Bibliography of the genus Apodemus (Rodentia, Muridae)

A complete bibliography of the genus Apodemus for the period 1970–1980 is presented, with a selection of the more important papers from earlier years, and a few references for 1981. A coded index to species and subjects is provided. All titles have been translated into English.     

Molecular phylogeny and distribution of three Apodemus species (Muridae, Rodentia) in Serbia

Phylogenetic relationships among three species of the genus Apodemus ( A. flavicollis, A. sylvaticus and A. agrarius ) from seven different localities in Serbia were estimated using arbitrarily primed PCR (AP-PCR) profiling, which allowed clear distinction between the sibling species A. flavicollis and A. sylvaticus . Eight oligonucleotide primers out of the 22 screened, gained a total of 397 amplified bands. The average pairwise genetic distances within Apodemus species ranged from 0.51 between A. flavicollis and A. sylvaticus , to 0.74 between A. sylvaticus and A. agrarius. The large genetic distances obtained among populations of A. flavicollis (0.13) indicate that this part of the Balkan Peninsula was probably a refuge during the last glaciation. Furthermore, differences obtained between populations south and north from the river Danube suggest that this species survived the Last Glacial Maximum in at least two separate refuges. Although our data for molecular markers are from a limited number of localities, extended analyses of C-band distribution on chromosomes from previously studied localities south of the rivers Danube and Sava, indicate that distribution of A. sylvaticus is limited to northern Serbia. Therefore, it is possible that this part of the Balkan Peninsula was not a refuge for this species during the last glaciation.     

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 and morphometric variation in two sibling species of the genus Praomys (Rodentia: Muridae): implications for biogeography

The rodent genus Praomys is widely distributed in the African tropics. The species are cryptic, rendering the species taxonomy unclear. There are differences of opinion concerning the specific status of Praomys misonnei and Praomys tullbergi, and their geographical distribution. We sequenced the cytochrome b and/or the 16S gene of 221 specimens from 12 countries in order to evaluate the genetic variability within these two species, and to precisely determine their geographical distribution. Morphological and morphometrical analyses on the sequenced specimens were also performed to find criteria useful for the identification of museum specimens. Our results confirm that P. misonnei and P. tullbergi are two valid species that can be separated by molecular data. However, no single discrete morphological character or simple metric measurement can be used to discriminate them. The percentage of misclassified individuals in multivariate discriminant analysis is relatively high (10%). The two species have allopatric distributions: P. tullbergi occurs in West Africa, from eastern Guinea to western Ghana, and P. misonnei is widely distributed from eastern Ghana to western Kenya. Within P. misonnei we identified three or four major geographical clades: a West Central African clade, an East African clade, a Nigerian clade, and a possible West African clade. Within P. misonnei, high geographical morphometrical variability was also identified. The role of both rivers and Pleistocene forest refugia in promoting speciation within the genus Praomys is discussed. © 2010 The Linnean Society of London, Zoological Journal of the Linnean Society, 2010, 160 , 397–419.     

Molecular phylogenetic analyses indicate paraphyly of the genus Hybomys (Rodentia: Muridae): Taxonomic implications

Widely distributed in Guineo‐Congolian forests, the genus Hybomys is represented by two species complexes (univittatus and trivirgatus), each restricted to one distinct forest block. In the last revision, these two species complexes were considered as distinct subgenera (Hybomys and Typomys). Previous morphological and karyological studies identified an important divergence between these two subgenera and raised the question of their taxonomic status (subgenus or genus). The number of species within this genus is also a matter of discussion: nine forms were described but only six (H. badius, H. basilii, H. lunaris, H. planifrons, H. trivirgatus, and H. univitttatus) are currently recognized as distinct species, the three others (H. pearcei, H. eisentrauti, and H. rufocanus) being considered as synonyms. The monophyly of the genus and its species have never been previously investigated with DNA sequence data. In this study, we combined mitochondrial and nuclear data (for a total of 3,264 nucleotide characters) to test the monophyly of Hybomys and to assess the specific status of H. eisentrauti and H. rufocanus. Our results highlight the paraphyly of the genus: members of the H. univittatus species complex appeared closely related to the genera Stochomys and Dephomys; representatives of H. trivirgatus are the sister clade of the node grouping Stochomys, Dephomys and member of the H. univittatus species complex. Combined with previous morphological findings, our results suggest that Typomys and Hybomys should be considered as two distinct genera. Based on tree topology and genetic distances, we propose to consider H. rufocanus as a valid species, distinct from H. univittaus, and to consider H. badius and H. eisentrauti as junior synonyms of H. rufocanus.     

Epigenetic polymorphism in populations of Apodemus sylvaticus and Apodemus flavicollis (Rodentia, Muridae)

The main object of this study was to use discontinuous variation as a means of measuring divergence between populations of A. sylvaticus (L.) and A. flavicollis (Melchior) from Britain and Eurasia. Samples from 17 populations (671 skulls) were each classified for 20 discontinuous morphological variants. The investigation has shown that certain epigenetic variants have a characteristic incidence in populations of the two species and that the relative incidence of the variants could be used as an aid to specific separation. The calculation of degree of divergence between the populations has made it possible to suggest the order in which populations are related to each other.     

Phylogeographic study of Apodemus ilex (Rodentia: Muridae) in Southwest China

Background

The Mountains of southwest China have complex river systems and a profoundly complex topography and are among the most important biodiversity hotspots in the world. However, only a few studies have shed light on how the mountains and river valleys promote genetic diversity. Apodemus ilex is a fine model for investigating this subject.

Methodology/Principal Findings

To assess the genetic diversity and biogeographic patterns of Apodemus ilex, the complete cytochrome b gene sequences (1,140 bp) were determined from 203 samples of A. draco/ilex that were collected from southwest China. The results obtained suggested that A. ilex and A. draco are sistergroups and diverged from each other approximately 2.25 million years ago. A. ilex could be divided into Eastern and Western phylogroups, each containing two sub-groups and being widespread in different geographical regions of the southern Hengduan Mountains and the western Yunnan - Guizhou Plateau. The population expansions of A. ilex were roughly from 0.089 Mya to 0.023 Mya.

Conclusions

Our result suggested that A. ilex is a valid species rather than synonym of A. draco. As a middle-high elevation inhabitant, the phylogenetic pattern of A. ilex was strongly related to the complex geographical structures in southwest China, particularly the existence of deep river valley systems, such as the Mekong and Salween rivers. Also, it appears that the evolutionary history of A. ilex, such as lineage divergences and population expansions were strongly affected by climate fluctuation in the Late Pleistocene.     

Chromosomal diversity in the genus Arvicanthis (Rodentia, Muridae) from East Africa: a taxonomic and phylogenetic evaluation

In this paper we discuss the contribution of cytogenetics to the systematics of Arvicanthis in East Africa, by reviewing all the known chromosomal cytotypes of the genus in the area. We also provide G‐ and C‐banding comparisons for two recently described karyotypes, provisionally named ANI‐5 (2n = 56, NFa = 62) and ANI‐6 (2n = 60, NFa = 72). This, therefore, brings the total number of known cytotypes in this area to 10. Five of these correspond to the species recognized by the latest rodent checklist, i.e. A. nairobae (2n = 62, NFa = 78), A. neumanni (2n = 52–53, NFa = 62), A. blicki (2n = 48, NFa = 62), A. abyssinicus (2n = 62, NFa = 64) and A. niloticus (2n = 62, NFa = 60–62). The taxonomic status of the remaining five cytotypes (A. cf. somalicus, 2n = 62 NFa = 62–63; ANI‐5, 2n = 56, NFa = 62; ANI‐6/6a 2n = 60, NFa = 72/76; ANI‐7, 2n = 56, NFa = 78; and ANI‐8, 2n = 44, NF = 72) is discussed. Finally, we reconstruct the phylogenetic relationships among all the known karyotypes on the basis of banding data available for the genus in Africa and show the occurrence of two main clades, each characterized by different types of chromosomal rearrangements. The times of the cladogenetic events, inferred by a molecular clock, indicate that karyotype evolution has accomplished almost all the dichotomic events from the end of the Miocene to the present day. The discovery of a large chromosomal differentiation between populations showing low genetic distances and intrapopulation chromosomal polymorphism suggests that the process of chromosomal differentiation in Arvicanthis is still ongoing and may possibly be responsible for speciation.     

Population structure and dynamics of sympatric Apodemus species (Rodentia: Muridae)

This paper describes the population biology of sympatric populations of Apodemus sylvaticus and A. flavicollis in western England. Annual changes in population siie closely resembled those seen in allopatric populations such that simultaneous peaks in number occurred only in autumn and early winter. Numbers of A. sylvaticus were low and stable in early summer increasing rapidly in late summer and autumn and remaining high throughout winter before a sharp decline in spring. Numbers of A. flavicollis increased after the start of reproduction and continued to rise throughout summer and autumn. The period of major decline of this species was during early winter. Densities of A. sylvaticus and A. flavicollis were comparable with those cited in allopatric studies. Spring populations of both species consisted of cohorts first appearing in the late summer and autumn of the previous year. Few individuals present in spring survived the summer. Reproduction of A. flavicollis commenced four to six weeks before that of A. sylvaticus . Seasonal variation in mean weight of adult males and females also indicates that those changes, due to the acquisition of secondary sex characteristics and reproductive maturity, occur earlier in A. flavicollis than in A. sylvaticus . Data presented contain no evidence of interspecific competition and it is concluded that interspecific differences, chiefly asynchrony in reproduction and annual population cycles, contribute to their stable coexistence.     

Phylogenetics of the woodrat genus Neotoma (Rodentia: Muridae): implications for the evolution of phenotypic variation in male external genitalia

Interspecific morphological variation in animal genitalia has long attracted the attention of evolutionary biologists because of the role genital form may play in the generation and/or maintenance of species boundaries. Here we examine the origin and evolution of genital variation in rodents of the muroid genus Neotoma. We test the hypothesis that a relatively rare genital form has evolved only once in Neotoma. We use four mitochondrial and four nuclear markers to evaluate this hypothesis by establishing a phylogenetic framework in which to examine genital evolution. We find intron seven of the beta-fibrinogen gene to be a highly informative nuclear marker for the levels of differentiation that characterize Neotoma with this locus evolving at a rate slower than cytochrome b but faster than 12S. We estimate phylogenetic relationships within Neotoma using both maximum parsimony and maximum likelihood-based Bayesian methods. Our Bayesian and parsimony reconstructions differ in significant ways, but we show that our parsimony analysis may be influenced by long-branch attraction. Furthermore, our estimate of Neotoma phylogeny remains consistent across various data partitioning strategies in the Bayesian analyses. Using ancestral state reconstruction, we find support for the monophyly of taxa that possess the relatively rare genital form. However, we also find support for the independent evolution of the common genital form and discuss possible underlying developmental shifts that may have contributed to our observed patterns of morphological evolution.     

Sex chromosomes at early meiosis in three wood mice species of the genus Apodemus (Rodentia, Muridae)

The prophase of the first meiotic division was studied in field mice of the species Apodemus (Sylvaemus) flavicollis, A. (S.) ponticus, and A. (S.) uralensis by light and electron microscopy. The karyotypes of the species were described on the base of electron microscopy of synaptonemal complexes in spermatocytes I. The axial elements of the sex chromosomes at early-middle pachytene can synapse along the major portion of the Y axis; at late pachytene-early diplotene, the synapsis region shrinks; and at diakinesis-metaphase I, X and Y chromosomes associate tail-to-tail in all species studied. The behavior of sex chromosomes in the synapsis in the species studied was quite uniform. The results are discussed in the context of earlier data on the behavior of sex chromosomes in various rodent species in meiosis prophase I and their banding.     

Chromosomal variability of the field mouse Apodemus agarius (Rodentia, Muridae)

Chromosome sets of 114 Apodemus agrarius mice from 29 localities in Moldova, Ukraine, Siberia, and Far East were studied by means of G-, C-, and NOR-banding. In all populations studied, the Y chromosome was shown to be a medium-size acrocentric chromosome consisting of heterochromatin. Chromosome polymorphism observed in populations from Primorskii krai concerned (1) the morphology of the first two autosome pairs (variants A/A, A/ST, and ST/ST), (2) the number of metacentric chromosomes (from 6 to 8), and (3) heterochromatin localization in the pericentromeric regions of two metacentric chromosome pairs. A karyotype with an additional heterochromatic microchromosome found in all the metaphases studied was described in one mouse from a locality of western Primorye that has not been studied previously. In the karyotype of 15 mice from four populations of Primorye, the pool of nucleolus organizer regions is distributed over three autosome pairs rather than over four, as is the case A. agrarius from Europe. Based on the analysis of literature sources and our own data, the problem of chromosome polymorphism in the field mouse is discussed.     

Arboreal gaits in three sympatric rodents Apodemus agrarius,Apodemus flavicollis (Rodentia,Muridae) and Myodes glareolus (Rodentia,Cricetidae)

Vertical stratification of the arboreal habitat allows the coexistence of several species in a given area, because the complex arboreal strata can be used in different ways by arboreal and scansorial mammals. The present report experimentally investigated the gait metrics on different arboreal substrates, of three sympatric rodents living in a deciduous forest in Poznań, Poland. Arboreal locomotion was compared between the burrowing striped field mouse, Apodemus agrarius, the scansorial bank vole, Myodes glareolus, and the more arboreal yellow-necked mouse, Apodemus flavicollis. We filmed two wild-caught individuals from each species walking on four different substrate diameters (2 mm, 5 mm, 10 mm, 25 mm) and three different inclinations (45° descending, horizontal, 45° ascending) at 240 fps and collected a set of gait parameters from a total of 273 complete cycles. Our results did not demonstrate clear relationships between arboreal locomotion and the ecology of the three species. Only A. flavicollis exhibited locomotor features partly associated with arboreal competence, including lower velocity and diagonality on narrow substrates and asymmetrical gaits on wider ones. On the other hand, the two Apodemus species, despite their different ecologies, shared a few locomotor similarities, such as velocity regulation primarily by stride frequency, and similar effects of substrate size and inclination on diagonality, duty factor, and duty factor index indicating the possibility of a phylogenetic signal. Because the selected gait parameters provided limited insight into the ability of small mammals to move competently through an arboreal habitat, these findings indicate that the relationship between behaviour and ecology is complex.     

Biochemical genetic variation in the genus Littorina (Prosobranchia:Mollusca)

The genus Littorina has been subject to many studies of electrophoretically detectable variation, mostly aimed either at clarifying questions concerned with population structure, or at clarifying difficult taxonomic/systematic problems. This paper reviews many of these studies. Topics covered include Hardy-Weinberg deviations, the extent of genetic differentiation among populations within species, founder effects and the effects of human introductions on genetic variation, the biological significance of allozyme variation, and the uses of allozyme variation in Littorina systematics.     

Social differences in the subcaudal scent gland secretion of Apodemus sylvaticus (Rodentia: Muridae)

This paper presents a preliminary chemical analysis of the secretion of the subcaudal scent gland of the Woodmouse Apodemus sylvaticus . A statistical analysis of samples from various sites in the United Kingdom and Eire shows that there are individual differences in the secretion, differences between the sexes, differences between juveniles and adults and differences between populations.     

Cytogenetic differentiation of Apodemus peninsulae populations (Rodentia, Muridae) in eastern Siberia

Population and cytogenetics studies of geographical karyotype changes in East Asiatic mice in East Siberia showed that each population has unique cytogenetic structure, owing to different variants of B-chromosomes system, including 1 to 18 B-chromosomes differing in morphology and size. For each population, we observed the prevalence of mice with a definite number and morphology of B-chromosomes, which is probably the result of homeostatic processes in the population. Local changes were revealed, due to increase in the number of dot-like B-chromosomes in the direction from the West to the East.     

Comparative study of the phylogenetic structure in six Apodemus species (Mammalia,Rodentia) inferred from ISSR-PCR data

The utility of the Inter Simple Sequence Repeat-Polymerase Chain Reaction (ISSR-PCR) was explored in order to determine genetic variation in six species of the genus Apodemus (A. flavicollis, A. sylvaticus, A. uralensis, A. agrarius, A. mystacinus and A. epimelas) at the individual level, population level, in separate geographic samples and in the species as a whole. Six optimized primers produced highly reproducible and polymorphic DNA markers with 98.3% polymorphic bands on a total sample of 91 individuals from 32 localities in Europe and Asia. Moreover, each primer allowed for an exact diagnosis of each of the six Apodemus species and thus provides a simple and reliable tool for the hitherto problematic discrimination of species from the subgenus Sylvaemus. Genetic distances between species ranged from 0.079, among the closely related A. flavicollis and A. sylvaticus, to 0.203 between A. mystacinus and A. agrarius. A. flavicollis, A. uralensis and A. sylvaticus display a strong population substructure. The range of genetic distances among geographic samples within last two species reaches the values obtained for closely related species. ISSR markers proved to be a simple and reliable tool for species diagnosis, as well as for estimating genetic diversity below the species level and for closely related species, but they showed questionable reliability for larger genetic distances.     

云南4个地区高山姬鼠线粒体控制区种群遗传分化研究

对云南4个种群38个个体的线粒体控制区（D-loop）905 bp的核苷酸序列遗传变异进行分析,探讨了高山姬鼠种群遗传结构和分化。在905 bp D-loop基因的碱基序列中,共发现了57个变异位点（全变异的6.30%）,共定义了23个单倍型,其中有一个单倍型（Hap1）为横断山3个种群（中甸、丽江和剑川）所共享,其余22个单倍型均为各个种群所特有。分子变异分析（AMOVA）表明,种群间的遗传变异占33.7%,种群内的遗传变异占66.3%。FST统计结果表明,除昆明种群和横断山种群之间差异显著（P〈0.05）,其它地理种群间的差异均不显著（P〉0.05）,说明昆明种群与横断山种群之间出现了明显的遗传分化。     

The phylogeny of the Praomys complex (Rodentia: Muridae) and its phylogeographic implications

Among the African Murinae (Rodentia, Muridae), the Praomys complex, whose systematics has been studied by different approaches, has raised numerous taxonomic problems. Different taxa, namely Praomys, Mastomys , Myomys and Hylomyscus have been considered either as separate genera or subgenera of Praomys . In order to understand the relationships within the Praomys complex and to test the monophyly of the genus Praomys , a cladistic analysis was conducted, based on morpho-anatomical factors involving different species of Praomys , Mastomys , Myomys and Hylomyscus. The results indicate that the Praomys complex is monophyletic, as are the genera Hylomyscus , Mastomys and Myomys , whereas the genus Praomys appears paraphyletic. Indeed, a group of species including Praomys jacksoni was found to be more closely related to the genera Mastomys and Myomys than to a Praomys tullbergi -group. The biotopes and the distribution areas of the species were mapped on the phylogeny. It appears that the different clades each present a relative ecological cohesion and are arranged according to a gradient from closed to open habitats. From there, an evolutionary scenario is proposed for the emergence of the different clades and species of the genus Praomys sensu stricto.