A Biogeographic View of Apodemus in Asia and Europe Inferred From Nuclear and Mitochondrial Gene Sequences

Range Dynamics of Striped Field Mouse (Apodemus agrarius) in Northern Eurasia under Global Climate Change Based on Ensemble Species Distribution Models

The striped field mouse (Apodemus agrarius Pallas, 1771) is a widespread species in Northern Eurasia. It damages crops and carries zoonotic pathogens. Its current and future range expansion under climate change may negatively affect public health and the economy, warranting further research to understand the ecological and invasive characteristics of the species. In our study, we used seven algorithms (GLM, GAM, GBS, FDA, RF, ANN, and MaxEnt) to develop robust ensemble species distribution models (eSDMs) under current (1970-2000) and future climate conditions derived from global circulation models (GCMs) for 2021-2040, 2041-2060, 2061-2080, and 2081-2100. Simulation of climate change included high-, medium-, and low-sensitivity GCMs under four scenarios (SSP1-2.6, SSP2-4.5, SSP3-7.0, and SSP5-8.5). We analyzed the habitat suitability across GCMs and scenarios by constructing geographical ranges and calculating their centroids. The results showed that the range changes depended on both the sensitivity of GCMs and scenario. The main trends were range expansion to the northeast and partial loss of habitat in the steppe area. The striped field mouse may form a continuous range from Central Europe to East Asia, closing the range gap that has existed for 12 thousand years. We present 49 eSDMs for the current and future distribution of A. agrarius (for 2000-2100) with quantitative metrics (gain, loss, change) of the range dynamics under global climate change. The most important predictor variables determining eSDMs are mean annual temperature, mean diurnal range of temperatures, the highest temperature of the warmest month, annual precipitation, and precipitation in the coldest month. These findings could help limit the population of the striped field mouse and predict distribution of the species under global climate change.

Spatio-temporal genetic structure of the striped field mouse (Apodemus agrarius) populations inhabiting national parks in South Korea: Implications for conservation and management of protected areas

Population or habitat connectivity is a key component in maintaining species and community-level regional biodiversity as well as intraspecific genetic diversity. Ongoing human activities cause habitat destruction and fragmentation, which exacerbate the connectivity due to restricted animal movements across local habitats, eventually resulting in the loss of biodiversity. The Baekdudaegan Mountain Range (BMR) on the Korean Peninsula represents “biodiversity hotspots” and eight of the 22 Korean national parks are located within the BMR. Given the striped field mouse (Apodemus agrarius) is the most common and ecologically important small mammals in these protected areas, the population genetic assessment of this species will allow for identifying “genetic diversity hotspots” and also “genetic barriers” that may hinder gene flow, and will therefore inform on effective conservation and management efforts for the national park habitats. We collected samples from hair, tail, or buccal swabs for 252 A. agrarius individuals in 2015 and 2019. By using mitochondrial DNA cytochrome b (cyt b) sequences and nine microsatellite loci, we determined levels of genetic diversity, genetic differentiation, and gene flow among eight national park populations of A. agrarius along the BMR. We found high levels of genetic diversity but the occurrences of inbreeding for all the nine samples analyzed. Our results also indicated that there was detectable temporal genetic variation between the 2015 and 2019 populations in the Jirisan National Park, which is probably due to a short-term decline in genetic diversity caused by reduced population sizes. We also found a well-admixed shared gene pool among the national park populations. However, a significant positive correlation between geographic and genetic distances was detected only in mtDNA but not microsatellites, which might be attributed to different dispersal patterns between sexes. There was a genetic barrier to animal movements around the Woraksan National Park areas. The poor habitat connectivity surrounding these areas can be improved by establishing an ecological corridor. Our findings of the presence of genetic barriers in some protected areas provide insights into the conservation and management efforts to improve the population or habitat connectivity among the national parks.

Phylogeography of the striped field mouse (Apodemus agrarius Pallas, 1771) in light of new data from central part of Northern Eurasia

A phylogeographic analysis of A. agrarius based on the complete mtDNA cytochrome b and control region sequences has been performed using data obtained for the first time for the species from large regions of the central part of Northern Eurasia (23 localities of Altai, Western Siberia, and the Urals). The obtained results have demonstrated a complex intraspecific differentiation of A. agrarius, which has manifested not only in the isolation of the isles populations in Southeast Asia (Jeju and Taiwan), but also in the genetic heterogeneity of mainland populations, which has reflected the history of the modern intraspecific genetic diversity formation against the background of changing physiographic conditions of Eurasia in the Quaternary. The divergence of genetic lineages has taken place apparently simultaneously (in mid-Pleistocene) on the territory of the Eastern part of the modern disjunctive range, where all the identified lineages are present today. The demographic history and possible evolutionary scenarios for A. agrarius in the Western part of the range have been considered. TMRC reconstructions have shown that the lifetime of the common ancestor of the lineage that expanded in the Western Palearctic is about 17.7 [95% HPD 13.2–22.5] kyr. This suggests that the transcontinental expansion of A. agrarius is a relatively recent event that has occurred after the LGM.

Ancient rivers shaped the current genetic diversity of the wood mouse (Apodemus speciosus) on the islands of the Seto Inland Sea, Japan

The current distributions of organisms have been shaped by both current and past geographical barriers. However, it remains unclear how past geographical factors-currently cryptic on the sea floor-affected the current distributions of terrestrial animals. Here, we examined the effects of currently cryptic ancient rivers on current genetic differentiation of the large Japanese wood mouse, Apodemus speciosus, which inhabits islands in the Seto Inland Sea, Japan. Genome-wide polymorphisms were identified by GRAS-Di (Genotyping by Random Amplicon Sequencing, Direct) analysis of 92 A. speciosus individuals. Maximum-likelihood analysis was performed with 94,142 single nucleotide polymorphisms (SNPs) identified by GRAS-Di analyses. Ancient rivers were visualized by Geographic Information System (GIS) channel analysis. Maximum-likelihood analysis showed strong support for the monophyly of each population in the islands in the Seto Inland Sea; it also showed close relationships between Innoshima-Ikuchijima, Ohmishima-Hakatajima-Oshima, Ohmishima-Hakatajima, Ohsakikamijima-Ohsakishimojima, Kamikamagarijima-Shimokamagarijima, and Kurahashijima-Etajima islands. The principal component analyses of the SNPs also supported these relationships. Furthermore, individuals from islands located on the east and west sides of the main stream of the ancient river were clustered on each side with strong support. These phylogenetic relationships were completely congruent with the paleogeographic relationships inferred from ancient rivers. In conclusion, the findings demonstrated that the current distribution of genetically distinct island lineages was shaped by ancient rivers that are currently submerged beneath the Seto Inland Sea, Japan.

Aggregated occurrence records of the invasive alien striped field mouse (Apodemus agrarius Pall.) in the former USSR

Background

Open access to occurrence records of the most dangerous invasive species in a standardised format have important potential applications for ecological research and management, including the assessment of invasion risks, formulation of preventative and management plans in the context of global climate and land use changes in the short and long perspective. The striped field mouse (Apodemusagrarius Pallas, 1771) is a common species in the temperate latitudes of the Palaearctic. Due to land use and global climate changes, several waves of expansion of the range of this species have been observed or inferred. By intrusion into new regions, the striped field mouse has become an alien species there. Apodemusagrarius causes significant harm to agriculture and is one of the most important pests of grain crops. In tree nurseries, A.agrarius destroys seeds of valuable tree species and gnaws at the bark of saplings of broadleaf species and berry bushes. It is one of the most epidemiologically important rodents, involved in the circulation of the causative agents of haemorrhagic fever with renal syndrome (HFRS) and many other zoonotic infections. The foregoing allows us to classify the striped field mouse as a dangerous invasive alien species in the expanding part of the range. A lot of data accumulated for this species are of interest from both ecological and applied points of view. The accumulation and aggregation of data on the occurrence records of A.agrarius is relevant for the study of ecology, biogeography and construction of the spatial distribution and ecological niche models in the context of global climate change. We have created a dataset of 1603 occurrence records of this species, collected from 1936 to December 2020 by various zoologists, previously published or original. These records relate to a significant part of the striped field mouse’s range in Russia (1264 records) and neighbouring countries (339 records). The dataset shows the position of the northern and central parts of A.agrarius range, the disjunction of the range in Transbaikalia and isolated populations in the north of the range. The data were obtained in different formats from literature, indicating different degrees of accuracy of geographic coordinates and with several variations of the species' name. In the process of aggregating and fixing errors, we created a set of georeferenced occurrence records, adopted a controlled vocabulary, removed duplicates and standardised the format of records using unified data structure. We examined the dataset for inconsistencies with the taxonomic position of A.agrarius and removed the incorrect records. This paper presents the resulting dataset of A.agrarius occurrence records in the territory of Russia and neighbouring countries in a standardised format.

New information

This is a validated and comprehensive dataset of occurrence records of A.agrarius, including both our own observations and records from literature. This dataset is available for extension by other researchers using a standard format in accordance with Darwin Core standards. In different countries, there are a lot of occurrence records for the striped field mouse, but the overwhelming part of them is presented in separate literary sources, stored in the form of maps and in zoological collections. Prior to this project, such information was not available to a wide range of researchers and did not allow the use of these spatial data for further processing by modern methods of analysis, based on geographic information systems (GIS technologies). The created dataset combines species occurrence records of many Soviet zoologists who studied the distribution of the striped field mouse over a significant part of its recent range, in Russia and neighbouring countries (within the former USSR). The final set of records was created by combining the species occurrence records using a uniform data structure, checking geographic coordinates and removing duplicate and erroneous records. The dataset expands the available information on the spatial and temporal distribution of the dangerous invasive species in Russia and neighbouring countries of the former USSR (Estonia, Latvia, Lithuania, Belarus, Ukraine, Moldova, Georgia, Azerbaijan, Kazakhstan and Kyrgyzstan).

Comparable response of wild rodent gut microbiome to anthropogenic habitat contamination

Species identity is thought to dominate over environment in shaping wild rodent gut microbiota, but it remains unknown whether the responses of host gut microbiota to shared anthropogenic habitat impacts are species-specific or if the general gut microbiota response is similar across host species. Here, we compare the influence of exposure to radionuclide contamination on the gut microbiota of four wild mouse species: Apodemus flavicollis, A. sylvaticus, A. speciosus and A. argenteus. Building on the evidence that radiation impacts bank vole (Myodes glareolus) gut microbiota, we hypothesized that radiation exposure has a general impact on rodent gut microbiota. Because we sampled (n = 288) two species pairs of Apodemus mice that occur in sympatry in habitats affected by the Chernobyl and Fukushima nuclear accidents, these comparisons provide an opportunity for a general assessment of the effects of exposure to environmental contamination (radionuclides) on gut microbiota across host phylogeny and geographical areas. In general agreement with our hypothesis, analyses of bacterial 16S rRNA gene sequences revealed that radiation exposure alters the gut microbiota composition and structure in three of the four species of Apodemus mice. The notable lack of an association between the gut microbiota and soil radionuclide contamination in one mouse species from Fukushima (A. argenteus) probably reflects host "radiation escape" through its unique tree-dwelling lifestyle. The finding that host ecology can modulate effects of radiation exposure offers an interesting counterpoint for future analyses into effects of radiation or any other toxic exposure on host and its associated microbiota. Our data show that exposure to radionuclide contamination is linked to comparable gut microbiota responses across multiple species of rodents.

Some Examples of the Use of Molecular Markers for Needs of Basic Biology and Modern Society

Application of molecular genetic markers appeared to be very fruitful in achieving many goals, including (i) proving the theoretic basements of general biology and (ii) assessment of worldwide biodiversity. Both are provided in the present meta-analysis and a review as the main signal. One of the basic current challenges in modern biology in the face of new demands in the 21st century is the validation of its paradigms such as the synthetic theory of evolution (STE) and biological species concept (BSC). Another of most valuable goals is the biodiversity assessment for a variety of social needs including free web-based information resources about any living being, renovation of museum collections, nature conservation that recognized as a global project, iBOL, as well as resolving global trading problems such as false labeling of species specimens used as food, drug components, entertainment, etc. The main issues of the review are focused on animals and combine four items. (1) A combination of nDNA and mtDNA markers best suits the identification of hybrids and estimation of genetic introgression. (2) The available facts on nDNA and mtDNA diversity seemingly make introgression among many taxa obvious, although it is evident, that introgression may be quite restricted or asymmetric, thus, leaving at least the "source" taxon (taxa) intact. (3) If we consider sexually reproducing species in marine and terrestrial realms introgressed, as it is still evident in many cases, then we should recognize that the BSC, in view of the complete lack of gene flow among species, is inadequate because many zoological species are not biological ones yet. However, vast modern molecular data have proven that sooner or later they definitely become biological species. (4) An investigation into the fish taxa divergence using the BOLD database shows that most gene trees are basically monophyletic and interspecies reticulations are quite rare.

Late Pleistocene Expansion of Small Murid Rodents across the Palearctic in Relation to the Past Environmental Changes

We investigated the evolutionary history of the striped field mouse to identify factors that initiated its past demographic changes and to shed light on the causes of its current genetic structure and trans-Eurasian distribution. We sequenced mitochondrial cyt b from 184 individuals, obtained from 35 sites in central Europe and eastern Mongolia. We compared genetic analyses with previously published historical distribution models and data on environmental and climatic changes. The past demographic changes displayed similar population trends in the case of recently expanded clades C1 and C3, with the glacial (MIS 3–4) expansion and postglacial bottleneck preceding the recent expansion initiated in the late Holocene and were related to environmental changes during the upper Pleistocene and Holocene. The past demographic trends of the eastern Asian clade C3 were correlated with changes in sea level and the formation of new land bridges formed by the exposed sea shelf during the glaciations. These data were supported by reconstructed historical distribution models. The results of our genetic analyses, supported by the reconstruction of the historical spatial distributions of the distinct clades, confirm that over time the local populations mixed as a consequence of environmental and climatic changes resulting from cyclical glaciation and the interglacial period during the Pleistocene.

Ring distribution patterns-diversification or speciation? Comparative phylogeography of two small mammals in the mountains surrounding the Sichuan Basin

Studying the genetic differentiation in a unique geographical area contributes to understanding the process of speciation. Here, we explore the spatial genetic structure and underlying formation mechanism of two congeneric small mammal species (Apodemus draco and A. chevrieri), which are mainly distributed in the mountains surrounding the lowland Sichuan Basin, southwest China. We applied a set of comparative phylogeographical analyses to determine their genetic diversification patterns, combining mitochondrial (Cytb and COI) and nuclear (microsatellite loci) markers, with dense sampling throughout the range (411 A. draco from 21 sites and 191 A. chevrieri from 22 sites). Moreover, we performed three complementary statistical methods to investigate the correlation between genotype and geographical and environmental components, and predicted the potential suitable distributional range under the present and historical climate conditions. Our results suggest that both species have experienced allopatric differentiation and admixture in historical periods, resulting in a ring-shape diversification, under the barrier effect of the Sichuan Basin. We infer that the tectonic events of the Qinghai-Tibetan Plateau and climatic oscillations during the Quaternary played an important role on the genetic divergence of the two species by providing environmental heterogeneity and geographical variation. Our study reveals a case of two sympatric small mammals following a ring-shaped diversification pattern and provides insight into the process of differentiation.

Taxonomy, phylogeny and evolution of the bumblebee bot flies (Oestridae: Hypodermatinae: Portschinskia)

The first phylogenetic study of Portschinskia is presented based on 42 adult morphological characters scored for all 11 species, including four new species Portschinskia burmensis sp. nov., Portschinskia sichuanensis sp. nov., Portschinskia xizangensis sp. nov. and Portschinskia yunnanensis sp. nov.Portschinskia luliangensis is established as a junior synonym of Portschinskia magnifica. Monophyly of Portschinskia is strongly supported by nine non-homoplasious synapomorphies. All cladograms resolve P. yunnanensis as a basal taxon and a well-resolved Portschinskia gigas clade {P. gigas + ((Portschinskia bombiformis + (P. burmensis + (P. magnifica + P. xizangensis))) + (Portschinskia himalayana + (Portschinskia przewalskyi + P. sichuanensis)))}. The only topological difference is Portschinskia loewii and Portschinskia neugebaueri either being sister taxa or branching off successively at the base of the P. gigas clade. Three colour-pattern types are recognized, with the yellow-tailed pattern optimized as the ancestral state. Our data show that the modal colour pattern of Portschinskia species is the same as in bumblebees, and a regional correlation in species diversity and colour patterns can be detected between sympatric Portschinskia and Bombus species. As a result, we suggest that colour patterns of Portschinskia can be explained as Batesian mimicry tracking locally dominant bumblebees.

Hepatic effects of low-dose rate radiation in natural mouse populations (Apodemus uralensis and Apodemus agrarius): comparative interspecific analysis

Hypothesis: Natural mouse populations in radioactive contamination zone provide adequate information about dose loads and biological effects for 'non-human biota'. The comparative analysis of the responses of different species of mice allows us to reveal the possible variation in the effects of low-dose rate radiation relative to the ecological-physiological and functional-metabolic features of the species.Materials and methods: Objects of study - two sympatric rodent species [pygmy wood mouse (Apodemus uralensis Pallas, 1811) and striped field mouse (Apodemus agrarius Pallas, 1771)] caught on the territory of the East-Ural radioactive trace (EURT). The EURT zone is consequence the Kyshtym accident in South Urals in 1957. Nowadays, the main dose-forming radionuclide is β-emitting ⁹⁰Sr. The individual dose rate of impacted mice caused by internal exposure to ⁹⁰Sr varied from 0.021 to 0.152 mGy/day. The baseline functional-metabolic characteristics of the liver were researched: protein-, lipid-, and glycogen-synthesizing processes; glycolysis; aerobic synthesis of ATP; lipid peroxidation; and the H₂O₂-scavenging enzymatic status; and the functional activity of the genome.Results: The hepatic shifts for impacted populations are amplified with increasing dose rate of irradiation, regardless of which species is considered. But, the response of closely related species of rodents to irradiation is different both in the vector and the level (in A. agrarius sample was 2 time higher than that for A. uralensis).Conclusion: The radiation-induced hepatic shifts in A. uralensis from the EURT area correspond to the chronic response under stressful environmental conditions. The impacted population of A. agrarius can be considered the more reactive species to the radiation burden, demonstrating an acute effect. The interspecies contrast in the radiation response is associated with the original interspecies differences (background rodents' samples in 28 km from the impact study site), and also the degree of residency of the species in the impact plots.

Molecular Characterization of Species of the Subgenus Mus from Myanmar

The species composition and genetic diversity of the subgenus Mus in Myanmar are not yet fully understood. In this study, mice were trapped in rural areas near the Ayeyarwady River basin, spanning five Myanmar cities from north to south: Mandalay, Bagan, Magway, Pyay, and Yangon. Mitochondrial cytochrome b (Cytb) and nuclear melanocortin 1 receptor (Mc1r) gene sequences were determined for mice sampled and revealed a widespread occurrence of Mus nitidulus in central Myanmar in addition to its previously known occurrence in the Yangon district of southern Myanmar. Analyses of Cytb revealed two haplogroups with a genetic distance of 2.0%, suggestive of divergence several hundred thousand years ago. Mus caroli and M. musculus were confined to Yangon and Mandalay/Bagan/Magway, respectively. Mice collected from a locality on the eastern side of the Ayeyarwady River in Pyay were identified using Cytb and Mc1r sequences as M. fragilicauda, which was previously identified only in Laos and Thailand. The species M. booduga and M. cervicolor previously predicted to be common in the study area were not found. These findings elucidate the species and genetic diversity of the subgenus Mus in the Indo-Malayan Region.

Evolutionary history of field mice (Murinae: Apodemus), with emphasis on morphological variation among species in China and description of a new species

Mice of the genus Apodemus are widely distributed across Eurasia. Several species of this genus are hosts of important zoonotic diseases and parasites. The evolutionary history and dispersal routes of these mice remain unclear and the distribution of these species in China was poorly explored in previous studies. We here investigate the divergence times and historical geographical evolution of Apodemus and study the taxonomy of species in China by integrating molecular and morphological data. The crown age of this genus is dated to the Late Miocene, approximately 9.84 Mya. Western and Central Asia were inferred as the most likely ancestral area of this genus. Moreover, we recognize nine living species of Apodemus in China: Apodemus uralensis, A. agrarius, A. chevrieri, A. latronum, A. peninsulae, A. draco, A. ilex, A. semotus and A. nigrus sp. nov., the last from the highlands (elevation > 1984 m) of Fanjing Mountain in Guizhou Province and Jinfo Mountain in Chongqing Province. This new species diverged from A. draco, A. semotus and A. ilex approximately 4.53 Mya. The discovery of A. nigrus highlights the importance of high mountains as refugia and ‘isolated ecological islands’ for temperate species in south-eastern China.

Establishment, characterization, and toxicological application of a spontaneous immortalized cell line from the striped field mouse, Apodemus agrarius

It is important to secure various biological resources in situations of diminishing wildlife genetic diversity. Cultured cells are useful bioresources because they can stably store genetic information for a long time and can be expanded efficiently. Here, we established fibroblast cell lines from Apodemus agrarius as a new living resource. A. agrarius is an important sub-predator species in ecosystem food chains and for the study of infection epidemiology. Established cell lines were characterized by chromosome and mitochondrial gene analysis, the observation of cell morphology, and their anchorage-dependent growth pattern. We also examined susceptibility to endocrine disruptors (EDCs), which threaten biodiversity, using these established cell lines. Nonylphenol (NP) is a well-known EDC that threatens wildlife; however, its impact is poorly understood. Sensitivity to NP was confirmed based on two cell viability assays, namely MTT and lactate dehydrogenase. Cells exposed to NP were analyzed for abnormalities in cell growth and mitochondrial function by evaluating the expression of genes (specifically, those encoding growth hormone receptor and cytochrome C oxidase). This newly established cell line represents a valuable tool for the evaluation of toxic substances such as EDCs and this cell was biobanked for study about relationship between various environmental pollution and decreasing biodiversity.

Karyotypes of field mice of the genus Apodemus (Mammalia: Rodentia) from China

Karyotypes of four Chinese species of field mice of the genus Apodemus were examined, including Apodemus chevrieri (diploid chromosome number, 2n=48, fundamental number of autosomal arms, FNa=56), A. draco (2n=48, FNa=48), A. ilex (2n=48, FNa=48), and A. latronum (2n=48, FNa=48). Karyotypes of A. chevrieri, A. draco, and A. ilex are reported here for the first time, providing useful information for their species taxonomy. Determining the karyotypes of all species of Apodemus in Asia, both in this and previous studies, provides a solid overview of the chromosome evolution and species differentiation of the genus in East Asia. In addition to allopatric speciation, chromosome rearrangements likely played an important role in the formation of the four Apodemus species groups as well as speciation within each group in East Asia. For example, increased centromeric heterochromatin in A. latronum may have contributed to the post-mating reproductive isolation from the A. draco-A. ilex-A. semotus clade.

Mysteries of host switching: Diversification and host specificity in rodent-coccidia associations

Recent studies show that host switching is much more frequent than originally believed and constitutes an important driver in evolution of host-parasite associations. However, its frequency and ecological mechanisms at the population level have been rarely investigated. We address this issue by analyzing phylogeny and population genetics of an extensive sample, from a broad geographic area, for commonly occurring parasites of the genus Eimeria within the abundant rodent genera Apodemus, Microtus and Myodes, using two molecular markers. At the most basal level, we demonstrate polyphyletic arrangement, i.e. multiple origin, of the rodent-specific clusters within the Eimeria phylogeny, and strong genetic/phylogenetic structure within these lineages determined at least partially by specificities to different host groups. However, a novel and the most important observation is a repeated occurrence of host switches among closely related genetic lineages which may become rapidly fixed. Within the studied model, this phenomenon applies particularly to the switches between the eimerians from Apodemus flavicollis/Apodemus sylvaticus and Apodemus agrarius groups. We show that genetic differentiation and isolation between A. flavicollis/A. sylvaticus and A. agrarius faunas is a secondary recent event and does not reflect host-parasite coevolutionary history. Rather, it provides an example of rapid ecology-based differentiation in the parasite population.

Late Pleistocene-Holocene paleobiogeography of the genus Apodemus in Central Europe

Wood mice of the genus Apodemus are an essential component of small mammal communities throughout Europe. Molecular data suggest the postglacial colonization of current ranges from south European glacial refugia, different in particular species. Yet, details on the course of colonization and Holocene history of particular species are not available, partly because of a lack of reliable criteria for species identification in the fossil record. Using a sample of extant species, we analyzed variation patterns and between-species overlaps for a large set of metric and non-metric dental variables and established the criteria enabling the reliable species identification of fragmentary fossil material. The corresponding biometrical analyses were undertaken with fossil material of the genus (2528 items, 747 MNI) from 22 continuous sedimentary series in the Czech Republic and Slovakia, from LGM to Recent. In Central Europe, the genus is invariantly absent in LGM assemblages but regularly appears during the Late Vistulian. All the earliest records belong to A. flavicollis, the species clearly predominating in the fossil record until the Late Holocene. A. uralensis accompanied it in all regions until the late Boreal when disappeared from the fossil record (except for Pannonia). A few items identified as A. sylvaticus had already appeared in the early Holocene assemblages, first in the western part of the region, yet the regular appearance of the species is mostly in the post-Neolithic age. A. agrarius appeared sparsely from the Boreal with a maximum frequency during the post-Neolithic period. The results conform well to the picture suggested by molecular phylogeography but demonstrate considerable differences among particular species in dynamic of the range colonization. Further details concerning Holocene paleobiogeography of individual species in the medium latitude Europe are discussed.

Mitochondrial genome of the Sichuan field mouse (Apodemus latronum)

Wood mice of the genus Apodemus are the most common small rodents in fields and broad-leaf forests in the temperate zone. In this study, we determined the complete mitochondrial genome of Apodemus latronum. It was endemic species to China, which mainly inhabited at the high land of the eastern Tibetan Plateau. The complete mitochondrial genome sequences of A. latronum was estimated to be 16,288 bases. Its organization and order were similar to that of typical vertebrate and other rodents' mitochondrial genomes, which consisting of 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes, and 1 control region. Most protein-coding genes used ATG as the initiation codon. However, ND1, ND2 and ND5 began with ATA, whereas ND3 initiated with ATT. The termination codon also showed some degree of variation, and three types of stop codons were observed. The mitogenome sequence of A. latronum could provide helpful data to study the phylogeny of Apodemus.

Spatial and temporal aspects of occurrence of Mogera species in the Japanese islands inferred from mitochondrial and nuclear gene sequences

We assessed dispersal and vicariant events in four species of Japanese moles in the genera Mogera and Euroscaptor to better understand the factors shaping intra- and interspecific differentiation in Japanese moles. We used the combined viewpoints of molecular phylogeny and historical geology using nucleotide sequences of mitochondrial (cytochrome b; Cytb) and nuclear (A2ab, Bmp4, Tcf25, vWf) genes. The divergence times estimated from the molecular data were verified with available geological data on the chronology of fluctuations in sea level in the Korea Strait, assuming sequential migration and speciation events. This produced possible migration times of 5.6, 3.5, 2.4, and 1.3 million years ago for four species of Japanese moles, Euroscaptor mizura, Mogera tokudae, M. imaizumii, and M. wogura, respectively. For the western Japanese mole M. wogura, Cytb sequences revealed four major phylogroups with strong geographic affinities in southwestern Central Honshu (I), western Honshu/Shikoku (II), Kyushu/westernmost Honshu (III), and Korea/Russian Primorye (IV). The nuclear gene sequences supported the distinctiveness of phylogroups I and IV, indicating long, independent evolutionary histories. In contrast, phylogroups II and III were merged into a single geographic group based on the nuclear gene data. Intraspecific divergences in M. imaizumii and M. tokudae were rather apparent in Cytb but not in nuclear gene sequences. The results suggest that repeated dispersal events have occurred between the Asian continent and the Japanese Islands, and intensive vicariant events associated with abiotic and biotic factors have created higher levels of species and genetic diversities in moles occurring on the Japanese Islands.

Variation in apical hook length reflects the intensity of sperm competition in murine rodents

Background

Post-copulatory sexual selection has been shown to shape morphology of male gametes. Both directional and stabilizing selection on sperm phenotype have been documented in vertebrates in response to sexual promiscuity.

Methodology

Here we investigated the degree of variance in apical hook length and tail length in six taxa of murine rodents.

Conclusions

Tail sperm length and apical hook length were positively associated with relative testis mass, our proxy for levels of sperm competition, thus indicating directional post-copulatory selection on sperm phenotypes. Moreover, our study shows that increased levels of sperm competition lead to the reduction of variance in the hook length, indicating stabilizing selection. Hence, the higher risk of sperm competition affects increasing hook length together with decreasing variance in the hook length. Species-specific post-copulatory sexual selection likely optimizes sperm morphology.

Migration route estimation of the Jeju striped field mouse Apodemus agrarius chejuensis (Rodentia, Muridae)

The taxonomic relationship between two Korean field mice species, Apodemus agrarius coreae and A. a. chejuensis, as well as their possible historic migration routes, was examined by molecular genetic analysis of the complete mitochondrial cytochrome b gene of 73 mice collected from the Korean Peninsula and Jeju Island. Our findings suggest that A. a. coreae and A. a. chejuensis populations expanded and dispersed rapidly. Bayesian and network analysis showed that A. a. chejuensis is a clearly distinct population, and that A. a. chejuensis originated from the ancestral lineage of A. a. coreae. Based on our data, we hypothesize that the A. a. coreae population originated from eastern China or elsewhere. After the last glacial epoch, the lineage isolated from A. a. coreae had adapted to the new environment of Jeju Island, and with the reproductive isolation caused by the geographic barrier, this lineage eventually became a distinct population.

Phylogeography of the South China field mouse (Apodemus draco) on the southeastern Tibetan Plateau reveals high genetic diversity and glacial refugia

The southeastern margin of the Tibetan Plateau (SEMTP) is a particularly interesting region due to its topographic complexity and unique geologic history, but phylogeographic studies that focus on this region are rare. In this study, we investigated the phylogeography of the South China field mouse, Apodemus draco, in order to assess the role of geologic and climatic events on the Tibetan Plateau in shaping its genetic structure. We sequenced mitochondrial cytochrome b (cyt b) sequences in 103 individuals from 47 sampling sites. In addition, 23 cyt b sequences were collected from GenBank for analyses. Phylogenetic, demographic and landscape genetic methods were conducted. Seventy-six cyt b haplotypes were found and the genetic diversity was extremely high (π = 0.0368; h = 0.989). Five major evolutionary clades, based on geographic locations, were identified. Demographic analyses implied subclade 1A and subclade 1B experienced population expansions at about 0.052-0.013 Mya and 0.014-0.004 Mya, respectively. The divergence time analysis showed that the split between clade 1 and clade 2 occurred 0.26 Mya, which fell into the extensive glacial period (EGP, 0.5-0.17 Mya). The divergence times of other main clades (2.20-0.55 Mya) were congruent with the periods of the Qingzang Movement (3.6-1.7 Mya) and the Kun-Huang Movement (1.2-0.6 Mya), which were known as the most intense uplift events in the Tibetan Plateau. Our study supported the hypothesis that the SEMTP was a large late Pleistocene refugium, and further inferred that the Gongga Mountain Region and Hongya County were glacial refugia for A. draco in clade 1. We hypothesize that the evolutionary history of A. draco in the SEMTP primarily occurred in two stages. First, an initial divergence would have been shaped by uplift events of the Tibetan Plateau. Then, major glaciations in the Pleistocene added complexity to its demographic history and genetic structure.

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.

A mitogenome of the Chevrier's field mouse (Apodemus chevrieri) and genetic variations inferred from the cytochrome b gene

The Chevrier's field mouse (Apodemus chevrieri) is an endemic species to China and is an important pest in agriculture and human diseases. In this study, the complete mitochondrial genome of this species was sequenced and its size was 16,298 bases (accession no.: HQ896683). The mitogenome structure was similar compared with other reported rodent mitochondrial genomes and includes 13 protein-coding genes, 2 rRNA genes (12S rRNA and 16S rRNA), 22 tRNA genes, and 1 control region. This was the first complete mitogenome sequenced in genus Apodemus. The phylogenetic analyses based on the sequences of 12 heavy-strand protein-coding genes demonstrated that A. chevrieri clustered together with genus Mus. Additionally, extremely high haplotype and nucleotide diversities (h=0.978, π=2.6%) were observed based on 44 mitochondrial cytochrome b (cyt b) gene sequences. This suggests adaptive divergence of this species to a variety of living habitats and potential refuges in the eastern margin of the Hengduan Mountains during the Quaternary ice ages. No population expansions or genetic bottlenecks were observed in demographic analyses. The phylogenetic analysis of cyt b sequences and haplotypes revealed a genetic differentiation between north and south populations. The divergence between north clade and south clade occurred probably in the middle Pleistocene 1.1815 million years ago (Mya) (95% highest posterior density 2.3189-0.2737 Mya), which was congruent with the periods of the most tense uplift events in the Tibetan Plateau.

Phylogenetic relationships of rodent pinworms (genus Syphacia) in Japan inferred from 28S rDNA sequences

The 28S rDNA from nine species of the genus Syphacia collected in Japan was sequenced, and the phylogenetic relationship was inferred from multiple sequence alignment of 28S rDNA by the MAFFT program. Phylogenetic tree indicates that S. petrusewiczi, which was the only species belonging to the subgenus Seuratoxyuris, has diverged earlier than other rodent pinworms examined and was distantly separated from the others genetically. It was revealed that S. agraria and S. vandenbrueli, whose subgeneric status has not been specified, belonged to the subgenus Syphacia together with other 6 species. Syphacia montana from Clethrionomys, Eothenomys and Microtus was very closely related to S. obvelata from Mus, and that S. frederici from Apodemus and S. vandenbrueli from Micromys were comparatively closely related to the former two species. The phylogenetic relationship among the three species of Syphacia found in Japanese Apodemus was inconsistent with the biogeography of host rodents. The co-evolutionary relationship between pinworm species and their host rodents may not be so strict and host switching has probably occurred frequently during the course of evolution.