Contribution to the species composition and taxonomic status of some Rattus inhabiting Southern Vietnam and Sundaland

Region-Specific Genetic Diversity of Black Rats (Rattus rattus Complex) in Southeast and East Asia Shaped by Rapid Population Expansion Events

Among the six mitochondrial DNA lineages of the black rat (Rattus rattus Complex; RrC), lineages II and IV are widespread in Southeast and East Asia. This study explored their demographic history using 17 new sequences from the Miyako Islands in the Ryukyu archipelago, together with 178 publicly available cytochrome b sequences. We defined six and two haplotype groups showing rapid population expansion signals in Lineages II and IV, respectively. The six haplotype groups of Lineage II were represented by haplotypes from 1) Myanmar/Bangladesh/Northeast India, 2) Laos, 3) Thailand, 4) Indonesia/Philippines, 5) Vietnam/southern China, and 6) the Ryukyu archipelago. These expansion times were estimated using time-dependent evolutionary rates to be 115,300 years ago (ya), 128,500 ya, 9600 ya, 10,600 ya, 7200 ya, and 1400 ya, respectively, although all had large confidence intervals. The two groups of Lineage IV were recovered from the mainland and islands of Southeast Asia with predicted expansion times of 197,000 ya and 5800 ya, respectively. These results suggest that climatic fluctuations during the last 200,000 years of the Quaternary, affected the population dynamics in subtropical areas at different times. Furthermore, the results of the younger rapid expansion events of RrC suggest the possibility of agricultural advancement and dispersal of Neolithic farmers to different areas within the mainland and islands of Southeast Asia during the Holocene. A subset of rats from the Miyako Islands were found to have the same lineage IV haplotypes as those in Southeast Asia, suggesting a recent introduction of these new lineages.

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.

Predicting the potential distribution of a previously undetected cryptic invasive synanthropic Asian house rat (Rattus tanezumi) in South Africa

Three species of Rattus, Norway rat (R. norvergicus), black rat (R. rattus) and Asian house rat (R. tanezumi) are currently known to occur in South Africa. The latter two species are cryptic and form part of the Rattus rattus species complex. Historically, R. norvegicus has been reported to occur along the coast and in urban centres, R. rattus is widespread in most urban areas, except in the drier areas, while R. tanezumi was only recorded to occur in the country (and Africa) ca. 15 years ago, and its distribution remains unknown. The aim of this study was to predict the potential distribution of R. tanezumi in South Africa and assess how it overlaps with that of R. norvegicus and R. rattus using species distribution modelling. Rattus tanezumi was predicted to mainly occur in most inland urban areas and along the coast. The distribution of R. rattus was as expected, in contrast, the predicted range of R. norvegicus was not restricted to the coast but also included inland urban areas. All three species showed broad potential distributional ranges that overlapped extensively indicating that their establishment and spread may be influenced by similar factors such as proximity to urban areas and a wet and moderate climate. These results allow insights into assessing their risk of establishment and for formulating appropriate intervention strategies for their management and control.

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

BACKGROUND

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

RESULTS

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

CONCLUSIONS

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

Genomic analyses identify multiple Asian origins and deeply diverged mitochondrial clades in inbred brown rats (Rattus norvegicus)

Over 500 strains of inbred brown rats (Rattus norvegicus) have been developed for use as a biomedical model organism. Most of these inbred lines were derived from the colony established at the Wistar Institute in 1906 or its descendants following worldwide distribution to research and breeding centers. The geographic source of the animals that founded the Wistar colony has been lost to history; thus, we compared 25 inbred rat strains to 326 wild rats from a global diversity dataset at 32 k SNPs, and 47 mitochondrial genomes to identify the source populations. We analyzed nuclear genomic data using principal component analyses and co-ancestry heat maps, and mitogenomes using phylogenetic trees and networks. In the nuclear genome, inbred rats clustered together indicating a single geographic origin for the strains studied and showed admixed ancestral variation with wild rats in eastern Asia and western North America. The Sprague Dawley derived, Wistar derived, and Brown Norway strains each had mitogenomes from different clades which diverged between 13 and 139 kya. Thus, we posit that rats originally collected for captive breeding had high mitochondrial diversity that became fixed through genetic drift and/or artificial selection. Our results show that these important medical models share common genomic ancestry from a few source populations, and opportunities exist to create new strains with diverse genomic backgrounds to provide novel insight into the genomic basis of disease phenotypes.

Molecular phylogenetic characterization of common murine rodents from Manipur, Northeast India

The Indian subcontinent and Southeast Asia are hotspots of murine biodiversity, but no species from the Arakan Mountain system that demarcates the border between the two areas has been subjected to molecular phylogenetic analyses. We examined the mitochondrial cytochrome b gene sequences in six murine species (the Rattus rattus species complex, R. norvegicus, R. nitidus, Berylmys manipulus, Niviventer sp. and Mus musculus) from Manipur, which is located at the western foot of the mountain range. The sequences of B. manipulus and Niviventer sp. examined here were distinct from available congeneric sequences in the databases, with sequence divergences of 10-15%. Substantial degrees of intrapopulation divergence were detected in R. nitidus and the R. rattus species complex from Manipur, implying ancient habitation of the species in this region, while the recent introduction by modern and prehistoric human activities was suggested for R. norvegicus and M. musculus, respectively. In the nuclear gene Mc1r, also analyzed here, the R. rattus species complex from Manipur was shown to possess allelic sequences related to those from the Indian subcontinent in addition to those from East Asia. These results not only fill gaps in the phylogenetic knowledge of each taxon examined but also provide valuable insight to better understand the biogeographic importance of the Arakan Mountain system in generating the species and genetic diversity of murine rodents.

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

Based on molecular data for mitochondrial (Cyt b, COI) and nuclear (IRBP, GHR) genes, and morphological examinations of museum specimens, we examined diversity, species boundaries, and relationships within and between the murine genera Chiromyscus and Niviventer. Phylogenetic patterns recovered demonstrate that Niviventer sensu lato is not monophyletic but instead includes Chiromyscuschiropus, the only previously recognized species of Chiropus. To maintain the genera Niviventer and Chiropus as monophyletic lineages, the scope and definition of the genus Chiromyscus is revised to include at least three distinct species: Chiromyscuschiropus (the type species of Chiromyscus), Chiromyscuslangbianis (previously regarded as a species of Niviventer), and a new species, described in this paper under the name Chiromyscusthomasi sp. n.

Phylogenetic species identification in Rattus highlights rapid radiation and morphological similarity of New Guinean species

The genus Rattus is highly speciose, the taxonomy is complex, and individuals are often difficult to identify to the species level. Previous studies have demonstrated the usefulness of phylogenetic approaches to identification in Rattus but some species, especially among the endemics of the New Guinean region, showed poor resolution. Possible reasons for this are simple misidentification, incomplete gene lineage sorting, hybridization, and phylogenetically distinct lineages that are unrecognised taxonomically. To assess these explanations we analysed 217 samples, representing nominally 25 Rattus species, collected in New Guinea, Asia, Australia and the Pacific. To reduce misidentification problems we sequenced museum specimens from earlier morphological studies and recently collected tissues from samples with associated voucher specimens. We also reassessed vouchers from previously sequenced specimens. We inferred combined and separate phylogenies from two mitochondrial DNA regions comprising 550 base pair D-loop sequences and both long (655 base pair) and short (150 base pair) cytochrome oxidase I sequences. Our phylogenetic species identification for 17 species was consistent with morphological designations and current taxonomy thus reinforcing the usefulness of this approach. We reduced misidentifications and consequently the number of polyphyletic species in our phylogenies but the New Guinean Rattus clades still exhibited considerable complexity. Only three of our eight New Guinean species were monophyletic. We found good evidence for either incomplete mitochondrial lineage sorting or hybridization between species within two pairs, R. leucopus/R. cf. verecundus and R. steini/R. praetor. Additionally, our results showed that R. praetor, R. niobe and R. verecundus each likely encompass more than one species. Our study clearly points to the need for a revised taxonomy of the rats of New Guinea, based on broader sampling and informed by both morphology and phylogenetics. The remaining taxonomic complexity highlights the recent and rapid radiation of Rattus in the Australo-Papuan region.