Phylogenetic relationships in the Niviventer-Chiromyscus complex (Rodentia, Muridae) inferred from molecular data, with description of a new species

Explorational analysis of the abundance and prevalence of chigger and gamasid mites parasitic on small mammals in Vietnam

We studied chigger and gamasid mite loads on small mammals during the dry season in Vietnam and used both our field data and museum collections to estimate the influence of environmental factors on mite abundance and prevalence. Generalized linear (mixed effect) models were used to analyze the data. We examined 1,239 small mammal individuals, which were obtained from field expeditions and museum collections belonging to 59 species. In different localities, Rattus Fischer (Rodentia: Muridae), Niviventer Marshall (Rodentia: Muridae), and Maxomys Sody (Rodentia: Muridae) were the most common animals captured. The prevalence of chigger and gamasid mites in our expedition data was high: 72% and 62%, respectively. We found differences in the abundance of chigger mites between different populations of the same species of small mammals. Season and locality were the main factors that influenced chigger mite abundance and prevalence. The best model that predicted the abundance and prevalence of chigger mites included geography (province) as a predictor and host species and season as random effects. For the first time, we analyzed factors connected with climate and weather affecting chigger mites of small mammals in Vietnam.

New occurrence records on the rodent species inhabiting Vietnam, based on Joint Russian-Vietnamese Tropical Research and Test Center genetic samples collection

Background

Open access to occurrence records in a standardised format has strong potential applications for many kinds of ecological research and bioresources management, including the assessment of invasion risks, formulation of nature protection, biomedical and management plans in the context of global climate and land-use changes both in the short and long perspective. The accumulation and aggregation of data on the occurrence records of small mammals are relevant for the study of biogeography and for ecological surveys including construction of the spatial distribution and ecological niche modelling of species ' distributions in the context of global climate change. The author has created a dataset of 2408 rodents and tree shrews occurrence records from Vietnam, collected from November 2007 to May 2022. A number of zoologist colleagues also provided genetic samples. A considerable part of these data has been published previously in a number of papers; however, most of these data have yet to be presented. These records cover a significant part of the range of many rodent species in Southeast Asia and provide new data on their distribution. The data were obtained during a number of different field expeditions, where some animals were caught by the author and some were provided by other researchers, resulting in different accuracy levels of geographic coordinates and altitude estimates may range from 10 to 1000 metres in area and from 1 to 100 metres for elevation. A number of samples were genetically examined to avoid inconsistencies with the taxonomic identification. With the help of colleagues, the author created a set of georeferenced occurrence records, adapted to the controlled vocabulary of Darwin Core format datasets, removed duplicates and standardised the format of records using commonly-used unified data structure. This paper presents the resulting dataset of rodents (mostly of Muridae and Sciuridae) along with other small terrestrial species (Scandentia Tupaidae) occurrence records in the territory of Vietnam and Laos.

New information

Much of the distribution data are currently available as open source GBIF databases and potentially may be combined into a united framework for better data resolution. The dataset presented here combines occurrence records of many species over a significant part of their recent natural range, in Vietnam and Laos. The author presents a validated and comprehensive dataset of rodents' occurrence records, based on genetic samples collection compiled during 15 years working in Vietnam (from 2007 to date). Prior to this project, a considerable part of the information about Vietnamese rodents was not available to a wide range of researchers to use these spatial data for analyses by modern methods, for example, for analysis based on geographic information systems (GIS technologies). This dataset now is available for any researchers who use the data format prepared in accordance with Darwin Core standards.For different countries of Southeast Asia and beyond, there are a lot of additional occurrence records for a number of species listed here which may be combined, but a considerable part of them is still scattered over a number of separate literary sources, while another is still presented as maps, field notes and huge amount of museum zoological collections records. The final set was created by a combination of species occurrence records and uniform data structure with verification of the samples' geographic coordinates. Most samples were genetically or/and morphologically verified for correct taxonomical identification, because the most part of the samples presented was carefully investigated by the author himself, both for morphology and genetic attribution. Therefore, the dataset expands the available information on the spatial and temporal distribution of a number of small mammals' species in Southeast Asia. All original notes and geographical localities were carefully checked and any duplicate and erroneous records have been removed from the final dataset.To the date of publication of these data, the GBIF database https://www.gbif.org contained 1408 rodent occurrence records from Vietnam (Fig. 1) along with 240 Scandentia records (Fig. 2), primarily the data on museum materials, including four large collections, such as the Field Museum of Natural History (Zoology) Mammal Collection (646 samples), Australian National Wildlife Collection provider for OZCAM (537), MVZ Mammal Collection Arctos (109), Museum of Comparative Zoology, Harvard University (69) and six other minor collections comprising single specimens.Actually, as for the small terrestrial mammals, Vietnam remains one of the least representative regions in Southeast Asia. Here, we present new data containing 2408 occurrence records, including 2237 rodent records, along with 171 Scandentia ones (Fig. 3). Thus, the data significantly expand our knowledge about actual ranges of a number of species, including rare and endangered ones.

Rodent-Borne Orthohantaviruses in Vietnam, Madagascar and Japan

Hantaviruses are harbored by multiple small mammal species in Asia, Europe, Africa, and the Americas. To ascertain the geographic distribution and virus-host relationships of rodent-borne hantaviruses in Japan, Vietnam, Myanmar, and Madagascar, RNAlater™-preserved lung tissues of 981 rodents representing 40 species, collected in 2011-2017, were analyzed for hantavirus RNA by RT-PCR. Our data showed Hantaan orthohantavirus Da Bie Shan strain in the Chinese white-bellied rat (Niviventer confucianus) in Vietnam, Thailand; orthohantavirus Anjo strain in the black rat (Rattus rattus) in Madagascar; and Puumala orthohantavirus Hokkaido strain in the grey-sided vole (Myodes rufocanus) in Japan. The Hokkaido strain of Puumala virus was also detected in the large Japanese field mouse (Apodemus speciosus) and small Japanese field mouse (Apodemus argenteus), with evidence of host-switching as determined by co-phylogeny mapping.

Distribution pattern and phylogeography of tree rats Chiromyscus (Rodentia, Muridae) in eastern Indochina

The study combines available data on species distribution in eastern Indochina to investigate the phylogeographical genetic and morphological diversity of tree rats (Chiromyscus, Rodentia, Muridae) and to specify their natural ranges. We examined the diversity and distribution of tree rats over its range, based on recent molecular data for mitochondrial (Cyt b, COI) and nuclear (IRBP, RAG1 and GHR) genes. The study presents the most complete and up-to-date data on the distribution and phylogeography of the genus in eastern Indochina. As revealed by mitochondrial genes, C. langbianis splits into at least four coherent geographically-distributed clades, whereas C. thomasi and C. chiropus form two distinctive mitochondrial clades each. Chiromyscus langbianis and C. chiropus show significant inconsistency in nuclear genes, whereas C. thomasi shows the same segregation pattern as can be traced by mitochondrial markers. The Northern and Southern phylogroups of C. thomasi appear to be distributed sympatrically with northern phylogroups of C. langbianis in most parts of eastern Indochina. The mitochondrial clades discovered are geographically subdivided and divergent enough to suspect independent subspecies within C. langbianis and C. thomasi. However, due to the insufficiency of obvious morphological traits, a formal description is not carried out here. The processes of recent fauna formation, species distribution patterns, dispersion routes and possible natural history in Indochina are discussed.

Molecular phylogeny and morphological diversity of the Niviventer fulvescens species complex with emphasis on species from China

The Niviventer fulvescens species complex (NFSC), a group of abundant and taxonomically ambiguous rodent taxa, is distributed from Southeast Asia to south-eastern China. We combined molecular and morphological datasets to clarify the species composition and variation of the NFSC. Our phylogenetic analyses, using molecular data, recovered eight genetic lineages in the NFSC, including a novel, distinct lineage from Jilong, Tibet, China, which is described as a new species, N. fengi sp. nov. The species status of N. fengi is supported by a species delimitation analysis, and it is morphologically distinguished from other members of the NFSC by its greyish dorsal fur, soft hairs covering the whole body and a hairy tail. NFSC species bearing well-developed spines are found at lower elevations. A comprehensive taxonomic revision of the NFSC within China is provided, represented by five species: N. cremoriventer, N. fulvescens, N. huang, N. mekongis comb. nov. and N. fengi. A further study of this species complex, including samples from Southeast Asia, is needed.

Multi-locus phylogeny using topotype specimens sheds light on the systematics of Niviventer (Rodentia, Muridae) in China

Background

Niviventer is a genus of white-bellied rats that are among the most common rodents in the Indo-Sundaic region. The taxonomy of the genus has undergone extensive revisions and remains controversial. The current phylogeny is unresolved and was developed primarily on the basis of mitochondrial genes. Identification is extremely difficult, and a large number of GenBank sequences seem to be problematic. We extensively sampled specimens of Niviventer in China and neighboring northern Vietnam, including topotypes of the most reported species (n = 6), subspecies (n = 8), and synonyms (n = 4). We estimated phylogenetic relationships on the basis of one mitochondrial and three nuclear genes, using concatenation and coalescent-based approaches. We also employed molecular species delimitation approaches to test the existence of cryptic and putative new species.

Results

Our phylogeny was finely resolved, especially for the N. confucianus-like species. Our data provided the first support for N. brahma and N. eha as sister species, an assignment that is congruent with their morphological similarities. Species delimitation analyses provided new insight into species diversity and systematics. Three geographic populations of N. confucianus and one of N. fulvescens were supported as genetically distinct in our species delimitation analyses, while three recognized species (N. coninga, N. huang, and N. lotipes) were not strongly supported as distinct.

Conclusions

Our results suggested that several genetically distinct species may be contained within the species currently known as N. confucianus and N. fulvescens. In addition, the results of Bayesian Phylogenetics and Phylogeography (BPP) for N. coninga, N. huang, and N. lotipes indicated that either inter-specific gene flow had occurred or imperfect taxonomy was present. Morphological examinations and morphometric analyses are warranted to examine the molecular results.

Electronic supplementary material

The online version of this article (doi:10.1186/s12862-016-0832-8) contains supplementary material, which is available to authorized users.