Phylogeography of Nanorana parkeri (Anura: Ranidae) and multiple refugia on the Tibetan Plateau revealed by mitochondrial and nuclear DNA

Abstract

Quaternary climatic changes have been recognized to influence the distribution patterns and evolutionary histories of extant organisms, but their effects on alpine species are not well understood. To investigate the Pleistocene climatic oscillations on the genetic structure of amphibians, we sequenced one mitochondrial and three nuclear DNA fragments in Nanorana parkeri, a frog endemic to the Tibetan Plateau, across its distribution range in the southern plateau. Mitochondrial cytochrome b (Cytb) and three nuclear genes (c-Myc2, Rhod, and Tyr) revealed two distinct lineages (i.e. the lineages East and West), which were strongly geographically structured. The split of the two divergent lineages was dated back earlier than the Middle Pleistocene, probably being associated with climatic and ecological factors. Species distribution modeling, together with the phylogeographic structuring, supported the hypothesis of multiple refugia for N. parkeri on the Tibetan Plateau during the Pleistocene glaciations, and suggested the Yarlung Zangbo valley and the Kyichu catchment to be the potential refugia. Our findings indicate that Pleistocene climatic changes have had a great impact on the evolution and demographic history of N. parkeri. Our study has important implications for conservation of this and other frog species in the Tibetan Plateau.

Phylogeography of Schizopygopsis stoliczkai (Cyprinidae) in Northwest Tibetan Plateau area

“…Geological movement and climatic fluctuations play an essential role in the phylogeography pattern of many species endemic to the TP (Jin & Liu, 2010; Li et al., 2015, 2016; Liu et al., 2015; Zhang et al., 2013; Zhao et al., 2011). In our study, the estimation of the divergence time for S. stoliczkai (Figure 4) was broadly consistent with these studies.…”

“…Many species endemic to the TP area has multiple glacial refugia, such as Gymnocypris chilianensis (Zhao et al., 2011) and Nanorana parkeri (Liu et al., 2015). In the current study, we found the separation of clade N and S (4.27 Mya) was much earlier than the onset of the ice age (2.6 Mya) (Gribbin, 1983), which implicated that the clade N and S occupied different refugia during Quaternary glaciations.…”

“…The Quaternary geographic and climatic changes across the Tibetan Plateau (TP) area shift the habitats of the endemic species, shaping the current distribution of the endemic fauna and intraspecific phylogeographic patterns (Jin & Liu, 2010; Li et al., 2015; Liu et al., 2015; Zhao et al., 2011). Therefore, the investigation of the phylogeography of the species endemic to the TP helps to achieve the following goals: to clarify the genetic structure and historical demography of the local population and to identify the relative roles of contemporary verses historical processes that have facilitated to shape the modern distribution (Avise, 2000).…”

Phylogeography of the Tibetan hamster Cricetulus kamensis in response to uplift and environmental change in the Qinghai–Tibet Plateau

“…draco (Fan et al, 2012), and N. parkeri (Liu et al, 2015). draco (Fan et al, 2012), and N. parkeri (Liu et al, 2015).…”

“…Several recent studies have suggested that the uplifting of the QTP plays a major role in shaping plateau biodiversity due to strong ecological gradients in temperature, precipitation, and topography which contribute to the generation of a variety of terrestrial habitats Favre et al, 2015;Lei et al, 2014). A large number of studies demonstrated that the phylogeny, speciation, and demography of organisms are associated with the uplift of the QTP and simultaneous changes of climate, for example in frogs, lizards, birds, and mammals (James et al, 2003;Jin, Brown, & Liu, 2008;Liu et al, 2015;Tseng et al, 2014). With respect to mammals, Yu et al (1992) proposed that the diversification of pika correlates with the uplift of the QTP in China; furthermore, geographic isolation created numerous diversified microhabitats for pika survival.…”