Sunday, December 23, 2012

[Mammalogy • 2012] A Remarkable Case of Micro-Endemism in Laonastes aenigmamus (Diatomyidae, Rodentia) Revealed by Nuclear and Mitochondrial DNA Sequence Data


Laonastes aenigmamus is endemic to the limestone formations of the Khammuan Province (Lao PDR), and is strongly specialized ecologically. From the survey of 137 individuals collected from 38 localities, we studied the phylogeography of this species using one mitochondrial (Cyt b) and two nuclear genes (BFIBR and GHR). Cyt b analyses reveal a strong mtDNA phylogeographical structure: 8 major geographical clades differing by 5–14% sequence divergence were identified, most of them corresponding to distinct karst areas. Nuclear markers display congruent results but with a less genetic structuring. Together, the data strongly suggest an inland insular model for Laonastes population structure. With 8 to 16 evolutionary significant units in a small area (about 200×50 km) this represents an exceptional example of micro-endemism. Our results suggest that L. aenigmamus may represent a complex of species and/or sub-species. The common ancestor of all Laonastes may have been widely distributed within the limestone formations of the Khammuan Province at the end of Miocene/beginning of the Pliocene. Parallel events of karst fragmentation and population isolation would have occurred during the Pleistocene or/and the end of the Pliocene. The limited gene flow detected between populations from different karst blocks restrains the likelihood of survival of Laonastes. This work increases the necessity for a strict protection of this rare animal and its habitat and provides exclusive information, essential to the organization of its protection.


Eroded limestone outcrops form a prominent part of the landscape in Southeast Asia. Because of high limestone weathering erosion in these areas resulted in scattered, isolated limestone hills with steep flanks called karsts towers. Despite a high diversity of habitat specialists and endemic taxa, these limestone karsts remain among the least studied ecosystems in Southeast Asia. Between 1985 and 2004 they contributed only to 1% of the global and regional biodiversity research output from terrestrial and freshwater ecosystems, while they cover around 10% of the land area in Southeast Asia. However, in the Khammuan Province of Lao PDR, several new endemic vertebrate species were recently described: a bird, Pycnonotus hualon, a bat, Hipposideros scutinares, a gymnure, Hylomys megalotis, and a murid rodent, Saxatilomys paulinae.

Laonastes aenigmamus, recently described from this region by Jenkins et al., is of special interest. Using comparative morphological and molecular data, this new species was initially described as a member of a new genus and ranked within the Hystricognathi rodents in a new family: the Laonastidae. But, further studies demonstrated: first, that L. aenigmamus is a member of the Diatomyidae, a fossil family known from early Oligocene to late Miocene in Pakistan, India, Thailand, China, and Japan; second, that the Diatomyidae are the sister group of the Ctenodactylidae, a family of small rodents found in rocky deserts across the northern parts of Africa; third, that together with the Hystricognathi, the Diatomyidae and the Ctenodactylidae form the suborder Ctenohystrica.

In a previous study we presented a preliminary analysis of the genetic diversity of L. aenigmamus: 52 specimens were sampled and the population structure was surveyed by sequencing 887 base pairs of the Cytochrome b (Cyt b) gene. Phylogenetic and haplotypic network reconstructions revealed three well-supported and rather divergent lineages, suggesting that L. aenigmamus populations are geographically structured. However, altogether these samples represented a limited part of the estimated range of the species; most of them were sampled in local markets and their exact geographic origin was impossible to determine; this study was based on a fragment of a single mitochondrial gene.

Before its scientific discovery, the kanyou was considered as a kind of game, trapped and eaten by the villagers. Since 2008, the conservation of L. aegnimamus is regulated in Lao PDR and since 2009 this species is listed as «Endangered» on the IUCN Red List. During the last four years we add the unique opportunity to accompany local officers in the field when they explained this change to local populations, and to sample for molecular analyses the last specimens that were captured by traditional hunters. We were able to sample 137 individuals for which the exact locality of collect was known. It represents 38 localities probably spanning the whole geographical range of the species. Thus, the sampling obtained for this study is exceptional both in terms of number of individuals and number of localities sampled and will not be able to be carried out again. In the present study we: (1) improve evaluation of the genetic diversity and delineation of the phylogeographical structure of L. aenigmamus, by sequencing both nuclear and mitochondrial markers of a larger number of geographically referenced individuals; (2) obtain a better definition of the geographical distribution of the species; (3) highlight the spatial and temporal history of the limestone formation of the Khammuan Province, using the evolutionary history of this species as a guide. Our analysis strongly underlines the necessity for a strict protection of this rare animal and its habitat and provides exclusive information, essential to the organization of its protection.

 Nicolas V, Herbreteau V, Couloux A, Keovichit K, Douangboupha B, et al. 2012. A Remarkable Case of Micro-Endemism in Laonastes aenigmamus (Diatomyidae, Rodentia) Revealed by Nuclear and Mitochondrial DNA Sequence Data. PLoS ONE 7(11): . doi:10.1371/journal.pone.0048145