The evolutionary radiation of Arvicolinae rodents (voles and lemmings): relative contribution of nuclear and mitochondrial DNA phylogenies

Species Composition of a Small Mammal Community and Prevalence of Echinococcus spp. in the Alpine Pastoral Area of the Eastern Tibetan Plateau

We aimed to investigate the species composition of a small mammal community and the prevalence of Echinococcus spp. in a typical endemic area of the Tibetan Plateau. One pika and five rodent species were identified based on the morphological characteristics of 1278 small mammal specimens collected during 2014-2019. Detection of Echinococcus DNA in tissue samples from small mammal specimens revealed that Ochotona curzoniae (pika, total prevalence: 6.02%, 26/432), Neodon fuscus (5.91%, 38/643), N. leucurus (2.50%, 3/120), and Alexandromys limnophilus (21.74%, 10/46) were infected by both E. multilocularis and E. shiquicus; Cricetulus longicaudatus (16.67%, 1/6) was infected by E. shiquicus; and no infection was detected in N. irene (0/15). Neodon fuscus and O. curzoniae were the two most abundant small mammal species. There was no significant difference in the prevalence of pika and the overall rodent species assemblage (6.26%, 53/846); however, the larger rodent populations suggested that more attention should be paid to their role in the transmission of echinococcosis in the wildlife reservoir, which has long been underestimated. Moreover, although DNA barcoding provides a more efficient method than traditional morphological methods for identifying large numbers of small mammal samples, commonly used barcodes failed to distinguish the three Neodon species in this study. The close genetic relationships between these species suggest the need to develop more powerful molecular taxonomic tools.

A new perspective on the taxonomy and systematics of Arvicolinae (Gray, 1821) and a new time-calibrated phylogeny for the clade

Background

Arvicoline rodents are one of the most speciose and rapidly evolving mammalian lineages. Fossil arvicolines are also among the most common vertebrate fossils found in sites of Pliocene and Pleistocene age in Eurasia and North America. However, there is no taxonomically robust, well-supported, time-calibrated phylogeny for the group.

Methods

Here we present well-supported hypotheses of arvicoline rodent systematics using maximum likelihood and Bayesian inference of DNA sequences of two mitochondrial genes and three nuclear genes representing 146 (82% coverage) species and 100% of currently recognized arvicoline genera. We elucidate well-supported major clades, reviewed the relationships and taxonomy of many species and genera, and critically compared our resulting molecular phylogenetic hypotheses to previously published hypotheses. We also used five fossil calibrations to generate a time-calibrated phylogeny of Arvicolinae that permitted some reconciliation between paleontological and neontological data.

Results

Our results are largely congruent with previous molecular phylogenies, but we increased the support in many regions of the arvicoline tree that were previously poorly-sampled. Our sampling resulted in a better understanding of relationships within Clethrionomyini, the early-diverging position and close relationship of true lemmings (Lemmus and Myopus) and bog lemmings (Synaptomys), and provided support for recent taxonomic changes within Microtini. Our results indicate an origin of ∼6.4 Ma for crown arvicoline rodents. These results have major implications (e.g., diversification rates, paleobiogeography) for our confidence in the fossil record of arvicolines and their utility as biochronological tools in Eurasia and North America during the Quaternary.

Evolution and diversification of Mountain voles (Rodentia: Cricetidae)

The systematics of the Cricetid genus Neodon have long been fraught with uncertainty due to sampling issues and a lack of comprehensive datasets. To gain better insights into the phylogeny and evolution of Neodon, we systematically sampled Neodon across the Hengduan and Himalayan Mountains, which cover most of its range in China. Analyses of skulls, teeth, and bacular structures revealed 15 distinct patterns corresponding to 15 species of Neodon. In addition to morphological analyses, we generated a high-quality reference genome for the mountain vole and generated whole-genome sequencing data for 47 samples. Phylogenomic analyses supported the recognition of six new species, revealing a long-term underestimation of Neodon diversity. We further identified positively selected genes potentially related to high-elevation adaptation. Together, our results illuminate how climate change caused the plateau to become the centre of Neodon origin and diversification and how mountain voles have adapted to the hypoxic high-altitude plateau environment.

Comparison of detection methods and genome quality when quantifying nuclear mitochondrial insertions in vertebrate genomes

The integration of mitochondrial genome fragments into the nuclear genome is well documented, and the transfer of these mitochondrial nuclear pseudogenes (numts) is thought to be an ongoing evolutionary process. With the increasing number of eukaryotic genomes available, genome-wide distributions of numts are often surveyed. However, inconsistencies in genome quality can reduce the accuracy of numt estimates, and methods used for identification can be complicated by the diverse sizes and ages of numts. Numts have been previously characterized in rodent genomes and it was postulated that they might be more prevalent in a group of voles with rapidly evolving karyotypes. Here, we examine 37 rodent genomes, and an additional 26 vertebrate genomes, while also considering numt detection methods. We identify numts using DNA:DNA and protein:translated-DNA similarity searches and compare numt distributions among rodent and vertebrate taxa to assess whether some groups are more susceptible to transfer. A combination of protein sequence comparisons (protein:translated-DNA) and BLASTN genomic DNA searches detect 50% more numts than genomic DNA:DNA searches alone. In addition, higher-quality RefSeq genomes produce lower estimates of numts than GenBank genomes, suggesting that lower quality genome assemblies can overestimate numts abundance. Phylogenetic analysis shows that mitochondrial transfers are not associated with karyotypic diversity among rodents. Surprisingly, we did not find a strong correlation between numt counts and genome size. Estimates using DNA: DNA analyses can underestimate the amount of mitochondrial DNA that is transferred to the nucleus.

Phylogenomics reveals the evolution, biogeography, and diversification history of voles in the Hengduan Mountains

The Hengduan Mountains (HDM) of China are a biodiversity hotspot whose temperate flora and fauna are among the world's richest. However, the origin and evolution of biodiversity in the HDM remain poorly understood, especially in mammals. Given that the HDM shows the highest richness of vole species in the world, we used whole-exome capture sequencing data from the currently most comprehensive sampling of HDM voles to investigate their evolutionary history and diversification patterns. We reconstructed a robust phylogeny and re-estimated divergence times of the HDM voles. We found that all HDM voles could be divided into a western lineage (Volemys, Proedromys, and Neodon) and an eastern lineage (Caryomys and Eothenomys), and the two lineages originated from two migration events from North Eurasia to the HDM approximately 9 Mya. Both vole lineages underwent a significant acceleration of net diversification from 8-5 Mya, which was temporally congruent with the orogeny of the HDM region. We also identified strong intertribal gene flow among the HDM voles and hypothesized that frequent gene flow might have facilitated the speciation burst of the HDM voles. Our study highlights the importance of both environmental and biotic factors in shaping the biodiversity of mammals in mountain ecosystems.

Signatures of Adaptation in Mitochondrial Genomes of Palearctic Subterranean Voles (Arvicolinae, Rodentia)

This study evaluates signatures of selection in the evolution of the mitochondrial DNA of voles, subfamily Arvicolinae, during the colonization of subterranean environments. The comparative sequence analysis of mitochondrial protein-coding genes of eight subterranean vole species (Prometheomys schaposchnikowi, three species of the genus Ellobius: Ellobius talpinus, Ellobius fuscocapillus and Ellobius lutescens, two species of the genus Terricola: Terricola subterraneus and Terricola daghestanicus, Lasiopodomys mandarinus, and Hyperacrius fertilis) and their closest aboveground relatives was applied using codon-substitution models. The highest number of selection signatures was detected in genes ATP8 and CYTB. The relaxation of selection was observed in most mitochondrial DNA protein-coding genes for subterranean species. The largest amount of relaxed genes is discovered in mole voles (genus Ellobius). The number of selection signatures was found to be independent of the evolutionary age of the lineage but fits the degree of specialization to the subterranean niche. The common trends of selective pressures were observed among the evolutionary ancient and highly specialized subterranean rodent families and phylogenetically young lineages of voles. It suggests that the signatures of adaptation in individual mitochondrial protein-coding genes associated with the colonization of the subterranean niche may appear within a rather short evolutionary timespan.

A mitochondrial genome phylogeny of voles and lemmings (Rodentia: Arvicolinae): Evolutionary and taxonomic implications

Arvicolinae is one of the most impressive placental radiations with over 150 extant and numerous extinct species that emerged since the Miocene in the Northern Hemisphere. The phylogeny of Arvicolinae has been studied intensively for several decades using morphological and genetic methods. Here, we sequenced 30 new mitochondrial genomes to better understand the evolutionary relationships among the major tribes and genera within the subfamily. The phylogenetic and molecular dating analyses based on 11,391 bp concatenated alignment of protein-coding mitochondrial genes confirmed the monophyly of the subfamily. While Bayesian analysis provided a high resolution across the entire tree, Maximum Likelihood tree reconstruction showed weak support for the ordering of divergence and interrelationships of tribal level taxa within the most ancient radiation. Both the interrelationships among tribes Lagurini, Ellobiusini and Arvicolini, comprising the largest radiation and the position of the genus Dinaromys within it also remained unresolved. For the first time complex relationships between genus level taxa within the species-rich tribe Arvicolini received full resolution. Particularly Lemmiscus was robustly placed as sister to the snow voles Chionomys in the tribe Arvicolini in contrast with a long-held belief of its affinity with Lagurini. Molecular dating of the origin of Arvicolinae and early divergences obtained from the mitogenome data were consistent with fossil records. The mtDNA estimates for putative ancestors of the most genera within Arvicolini appeared to be much older than it was previously proposed in paleontological studies.

Comprehensive total evidence phylogeny of chinchillids (Rodentia, Caviomorpha): Cheek teeth anatomy and evolution

Rodents are the most diverse order of extant mammals, and caviomorph rodents, or New World hystricognaths, have a remarkable morphological disparity and a long fossil record that begins in the Eocene. Chinchilloidea is a poorly understood clade within Caviomorpha, from an evolutionary and phylogenetic perspective. It includes the extant families Chinchillidae and Dinomyidae, the extinct Neoepiblemidae and Cephalomyidae, and several extinct chinchilloids without a clear phylogenetic position, like Eoincamys, Borikenomys, Chambiramys, Ucayalimys, Incamys, Saremmys, Garridomys and Scotamys. The family Chinchillidae includes the extant Chinchilla and Lagidium, grouped in Chinchillinae, and the only living Lagostominae, Lagostomus maximus. Among extinct chinchillids, Eoviscaccia (early Oligocene-early Miocene of Argentina, Bolivia and Chile), Prolagostomus (early-middle Miocene of Argentina, Bolivia and Chile) and Pliolagostomus (early-middle Miocene of Argentina) are the only genera originally described as members of the family. Based on the study of specimens with unworn or little-worn cheek teeth, belonging to extinct and extant taxa, we propose homologies of the cheek teeth structures and perform a combined molecular and morphological phylogenetic analysis including extinct and extant taxa of all families of Chinchilloidea and all genera of Chinchillidae. Our phylogenetic analysis recovered three major lineages in the evolutionary history of Chinchilloidea. The first major lineage is composed of the extant taxa Chinchilla, Lagidium and Lagostomus, and the extinct genera Eoviscaccia, Prolagostomus, Pliolagostomus, Garridomys, Incamys, Loncolicu and Saremmys. Cephalomyid (Banderomys, Cephalomys, Litodontomys, Soriamys) and neoepiblemid (Neoepiblema, Perimys, Phoberomys, Scotamys) genera are part of the second major lineage, while dinomyids such as Dinomys, Drytomomys, Scleromys, 'Scleromys' and Tetrastylus constitute the third major lineage within Chinchilloidea. The phylogenetic position of some taxa previously considered as incertae sedis chinchilloids or without a clear suprageneric group (i.e. Incamys, Saremmys, Garridomys and Loncolicu) show that they belong to pan-Chinchillidae and conform the stem Chinchillidae along with Eoviscaccia. The euhypsodont crown Chinchillidae includes the living subfamilies Chinchillinae and Lagostominae. Dinomyidae and Eoincamys pascuali are recovered as the sisters of a major clade composed by 'Cephalomyidae'+Neopiblemidae and pan-Chinchillidae, and Chambiramys sylvaticus occupies a basal position to the same clade. Four major radiation events are identified in the evolutionary history of Chinchilloidea. The analysis of new morphological characters linked with molecular evidence as well as the addition of taxa of uncertain or unstable phylogenetic position or not considered in previous studies allowed us resolve part of the relationships within Chinchilloidea, particularly that of Chinchillidae, supporting preceding morphological hypotheses.

Mitochondrial Genome Evolution, Genetic Diversity, and Population Structure in British Water Voles (Arvicola amphibius)

The European water vole (Arvicola amphibius) is a rodent within the subfamily Arvicolinae. In Britain, water voles have declined rapidly during the last century, making them a conservation priority. The relationship of Arvicola to other genera within Arvicolinae remains debated. Additionally, the impact that captive breeding programs in Britain are having on the genetic diversity of water voles is unknown. We use available mitochondrial genomes to construct the phylogeny of species within Arvicolinae, followed by sequencing the mitochondrial DNA control region of 17 individuals from a captive population of water voles in Britain to assess their genetic diversity and population structure. Our study first provides an updated phylogenetic tree of Arvicolinae using the mitochondrial genome of 31 species. Second, our results show considerable genetic diversity in the captive population of water voles, when compared with natural populations in Britain. We confirm the grouping of British water voles into two clades, with all captive individuals found in the English/Welsh clade. Moreover, captive water voles clustered closely with populations in the South East and East of England. The mitochondrial genome provides a useful marker to study the phylogenetics of this rodent clade and in addition, our study provides support for the breeding program at Wildwood Trust and provides a framework for future conservation genetics studies in this species.

Complete Mitochondrial Genome of Three Species of the Genus Microtus (Arvicolinae, Rodentia)

The 65 species of the genus Microtus have unusual sex-related genetic features and a high rate of karyotype variation. However, only nine complete mitogenomes for these species are currently available. We describe the complete mitogenome sequences of three Microtus, which vary in length from 16,295 bp to 16,331 bp, contain 13 protein-coding genes (PCGs), two ribosomal RNA genes, 22 transfer RNA genes and a control region. The length of the 13 PCGs and the coded proteins is the same in all three species, and the start and stop codons are conserved. The non-coding regions include the L-strand origin of replication, with the same sequence of 35 bp, and the control region, which varies between 896 bp and 930 bp in length. The control region includes three domains (Domains I, II and III) with extended termination-associated sequences (ETAS-1 and ETAS-2) in Domain I. Domain II and Domain III include five (CSB-B, C, D, E and F) and three (CSB-1, CSB-2, and CSB-3) conserved sequence blocks, respectively. Phylogenetic reconstructions using the mitochondrial genomes of all the available Microtus species and one representative species from another genus of the Arvicolinae subfamily reproduced the established phylogenetic relationships for all the Arvicolinae genera that were analyzed.

Whole mitochondrial genome of long-clawed mole vole (Prometheomys schaposchnikowi) from Turkey, with its phylogenetic relationships

The mitogenome of Prometheomys schaposchnikowi was characterized for the first time as a circular DNA molecule (16.284 bp), containing 37 coding and 2 non-coding regions. In the mitogenome, ND6 and 8 tRNA genes were encoded on the light chain, while 12 PCGs, 14 tRNAs, 2 rRNAs, D-loop and O_L were encoded on the heavy chain. The most common initiation codon in PCGs was ATG. As in many mammals, incomplete stop codons in P. schaposchnikowi were in the COX3, ND1 and ND4. Phylogenetic relationships were revealed using Bayesian method and the 13 PCGs. Seven genera (Arvicola, Dicrostonyx, Lasiopodomys, Myodes, Ondatra, Proedromys and Prometheomys) formed a monophyletic group, while Eothenomys, Microtus and Neodon were paraphyletic. P. schaposchnikowi constituted the most basal group within Arvicolinae. Divergence time estimation suggested that P. schaposchnikowi diversified during the Miocene (16.28 Mya). Further molecular studies are needed to test the distinctiveness and diversity of the genus Prometheomys.

Evolutionary history of water voles revisited: confronting a new phylogenetic model from molecular data with the fossil record

Recent water voles (genus Arvicola) display a prominent morphological diversity with a strong ecotypical background but with unclear taxonomic associations. We provide a novel synthetic view on the evolutionary history and the current taxonomic richness in the genus. Our molecular reconstruction, based on a 1143-bp-long sequence of cytochrome b and a 926-bp interphotoreceptor retinoid binding protein (irbp) confirmed the monophyly of four species (amphibius, sapidus, monticola and italicus) recognized thus far, and retrieved a new deeply divergent lineage from West Iran. Genetic divergence of the Iranian lineage (>9.0%) is inside the range of interspecies distances, exceeding the interspecies divergences between the remaining Arvicola species (range, 4.3–8.7%). The oldest name available for the Iranian phylogroup is Arvicola persicus de Filippi, 1865, with the type locality in Soltaniyeh, Iran. The molecular clock suggests the divergence of A. persicus in the Early Pleistocene (2.545 Ma), and the current radiation of the remaining species between 1.535 Ma (Arvicola sapidus) and 0.671 Ma. While A. sapidus possibly evolved from Arvicola jacobaeus, a fossil ancestor to A. persicus is unknown. The aquatic life-style of Mimomys savini, a direct ancestor to some fossil Arvicola, is retained in recent stem species A. sapidus and A. persicus, while a major shift toward fossorial morphotype characterizes the terminal lineages (amphibius, italicus and monticola). We suggest that habitat-dependent morphological plasticity and positive enamel differentiation in Arvicola amphibius widened its ecological niche that might trigger a range expansion across c. 12 million km2, making it one of the largest among arvicolines.

Complete mitochondrial genomes confirm the generic placement of the plateau vole, Neodon fuscus

The plateau vole, Neodon fuscus is endemic to China and is distributed mainly in Qinghai Province. It is of public health interest, as it is, a potential reservoir of Toxoplasma gondii and the intermediate host of Echinococcus multilocularis. However, genetic data of this species are lacking, and its name and taxonomy are still a controversy. In the present study, we determined the nucleotide sequence of the entire mitochondrial (mt) genome of N. fuscus and analyzed its evolutionary relationship. The mitogenome was 16328 bp in length and contained 13 protein-coding genes, 22 genes for transfer RNAs (tRNA), two ribosomal RNA genes and two major noncoding regions (O_L region and D-loop region). Most genes were located on the heavy strand. All tRNA genes had typical cloverleaf structures except for tRNA^{Ser (GCU)}. The mt genome of N. fuscus was rich in A+T (58.45%). Maximum likelihood (ML) and Bayesian methods yielded phylogenetic trees from 33 mt genomes of Arvicolinae, in which N. fuscus formed a sister group with Neodon irene and Neodon sikimensis to the exclusion of species of Microtus and other members of the Arvicolinae. Further phylogenetic analyses (ML only) based on the cytb gene sequences also demonstrated that N. fuscus had a close relationship with N. irene. The complete mitochondrial genome was successfully assembled and annotated, providing the necessary information for the phylogenetic analyses. Although the name Lasiopodomys fuscus was used in the book ‘Wilson & Reeder’s Mammal Species of the World’, we have confirmed here that its appropriate name is N. fuscus through an analysis of the evolutionary relationships.

Further assessment of the Genus Neodon and the description of a new species from Nepal

Recent molecular systematic studies of arvicoline voles of the genera Neodon, Lasiopodomys, Phaiomys, and Microtus from Central Asia suggest the inclusion of Phaiomys leucurus, Microtus clarkei, and Lasiopodomys fuscus into Neodon and moving Neodon juldaschi into Microtus (Blanfordimys). In addition, three new species of Neodon (N. linzhiensis, N. medogensis, and N. nyalamensis) have recently been described from Tibet. Analyses of concatenated mitochondrial (Cytb, COI) and nuclear (Ghr, Rbp3) genes recovered Neodon as a well-supported monophyletic clade including all the recently described and relocated species. Kimura-2-parameter distance between Neodon from western Nepal compared to N. sikimensis (K2P = 13.1) and N. irene (K2P = 13.4) was equivalent to genetic distances observed between recognized species of this genus. The specimens sampled from western Nepal were recovered sister to N. sikimensis in the concatenated analysis. However, analyses conducted exclusively with mitochondrial loci did not support this relationship. The occlusal patterns of the first lower (m1) and third upper (M3) molars were simpler in specimens from western Nepal in comparison to N. sikimensis from eastern Nepal and India. Twelve craniodental characters and four external field measurements were examined from specimens of N. sikimensis from eastern Nepal and India, N. irene, and Neodon from western Nepal. Neodon from western Nepal were significantly different from N. sikimensis from eastern Nepal and India in ten out of 16 characters measured and from N. irene for all characters except ear height. Specimens from western Nepal were smaller in size than N. sikimensis from Eastern Nepal and India and larger than N. irene. Together the results of the molecular and morphological analyses indicate that Neodon from western Nepal are distinct under the phylogenetic, genetic and morpho species concepts.

Multiple intrasyntenic rearrangements and rapid speciation in voles

Remarkably stable genomic chromosome elements (evolutionary conserved segments or syntenies) are the basis of large-scale chromosome architecture in vertebrate species. However, these syntenic elements harbour evolutionary important changes through intrachromosomal rearrangements such as inversions and centromere repositioning. Here, using FISH with a set of 20 region-specific probes on a wide array of 28 species, we analyzed evolution of three conserved syntenic regions of the Arvicolinae ancestral karyotype. Inside these syntenies we uncovered multiple, previously cryptic intrachromosomal rearrangements. Although in each of the three conserved blocks we found inversions and centromere repositions, the blocks experienced different types of rearrangements. In two syntenies centromere repositioning predominated, while in the third region, paracentric inversions were more frequent, whereas pericentric inversions were not detected. We found that some of the intrachromosomal rearrangements, mainly paracentric inversions, were synapomorphic for whole arvicoline genera or tribes: genera Alexandromys and Microtus, tribes Ellobini and Myodini. We hypothesize that intrachromosomal rearrangements within conserved syntenic blocks are a major evolutionary force modulating genome architecture in species-rich and rapidly-evolving rodent taxa. Inversions and centromere repositioning may impact speciation and provide a potential link between genome evolution, speciation, and biogeography.

Population structure and genetic diversity of hatchery stocks as revealed by combined mtDNA fragment sequences in Indian major carp, Catla catla

Catla catla is the second most important Indian major carp due to high growth rate and acceptance to consumers for food value. It is widely cultured in the Indian subcontinent as monoculture or polyculture. In the present study, genetic diversity among hatchery stocks (total 218 samples of catla) collected from different geographical regions of India was examined using mtDNA fragment sequence of Cyt b (306 bp) and D loop (710 bp). High numbers (57) of population specific haplotypes were observed in the present study. The results revealed significant genetic heterogeneity for the sequence data (F_ST = 0.27546, p < .05). Analysis of molecular variance revealed significant genetic differentiation among different catla populations. The information generated in present study could be useful to develop broad genetic base populations of catla.

Disjunct distribution and distinct intraspecific diversification of Eothenomys melanogaster in South China

BACKGROUND

South China encompasses complex and diverse landforms, giving rise to high biological diversity and endemism from the Hengduan Mountains to Taiwan Island. Many species are widely distributed across South China with similar disjunct distribution patterns. To explore the causes of these disjunct distribution patterns and their genetic consequences, we investigated the endemic species Père David's Chinese Vole (Eothenomys melanogaster) by integrating geological and ecological factors. We analysed the genetic structure and divergence time of E. melanogaster based on fast-evolving mitochondrial and nuclear markers using Bayesian trees and coalescent species tree approaches. Historical scenarios of distribution range and demography were reconstructed based on spatial interpolations of genetic diversity and distance, extended Bayesian skyline plots, phylogeographic diffusion analysis, and ecological niche modelling (ENM) during different periods. We also assessed the relationships between geographical distance/ecological vicariance and genetic distance (isolation by distance, IBD; isolation by environment, IBE).

RESULTS

The genetic analysis revealed three deeply divergent clades-Southeast, Southwest and Central clades, centred on the Wuyi Mountains, the Yunnan-Guizhou Plateau (YGP) and the mountains around the Sichuan Basin, respectively-that have mostly developed since the Pleistocene. IBD played an important role in early divergence, and geological events (sedimentation of plains and linking of palaeo-rivers) and IBE further reinforced genetic differentiation. ENM shows the importance of suitable habitats and elevations.

CONCLUSIONS

Our results suggest that the primary cause of the disjunct distribution in E. melanogaster is the high dependence on middle-high-altitude habitat in the current period. Mountains in the occurence range have served as "sky islands" for E. melanogaster and hindered gene flow. Pleistocene climatic cycles facilitated genetic admixture in cold periods and genetic diversification in warm periods for inland clades. During cold periods, these cycles led to multiple colonization events between the mainland and Taiwan and erased genetic differentiation.

The complete mitochondrial genome of the common vole, Microtus arvalis (Rodentia: Arvicolinae)

The common vole, Microtus arvalis belongs to the genus Microtus in the subfamily Arvicolinae. In this study, the complete mitochondrial genome of M. arvalis was recovered using shotgun sequencing and an iterative mapping approach using three related species. Phylogenetic analyses using the sequence of 21 arvicoline species place the common vole as a sister species to the East European vole (Microtus levis), but as opposed to previous results we find no support for the recognition of the genus Neodon within the subfamily Arvicolinae, as this is, as well as the genus Lasiopodomys, found within the Microtus genus.

The Microtus voles: Resolving the phylogeny of one of the most speciose mammalian genera using genomics

Sequential rapid radiations pose some of the greatest difficulties in phylogenetics, especially when analysing only a small number of genetic markers. Given that most of the speciation events occur in quick succession at various points in time, this creates particular challenges in determining phylogenetic relationships, i.e. branching order and divergence times. With the development of high throughput sequencing, thousands of markers can now readily be used to tackle these issues. Microtus is a speciose genus currently composed of 65 species that evolved over the last 2 million years. Although it is a well-studied group, there is still phylogenetic uncertainty at various divergence levels. Building upon previous studies that generally used small numbers of mitochondrial and/or nuclear loci, in this genomic-scale study we used both mitochondrial and nuclear data to study the rapid radiation within Microtus, using partial mitogenomes and genotyping-by-sequencing (GBS) on seven species representing five Microtus subgenera and the main biogeographic ranges where this group occurs. Both types of genome (mitochondrial and nuclear) generated similar tree topologies, with a basal split of the Nearctic (M. ochrogaster) and Holarctic (M. oeconomus) species, and then a subdivision of the five Palearctic species into two subgroups. These data support the occurrence of two European radiations, one North American radiation, and a later expansion of M. oeconomus from Asia to both Europe and North America. We further resolved the positioning of M. cabrerae as sister group of M. agrestis and refute the claim that M. cabrerae should be elevated to its own genus (Iberomys). Finally, the data support ongoing speciation events, especially within M. agrestis, with high levels of genetic divergence between the three Evolutionarily Significant Units (ESUs) previously identified. Similar high levels of divergence were also found among ESUs within M. oeconomus and M. arvalis.

A new species of big-eared climbing rat, genus Ototylomys (Cricetidae: Tylomyinae), from Chiapas, Mexico

An allopatric population of big-eared climbing rats (Ototylomys) from the Northern Highlands of Chiapas, Mexico, is described as a new species. The new taxon is part of a unique montane rainforest community that includes several other endemic species in the limited geographic range between the Río Grijalva and the Central Depression of Chiapas. Several cranial, external, and molecular characters distinguish this new species of big-eared climbing rat from its more widely distributed congener, Ototylomys phyllotis. We performed principal component and discriminate function analyses of cranial measurements, and found that specimens of the new species consistently could be distinguished from other Ototylomys with strong statistical support. Compared with exemplars of Ototylomys from elsewhere in their range, the new species possesses a karyotype that differs by 3 additional biarmed chromosome pairs, is fixed or nearly fixed for distinct electromorphs at 12 allozyme loci, and the mean genetic distance exceeds 14%, based on comparisons of the mitochondrial cytochrome b gene between the new species of Ototylomys and representatives of O. phyllotis. The restricted distribution in montane karst rainforest suggests that the species and its habitat may be a matter of conservation concern.

Una población alopátrica de rata orejuda trepadora (Ototylomys) de las Tierras Altas del Norte de Chiapas, México se describe como una nueva especie. El nuevo taxón es parte de una comunidad única de bosque lluvioso montano que incluye varias especies endémicas en el área de distribución geográfica limitada entre el Río Grijalva y la Depresión Central de Chiapas. Varios caracteres craneales, externos, y moleculares distinguen la nueva rata orejuda trepadora de su congénere más ampliamente distribuido, Ototylomys phyllotis. Se realizaron análisis de componentes principales y de función discriminante de los caracteres craneales, y se encontró que los especímenes de La Pera fueron consistentemente distinguidos de otros Ototylomys con un fuerte soporte estadístico. En comparación con ejemplares de Ototylomys del rango, la nueva especie posee un cariotipo que difiere por 3 pares adicionales de cromosomas biarmados, está fijo o casi fijo por distintos electromorfos en 12 loci alozímicos. Adicionalmente, la media de la distancia genética comparada del gen mitochondrial citocromo b entre la nueva especie de Ototylomys y representantes de O. phyllotis, excede el 14%. La distribución restringida en el bosque lluvioso montano kárstico sugiere que la especie y su hábitat pueden ser de importancia para la conservación.

Intrachromosomal Rearrangements in Rodents from the Perspective of Comparative Region-Specific Painting

It has long been hypothesized that chromosomal rearrangements play a central role in different evolutionary processes, particularly in speciation and adaptation. Interchromosomal rearrangements have been extensively mapped using chromosome painting. However, intrachromosomal rearrangements have only been described using molecular cytogenetics in a limited number of mammals, including a few rodent species. This situation is unfortunate because intrachromosomal rearrangements are more abundant than interchromosomal rearrangements and probably contain essential phylogenomic information. Significant progress in the detection of intrachromosomal rearrangement is now possible, due to recent advances in molecular biology and bioinformatics. We investigated the level of intrachromosomal rearrangement in the Arvicolinae subfamily, a species-rich taxon characterized by very high rate of karyotype evolution. We made a set of region specific probes by microdissection for a single syntenic region represented by the p-arm of chromosome 1 of Alexandromys oeconomus, and hybridized the probes onto the chromosomes of four arvicolines (Microtus agrestis, Microtus arvalis, Myodes rutilus, and Dicrostonyx torquatus). These experiments allowed us to show the intrachromosomal rearrangements in the subfamily at a significantly higher level of resolution than previously described. We found a number of paracentric inversions in the karyotypes of M. agrestis and M. rutilus, as well as multiple inversions and a centromere shift in the karyotype of M. arvalis. We propose that during karyotype evolution, arvicolines underwent a significant number of complex intrachromosomal rearrangements that were not previously detected.

Muroid rodent phylogenetics: 900-species tree reveals increasing diversification rates

We combined new sequence data for more than 300 muroid rodent species with our previously published sequences for up to five nuclear and one mitochondrial genes to generate the most widely and densely sampled hypothesis of evolutionary relationships across Muroidea. An exhaustive screening procedure for publically available sequences was implemented to avoid the propagation of taxonomic errors that are common to supermatrix studies. The combined data set of carefully screened sequences derived from all available sequences on GenBank with our new data resulted in a robust maximum likelihood phylogeny for 900 of the approximately 1,620 muroids. Several regions that were equivocally resolved in previous studies are now more decisively resolved, and we estimated a chronogram using 28 fossil calibrations for the most integrated age and topological estimates to date. The results were used to update muroid classification and highlight questions needing additional data. We also compared the results of multigene supermatrix studies like this one with the principal published supertrees and concluded that the latter are unreliable for any comparative study in muroids. In addition, we explored diversification patterns as an explanation for why muroid rodents represent one of the most species-rich groups of mammals by detecting evidence for increasing net diversification rates through time across the muroid tree. We suggest the observation of increasing rates may be due to a combination of parallel increases in rate across clades and high average extinction rates. Five increased diversification-rate-shifts were inferred, suggesting that multiple, but perhaps not independent, events have led to the remarkable species diversity in the superfamily. Our results provide a phylogenetic framework for comparative studies that is not highly dependent upon the signal from any one gene.

Phylogenetic relationship and time of divergence of Mus terricolor with reference to other Mus species

Mitochondrial DNA control region of Mus terricolor, three aboriginal species M. spretus, M. macedonicus, M. spicilegus; the Asian lineage M. caroli, M. cervicolor, M. cookii; and the two house mice, M. musculus domesticus and M. m. castaneus were analysed to estimate the substitution rate, phylogenetic relationship and the probable time of divergence. Results showed that M. spretus, M. caroli and M. terricolor are highly diverged from each other (caroli/terricolor = 0.146, caroli/spretus = 0.147 and terricolor/spretus = 0.122), whereas M. spretus showed less divergence with two house mice species (0.070 and 0.071). Sequence divergence between M. terricolor and the Palearctic group were found to be ranging from 0.121 to 0.134. Phylogenetic analysis by minimum evolution, neighbour-joining, unweighed pair group method with arithmetic mean and maximum parsimony showed almost similar topology. Two major clusters were found, one included the Asian lineage, M. caroli, M. cookii and M. cervicolor and the other included the house mice M. m. domesticus, M. m. castaneus and the aboriginal mice M. macedonicus and M. spicilegus along with M. spretus, forming the Palearctic clade. M. terricolor was positioned between the Palearctic and Asian clades. Results showed that Palearctic-terricolor and the Asian lineages diverged 5.47 million years ago (Mya), while M. terricolor had split around 4.63 Mya from their ancestor. M. cervicolor, M. cookii and M. caroli diverged between 4.70 and 3.36 Mya, which indicates that M. terricolor and the Asian lineages evolved simultaneously. M. spretus is expected to have diverged nearly 2.9 Mya from their most recent common ancestor.

Taxonomic position of Chinese voles of the tribe Arvicolini and the description of 2 new species from Xizang, China

China has 26 species in the tribe Arvicolini. The taxonomic status of these voles remains controversial despite much effort. Herein, we evaluate the taxonomic position of 22 species plus 2 unidentified taxa using mitochondrial DNA gene sequences (cytb + CO1). We also evaluate 18 species and 2 unidentified taxa using morphological data. Phylogenetic analyses of cytb resolve monophyly for the genera Alexandromys, Lasiopodomys, Microtus, Neodon, Proedromys, and Volemys with strong support. Stenocranius clusters with Chionomys but with very weak support. Analyses of concatenated cytb + CO1 resolve the same genera with strong support, but the topology of the tree differs from that of cytb in that Chionomys roots at the base of the tree independent of Stenocranius, which forms the sister-group of Lasiopodomys in a more terminal position. The matrilineal genealogy excludes the type species Arvicola amphibius from the rest of the Arvicolini. This species forms the sister-group of Ondatra with high support. Neodon includes N. irene, N. linzhiensis, N. fuscus, N. leucurus, N. sikimensis, Microtus clarkei, and 2 unidentified specimens. Alexandromys includes the former species Microtus oeconomus, M. kikuchii, M. limnophilus, M. fortis, and M. maximowiczii. Finally, Microtus has the subgenera Blanfordimys, Microtus, Mynomes, Pedomys, Pitymys, and Terricola, which includes the Chinese species M. agrestis, M. arvalis, and Blanfordimys juldaschi. General mixed Yule-coalescent species delimitation modeling demarcates 6 currently recognized species and 2 new species of Neodon. A principal component analysis of the morphological data among 7 matrilines shows that all variables have positive loadings of high magnitude on the 1st component. Canonical discriminant analysis for Neodon (including M. clarkei and 2 unidentified species) correctly classifies 93.0% of specimens. Overall, our analyses support the recognition of Alexandromys, Lasiopodomys, Microtus, Neodon, Proedromys, and Volemys as genera. Stenocranius includes Microtus gregalis, and the genealogical position of Stenocranius remains uncertain. The status of Arvicola requires further study. We assign M. clarkei to Neodon and describe 2 new species of Neodon.

Make haste slowly: reproduction in the Zaisan mole vole (Ellobius tancrei)

Mole voles are the most specialized subterranean members of the subfamily Arvicolinae. We assess the basic reproductive parameters of the Zaisan mole vole (Ellobius tancrei Blasius, 1884) and compare our data with the characteristics reported for other Ellobius species and surface-dwelling voles. In most respects, reproduction of the E. tancrei follows the pattern that is typical for voles. Females undergo postpartum estrus, but rarely combine pregnancy with lactation. The rate of embryonic and postembryonic growth (0.13 and 0.54 g/day, respectively) are slightly lower, whereas the relative neonate and weanling masses (8% and 40% of maternal mass, respectively) are slightly higher than the respective values predicted for non-subterranean arvicolines. The combination of these trends results in the protracted pregnancy and lactation (both ∼30 days). The age at first breeding is delayed (>2.5 months). Despite heavy weanlings, total maternal investment per litter in E. tancrei is low due to small litter size (2.31). Although the species of Ellobius are similar to each other by the parameters of developmental time, they vary by litter size, total investment per litter, and possibly by relative neonate body mass. This is consistent with the idea that when body-size effect is removed, fecundity variables and degree of precociality at birth are dissociated from timing variables.

Genome-wide comparative chromosome maps of Arvicola amphibius, Dicrostonyx torquatus, and Myodes rutilus

The subfamily Arvicolinae consists of a great number of species with highly diversified karyotypes. In spite of the wide use of arvicolines in biological and medicine studies, the data on their karyotype structures are limited. Here, we made a set of painting probes from flow-sorted chromosomes of a male Palearctic collared lemming (Dicrostonyx torquatus, DTO). Together with the sets of painting probes made previously from the field vole (Microtus agrestis, MAG) and golden hamster (Mesocricetus auratus, MAU), we carried out a reciprocal chromosome painting between these three species. The three sets of probes were further hybridized onto the chromosomes of the Eurasian water vole (Arvicola amphibius) and northern red-backed vole (Myodes rutilus). We defined the diploid chromosome number in D. torquatus karyotype as 2n = 45 + Bs and showed that the system of sex chromosomes is X1X2Y1. The probes developed here provide a genomic tool-kit, which will help to investigate the evolutionary biology of the Arvicolinae rodents. Our results show that the syntenic association MAG1/17 is present not only in Arvicolinae but also in some species of Cricetinae; and thus, should not be considered as a cytogenetic signature for Arvicolinae. Although cytogenetic signature markers for the genera have not yet been found, our data provides insight into the likely ancestral karyotype of Arvicolinae. We conclude that the karyotypes of modern voles could have evolved from a common ancestral arvicoline karyotype (AAK) with 2n = 56 mainly by centric fusions and fissions.

Phylogeny, biogeography and systematic revision of plain long-nosed squirrels (genus Dremomys, Nannosciurinae)

The plain long-nosed squirrels, genus Dremomys, are high elevation species in East and Southeast Asia. Here we present a complete molecular phylogeny for the genus based on nuclear and mitochondrial DNA sequences. Concatenated mitochondrial and nuclear gene trees were constructed to determine the tree topology, and date the tree. All speciation events within the plain-long nosed squirrels (genus Dremomys) were ancient (dated to the Pliocene or Miocene), and averaged older than many speciation events in the related Sunda squirrels, genus Sundasciurus. Within the plain long-nosed squirrels, the most recent interspecific split occurred 2.9 million years ago, older than some splits within Sunda squirrels, which dated to the Pleistocene. Our results demonstrate that the plain long-nosed squirrels are not monophyletic. The single species with a distinct distribution, the Bornean mountain ground squirrel (Dremomys everetti), which is endemic to the high mountains of Borneo, is nested within the Sunda squirrels with high support. This species diverged from its sister taxa in the Sunda squirrels 6.62 million years ago, and other plain long-nosed squirrels over 11 million years ago. Our analyses of morphological traits in these related genera support the re-classification of the Bornean mountain ground squirrel, Dremomys everetti, to the genus Sundasciurus, which changes its name to Sundasciurus everetti. Past inclusion in the plain long-nosed squirrels (Dremomys) reflects convergent evolution between these high elevation species.

Sexual selection and the adaptive evolution of PKDREJ protein in primates and rodents

PKDREJ is a testis-specific protein thought to be located on the sperm surface. Functional studies in the mouse revealed that loss of PKDREJ has effects on sperm transport and the ability to undergo an induced acrosome reaction. Thus, PKDREJ has been considered a potential target of post-copulatory sexual selection in the form of sperm competition. Proteins involved in reproductive processes often show accelerated evolution. In many cases, this rapid divergence is promoted by positive selection which may be driven, at least in part, by post-copulatory sexual selection. We analysed the evolution of the PKDREJ protein in primates and rodents and assessed whether PKDREJ divergence is associated with testes mass relative to body mass, which is a reliable proxy of sperm competition levels. Evidence of an association between the evolutionary rate of the PKDREJ gene and testes mass relative to body mass was not found in primates. Among rodents, evidence of positive selection was detected in the Pkdrej gene in the family Cricetidae but not in Muridae. We then assessed whether Pkdrej divergence is associated with episodes of sperm competition in these families. We detected a positive significant correlation between the evolutionary rates of Pkdrej and testes mass relative to body mass in cricetids. These findings constitute the first evidence of post-copulatory sexual selection influencing the evolution of a protein that participates in the mechanisms regulating sperm transport and the acrosome reaction, strongly suggesting that positive selection may act on these fertilization steps, leading to advantages in situations of sperm competition.

DNA barcoding of Murinae (Rodentia: Muridae) and Arvicolinae (Rodentia: Cricetidae) distributed in China

Identification of rodents is very difficult mainly due to high similarities in morphology and controversial taxonomy. In this study, mitochondrial cytochrome oxidase subunit I (COI) was used as DNA barcode to identify the Murinae and Arvicolinae species distributed in China and to facilitate the systematics studies of Rodentia. In total, 242 sequences (31 species, 11 genera) from Murinae and 130 sequences (23 species, 6 genera) from Arvicolinae were investigated, of which 90 individuals were novel. Genetic distance, threshold method, tree-based method, online BLAST and BLOG were employed to analyse the data sets. There was no obvious barcode gap. The average K2P distance within species and genera was 2.10% and 12.61% in Murinae, and 2.86% and 11.80% in Arvicolinae, respectively. The optimal threshold was 5.62% for Murinae and 3.34% for Arvicolinae. All phylogenetic trees exhibited similar topology and could distinguish 90.32% of surveyed species in Murinae and 82.60% in Arvicolinae with high support values. BLAST analyses yielded similar results with identification success rates of 92.15% and 93.85% for Murinae and Arvicolinae, respectively. BLOG successfully authenticated 100% of detected species except Leopoldamys edwardsi based on the latest taxonomic revision. Our results support the species status of recently recognized Micromys erythrotis, Eothenomys tarquinius and E. hintoni and confirm the important roles of comprehensive taxonomy and accurate morphological identification in DNA barcoding studies. We believe that, when proper analytic methods are applied or combined, DNA barcoding could serve as an accurate and effective species identification approach for Murinae and Arvicolinae based on a proper taxonomic framework.

Hantavirus reservoirs: current status with an emphasis on data from Brazil

Since the recognition of hantavirus as the agent responsible for haemorrhagic fever in Eurasia in the 1970s and, 20 years later, the descovery of hantavirus pulmonary syndrome in the Americas, the genus Hantavirus has been continually described throughout the World in a variety of wild animals. The diversity of wild animals infected with hantaviruses has only recently come into focus as a result of expanded wildlife studies. The known reservoirs are more than 80, belonging to 51 species of rodents, 7 bats (order Chiroptera) and 20 shrews and moles (order Soricomorpha). More than 80genetically related viruses have been classified within Hantavirus genus; 25 recognized as human pathogens responsible for a large spectrum of diseases in the Old and New World. In Brazil, where the diversity of mammals and especially rodents is considered one of the largest in the world, 9 hantavirus genotypes have been identified in 12 rodent species belonging to the genus Akodon, Calomys, Holochilus, Oligoryzomys, Oxymycterus, Necromys and Rattus. Considering the increasing number of animals that have been implicated as reservoirs of different hantaviruses, the understanding of this diversity is important for evaluating the risk of distinct hantavirus species as human pathogens.

Evolution of protamine genes and changes in sperm head phenotype in rodents

Little is known about the genetic basis of evolutionary changes in sperm phenotype. Postcopulatory sexual selection is associated with differences in protamine gene sequences and promoters and is a powerful force acting on sperm form and function, although links between protamine evolution and sperm phenotype are scarce. Protamines are involved in sperm chromatin condensation, and protamine deficiency negatively affects sperm morphology and male fertility, thus suggesting that they are important for sperm design and function. We examined changes in protamine genes and sperm phenotype in rodents to understand the role of sexual selection on protamine evolution and sperm design. We performed a genotype-phenotype association study using root-to-tip dN/dS (nonsynonymous/synonymous substitutions rate ratio) to account for evolutionary rates and phylogenetic generalized least squares analyses to compare genetic and morphometric data. Evolutionary rates of protamine 1 and the protamine 2 domain cleaved off during chromatin condensation correlated with head size and elongation. Protamine 1 exhibited restricted positive selection on some functional sites, which seemed sufficient to preserve its role in head design. The cleaved-protamine 2, whose relaxation is halted by sexual selection, seems to ensure small, elongated heads that would make sperm more competitive. No association existed between mature-protamine 2 and head phenotype, suggesting little involvement during chromatin condensation and a likely role maintaining the condensed state. Our results suggest that evolutionary changes in protamines could be related to complex developmental modifications in the sperm head. This represents an important step toward understanding the role of changes in gene coding sequences in the divergence of germ cell phenotype.

Multilocus systematics and non-punctuated evolution of Holarctic Myodini (Rodentia: Arvicolinae)

The tribe Myodini consists of five genera of forest and alpine voles (Alticola, Caryomys, Eothenomys, Hyperacrius and Myodes) distributed throughout the Holarctic. Because mitochondrial evidence has revealed paraphyly and polyphyly among genera, we apply the first multilocus tests to clarify taxonomy and phylogenetic relationships. Our analyses of 28 of 36 species within Myodini, including three not previously sequenced (A. montosa, A. albicaudus, and H. fertilis), identify four distinct clades and provide the first molecular evidence that Hyperacrius may not belong in Myodini. Myodes is paraphyletic, while polyphyly of Alticola reflects apparent ancient mitochondrial introgression. Diversification in this tribe was hypothesized to be tightly linked to Late Cenozoic climatic events, however, lineage through time analysis indicates diversification over the last 4 My was gradual and not strongly punctuated.

Reconstructing the phylogenetic history of long-term effective population size and life-history traits using patterns of amino acid replacement in mitochondrial genomes of mammals and birds

The nearly neutral theory, which proposes that most mutations are deleterious or close to neutral, predicts that the ratio of nonsynonymous over synonymous substitution rates (dN/dS), and potentially also the ratio of radical over conservative amino acid replacement rates (Kr/Kc), are negatively correlated with effective population size. Previous empirical tests, using life-history traits (LHT) such as body-size or generation-time as proxies for population size, have been consistent with these predictions. This suggests that large-scale phylogenetic reconstructions of dN/dS or Kr/Kc might reveal interesting macroevolutionary patterns in the variation in effective population size among lineages. In this work, we further develop an integrative probabilistic framework for phylogenetic covariance analysis introduced previously, so as to estimate the correlation patterns between dN/dS, Kr/Kc, and three LHT, in mitochondrial genomes of birds and mammals. Kr/Kc displays stronger and more stable correlations with LHT than does dN/dS, which we interpret as a greater robustness of Kr/Kc, compared with dN/dS, the latter being confounded by the high saturation of the synonymous substitution rate in mitochondrial genomes. The correlation of Kr/Kc with LHT was robust when controlling for the potentially confounding effects of nucleotide compositional variation between taxa. The positive correlation of the mitochondrial Kr/Kc with LHT is compatible with previous reports, and with a nearly neutral interpretation, although alternative explanations are also possible. The Kr/Kc model was finally used for reconstructing life-history evolution in birds and mammals. This analysis suggests a fairly large-bodied ancestor in both groups. In birds, life-history evolution seems to have occurred mainly through size reduction in Neoavian birds, whereas in placental mammals, body mass evolution shows disparate trends across subclades. Altogether, our work represents a further step toward a more comprehensive phylogenetic reconstruction of the evolution of life-history and of the population-genetics environment.