Disjunct distribution and distinct intraspecific diversification of Eothenomys melanogaster in South China

Abstract

BackgroundSouth China encompasses complex and diverse landforms, giving rise to high biological diversity and endemism from the Hengduan Mountains to Taiwan Island. Many species are widely distributed across South China with similar disjunct distribution patterns. To explore the causes of these disjunct distribution patterns and their genetic consequences, we investigated the endemic species Père David’s Chinese Vole (Eothenomys melanogaster) by integrating geological and ecological factors. We analysed the genetic structure and divergence time of E. melanogaster based on fast-evolving mitochondrial and nuclear markers using Bayesian trees and coalescent species tree approaches. Historical scenarios of distribution range and demography were reconstructed based on spatial interpolations of genetic diversity and distance, extended Bayesian skyline plots, phylogeographic diffusion analysis, and ecological niche modelling (ENM) during different periods. We also assessed the relationships between geographical distance/ecological vicariance and genetic distance (isolation by distance, IBD; isolation by environment, IBE).ResultsThe genetic analysis revealed three deeply divergent clades—Southeast, Southwest and Central clades, centred on the Wuyi Mountains, the Yunnan-Guizhou Plateau (YGP) and the mountains around the Sichuan Basin, respectively—that have mostly developed since the Pleistocene. IBD played an important role in early divergence, and geological events (sedimentation of plains and linking of palaeo-rivers) and IBE further reinforced genetic differentiation. ENM shows the importance of suitable habitats and elevations.ConclusionsOur results suggest that the primary cause of the disjunct distribution in E. melanogaster is the high dependence on middle-high-altitude habitat in the current period. Mountains in the occurence range have served as “sky islands” for E. melanogaster and hindered gene flow. Pleistocene climatic cycles facilitated genetic admixture in cold periods and genetic diversification in warm periods for inland clades. During cold periods, these cycles led to multiple colonization events between the mainland and Taiwan and erased genetic differentiation.Electronic supplementary materialThe online version of this article (10.1186/s12862-018-1168-3) contains supplementary material, which is available to authorized users.

Phylogeography and niche modelling: reciprocal enlightenment

“…Phylogeographical studies often find a rough correlation with, or between, the geographical borders of genetic clades and potential barriers or bioclimatic transitions (see e.g. Smit et al 2007, Edwards et al 2011, Willows-Munro and Matthee 2011, Bittencourt-Silva et al 2017, Lavin et al 2018, Lv et al 2018, but proving causation is difficult. Phylogeographers must therefore often either stop at describing existing phylogeographical patterns or speculate as to their creation based on very little information (Peterson 2009).…”

Dynamics behind disjunct distribution, hotspot-edge refugia, and discordant RADseq/mtDNA variability: insights from the Emei mustache toad

“…The molecular results suggest a Late Pliocene to early Pleistocene origin for the West clade endemic to the hotspot edge, in which the area around sites 21–24 and 26 has consistently been modeled to be suitable for L. boringii in the LIG, LGM, MH, and current periods. Western marginal refugia and areas of long-term persistence within or overlapping with this hotspot edge have been proposed for some mountain amphibian [ 37 , 79 ], mammal [ 47 ], insect [ 50 ], and flowering plant species [ 38 , 39 , 52 , 53 , 80 – 82 ]. Additionally, gene flows from the east via mountains along the edges of the Sichuan Basin have recently been reported for different species [ 37 , 48 , 83 ].…”

“…Many others have disjunct distributions ranging from much of the surrounding mountains to one area in the mountains, with most species distributions somewhere between these two extremes [38][39][40], which can potentially be explained by a dynamic history involving recurrent range fragmentation and contractions. In the western part of the region, the disjunct distribution of a variety of plant and animal species overlaps with the eastern edge of the Mountains of Southwest China hotspot [41][42][43][44][45][46][47][48], contributing to the biodiversity of the global hotspot and implying a shared long-term refugium [38,39,[49][50][51][52][53]. Relevant studies that provided both species history inferences and multilocus estimates of genetic diversity distributions for such taxa are rare.…”

Ring distribution patterns—diversification or speciation? Comparative phylogeography of two small mammals in the mountains surrounding the Sichuan Basin

“…The mountains of Southwest China represent a global biodiversity hotspot with typical mountainous landscape features (high mountains which are cut by deep valleys and tumbling rivers), and these features have played an important role in the diversification process of organisms in this region (Chen et al, 2017; Lv et al, 2018; Myers et al, 2000; Wan et al, 2018). These mountains (except for the Eastern Himalaya Mountains and the southern part of the Hengduan Mountains) form an approximate ring surrounding the Sichuan Basin, which is mainly a lowland plain with an elevational range of 250–750 m (Liu et al, 2012).…”