title: Multi-locus phylogeny using topotype specimens sheds light on the systematics of Niviventer (Rodentia, Muridae) in China.
abstract: 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.
  
  
  
  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.
  
  
  
  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.
authors.affiliation: State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China.|Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan, China.
authors.forename: Bin
authors.initials: B
authors.lastname: Zhang
authors.affiliation: State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China. hekai@mail.kiz.ac.cn.|National Museum of Natural History, Smithsonian Institution, Washington D.C., USA. hekai@mail.kiz.ac.cn.|The Kyoto University Museum, Kyoto University, Kyoto, 606-8501, Japan. hekai@mail.kiz.ac.cn.
authors.forename: Kai
authors.initials: K
authors.lastname: He
authors.affiliation: State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China.
authors.forename: Tao
authors.initials: T
authors.lastname: Wan
authors.affiliation: Chengdu Research Base of Giant Panda Breeding, Sichuan Key Laboratory of Conservation Biology for Endangered Wildlife, Chengdu, Sichuan, China.
authors.forename: Peng
authors.initials: P
authors.lastname: Chen
authors.affiliation: China Forest Exploration and Design Institute on Kunming, Kunming, Yunnan, China.
authors.forename: Guozheng
authors.initials: G
authors.lastname: Sun
authors.affiliation: Sichuan Academy of Forestry, Chengdu, Sichuan, China.
authors.forename: Shaoying
authors.initials: S
authors.lastname: Liu
authors.affiliation: Department of Vertebrate Zoology Institute of Ecology and Biological Resources, Vietnam Academy of Sciences and Technology, Hanoi, Vietnam.
authors.forename: Truong Son
authors.initials: TS
authors.lastname: Nguyen
authors.affiliation: Department of Life Sciences, Laboratory of Wildlife Ecology, Tunghai University, Taichung, Taiwan.
authors.forename: Liangkong
authors.initials: L
authors.lastname: Lin
authors.affiliation: State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China. jiangxl@mail.kiz.ac.cn.
authors.forename: Xuelong
authors.initials: X
authors.lastname: Jiang
mesh_terms: D000818:Animals; D001499:Bayes Theorem; D002681:China; D004272:DNA, Mitochondrial / Q000235:genetics; D050259:Genes, Mitochondrial; D008928:Mitochondria / Q000235:genetics; D051189:Murinae / Q000145:classification / Q000235:genetics*; D010802:Phylogeny; D058974:Phylogeography
chemical_list: D004272:DNA, Mitochondrial
keywords: Cryptic species; Niviventer; Phylogenetics; Species delimitation; Taxonomy; Topotype