primates, indicate that positive selection promoting length variation in Catsper1 may be widespread in mammals. A structural model of Catsper1 suggested the importance of the exon 1-encoded region in regulating channel inactivation, which may affect sperm mobility and sperm competition. Our findings provide a necessary foundation for future experimental investigations of Catsper1's function in sperm physiology and role in sperm competition using rodent models.     

Tracing paternal ancestry in mice, using the Y-linked, sex-determining locus, Sry

The molecular evolution of mammalian Y-linked DNA sequences is of special interest because of their unique mode of inheritance: most Y- linked sequences are clonally inherited from father to son. Here we investigate the use of Y-linked sequences for phylogenetic inference. We describe a comparative analysis of a 515-bp region from the male sex- determining locus, Sry, in 22 murine rodents (subfamily Murinae, family Muridae), including representatives from nine species of Mus, and from two additional murine genera--Mastomys and Hylomyscus. Percent sequence divergence was < 0.01% for comparisons between populations within a species and was 0.19%-8.16% for comparisons between species. Our phylogenetic analysis of 12 murine taxa resulted in a single most- parsimonius tree that is highly concordant with phylogenies based on mitochondrial DNA and allozymes. A total evidence tree based on the combined data from Sry, mitochondrial DNA, and allozymes supports (1) the monophyly of the subgenus Mus, (2) its division into a Palearctic group (M. musculus, M. domesticus, M. spicilegus, M. Macedonicus, and M. spretus) and an Oriental group (M. cookii++, M. cervicolor, and M. caroli), and (3) sister-group relationships between M. spicilegus and M. macedonicus and between M. cookii and M. cervicolor. We argue that Y- chromosome DNA sequences represent a valuable new source of characters for phylogenetic inference.