Identification of Sarcocystis spp. in synanthropic (Muridae) and wild (Cricetidae) rodents from Argentina.

The occurrence of Sarcocystis species was investigated in synanthropic (Muridae) and wild (Cricetidae) rodents from Argentina. Nine species were captured (n = 356). Sarcocysts were detected in muscles of 8.7% (31/356) and 3.7% (4/106) of the rodents by histopathology and direct microscopic observation, respectively. PCR-sequencing targeting the 18S rRNA, cox1, and ITS1 regions was performed on samples with positive histopathology. Four different 18S rRNA sequences or sequence groups with high intra-group identities (99.6-100%) were detected in Mus musculus, Oxymycterus rufus, Akodon azarae, and Necromys lasiurus. Eight sequences showed 99.5-99.7% identity with S. dispersa. Thirteen sequences showed low identity (95.3-96.4%) with other Sarcocystis spp. The obtained coxI sequences (n = 9) were almost identical to each other and showed a high similarity with S. strixi (99.2-99.5%) and S. lutrae (99.1%), despite the 18S rRNA sequences from the same samples suggested the occurrence of at least two species. This suggests that coxI may not show high variability in Sarcocystis spp. that use rodents as intermediate hosts. Six ITS1 sequences were obtained, showing high identity but low coverage with several Sarcocystis spp. Multilocus sequence typing and BLAST analysis did not lead to an accurate species identification. Possible reasons are the detection of new species or the limited molecular information available from previously described Sarcocystis spp. Phylogeny suggests that the detected Sarcocystis spp. may use raptor birds or snakes as definitive hosts. This study represents the first molecular identification of Sarcocystis spp. in naturally infected rodents of the Cricetidae and Muridae families in South America.

Diversity and Evolution of Highly Repetitive DNA Sequences Constituting Chromosome Site-Specific Heterochromatin in Two Gerbillinae Species.

Constitutive heterochromatin, consisting of repetitive sequences, diverges very rapidly; therefore, its nucleotide sequences and chromosomal distributions are often largely different, even between closely related species. The chromosome C-banding patterns of two Gerbillinae species, Meriones unguiculatus and Gerbillus perpallidus, vary greatly, even though they belong to the same subfamily. To understand the evolution of C-positive heterochromatin in these species, we isolated highly repetitive sequences, determined their nucleotide sequences, and characterized them using chromosomal and filter hybridization. We obtained a centromeric repeat (MUN-HaeIII) and a chromosome 13-specific repeat (MUN-EcoRI) from M. unguiculatus. We also isolated a centromeric/pericentromeric repeat (GPE-MBD) and an interspersed-type repeat that was predominantly amplified in the X and Y chromosomes (GPE-EcoRI) from G. perpallidus. GPE-MBD was found to contain a 17-bp motif that is essential for binding to the centromere-associated protein CENP-B. This indicates that it may play a role in the formation of a specified structure and/or function of centromeres. The nucleotide sequences of the three sequence families, except GPE-EcoRI, were conserved only in Gerbillinae. GPE-EcoRI was derived from the long interspersed nuclear elements 1 retrotransposon and showed sequence homology throughout Muridae and Cricetidae species, indicating that the repeat sequence occurred at least in the common ancestor of Muridae and Cricetidae. Due to a lack of assembly data of highly repetitive sequences constituting heterochromatin in whole-genome sequences of vertebrate species published to date, the knowledge obtained in this study provides useful information for a deep understanding of the evolution of repetitive sequences in not only rodents but also in mammals.

Conservation and divergence of canonical and non-canonical imprinting in murids.

BACKGROUND: Genomic imprinting affects gene expression in a parent-of-origin manner and has a profound impact on complex traits including growth and behavior. While the rat is widely used to model human pathophysiology, few imprinted genes have been identified in this murid. To systematically identify imprinted genes and genomic imprints in the rat, we use low input methods for genome-wide analyses of gene expression and DNA methylation to profile embryonic and extraembryonic tissues at allele-specific resolution. RESULTS: We identify 14 and 26 imprinted genes in these tissues, respectively, with 10 of these genes imprinted in both tissues. Comparative analyses with mouse reveal that orthologous imprinted gene expression and associated canonical DNA methylation imprints are conserved in the embryo proper of the Muridae family. However, only 3 paternally expressed imprinted genes are conserved in the extraembryonic tissue of murids, all of which are associated with non-canonical H3K27me3 imprints. The discovery of 8 novel non-canonical imprinted genes unique to the rat is consistent with more rapid evolution of extraembryonic imprinting. Meta-analysis of novel imprinted genes reveals multiple mechanisms by which species-specific imprinted expression may be established, including H3K27me3 deposition in the oocyte, the appearance of ZFP57 binding motifs, and the insertion of endogenous retroviral promoters. CONCLUSIONS: In summary, we provide an expanded list of imprinted loci in the rat, reveal the extent of conservation of imprinted gene expression, and identify potential mechanisms responsible for the evolution of species-specific imprinting.

Backcrossing as a species restoration technique.

An investigation was conducted on the phenotypic results of mouse hybridization and seven generations of backcrossing, observing reciprocal F1 hybrids and backcrosses of Mus spretus and a laboratory strain of Mus domesticus C57BL/6J. F1 hybrids, backcrosses, and pure control specimens were measured for 6 body characteristics, 4 pelage coloration characteristics, 14 behaviors, and reproduction as reflected in litter size. Backcrossing was pursued for seven generations to FBC7 (i.e., "Backcross 7" or seven generations from commencement of backcrossing from an F1 hybrid female) where species restoration is mathematically calculated to be at 99.7%. Except for a minority of FBC7 M. spretus specimens failing to conform completely to one pelage characteristic, FBC7 specimens were indistinguishable from controls both subjectively and in all areas of measurement. The M. spretus backcross line was followed generation by generation and was largely conforming to controls by FBC4 at latest. The same effect was observed in the reciprocal M. domesticus backcross line. Fertility was negatively affected in F1 hybrids but restored or improved in backcross generations. Discussion is offered on hybridization and backcrossing as it occurs in nature and how it has been used or could be used as an additional ex situ tool in wildlife conservation efforts. It is concluded that conservation-oriented backcrossing is a practical species/subspecies restoration technique and has the potential to make genetic rescue feasible with minimal gene flow at the binomial level. Backcrossing is most applicable in closely monitored ex situ settings (1) where only one sex remains of a given taxon; and (2) where inbreeding depression seriously threatens a remnant taxon's ability to recover, and the only gene flow option is from another distinct species.

Comparative Mitogenome Analysis of Gerbils and the Mitogenome Phylogeny of Gerbillinae (Rodentia: Muridae).

To enrich the mitogenomic database of Gerbillinae (Rodentia: Muridae), mitogenomes of three gerbils from different genera, Meriones tamariscinus (16,393 bp), Brachiones przewalskii (16,357 bp), and Rhombomys opimus (16,352 bp), were elaborated and compared with those of other gerbils in the present study. The three gerbil mitogenomes consisted of 2 ribosomal RNA genes, 13 protein-coding genes (PCGs), 22 transfer RNA genes, and one control region. Here, gerbil mitogenomes have shown unique characteristics in terms of base composition, codon usage, non-coding region, and the replication origin of the light strand. There was no significant correlation between the nucleotide percentage of G + C and the phylogenetic status in gerbils, and between the GC content of PCGs and the leucine count. Phylogenetic relationships of the subfamily Gerbillinae were reconstructed by 7 gerbils that represented four genera based on concatenated mitochondrial DNA data using both Bayesian Inference and Maximum Likelihood. The phylogenetic analysis indicated that M. tamariscinus was phylogenetically distant from the genus Meriones, but has a close relationship with R. opimus. B. przewalskii was closely related to the genus Meriones rather than that of R. opimus.

Androgen-Binding Protein (Abp) Evolutionary History: Has Positive Selection Caused Fixation of Different Paralogs in Different Taxa of the Genus Mus?

Comparison of the androgen-binding protein (Abp) gene regions of six Mus genomes provides insights into the evolutionary history of this large murid rodent gene family. We identified 206 unique Abp sequences and mapped their physical relationships. At least 48 are duplicated and thus present in more than two identical copies. All six taxa have substantially elevated LINE1 densities in Abp regions compared with flanking regions, similar to levels in mouse and rat genomes, although nonallelic homologous recombination seems to have only occurred in Mus musculus domesticus. Phylogenetic and structural relationships support the hypothesis that the extensive Abp expansion began in an ancestor of the genus Mus. We also found duplicated Abpa27's in two taxa, suggesting that previously reported selection on a27 alleles may have actually detected selection on haplotypes wherein different paralogs were lost in each. Other studies reported that a27 gene and species trees were incongruent, likely because of homoplasy. However, L1MC3 phylogenies, supposed to be homoplasy-free compared with coding regions, support our paralog hypothesis because the L1MC3 phylogeny was congruent with the a27 topology. This paralog hypothesis provides an alternative explanation for the origin of the a27 gene that is suggested to be fixed in the three different subspecies of Mus musculus and to mediate sexual selection and incipient reinforcement between at least two of them. Finally, we ask why there are so many Abp genes, especially given the high frequency of pseudogenes and suggest that relaxed selection operates over a large part of the gene clusters.

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.

Molecular systematics and biogeographic history of the African climbing-mouse complex (Dendromus).

Climbing mice in the genus Dendromus (sensu lato) are widely distributed in Africa, south of the Saharan Desert. The 17 currently recognized species in the genus range from widespread taxa to single-mountain endemics, and there is considerable variation across species with respect to habitats occupied. These habitats range from arid grasslands and savannahs to sub-alpine and alpine vegetation. Using the most comprehensive geographic and genetic survey to date and after reviewing many type specimens, we assess the systematics and biogeography of Dendromus. Given the structure of our molecular phylogenetic hypotheses, in which we recover six major clades, we propose the recognition of three genera within the Dendromus group (sensu lato): in addition to Dendromus (26 lineages), we suggest the retention of Megadendromus (monotypic) and the resurrection of the genus Poemys (six lineages). From our model-based molecular phylogenetic results and morphological comparisons, we suggest that six formerly synonymized taxa should be resurrected, and we highlight 14 previously undescribed lineages. We also constructed time-calibrations on our phylogeny, and performed ancestral area reconstructions using BioGeoBEARS. Based on fossil evidence, Dendromus appears to have had a widespread African distribution dating back to the Late Miocene (8-10 Ma), and our basal ancestral area reconstruction (Ethiopians Highlands + Eastern African Mountains + Zambezian region) supports this. Divergence of the six major clades we recover (Poemys, Megadendromus and four within Dendromus) occurred prior to or at the Miocene-Pliocene boundary 5.3 Ma. Biogeographically, Megadendromus is restricted to the Ethiopian Highlands. The ancestral area for Poemys is reconstructed as the Zambezian region, with species distributions ranging from South Africa to Western Africa. The ancestral area for Dendromus is reconstructed as the Ethiopian Highlands, with the ancestral areas of the four major clades being reconstructed as Ethiopian Highlands, Albertine Rift, South Africa or Western Africa. None of the four Dendromus clades are reciprocally monophyletic with respect to distributional area.

Australian Rodents Reveal Conserved Cranial Evolutionary Allometry across 10 Million Years of Murid Evolution.

AbstractAmong vertebrates, placental mammals are particularly variable in the covariance between cranial shape and body size (allometry), with rodents being a major exception. Australian murid rodents allow an assessment of the cause of this anomaly because they radiated on an ecologically diverse continent notably lacking other terrestrial placentals. Here, we use 3D geometric morphometrics to quantify species-level and evolutionary allometries in 38 species (317 crania) from all Australian murid genera. We ask whether ecological opportunity resulted in greater allometric diversity compared with other rodents or whether conserved allometry suggests intrinsic constraints and/or stabilizing selection. We also assess whether cranial shape variation follows the proposed rule of craniofacial evolutionary allometry (CREA), whereby larger species have relatively longer snouts and smaller braincases. To ensure we could differentiate parallel versus nonparallel species-level allometric slopes, we compared the slopes of rarefied samples across all clades. We found exceedingly conserved allometry and CREA-like patterns across the 10-million-year split between Mus and Australian murids. This could support both intrinsic-constraint and stabilizing-selection hypotheses for conserved allometry. Large-bodied frugivores evolved faster than other species along the allometric trajectory, which could suggest stabilizing selection on the shape of the masticatory apparatus as body size changes.

Genomes, expression profiles, and diversity of mitochondria of the White-footed Deermouse Peromyscus leucopus, reservoir of Lyme disease and other zoonoses.

The cricetine rodents Peromyscus leucopus and P. maniculatus are key reservoirs for several zoonotic diseases in North America. We determined the complete circular mitochondrial genome sequences of representatives of 3 different stock colonies of P. leucopus, one stock colony of P. maniculatus and two wild populations of P. leucopus. The genomes were syntenic with that of the murids Mus musculus and Rattus norvegicus. Phylogenetic analysis confirmed that these two Peromyscus species are sister taxa in a clade with P. polionotus and also uncovered a distinction between P. leucopus populations in the eastern and the central United States. In one P. leucopus lineage four extended regions of mitochondrial pseudogenes were identified in the nuclear genome. RNA-seq analysis revealed transcription of the entire genome and differences from controls in the expression profiles of mitochondrial genes in the blood, but not in liver or brain, of animals infected with the zoonotic pathogen Borrelia hermsii. PCR and sequencing of the D-loop of the mitochondrion identified 32 different haplotypes among 118 wild P. leucopus at a Connecticut field site. These findings help to further establish P. leucopus as a model organism for studies of emerging infectious diseases, ecology, and in other disciplines.

Range-wide genetic structure of a cooperative mouse in a semi-arid zone: Evidence for panmixia.

Landscape topography and the mobility of individuals will have fundamental impacts on a species' population structure, for example by enhancing or reducing gene flow and therefore influencing the effective size and genetic diversity of the population. However, social organization will also influence population genetic structure. For example, species that live and breed in cooperative groups may experience high levels of inbreeding and strong genetic drift. The western pebble-mound mouse (Pseudomys chapmani), which occupies a highly heterogeneous, semi-arid landscape in Australia, is an enigmatic social mammal that has the intriguing behaviour of working cooperatively in groups to build permanent pebble mounds above a subterranean burrow system. Here, we used both nuclear (microsatellite) and mitochondrial (mtDNA) markers to analyse the range-wide population structure of western pebble-mound mice sourced from multiple social groups. We observed high levels of genetic diversity at the broad scale, very weak genetic differentiation at a finer scale and low levels of inbreeding. Our genetic analyses suggest that the western pebble-mound mouse population is both panmictic and highly viable. We conclude that high genetic connectivity across the complex landscape is a consequence of the species' ability to permeate their environment, which may be enhanced by "boom-bust" population dynamics driven by the semi-arid climate. More broadly, our results highlight the importance of sampling strategies to infer social structure and demonstrate that sociality is an important component of population genetic structure.

Winter Reproduction of Cyclomorphic Mammals: From a Case to the Phenomenon.

In 2010 (a year of drought), the true winter breeding (TWB) of the pygmy wood mouse (S. uralensis) was first recorded in the Southern Urals and confirmed by the morphological parameters and age markers. The young born in winter fulfilled successfully their reproductive potential under favorable climatic conditions. The true winter breeding and the age cross of animals during the year of drought promoted the maximum population growth and enhanced population genetic heterogeneity. In subsequent years, TWB of S. uralensis became common, which is regarded as a climatic pattern. Extreme drought rearranged the rodent community and caused TWB of S. uralensis, which resulted in a higher abundance of the species.

Molecular phylogeographic analyses and species delimitations reveal that Leopoldamys edwardsi (Rodentia: Muridae) is a species complex.

Leopoldamys edwardsi is a species with wide distribution ranges in southern China but is not discussed in studies on geographic variation and species differentiation. We used 2 mitochondrial (Cytb, CO1) and 3 nuclear (GHR, IRBP and RAG1) genes to clarify species phylogeography and geographical differentiation. Maximum likelihood (ML) and Bayesian phylogenetic inference (BI) trees consistently indicated that L. edwardsi is a species complex containing 3 main lineages with high Kimura-2-parameter (K2P) divergences (i.e. lineages LN , LS and LHN ) found in the northern and southern China and Hainan Island, respectively. The 3 species delimitation methods, automated barcoding gap discovery, Bayesian poisson tree process analysis and Bayesian phylogenetics and phylogeography, consistently supported the existence of cryptic species. Divergence times among the main lineages were inferred to be during the Pleistocene, with LHN /LS split at 1.33 Ma and LN /(LHN +LS ) at 2.61 Ma; the diversifications of L. edwardsi complex might be caused by the rapid uplifts of Tibetan Plateau, paleoclimate change and complex topography. The divergence between LHN and LS was probably related to the separation of Hainan Island from the mainland via the formation of the Qiongzhou Strait. Lineages LN and (LS +LHN ) likely diverged due to the Wuyi-Nanling mountain range forming a dispersal barrier. Our results suggested that L. edwardsi complex contains at least 3 distinct species: LHN represents L. hainanensis, endemic to Hainan Island and previously considered as a subspecies L. e. hainanensis; LS represents a cryptic species distributed throughout the southern Chinese continent; and LN represents the nominotypical species L. edwardsi.

Repeat associated mechanisms of genome evolution and function revealed by the Mus caroli and Mus pahari genomes.

Understanding the mechanisms driving lineage-specific evolution in both primates and rodents has been hindered by the lack of sister clades with a similar phylogenetic structure having high-quality genome assemblies. Here, we have created chromosome-level assemblies of the Mus caroli and Mus pahari genomes. Together with the Mus musculus and Rattus norvegicus genomes, this set of rodent genomes is similar in divergence times to the Hominidae (human-chimpanzee-gorilla-orangutan). By comparing the evolutionary dynamics between the Muridae and Hominidae, we identified punctate events of chromosome reshuffling that shaped the ancestral karyotype of Mus musculus and Mus caroli between 3 and 6 million yr ago, but that are absent in the Hominidae. Hominidae show between four- and sevenfold lower rates of nucleotide change and feature turnover in both neutral and functional sequences, suggesting an underlying coherence to the Muridae acceleration. Our system of matched, high-quality genome assemblies revealed how specific classes of repeats can play lineage-specific roles in related species. Recent LINE activity has remodeled protein-coding loci to a greater extent across the Muridae than the Hominidae, with functional consequences at the species level such as reproductive isolation. Furthermore, we charted a Muridae-specific retrotransposon expansion at unprecedented resolution, revealing how a single nucleotide mutation transformed a specific SINE element into an active CTCF binding site carrier specifically in Mus caroli, which resulted in thousands of novel, species-specific CTCF binding sites. Our results show that the comparison of matched phylogenetic sets of genomes will be an increasingly powerful strategy for understanding mammalian biology.

Adaptive Transcriptome Profiling of Subterranean Zokor, Myospalax baileyi, to High- Altitude Stresses in Tibet.

Animals living at high altitudes have evolved distinct phenotypic and genotypic adaptations against stressful environments. We studied the adaptive patterns of altitudinal stresses on transcriptome turnover in subterranean plateau zokors (Myospalax baileyi) in the high-altitude Qinghai-Tibetan Plateau. Transcriptomes of zokors from three populations with distinct altitudes and ecologies (Low: 2846 m, Middle: 3282 m, High: 3,714 m) were sequenced and compared. Phylogenetic and principal component analyses classified them into three divergent altitudinal population clusters. Genetic polymorphisms showed that the population at H, approaching the uppermost species boundary, harbors the highest genetic polymorphism. Moreover, 1056 highly up-regulated UniGenes were identified from M to H. Gene ontologies reveal genes like EPAS1 and COX1 were overexpressed under hypoxia conditions. EPAS1, EGLN1, and COX1 were convergent in high-altitude adaptation against stresses in other species. The fixation indices (F ST and G ST )-based outlier analysis identified 191 and 211 genes, highly differentiated among L, M, and H. We observed adaptive transcriptome changes in Myospalax baileyi, across a few hundred meters, near the uppermost species boundary, regardless of their relatively stable underground burrows' microclimate. The highly variant genes identified in Myospalax were involved in hypoxia tolerance, hypercapnia tolerance, ATP-pathway energetics, and temperature changes.

Phylogenomic Insights into Mouse Evolution Using a Pseudoreference Approach.

Comparative genomic studies are now possible across a broad range of evolutionary timescales, but the generation and analysis of genomic data across many different species still present a number of challenges. The most sophisticated genotyping and down-stream analytical frameworks are still predominantly based on comparisons to high-quality reference genomes. However, established genomic resources are often limited within a given group of species, necessitating comparisons to divergent reference genomes that could restrict or bias comparisons across a phylogenetic sample. Here, we develop a scalable pseudoreference approach to iteratively incorporate sample-specific variation into a genome reference and reduce the effects of systematic mapping bias in downstream analyses. To characterize this framework, we used targeted capture to sequence whole exomes (∼54 Mbp) in 12 lineages (ten species) of mice spanning the Mus radiation. We generated whole exome pseudoreferences for all species and show that this iterative reference-based approach improved basic genomic analyses that depend on mapping accuracy while preserving the associated annotations of the mouse reference genome. We then use these pseudoreferences to resolve evolutionary relationships among these lineages while accounting for phylogenetic discordance across the genome, contributing an important resource for comparative studies in the mouse system. We also describe patterns of genomic introgression among lineages and compare our results to previous studies. Our general approach can be applied to whole or partitioned genomic data and is easily portable to any system with sufficient genomic resources, providing a useful framework for phylogenomic studies in mice and other taxa.

Consequences of Secondary Calibrations on Divergence Time Estimates.

Secondary calibrations (calibrations based on the results of previous molecular dating studies) are commonly applied in divergence time analyses in groups that lack fossil data; however, the consequences of applying secondary calibrations in a relaxed-clock approach are not fully understood. I tested whether applying the posterior estimate from a primary study as a prior distribution in a secondary study results in consistent age and uncertainty estimates. I compared age estimates from simulations with 100 randomly replicated secondary trees. On average, the 95% credible intervals of node ages for secondary estimates were significantly younger and narrower than primary estimates. The primary and secondary age estimates were significantly different in 97% of the replicates after Bonferroni corrections. Greater error in magnitude was associated with deeper than shallower nodes, but the opposite was found when standardized by median node age, and a significant positive relationship was determined between the number of tips/age of secondary trees and the total amount of error. When two secondary calibrated nodes were analyzed, estimates remained significantly different, and although the minimum and median estimates were associated with less error, maximum age estimates and credible interval widths had greater error. The shape of the prior also influenced error, in which applying a normal, rather than uniform, prior distribution resulted in greater error. Secondary calibrations, in summary, lead to a false impression of precision and the distribution of age estimates shift away from those that would be inferred by the primary analysis. These results suggest that secondary calibrations should not be applied as the only source of calibration in divergence time analyses that test time-dependent hypotheses until the additional error associated with secondary calibrations is more properly modeled to take into account increased uncertainty in age estimates.

Repeated evolution of carnivory among Indo-Australian rodents.

Convergent evolution, often observed in island archipelagos, provides compelling evidence for the importance of natural selection as a generator of species and ecological diversity. The Indo-Australian Archipelago (IAA) is the world's largest island system and encompasses distinct biogeographic units, including the Asian (Sunda) and Australian (Sahul) continental shelves, which together bracket the oceanic archipelagos of the Philippines and Wallacea. Each of these biogeographic units houses numerous endemic rodents in the family Muridae. Carnivorous murids, that is those that feed on animals, have evolved independently in Sunda, Sulawesi (part of Wallacea), the Philippines, and Sahul, but the number of origins of carnivory among IAA murids is unknown. We conducted a comprehensive phylogenetic analysis of carnivorous murids of the IAA, combined with estimates of ancestral states for broad diet categories (herbivore, omnivore, and carnivore) and geographic ranges. These analyses demonstrate that carnivory evolved independently four times after overwater colonization, including in situ origins on the Philippines, Sulawesi, and Sahul. In each biogeographic unit the origin of carnivory was followed by evolution of more specialized carnivorous ecomorphs such as vermivores, insectivores, and amphibious rats.

The complete mitochondrial genome of the Leopoldamys edwardsi (Rodentia: Muridae).

The complete mitochondrial genome of L. edwardsi was first sequenced and characterized. The genome was 16,284 bases in length and the composition and arrangement of its genes are analogous to most other rodents. The nucleotide sequence date of 12 heavy-strand protein-coding genes of L. edwardsi and other 26 Muridae species were used for phylogenetic analyses. Trees constructed using Maximum Likelihood, Neighbor Joining and Minimum Evolution demonstrated that L. edwardsi was closer to the genus Niviventer than Rattus. Combing previous research, it suggests that Edward's long-tailed rat is more suitable to be classified into genus Leopoldamys and named as Leopoldamys edwardsi. This study suggested that R. edwardsi is inappropriate for the other name of L. edwardsi.

Sequencing and analysis of complete mitochondrial genome of Niviventer fulvescens (Muridae).

The complete mitochondrial genome was sequenced and annotated newly from an individual of Niviventer fulvescens (Muridae) from Sichuan province. The total length of the N. fulvescens mitogenome is 16 296 bp and contains 13 protein-coding genes, 2 ribosomal RNA genes, 22 transfer RNA genes and a control region, with a base composition of 34.3%A, 29.1%T, 24.2%C and 12.4%G. The nucleotide sequence data of 12 heavy-strand protein-coding genes of N. fulvescens and other 18 rodents were used for mitochondrial genome phylogenetic analyses. Bayesian phylogenetic tree demonstrated the genus Niviventer was embedded within the genus Leopoldamys, although three Niviventer species constituted a monophyletic group. More complete mitochondrial genome sequences are required to illuminate the molecular phylogenetic relationship between Niviventer and Leopoldamys.