A molecular phylogenetic framework for the Ryukyu endemic rodents Tokudaia osimensis and Diplothrix legata

Diplothrix legata and Tokudaia osimensis are rodent species endemic to the Ryukyu Islands (Okinawa area) of the southern part of Japan. To place them within a phylogenetic framework of Asian rodent species, we examined the molecular relationships among these species and Apodemus, Micromys, Mus, and Rattus, using an analysis of mitochondrial cytochrome b gene (1140 bp) and nuclear IRBP gene (782 bp) sequences. The results indicate that the four main murine genera and Tokudaia diverged at similar evolutionary times, namely at the time of the radiation of Murinae, 14 to 40 million years ago, depending on different concepts for the divergence times of Rattus and Mus. In contrast, Diplothrix separated from the Rattus group more recently. Our results indicate that D. legata and the Rattus group diverged at 20-30% of the divergence time of Rattus and Mus under the assumption of the molecular clock, suggesting that D. legata established its lineage at least by the beginning of the Pleistocene era. It is thus evident that the Okinawa area preserves rare indigenous species with various levels of genetic endemicity.     

Albumin evolution and phylogenetic relationships among Greek rodents of the families Arvicolidae and Muridae

The phylogenetic relationships of seven rodent species Microtus atticus, M. thomasi, M. epiroticus (family Arvicolidae) and Mus domesticus, Rattus norvegicus, Apodemus flavicollis and A. mystacinus (family Muridae) have been studied. In order to define these relationships we study the albumin evolution using the micro-complement fixation test (MC'F). No phylogenetic (immunological) distance between M. atticus and M. thomasi was found, a fact which confirms from the biochemical point of view the opinion that the former taxon is a synonym of the latter one. A molecular time scale relating MC'F immunological distances and geological time was established based on the assumption of a rate of 100 amino acid substitutions per–20 million years. The time of divergence between M. epiroticus and M. thomasi was estimated to be 0.5–0.6 million years ago (Pleistocene). Such a recent divergence corroborates the opinion based on morphological and protein electrophoretic criteria according to which Terricola (formerly Pitymys ) must be considered as a subgenus of the genus Microtus and not as a distinct genus Pitymys , as previously had been accepted. Apodemus flavicollis and A. mystacinus were separated about 0.65–0.8 million years ago (Pleistocene). The Rattus norvegicus lineage was separated–12.5 million years ago (end of Miocene), shortly before the Mus and Apodemus divergence. Our data indicate that the common ancestor of Arvicolidae and Muridae lived–25 million years ago (early Miocene). All these results are in agreement with paleontological and some recent DNA-DNA hybridization and electrophoretic data.     

A phylogenetic study of the genus Apodemus by sequencing the mitochondrial DNA control region

The sequences of the mitochondrial DNA control region (D-loop) and flanking tRNA genes (about 1000 bp) of 20 samples of wood mice (genus Apodemus ) were analyzed in order to clarify the relationships between different species belonging to the genus. The phylogenetic trees obtained using different methods showed similar topologies with distinct Karstomys ( Apodemus epimelas and Apodemus mystacinus ) and Sylvaemus ( Apodemus alpicola , Apodemus flavicollis , Apodemus hermonensis , Apodemus sylvaticus and Apodemus uralensis ) subtrees. Within Sylvaemus all species appeared to be closely related to each other, probably as result of a bush-like radiation event. Nevertheless, A. hermonensis seemed to be the first diverging branch followed by A. sylvaticus ; A. alpicola and A. flavicollis appeared to be very closely related. Three individuals of uncertain taxonomical status were included in the analysis: hypotheses as to their status are discussed. Further phylogenetic analysis was carried out combining the D-loop sequences of part of the samples of certain taxonomical status with 12S rRNA and cytochrome b sequences obtained by other researchers. Furthermore, I present a structure analysis of the D-loop in Apodemus as compared other rodent species.     

Molecular phylogeny and taxonomy of wood mice (genus Apodemus Kaup, 1829) based on complete mtDNA cytochrome b sequences, with emphasis on Chinese species

Phylogenetic relationships among 15 species of wood mice (genus Apodemus) were reconstructed to explore some long-standing taxonomic problems. The results provided support for the monophyly of the genus Apodemus, but could not reject the hypothesis of paraphyly for this genus. Our data divided the 15 species into four major groups: (1) the Sylvaemus group (A. sylvaticus, A. flavicollis, A. alpicola, and A. uralensis), (2) the Apodemus group (A. peninsulae, A. chevreri, A. agrarius, A. speciosus, A. draco, A. ilex, A. semotus, A. latronum, and A. mystacinus), (3) A. argenteus, and (4) A. gurkha. Our results also suggested that orestes should be a valid subspecies of A. draco rather than an independent species; in contrast, A. ilex from Yunnan may be regarded as a separate species rather than a synonym of orestes or draco. The species level status of A. latronum, tscherga as synonyms of A. uralensis, and A. chevrieri as a valid species and the closest sibling species of A. agrarius were further corroborated by our data. Applying a molecular clock with the divergences of Mus and Rattus set at 12 million years ago (Mya) as a calibration point, it was estimated that five old lineages (A. mystacinus and four major groups above) diverged in the late Miocene (7.82-12.74 Mya). Then the Apodemus group (excluding A. mystacinus) split into two subgroups: agrarius and draco, at about 7.17-9.95 Mya. Four species of the Sylvaemus group were estimated to diverge at about 2.92-5.21 Mya. The Hengduan Mountains Region was hypothesized to have played important roles in Apodemus evolutionary histories since the Pleistocene.     

Genetic relationships between European and Transcaucasian mice of the genus Apodemus Kaup]

Genetic relations between four European mice species of the genus Apodemus (Apodemus sylvaticus, A. flavicollis, A. microps and A. falzfeini) and five Transcaucasian ones (A. mystacinus, A. microps, and the forms No 2, 3p, 3f) were studied for 37 biochemical loci. Close genetic relations were demonstrated between the mice of subgenus Sylvaemus and A. mystacinus. A. microps and A. falzfeini from the Caucasus were shown conspecific to these species from the Ukraine and the presence of the two new different species--the form No 2 and 3p in the Caucasus was established.     

Genetic variation and evolution in the genus Apodemus (Muridae: Rodentia)

Genetic variation was studied using protein electrophoresis of 28–38 gene loci in 1347 specimens of Apodemus agrar-ius, A. peninsulae, A. flavicollis, A. sylvaticus, A. alpicola, A. uralensis, A . cf. hyrcanicus, A. hermonensis, A. m. mystacinus and A. m. epimelas , representing 121 populations from Europe, the Middle East, and North Africa. Mean values of heterozygosity per locus for each species ranged from 0.02 to 0.04. Mean values of Nel's genetic distance ( D ) between the taxa ranged from 0.06 (between A. flavicollis and A. alpicola) to 1.34 (between A. uralensis and A. agrarius ). The highest values of D were found between A. agrarius and other Apodemus species (0.62-1.34). These values correspond to those generally observed between genera in small mammals. Our data show that A. agrarius and A. peninsulae are sister species, well-differentiated from other taxa. High genetic distance between A. m. mystacinus and A. m. epimelas leads us to consider them distinct species and sister taxa to other Western Palaearctic species of the subgenus Sylvaemus . The data also suggest a recent separation of members of the latter group from a common ancestor, and subsequent rapid radiation, making it difficult to infer phylogenetic relationships. Some taxonomic implications of the results are discussed further.© 2002 The Linnean Society of London, Biological Journal of the Linnean Society , 2002, 75 , 395–419.     

Molecular phylogeny of the genus Mus (Rodentia: Murinae) based on mitochondrial and nuclear data

The genus Mus encompasses at least 38 species divided into four subgenera: Mus , Pyromys , Nannomys and Coelomys . The subgenus Mus , which comprises the house mouse and related species, is by far the most extensively studied, although the subgenus Nannomys is the most speciose. Although the relationships within the subgenus Mus are rather well characterized, those between subgenera are still unclear. In the present study, phylogenetic analyses of the whole genus were performed using a larger species sample of Nannomys than in previous studies, and a nuclear gene (IRBP) in addition to mitochondrial data (cytochrome b and 12S rRNA). Members of the Acomyinae and Murinae were used as outgroups. Separate and combined analyses were performed with maximum parsimony, maximum likelihood and Bayesian methods, and divergence times were estimated. The results showed that the monophyly of the genus Mus and of each subgenus was strongly supported by the three genes and the combined analysis. The phylogenies derived from the three genes were on the whole congruent; however, several conflicting topologies were observed such as the relationships between the three Asian species of the subgenus Mus ( caroli , cervicolor and cookii ). Increasing the taxonomic sampling of Nannomys did not satisfactorily improve the resolution of relationships between the four subgenera. In addition, molecular calibrations indicate that the Mus and Nannomys radiation coincided with major environmental changes.  © 2005 The Linnean Society of London, Biological Journal of the Linnean Society , 2005, 84 , 417–427.     

Evolutionary systematics of the Indian mouse Mus famulus Bonhote, 1898: molecular (DNA/DNA hybridization and 12S rRNA sequences) and morphological evidence

The genus Mus encompasses 38 species of mice divided into four subgenera: Mus , Pyromys , Nannomys and Coelomys . Each of these four taxa is characterized by discrete morphological as well as biochemical traits. We used two different molecular approaches to determine the relationships between these subgenera: DNA/DNA hybridization and 12S rRNA mitochondrial sequences. We compared the resulting phylogenies from each method and with phylogenies derived from morphological data. The degree of resolution of each molecular approach is discussed. The two molecular studies indicate that Mus , Pyromys , Nannomys and Coelomys are clearly distinct monophyletic groups, as previously indicated by morphological data and other biochemical and molecular approaches. There is one divergence between previous morphological and the molecular and morphological studies presented here: the position of the Indian species Mus famulus . This taxon, which was formerly included in the subgenus Coelomys , is demonstrated here to belong to the subgenus Mus. We also propose the following relationships within Mus sensu lato : Mus and Pyromys are the closest relatives, followed by Nannomys and Coelomys , whose relationships are still unclear. This arrangement is more robustly supported by DNA/DNA hybridization than by 12S rRNA data. A molecular time scale for the evolution within Mus sensu lato is proposed, using as a reference the Mus/Rattus divergence estimated by the fossil record at around 12 mya.  © 2003 The Linnean Society of London, Zoological Journal of the Linnean Society , 2003, 137 , 385–401.     

Molecular phylogeny of European muroid rodents based on complete cytochrome b sequences

Phylogenetic relationships among 18 species of mainly European muroid rodents that belong to three subfamilies were estimated using complete sequences of the mitochondrial cytochrome b gene. The inferred monophyly of the subfamilies Murinae (mice and rats) and Arvicolinae (voles, lemmings, and muskrats) is in agreement with previous studies. Within the Murinae, the morphology-based division of the genus Apodemus into three subgenera is supported by these DNA sequence data. The relationships among the different genera of the Murinae were generally poorly resolved, and the relationships of Micromys and Acomys to the other murine genera remained unresolved. Within the subfamily Arvicolinae, the relations of the genera Arvicola, Clethrionomys, and Microtus remained tentative with our data. However, within the Microtus group, there is a good molecular support for the phylogenetic relationships. These findings suggest that the origin of the different murine and arvicoline lineages was rapid, indicating an adaptive radiation with fast speciation.     

Y Chromosome Evolution in the Subgenus Mus (Genus Mus)

A 305 base pair DNA sequence isolated from the Y chromosome of the inbred mouse strain C57BL/10 was used to investigate the pattern and tempo of evolution of Y chromosome DNA sequences for five species in the subgenus Mus, including Mus spretus, Mus hortulanus, Mus abbotti, Mus musculus and Mus domesticus. Variation in hybridization patterns between species was characterized by differences in fragment lengths of both intensely and faintly hybridizing fragments, whereas variation in hybridization patterns within species was characterized primarily by differences in fragment lengths of faintly hybridizing fragments. Phylogenetic analyses were conducted based on fragment size variation within and among species. Phylogenetic relationships inferred from these analyses partly agree with the phylogenetic relationships obtained from biochemical and mitochondrial DNA data. We conclude that a set of DNA sequences common to the Y chromosomes of a closely related group of species in the subgenus Mus has evolved rapidly as reflected by sequence divergence and sequence amplification.     

Satellite DNA as a phylogenetic marker: Case study of three genera of the murine subfamily

Satellite DNA (satDNA) represent tens of percent of the vertebrate genome. However, no full set of satDNA fragments has been determined for even one species. It is known that some genera possess a satDNA characteristic for that genus with species-specific modifications. We found that the pattern of hybridization of Mus musculus satDNA probes with M. spicilegus metaphase chromosomes was similar to, with slight differences from, that of M. musculus. No hybridization signal was observed if Mus musculus satDNA probes were hybridized with representatives of Sylvaemus and Apodemus genera. The amount of Mus musculus satDNA in the genomes of various species was evaluated by dot-hybridization. We revealed that genomes of close murine species had cenromeric and pericentromeric repeats belonging to the same families and were not found in remote species.     

Molecular evolution of the murine tspy genes

Molecular aspects of murine evolution were studied by sequencing, and subsequently comparing, introns of the Y-chromosomal tspy genes from Apodemus agrarius, A. sylvaticus, A. flavicollis, Mus platythrix (subgenus Pyromys), M. booduga (subgenus Leggada), and from species of the subgenus Mus, including M. cervicolor, M. macedonicus and M. spretus. Estimates of nucleotide substitution rates in these lineages were in perfect agreement with phylogenetic data previously published by She et al. (1990), Catzeflis et al. (1992; 1993), and Lyon et al. (1996). The only exception was provided by a comparatively late divergence of M. spretus and M. macedonicus. Our data also suggest that M. booduga diverged from the subgenus Mus about 3 Myr ago.     

Temporal, spatial, and ecological modes of evolution of Eurasian Mus based on mitochondrial and nuclear gene sequences

We sequenced mitochondrial (cytochrome b, 12S rRNA) and nuclear (IRBP, RAG1) genes for 17 species of the Old World murine genus Mus, drawn primarily from the Eurasian subgenus Mus. Phylogenetic analysis of the newly and previously available sequences support recognition of four subgenera within Mus (Mus, Coelomys, Nannomys, and Pyromys), with an unresolved basal polytomy. Our data further indicate that the subgenus Mus contains three distinct 'species groups': (1) a Mus booduga Species Group, also including Mus terricolor and Mus fragilicauda (probably also Mus famulus); (2) a Mus cervicolor Species Group, also including Mus caroli and Mus cookii; and (3) a Mus musculus Species Group, also including Mus macedonicus, Mus spicilegus, and Mus spretus. Species diversity in Eurasian Mus is probably explicable in terms of several phases of range expansion and vicariance, and by a propensity within the group to undergo biotope transitions. IRBP and RAG1 molecular clocks for Mus date the origin of subgenera to around 5-6 mya and the origin of Species Groups within subgenus Mus to around 2-3 mya. The temporal pattern of evolution among Eurasian Mus is more complex than that within the Eurasian temperate genus Apodemus.     

六种鼠组织中过氧化物酶和酯酶变异的比较

本文研究姬鼠属（Ａｐｏｄｅｍｕｓ）２种鼠和鼠属（Ｒａｔｕｓ）４种鼠的心组织过氧化物酶和肝组织酯酶同工酶等位基因的变异。结果表明,６种鼠心组织过氧化物酶皆为４条区带,其中社鼠和白腹巨鼠的酶带泳动速度略快于褐家鼠和黄毛鼠的酶带;鼠属４种鼠的酶带间距大致相同,而姬鼠属的酶带间距略大于鼠属,这种谱型的区别就所分析的６种鼠而言,可以认为是该同工酶表现的属间区别。肝组织酯酶区带较多,其酶带数和泳动速度的差异具有明显的种间特征;泳动最快的酶带在姬鼠中是２条,在鼠属中是１条,可以认为是属间特征的区别。从９项生化指标的异同作动物配对比较,表明褐家鼠与黄毛鼠亲缘上较近,社鼠与白腹巨鼠亲缘上也较近,而且白腹巨鼠在进化上可能要比其余３种鼠属动物更接近于姬鼠属     

Satellite DNA as a phylogenetic marker: case study of three genera of the Murinae subfamily

Satellite DNA (satDNA) represent tens percent of any of the vertebrate genome. Still, a complete set of sat-DNA fragments is not determined for either species. It is known that some genus with species-specific modifications possess a satDNA characteristic for the genus. So, satDNA was used as a phylogenetic marker in some cases when precise satDNA fragment was cloned. We used the probe of the whole pericentromeric region and 4 cloned satDNA fragments of Mus musculus in order to consider probes value for phylogenesis of 3 Murinae genera. Fluorescent in situ hybridization (FISH) revealed similar pattern on metaphase spreads inside genus Mus, though some difference was noted. None of the satDNA fragment gave signal in the centromeric region on chromosomes from genera Sylvaemus and Apodemus. These data are in agreement with those on satDNA fragments in the genome determined by dot-blot hybridization: M musculus satDNA fragments are absent in the genomes of both remote genera while they are present in the genomes of the genera Mus, though in different amounts. SatDNA of each genera should be cloned for the phylogenetic purposes.     

Polymorphism of C lambda genes and units of duplication in the genus Mus

The number of Ig C lambda genes in nine geographically widespread species from the four subgenera in the genus Mus was estimated from the number of Bam HI and Eco RI restriction fragments that hybridize under high stringency conditions to cDNA probes of BALB/c inbred mouse origin (Mus musculus domesticus). Three closely related species in the subgenus Mus, M. musculus, M. spretus, and M. spicelegus, show considerable variation in the number of C lambda genes. Estimates of gene numbers in these animals range from two C lambda genes in M. spretus from Puerto Real, Spain to 12 C lambda genes in M. musculus musculus from Studenec, Czechoslovakia. Strains of mice carrying either six or 10 C lambda genes were derived from a single population of M. musculus domesticus from Centreville, MD. The hybridization patterns of mice exhibiting C lambda gene amplification indicate that duplications are of relatively recent origin and probably occurred by reiteration of a DNA segment closely related to the 6.5 kb [C lambda 3 - C lambda 1] unit found in BALB/c inbred mice. Three more distantly related species in the subgenus Mus, and a species representing the Nannomys subgenus all appear to carry only four C lambda genes. DNA of species representing the Coelomys and Pyromys subgenera hybridized weakly to the C lambda cDNA probes, but these animals also have no more than four C lambda genes. Thus, there may be a base number of four C lambda genes in most species in the genus Mus. All inbred strains of mice so far examined also have only four C lambda genes, but no feral M. musculus examined have fewer than six C lambda genes. One explanation of the discrepancy in the number of genes between inbred and feral M. musculus is that C lambda genes were deleted during the process of inbreeding.     

Multigene phylogeny of the Old World mice, Murinae, reveals distinct geographic lineages and the declining utility of mitochondrial genes compared to nuclear genes

Despite its great diversity and biomedical importance, the rodent subfamily Murinae is poorly resolved phylogenetically. We present the first cladistic analysis sampling multiple representatives of most major groups based on DNA sequence for three nuclear (GHR, RAG1, and AP5) and one mitochondrial (COII and parts of COI and ATPase 8) fragments. Analyzed separately, the four partitions agree broadly with each other and the combined analysis. The basal split is between a clade of Philippine Old Endemics and all remaining murines. Within the latter, rapid radiation led to at least seven geographically distinct lineages, including a Southeast Asian Rattus clade; a diverse Australo-Papuan and Philippine clade; an African arvicanthine group including the otomyines; an African Praomys group; and three independent genera from Africa and Asia, Mus, Apodemus, and Malacomys. The murines appear to have originated in Southeast Asia and then rapidly expanded across all of the Old World. Both nuclear exons provide robust support at all levels. In contrast, the bootstrap proportions from mitochondrial data decline rapidly with increasing depth in the tree, together suggesting that nuclear genes may be more useful even for relatively recent divergences (< 10MYA).     

Phylogenetic relationships in the coral family acroporidae, reassessed by inference from mitochondrial genes

Phylogenetic relationships within the dominant reef coral family Acroporidae were inferred from the mitochondrial genes cytochrome b and ATPase 6. The rate of nucleotide substitution in the genes gave proper resolution to deduce genetic relationships between the genera in this family. The molecular phylogeny divided this family into three major lineages: the genera Astreopora, Montipora and Acropora. The genus Anacropora was included in the same clade as the genus Montipora, suggesting its recent speciation from Montipora. The subgenus Isopora was significantly distant from the subgenus Acropora. Taken together with morphological and reproductive differences, we propose that these two subgenera be classified as independent genera. The divergence times deduced from the genetic distances were consistent with the fossil record for the major genera. The results also suggest that the extant reef corals speciated and expanded very recently, probably after the Miocene, from single lineage which survived repeated extinction by climate changes during the Cenozoic era.     

Taxonomy, evolutionary history and biogeography of the broad-toothed field mouse (Apodemus mystacinus) in the eastern Mediterranean area based on mitochondrial and nuclear genes

The broad-toothed field mouse ( Apodemus mystacinus ) is distributed throughout the Balkan Peninsula, Asia Minor and the Middle East. It is generally split into two different specific entities: Apodemus epimelas occurs on the Balkan Peninsula and A. mystacinus inhabits Asia Minor and the Middle East. This analysis, based on two mitochondrial regions (cytochrome b and the D-loop) and the interstitial retinol binding protein (IRBP) nuclear gene, confirms an important level of genetic divergence between the animals from these regions and their separation from each other at least 4.2–5.1 Mya, which is in favour of a distinct specific status. Finally, the broad-toothed field mice from south-western Turkey appear to be closely related to the animals from Crete but highly distinct from the populations of the other Oriental regions. This supports a distinct subspecific level ( A. m. rhodius ) for the insular animals and also for those from south-western Turkey. From a biogeographical point of view, it can be assumed that either late Pliocene or early Pleistocene cooling led to the isolation of two main groups of A. mystacinus , one in the Balkan region and the other one in Turkey and the Near East (Syria and Israel). In this region, it is suggested that a more recent event appeared during the Quaternary period, isolating broad-toothed field mice in Crete and leading to the appearance of two well-differentiated genetic groups: one in Crete and south-western Turkey, and the other widespread in northern and eastern Turkey as well as in the Near East.  © 2005 The Linnean Society of London, Biological Journal of the Linnean Society , 2005, 85 , 53–63.     

Systematics of Maxomys Sody, 1936. (Rodentia: Muridae: Murinae): DNA/DNA hybridization studies of some Borneo-Javan species and allied Sundaic and Australo-Papuan genera

We compared five species of the murine genus Maxomys and representatives of nine other murid genera in a complete 15 × 15 DNA-hybridization matrix. FITCH trees were calculated for the entire suite of taxa and for subsets including only the five Maxomys and these together with the four nearest outgroups. All trees were validated by 'bootstrapping' and by jackknifing, performing both single- and multiple-deletions of taxa. The full 15 times 15 data set indicated a sister-group relationship between Maxomys and two pairs of genera ( Sundamys-Rattus sensu stricto and Mviventer-Leopoldamys ) that are more closely related to each other than to Maxomys; addition of data on Bandicota and Berylmys from another recent DNA-hybridization study confirmed that these genera are successive sister-taxa to the Sundamys-Rattus pair. Mus-Myomys and Uromys-Melomys were each distinct lineages from the above grouping of Rattus sensu lata species, and from the putative outgroup sigmodontine Peromyscus, but the interrelations of the three murine clades were unresolved. Within Maxomys, M. surifer and M. bartelsii are a related pair, and M. ochraceiventer probably forms an unresolved trio with M. rajah and M. whiteheadi. Calibration of a tree generated from saturation-corrected distances against a likely divergence-date of 12.2 Mybp for the separation of Mus and Rattus confirms a high rate of single-copy DNA change in murids (2.1%/Myr); and suggests that Sigmodontinae and Murinae diverged at around 15.3 Mybp, that Maxomys and the group of six other Rattus sensu lato separated approximately 7.6 Myr ago, and that Maxomys began to diversify 4.8 Myr ago.