Molecular phylogeny and the underestimated species diversity of the endemic white‐bellied rat (Rodentia: Muridae:Niviventer) in Southeast Asia and China

Abstract

Q. (2015). Molecular phylogeny and the underestimated species diversity of the endemic white-bellied rat (Rodentia: Muridae: Niviventer) in Southeast Asia and China. -Zoologica Scripta, 44, 475-494.The white-bellied rat, Niviventer, is a genus endemic to Southeast Asia and China. However, the interspecific phylogenetic relationships and species diversity of this genus remain poorly understood. In the present study, single and multi-locus analyses were performed. Phylogenetic reconstruction on Cytochrome b (512 individuals, including data from Genbank) revealed five major clades with approximately 35 operational taxonomic units (OTUs), a number twice the existing taxonomy. The first clade (N. langbianis species group) was the earliest diverged. The second clade (N. fulvescens species group) diverged in Southeast Asia, the south and lower altitude regions of the Hengduan Mountains, and Southeast China. The third clade (the N. eha species group) is endemic to high altitudes in Northwest Yunnan and the central region of Himalaya. The fourth clade (the N. andersoni species group), is mainly confined to alpine regions of the Hengduan Mountains. The fifth clade (N. confucianus species group) is mainly distributed in the north and higher altitude regions of eastern Himalaya, the Hengduan Mountains and Taiwan, with the complex also invading central and northern China. Results from the combined dataset of four genes (Cytochrome b, Cytochrome oxidase subunit I, the D-loop sequence of the mitochondrial genome and the first exon of the nuclear interphotoreceptor retinoid binding protein) for 82 representative individuals from China generally coincide with the result of the single gene, with 12 OTUs identified. These results provide a preliminary framework for the existing classification of this highly diversified genus. The divergence time of Niviventer based on the four gene topology was dated to the late Miocene~6.41 Ma. Significant differences were detected in the general body form changes among these units based on voucher specimens. Moreover, geometric morphometric analysis of the cranium shape of voucher specimens indicated significant differences among five major species groups. Shape divergence of the cranium among several OTUs within the N. confucinaus complex is also significant. Our results provide further evidence for rapid and highly underestimated diversification of Niviventer both in genetics and morphology.

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

“… a : The topotype of N. ling was sequenced in Lu et al (2015) [14] and was included in the present study. Sample locality is not shown in Fig.…”

“…Molecular phylogenetic studies further found that the widely distributed species were paraphyletic or even polyphyletic (e.g., N. andersoni, N. confucianus, N. excelsior, and N. fulvescens ) [13]. Despite the possibility of misidentification, the number of putative species always exceeded that of recognized species [13, 14], implying that species diversity was underestimated. Thus, it was reasonable to re-evaluate the large body of remaining subspecies/synonyms within this genus.…”

“…For example, geometric morphometric analyses in a previous study showed that two distinctive genetic lineages largely overlapped (i.e., N. confucianus and N. fulvescens ; Fig. 6 in Lu et al [14]). Examination of type specimens is always crucial for taxonomic revision and essential for re-evaluating the synonyms.…”

“…More than 540 Niviventer specimens have been sequenced, but most of the previous studies were conducted using only mitochondrial cytochrome b ( CYT B ) and cytochrome c oxidase ( COI ) genes [11, 13, 15, 16]. In another previous study using both mitochondrial ( CYT B, COI , and D-loop ) and nuclear ( IRBP ) loci, the gene trees were conflicting, suggesting that inclusion of multiple nuclear genes is warranted [14]. …”

“…Another 24 taxa are recognized as synonyms or subspecies of N. andersoni ( n  = 3), N. confucianus ( n  = 14), N. eha ( n  = 1), N. excelsior ( n  = 1), N. fulvescens ( n  = 1), and N. huang ( n  = 4). Moreover, according to Lu et al [14], undescribed species may exist in the mountains of southwestern China, an area characterized by extremely complex topography [17]. …”