Abstract
BackgroundHistorical biogeography and evolutionary processes of cave taxa have been widely studied in temperate regions. However, Southeast Asian cave ecosystems remain largely unexplored despite their high scientific interest. Here we studied the phylogeography of Leopoldamys neilli, a cave-dwelling murine rodent living in limestone karsts of Thailand, and compared the molecular signature of mitochondrial and nuclear markers.Methodology/Principal FindingsWe used a large sampling (n = 225) from 28 localities in Thailand and a combination of mitochondrial and nuclear markers with various evolutionary rates (two intronic regions and 12 microsatellites). The evolutionary history of L. neilli and the relative role of vicariance and dispersal were investigated using ancestral range reconstruction analysis and Approximate Bayesian computation (ABC).Both mitochondrial and nuclear markers support a large-scale population structure of four main groups (west, centre, north and northeast) and a strong finer structure within each of these groups. A deep genealogical divergence among geographically close lineages is observed and denotes a high population fragmentation. Our findings suggest that the current phylogeographic pattern of this species results from the fragmentation of a widespread ancestral population and that vicariance has played a significant role in the evolutionary history of L. neilli. These deep vicariant events that occurred during Plio-Pleistocene are related to the formation of the Central Plain of Thailand. Consequently, the western, central, northern and northeastern groups of populations were historically isolated and should be considered as four distinct Evolutionarily Significant Units (ESUs).Conclusions/SignificanceOur study confirms the benefit of using several independent genetic markers to obtain a comprehensive and reliable picture of L. neilli evolutionary history at different levels of resolution. The complex genetic structure of Leopoldamys neilli is supported by congruent mitochondrial and nuclear markers and has been influenced by the geological history of Thailand during Plio-Pleistocene.
Highlights
Subterranean habitats and their singular fauna have fascinated biologists and biogeographers for centuries
In order to improve our knowledge of karst biodiversity in southeast asian limestone karsts and to better understand the biogeographic processes operating in these habitats, we studied the phylogeography and evolutionary history of Neill’s rat Leopoldamys neilli (Marshall, 1976), a murine rodent species endemic to limestone karsts of Thailand, within the Indo-Burmese biodiversity hotspot
Due to the considerable lack of ecological data on L. neilli, we can only propose some hypotheses on this point but we suggest that this ecological shift could affect the reproductive behaviour of these rodents and we suspect L. neilli to use caves for breeding and nursing as young individuals and babies have been observed within caves during our survey
Summary
Subterranean habitats and their singular fauna have fascinated biologists and biogeographers for centuries. To explain the evolution of subterranean fauna in the tropics, an alternative model, the ASH, was proposed This model assumes an active colonization of subsurface habitats to exploit new resources coupled with an adaptive differentiation of surface and subterranean populations and possible gene flow between them for some time before genetic isolation and parapatric speciation occurred. Support for both models has been obtained for diverse species in different regions of the world using phylogenetic analysis, molecular dating and analysis of the current geographical distributions of taxa [10,11,12]. We studied the phylogeography of Leopoldamys neilli, a cave-dwelling murine rodent living in limestone karsts of Thailand, and compared the molecular signature of mitochondrial and nuclear markers
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