Diet analysis of Leopoldamys neilli, a cave-dwelling rodent in Southeast Asia, using Next-Generation Sequencing from feces

peer reviewedLeopoldamys neilli is a Murinae rodent endemic to limestone karst of Thailand and the Lao PDR, but its ecology and the reasons of its endemism to karst are still totally unknown. The aim of this pilot study was to examine the plant composition of the diet of L. neilli at the level of order and family using DNA for molecular identification and to compare it with two other forest-dwelling Leopoldamys species, L. herberti and L. sabanus. A 202bp fragment of the rbcL gene was amplified and sequenced for twenty-three fecal samples of the three species using 454 pyrosequencing. We successfully identified a total of seventeen orders and twenty-one plant families, corresponding to thirty-three putative species, in the feces of these three Leopoldamys species. Solanaceae were the most common plants in the diet of L.neilli regardless of the region and sampling season, and they were also present in feces of both L. herberti and L. sabanus. The Araceae, Fabaceae, and Apocynaceae families were also identified in feces of L. neilli collected in various regions of Thailand and at different seasons. Plants of the Oleaceae family are consumed by both L. herberti and L. sabanus but were not found in the diet of L. neilli. Further improvements of the study, such as the use of additional genes, the creation of a reference collection, the microhistological examination of plant fragments to determine which parts of the plant are consumed, and the analysis of the animal diet of Leopoldamys are suggested to enhance the quality and accuracy of the results obtained

Median-joining networks based on mitochondrial (A) and nuclear (B) datasets.

<p>Circles represent haplotypes obtained in this study and the circle size is proportional to the number of individuals sharing a haplotype. Squares represent median vectors. Numbers on branches represent the number of mutational steps between haplotypes.</p

Maximum likelihood tree based on mitochondrial dataset (GTR+G).

<p>Bootstrap support (1000 replicates) and posterior probabilities of nodes are indicated above and below the branches, respectively. Node support values from within lineages were removed for clarity.</p

Dating of the most recent common ancestors with 95% HPD (blue node bars) computed with BEAST and graphical representation of the biogeographic scenario of <i>L. neilli</i> according to four time periods (A, B, C, D) inferred by VIP, LAGRANGE and DIYABC.

<p>The four maps depict the hypothetical distribution of <i>L. neilli</i> ancestral population (dark grey) (obtained with LAGRANGE), western (mauve), central (yellow), northern (light blue) and northeastern (red) groups and the localisation of barriers (black lines) leading to three vicariant events (obtained with VIP).</p

Prior distribution of parameters used in our ABC analysis.

<p>Prior distribution of parameters used in our ABC analysis.</p

Sampling localities of the 225 <i>L. neilli</i> analyzed in this study.

<p>Sampling localities of the 225 <i>L. neilli</i> analyzed in this study.</p

Pairwise <i>F</i>_ST among lineages containing more than three individuals calculated on mitochondrial (below diagonal) and nuclear (above diagonal) datasets.

<p>Non significant values are marked with asterisks (significance level = 0.05).</p

Is Leopoldamys neilli (Rodentia, Muridae) a synonym of Leopoldamys herberti ? A reply to Balakirev et al. (2013)

International audienceRecently, Balakirev et al. (2013) presented a taxonomic revision of the genus Leopoldamys based on phylogenetic analyses. They identified five main Leopoldamys genetic lineages and suggested to rename several of them. According to these authors, the genetic lineage previously thought to belong to L. edwardsi (lineage L1) should be assigned to L. revertens while L. neilli (lineage L2) should be considered as a junior synonym of L. herberti. Using molecular and morphological data from a large sampling of Leopoldamys specimens, the aim of the present study was to investigate the taxonomic status of L. herberti and L. neilli. This study reveals that, contrary to Balakirev et al.’s statement, both genetic lineages L1 and L2 occur in Nakhon Ratchasima Province, close to the type locality of L. herberti. We also show that the external measurements and color pattern of L. herberti are highly similar to those of L1 specimens but are not consistent with the morphology of L2 specimens. Therefore these results strongly suggest that L. herberti should be assigned to the genetic lineage L1. Consequently L. neilli should not be considered as a junior synonym of L. herberti and this study confirms that the appropriate name of the genetic lineage L2 is L. neilli. Moreover, as our results show that L. herberti should be assigned to the lineage L1, this name has nomenclatural priority over L. revertens, the species name suggested by Balakirev et al. (2013) for this lineage

TMRCA (mean values and 95% HPD) of the clades observed in phylogenetic trees.

<p>TMRCA (mean values and 95% HPD) of the clades observed in phylogenetic trees.</p

Genetic diversity within <i>L. neilli</i> populations based on microsatellite dataset.

<p>Genetic diversity within <i>L. neilli</i> populations based on microsatellite dataset.</p