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Evidence of complex phylogeographic structure for the threatened rodent Leopoldamys neilli, in Southeast Asia

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Abstract

Leopoldamys neilli is a threatened murine rodent species endemic to limestone karsts of Thailand. We have studied the phylogeography of L. neilli using two mitochondrial markers (cytb, COI) and one nuclear fragment (bfibr), in order to assess the influence of its endemicity to karst habitat. One hundred fifteen individuals of L. neilli were collected in 20 localities throughout the geographic range of this species in Thailand. Our study revealed strong geographic structure of the mtDNA genetic diversity: six highly differentiated, allopatric genetic lineages were observed in our dataset. They exhibit a very high degree of genetic divergence, low gene flow among lineages and low levels of haplotype and nucleotide diversities within lineages. Our results suggest that L. neilli’s populations are highly fragmented due to the scattered distribution of its karst habitat. The most divergent lineage includes the populations from western Thailand, which have been separated from the other genetic lineages since at least the Early Pleistocene. The other lineages are more closely related and have diverged since the Middle Pleistocene. This study revealed an unexpected high level of genetic differentiation within L. neilli and highlighted the high endemicity of this species to limestone karsts. Our results enhance the importance of protecting limestone habitats to preserve not only the species but also intraspecific diversity.

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Acknowledgments

We thank Boonchai Tontan who worked hard in the field and help us to collect the samples used in this study. We are grateful to G. Vanhamel for his help in the lab. We express gratitude to S. Jittapalapong for his administrative help. We thank Drs D. Aigoin, C. Berthouly, C. Ek, S. Morand, M. Pagès for their great help and/or comments on the manuscript. We thank E. Latinne for her help in the drafting of the figures. We wish to acknowledge Dr Andy Jennings for English corrections and scientific comments. This work was supported by a Belgian FRS-FNRS (Fonds de la Recherche Scientifique) fellowship to A. Latinne (mandate “aspirant”) and to J.R. Michaux (mandate “chercheur qualifié”), and a financial grant from the Belgian FNRS (crédits pour brefs séjours à l’étranger to A. Latinne), from the University of Liège (Patrimoine) and from the Communauté française de Belgique. This study is part of the “CERoPath project” (Community Ecology of Rodents and their Pathogens in South-East Asia: effects of biodiversity changes and implications in health ecology), ANR Biodiversity ANR 07 BDIV 012, funded by the French National Agency for Research.

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Authors and Affiliations

  1. Institut de Botanique, B 22, Université de Liège, 4000, Liège (Sart Tilman), Belgium

    Alice Latinne & Johan R. Michaux

  2. Environment and Resources Technology Department, Thailand Institute of Scientific and Technological Research, 35 Mu 3 Tambon Khlong Ha, Amphoe Khlong Luang, Changwat Pathum Thani, 12120, Thailand

    Surachit Waengsothorn

  3. CIRAD, UR AGIRs (Animal et Gestion Intégrée des Risques), Campus International de Baillarguet, CS 30016, 34988, Montferrier-sur-Lez Cedex, France

    Vincent Herbreteau

  4. CBGP (Centre de Biologie et de Gestion des Populations), UMR INRA/IRD/Cirad/Montpellier SupAgro, Campus International de Baillarguet, CS 30016, 34988, Montferrier-sur-Lez Cedex, France

    Johan R. Michaux

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  1. Alice Latinne
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Correspondence to Alice Latinne.

Appendices

Appendix 1

See Table 5.

Table 5 Sampling locality, samples used for sequencing (N) for each dataset and haplotype/allele distribution
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Appendix 2

See Tables 6 and 7.

Table 6 Genbank accession numbers for cytb and COI haplotypes and for bfibr alleles of L. neilli
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Table 7 Vouchers specimens from the CERoPath tissue collection (Pagès et al. 2010) used in this study and their Genbank accession numbers
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Appendix 3

See Tables 8 and 9.

Table 8 Mitochondrial haplotype definitions
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Table 9 Three combined genes haplotypes definitions
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Latinne, A., Waengsothorn, S., Herbreteau, V. et al. Evidence of complex phylogeographic structure for the threatened rodent Leopoldamys neilli, in Southeast Asia. Conserv Genet 12, 1495–1511 (2011). https://doi.org/10.1007/s10592-011-0248-3

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