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

The genomic landscape, causes, and consequences of extensive phylogenomic discordance in Old World mice and rats

A species tree is a central concept in evolutionary biology whereby a single branching phylogeny reflects relationships among species. However, the phylogenies of different genomic regions often differ from the species tree. Although tree discordance is often widespread in phylogenomic studies, we still lack a clear understanding of how variation in phylogenetic patterns is shaped by genome biology or the extent to which discordance may compromise comparative studies. We characterized patterns of phylogenomic discordance across the murine rodents (Old World mice and rats) - a large and ecologically diverse group that gave rise to the mouse and rat model systems. Combining new linked-read genome assemblies for seven murine species with eleven published rodent genomes, we first used ultra-conserved elements (UCEs) to infer a robust species tree. We then used whole genomes to examine finer-scale patterns of discordance and found that phylogenies built from proximate chromosomal regions had similar phylogenies. However, there was no relationship between tree similarity and local recombination rates in house mice, suggesting that genetic linkage influences phylogenetic patterns over deeper timescales. This signal may be independent of contemporary recombination landscapes. We also detected a strong influence of linked selection whereby purifying selection at UCEs led to less discordance, while genes experiencing positive selection showed more discordant and variable phylogenetic signals. Finally, we show that assuming a single species tree can result in high error rates when testing for positive selection under different models. Collectively, our results highlight the complex relationship between phylogenetic inference and genome biology and underscore how failure to account for this complexity can mislead comparative genomic studies.

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.

Characterization of Two New Apodemus Mitogenomes (Rodentia: Muridae) and Mitochondrial Phylogeny of Muridae

Apodemus is the most common small rodent species in the Palearctic realm and an ideal species for biogeographical research and understanding environmental changes. Elucidating phylogenetic relationships will help us better understand species adaptation and genetic evolution. Due to its stable structure, maternal inheritance, and rapid evolution, the mitogenome has become a hot spot for taxonomic and evolutionary studies. In this research, we determined the mitochondrial genome of Apodemus agrarius ningpoensis and Apodemus draco draco and studied the phylogeny of Muridae using ML and BI trees based on all known complete mitogenomes. The mitochondrial genome of Apodemus agrarius ningpoensis was 16,262 bp, whereas that of Apodemus draco draco was 16,222 bp, and both encoded 13 protein-coding genes, 2 ribosomal RNA genes, and 22 transfer RNA genes. Analysis of base composition showed a clear A-T preference. All tRNAs except tRNASer and tRNALys formed a typical trilobal structure. All protein-coding genes contained T- and TAA as stop codons. Phylogeny analysis revealed two main branches in the Muridae family. Apodemus agrarius ningpoensis formed sister species with Apodemus chevrieri, whereas Apodemus draco draco with Apodemus latronum. Our findings provide theoretical basis for future studies focusing on the mitogenome evolution of Apodemus.

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.

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.

Genetic diversity and evolution of Hantaan virus in China and its neighbors

BACKGROUND

Hantaan virus (HTNV; family Hantaviridae, order Bunyavirales) causes hemorrhagic fever with renal syndrome (HFRS), which has raised serious concerns in Eurasia, especially in China, Russia, and South Korea. Previous studies reported genetic diversity and phylogenetic features of HTNV in different parts of China, but the analyses from the holistic perspective are rare.

METHODOLOGY AND PRINCIPAL FINDINGS

To better understand HTNV genetic diversity and gene evolution, we analyzed all available complete sequences derived from the small (S) and medium (M) segments with bioinformatic tools. Eleven phylogenetic groups were defined and showed geographic clustering; 42 significant amino acid variant sites were found, and 19 of them were located in immune epitopes; nine recombinant events and eight reassortments with highly divergent sequences were found and analyzed. We found that sequences from Guizhou showed high genetic divergence, contributing to multiple lineages of the phylogenetic tree and also to the recombination and reassortment events. Bayesian stochastic search variable selection analysis revealed that Heilongjiang, Shaanxi, and Guizhou played important roles in HTNV evolution and migration; the virus may originate from Zhejiang Province in the eastern part of China; and the virus population size expanded from the 1980s to 1990s.

CONCLUSIONS/SIGNIFICANCE

These findings revealed the original and evolutionary features of HTNV, which will help to illustrate hantavirus epidemic trends, thus aiding in disease control and prevention.

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.

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.

Dispersal route of the Asian house rat (Rattus tanezumi) on mainland China: insights from microsatellite and mitochondrial DNA

BACKGROUND

Rattus tanezumi is a common commensal rat and an important host animal of bubonic plague in South China and Southeast Asia. The northward dispersal of this species in mainland China has been reported in recent decades, along with more recent intercontinental expansion. Population genetics of R. tanezumi in mainland China were studied to explain the relationship between dispersal history and the ancient and modern transportation networks of China.

RESULTS

In total, 502 individuals belonging to 18 populations were collected from 13 provincial areas. Nine microsatellite loci and two mtDNA sequences were analyzed. The results indicate that R. tanezumi populations from Yunnan have highest genetic diversity and populations from Tibet with lowest genetic diversity. 18 populations can be divided into four clusters, the first cluster including populations from southwest Yunnan, the second including two populations of Tibet, the third for populations from middle and east of mainland China, and the forth for two populations from north Yunnan. Both microsatellite and mtDNA data reveal that the populations from coastal areas are closely related to populations from Yunnan, whereas populations from Tibet are closely related with populations from Sichuan.

CONCLUSIONS

The results suggest that early dispersal of R. tanezumi in mainland China depended on shipping transportation, with subsequent expansion from coastal areas into Central China occurring along the Yangzi River. Further, the linkages between populations in Tibet and Sichuan point to a modern era introduction via the Chuan-Zang highway, rather than along the Tea Horse Ancient Road.

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.

How many species of Apodemus and Rattus occur in China? A survey based on mitochondrial cyt b and morphological analyses

Apodemus (mice) and Rattus (rats) are the top rodent reservoirs for zoonoses in China, yet little is known about their diversity. We reexamined the alpha diversity of these two genera based on a new collection of specimens from China and their cyt b sequences in GenBank. We also tested whether species could be identified using external and craniodental measurements exclusively. Measurements from 147 specimens of Apodemus and 236 specimens of Rattus were used for morphological comparisons. We analysed 74 cyt b sequences of Apodemus and 100 cyt b sequences of Rattus to facilitate phylogenetic estimations. Results demonstrated that nine species of Apodemus and seven species of Rattus, plus a new subspecies of Rattus nitidus, are distributed in China. Principal component analysis using external and craniodental measurements revealed that measurements alone could not separate the recognized species. The occurrence of Rattus pyctoris in China remains uncertain.

Cryptosporidium apodemi sp. n. and Cryptosporidium ditrichi sp. n. (Apicomplexa: Cryptosporidiidae) in Apodemus spp

Faecal samples from striped field mice (n = 72) and yellow-necked mice (n = 246) were screened for Cryptosporidium by microscopy and PCR/sequencing. Phylogenetic analysis of small-subunit rRNA, Cryptosporidium oocyst wall protein and actin gene sequences revealed the presence of C. parvum, C. hominis, C. muris and two new species, C. apodemi and C. ditrichi. Oocysts of C. apodemi are smaller than C. ditrichi and both are experimentally infectious for yellow-necked mice but not for common voles. Additionally, infection by C. ditrichi was established in one of three BALB/c mice. The prepatent period was 7-9 and 5-6 days post infection for C. apodemi and C. ditrichi, respectively. The patent period was greater than 30 days for both species. Infection intensity of C. ditrichi ranged from 4000-50,000 oocyst per gram of faeces and developmental stages of C. ditrichi were detected in the jejunum and ileum. In contrast, neither oocysts nor endogenous developmental stages of C. apodemi were detected in faecal or tissue samples, although C. apodemi DNA was detected in contents from the small and large intestine. Morphological, genetic, and biological data support the establishment of C. apodemi and C. ditrichi as a separate species of the genus Cryptosporidium.

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.

High-throughput collagen fingerprinting of intact microfaunal remains; a low-cost method for distinguishing between murine rodent bones

RATIONALE

Microfaunal skeletal remains can be sensitive indicators of the contemporary ecosystem in which they are sampled and are often recovered in owl pellets in large numbers. Species identification of these remains can be obtained using a range of morphological criteria established for particular skeletal elements, but typically dominated by a reliance on cranial characters. However, this can induce biases under different environmental and taphonomic conditions. The aim of this research was to develop a high-throughput method of objectively identifying rodent remains from archaeological deposits using collagen fingerprinting, most notably the identification of rats from other myomorph rodents as a means to identify disturbances in the archaeofauna through the presence of invasive taxa not contemporary with the archaeological deposits.

METHODS

Collagen was extracted from complete microfaunal skeletal remains in such a manner as to leave the bones morphologically intact (i.e., weaker concentration of acid than previously used over shorter length of time). Acid-soluble collagen was then ultrafiltered into ammonium bicarbonate and digested with trypsin prior to dilution in the MALDI matrix and acquisition of peptide mass fingerprints using a matrix-assisted laser desorption/ionisation time-of-flight (MALDI-TOF) mass spectrometer.

RESULTS

Collagen fingerprinting was able to distinguish between Rattus, Mus, Apodemus and Micromys at the genus level; at the species level, R. rattus and R. norvegicus could be separated whereas A. flavicollis and A. sylvaticus could not. A total of 12,317 archaeological microvertebrate samples were screened for myomorph signatures but none were found to be invasive rats (Rattus) or mice (Mus). Of the contemporary murine fauna, no harvest mice (Micromys) were identified and only 24 field mouse (Apodemus) discovered.

CONCLUSIONS

As a result, no evidence of recent bioturbation could be inferred from the faunal remains of these archaeological deposits. More importantly this work presents a method for high-throughput screening of specific taxa and is the first application of collagen fingerprinting to microfaunal remains of archaeological specimens.

Selective constraints on protamine 2 in primates and rodents

BACKGROUND

Protamines are sperm nuclear proteins with a crucial role in chromatin condensation. Their function is strongly linked to sperm head morphology and male fertility. Protamines appear to be affected by a complex pattern of selective constraints. Previous studies showed that sexual selection affects protamine coding sequence and expression in rodents. Here we analyze selective constraints and post-copulatory sexual selection acting on protamine 2 (Prm2) gene sequences of 53 species of primates and rodents. We focused on possible differences in selective constraints between these two clades and on the two functional domains of PRM2 (cleaved- and mature-PRM2). We also assessed if and how changes in Prm2 coding sequence may affect sperm head dimensions.

RESULTS

The domain of Prm2 that is cleaved off during binding to DNA (cleaved-Prm2) was found to be under purifying selection in both clades, whereas the domain that remains bound to DNA (mature-Prm2) was found to be positively selected in primates and under relaxed constraint in rodents. Changes in cleaved-Prm2 coding sequence are significantly correlated to sperm head width and elongation in rodents. Contrary to expectations, a significant effect of sexual selection was not found on either domain or clade.

CONCLUSIONS

Mature-PRM2 may be free to evolve under less constraint due to the existence of PRM1 as a more conserved and functionally redundant copy. The cleaved-PRM2 domain seems to play an important role in sperm head shaping. However, sexual selection on its sequence may be difficult to detect until it is identified which sperm head phenotype (shape and size) confers advantages for sperm performance in different mammalian clades.

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.

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.

Historical effects on local variation in walnut-feeding behavior by the Japanese wood mouse, Apodemus speciosus

The Japanese wood mouse Apodemus speciosus eats large, hard-walled walnuts of Juglans ailanthifolia immediately after finding or after hoarding them. However, not all individuals can efficiently eat the nuts. In this study, to examine local variation in the ability to eat walnuts, feeding behavior was compared among nine wood mouse populations, four from mainland Honshu, where the walnut tree is distributed, and five from the Izu Islands (30-100 km south of Honshu), which lack the tree species. To avoid the effects of pre-capture experience with walnuts, mice from areas lacking the walnut trees were used for testing, even in the Honshu sites. Most mice from Honshu were able to eat walnuts after a 14-day training period, whereas most insular mice could not, with the exception of mice on Kouzushima Island. An analysis of the population genetic structures of these mice based on sequences of the mitochondrial control (D-loop) region revealed that the four insular populations are genetically distinct from the mainland populations, whereas the Kouzushima population remains genetically similar to the mainland populations. The relatively recent colonization of Kouzushima may explain why mice from this island were able to feed on walnuts despite the lack of walnut trees on the island. Thus, walnut-feeding ability appears to have some innate basis in the Japanese wood mouse, and this trait would be selected for in a walnut-available environment as it would better enable mice to survive during food shortages.

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.

Classification tree methods provide a multifactorial approach to predicting insular body size evolution in rodents

Many hypotheses have been proposed to explain size changes in insular mammals, but no single variable suffices to explain the diversity of responses, particularly within Rodentia. Here in a data set on insular rodents, we observe strong consistency in the direction of size change within islands and within species but (outside of Heteromyidae) little consistency at broader taxonomic scales. Using traits of islands and of species in a classification tree analysis, we find the most important factor predicting direction of change to be mainland body mass (large rodents decrease, small ones increase); other variables (island climate, number of rodent species, and area) were significant, although their roles as revealed by the classification tree were context dependent. Ecological interactions appear relatively uninformative, and on any given island, the largest and smallest rodent species converged or diverged in size with equal frequency. Our approach provides a promising framework for continuing examination of insular body size evolution.

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.

Molecular diversity and phylogeny of Hantaan virus in Guizhou, China: evidence for Guizhou as a radiation center of the present Hantaan virus

To gain further insight into the molecular epidemiology of Hantaan virus (HTNV) in Guizhou, China, rodents were captured in this region in 2004 and 2005. In addition, serum samples were collected from four patients. Ten hantaviruses were isolated successfully in cell culture from four humans, two Apodemus agrarius, three Rattus norvegicus and one Rattus nitidus. The nucleotide sequences for their small (S), medium (M) and partial large (L) segments were determined. Phylogenetic analysis of the S and M segment sequences revealed that all of these isolates belong to the species HTNV, suggesting a spillover of HTNV from A. agrarius to Rattus rats. All available isolates from Guizhou were divided into four distinct groups either in the S segment tree or in the M segment tree. The clustering pattern of these isolates in the S segment tree was not in agreement with that in the M or L segment tree, showing that genetic reassortment between HTNV had occurred naturally. Analysis of the S segment sequences from available HTNV strains indicated that they formed three clades. The first clade, which comprised only viruses from Guizhou, was the outgroup of clades II and III. The viruses in the second clade were found in Guizhou and mainly in the far-east Asian region, including China. However, the viruses in the third clade were found in most areas of China, including Guizhou, in which haemorrhagic fever with renal syndrome (HFRS) is endemic. Our results reveal that the highest genetic diversity of HTNV is in a limited geographical region of Guizhou, and suggest that Guizhou might be a radiation centre of the present form of HTNV.

Phylogenetic relationships in genus Niviventer (Rodentia: Muridae) in China inferred from complete mitochondrial cytochrome b gene

Chinese species of the genus Niviventer, predominantly distributed in the southeastern Tibetan Plateau and in Taiwan, are a diverse group and have not yet received a thorough molecular phylogenetic analysis. Here, we reconstructed the phylogenetic relationships of 32 specimens representing nine Chinese species of Niviventer, based on sequences of the complete mitochondrial cytochrome b gene. Maximum parsimony, maximum likelihood and Bayesian analysis resulted in three consistent trees, each supported by high bootstrap values. The results showed that the Niviventer species included here are monophyletic. The nine species were classified into three distinct clades: clade A with Niviventer brahma, N. confucianus, N. coxingi, N. culturatus, N. eha and N. fulvescens; clade B with N. andersoni and N. excelsior; clade C with N. cremoriventer. Our results also suggested that N. culturatus should be a valid species rather than a subspecies of N. confucianus. Divergence times among species were calibrated according to the middle-late Pleistocene (1.2-0.13 Mya) fossil records of N. confucianus. The results demonstrated that the first radiation event of the genus Niviventer occurred in early Pleistocene (about 1.66 Mya), followed by the divergence of clades A and B at about 1.46 Mya. Most of the extant Niviventer species appeared during early to middle Pleistocene (about 1.29-0.67 Mya). These divergence times are coincidental with the last uplift events of the Tibetan Plateau, Kun-Huang movement, Pleistocene glaciations and the vicariant formation of Taiwan Strait. Consequently geographical events and Pleistocene glaciations have played a great role in the diversification of Niviventer.

Primate molecular divergence dates

With genomic data, alignments can be assembled that greatly increase the number of informative sites for analysis of molecular divergence dates. Here, we present an estimate of the molecular divergence dates for all of the major primate groups. These date estimates are based on a Bayesian analysis of approximately 59.8 kbp of genomic data from 13 primates and 6 mammalian outgroups, using a range of paleontologically supported calibration estimates. Results support a Cretaceous last common ancestor of extant primates (approximately 77 mya), an Eocene divergence between platyrrhine and catarrhine primates (approximately 43 mya), an Oligocene origin of apes and Old World monkeys (approximately 31 mya), and an early Miocene (approximately 18 mya) divergence of Asian and African great apes. These dates are examined in the context of other molecular clock studies.

Two new species of Eimeria Schneider 1875 (Apicomplexa: Eimeriidae) from the broad-toothed field mouse, Apodemus mystacinus Danford and Alston 1877 (Rodentia: Muridae) from Jordan

Coprological examination of 40 Apodemus mystacinus Danford and Alston 1877 from Jordan revealed oocysts of three species of genus Eimeria. Two species are described as new. Eimeria zuhairamri sp. n. has broadly ellipsoidal oocysts 29.6 (27.0-34.0) x 23.3 (22.0-25.0) mum with distinctly granulated wall and oocyst residuum. Endogenous development occurs in jejunum and ileum. Eimeria alorani sp. n. has oocysts 26.9 (23.0-29.0) x 19.3 (18.0-22.0) mum with smooth wall and absent residuum. Endogenous development is confined to the caecum. The third species, developing in jejunum, has oocysts morphologically indistinguishable from Eimeria uptoni. The identity of E. uptoni and the taxonomy of Eimeria of Apodemus are discussed.