[en] Leopoldamys 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.
Disciplines :
Zoology
Author, co-author :
Latinne, Alice ; Université de Liège - ULiège > R&D Direction : Chercheurs ULiège en mobilité
Galan, Maxime
Waengsothorn, Surachit
Rojanadilok, Prateep
Eiamampai, Krairat
Sribuarod, Kriangsak
Michaux, Johan ; Université de Liège - ULiège > Département des sciences de la vie > Génétique et physiologie des microalgues
Language :
English
Title :
Diet analysis of Leopoldamys neilli, a cave-dwelling rodent in Southeast Asia, using Next-Generation Sequencing from feces
Publication date :
2014
Journal title :
Journal of Cave and Karst Studies
ISSN :
1090-6924
Publisher :
National Speleological Society, United States - Alabama
Balakirev, A.E., Abramov, A.V., and Rozhnov, V.V., 2013, Revision of the genus Leopoldamys (Rodentia, Muridae) as inferred from morphological and molecular data, with a special emphasis on the species composition in continental Indochina: Zootaxa, v. 3640, no. 4, p. 521-549. doi:10.11646/zootaxa.3640.4.2.
Bradley, B.J., Stiller, M., Doran-Sheehy, D.M., Harris, T., Chapman, C.A., Vigilant, L., and Poinar, H., 2007, Plant DNA sequences from feces: Potential means for assessing diets of wild primates: American Journal of Primatology, v. 69, no. 6, p. 699-705. doi:10.1002/ajp. 20384.
Bremer, B., Bremer, K., Chase, M.W., Fay, M.F., Reveal, J.L., Soltis, D.E., Soltis, P.S., and Stevens, P.F., 2009, An update of the Angiosperm Phylogeny Group classification for the orders and families of flowering plants: APG III: Botanical Journal of the Linnean Society, v. 161, no. 2, p. 105-121. doi:10.1111/j.1095-8339. 2009.00996.x.
Cheng, Jinrui,Xiao, Zhishu, and Zhang, Zhibin, 2005, Seed consumption and caching on seeds of three sympatric tree species by four sympatric rodent species in a subtropical forest, China: Forest Ecology and Management, v. 216, no. 1-3, p. 331-341. doi:10.1016/j.foreco.2005.05.045.
Emmons, L.H., 2000, Tupai: A Field Study of Bornean Treeshrews, Berkeley, University of California Press, Organisms and Environments Series 2, 280 p.
Galan, M., Guivier, E., Caraux, G., Charbonnel, N., and Cosson, J.-F., 2010, A 454 multiplex sequencing method for rapid and reliable genotyping of highly polymorphic genes in large-scale studies: BMC Genomics, v. 11, article 296, 15 p. doi:10.1186/1471-2164-11-296.
Galan, M., Pagès, M., and Cosson, J.-F., 2012, Next-Generation Sequencing for Rodent Barcoding: Species Identification from Fresh, Degraded and Environmental Samples: PLoS ONE, v. 7, no. 11, e48374 p.
Hajibabaei, M., Shokralla, S., Zhou, Xin, Singer, G.A.C., and Baird, D.J., 2011, Environmental barcoding: a next-generation sequencing approach for biomonitoring applications using river benthos: PLoS ONE, v. 6, article e17497, 7 p. doi:10.1371/journal.pone.0017497.
Hofreiter, M., Poinar, H.N., Spaulding, W.G., Bauer, K., Martin, P.S., Possnert, G., and Pääbo, S., 2000, A molecular analysis of ground sloth diet through the last glaciation: Molecular Ecology, v. 9, no. 12, p. 1975-1984. doi:10.1046/j.1365-294X.2000.01106.x.
Hollingsworth, M.L., Clark, A.A., Forrest, L.L., Richardson, J., Pennington, R.T., Long, D.G., Cowan, R., Chase, M.W., Gaudeul, M., and Hollingsworth, P.M., 2009, Selecting barcoding loci for plants: evaluation of seven candidate loci with species-level sampling in three divergent groups of land plants: Molecular Ecology Resources, v. 9, p. 439-457. doi:10.1111/j.1755-0998.2008.02439.x.
International Finance Corporation, World Bank Group, 2002, Limestone Biodiversity Study, Hon Chong, Executive summary.
Kim, Baek Jun, Lee, Nam Sook, and Lee, Sang Don, 2011, Feeding diets of the Korean water deer (Hydropotes inermis argyropus) based on a 202 bp rbcL sequence analysis: Conservation Genetics, v. 12, no. 3, p. 851-856. doi:10.1007/s10592-011-0192-2.
Kress, W.J., and Erickson, D.L., 2007, A two-locus global DNA barcode for land plants: The coding rbcL gene complements the non-coding trnH-psbA spacer region: PLoS ONE, v. 2, article e508, 10 p. doi:10.1371/journal.pone.0000508.
Langham, N., 1983, Distribution and ecology of small mammals in three rain forest localities of Peninsula Malaysia with particular reference to Kedah Peak: Biotropica, v. 15, no. 3, p. 199-206.
Latinne, A., 2012, Diversity and endemism of Murinae rodents in Thai limestone karsts: a genetic approach [PhD dissertation], University of Liège, 254 p.
Latinne, A., Waengsothorn, S., Herbreteau, V., and Michaux, J.R., 2011, Evidence of complex phylogeographic structure for the threatened rodent Leopoldamys neilli, in Southeast Asia: Conservation Genetics, v. 12, no. 6, p. 1495-1511doi:10.1007/s10592-011-0248-3. p.
Latinne, A., Chaval, Y., Waengsothorn, S., Rojanadilok, P., Eiamampai, K., Sribuarod, K., Herbreteau, V., Morand, S., and Michaux, J.R., 2013a, Is Leopoldamys neilli (Rodentia, Muridae) a synonym of Leopoldamys herberti? A reply to Balakirev et al. (2013): Zootaxa, v. 3731, no. 4, p. 589-598. doi:10.11646/zootaxa.3731.4.10.
Latinne, A., Waengsothorn, S., Rojanadilok, P., Eiamampai, K., Sribuarod, K., and Michaux, J.R., 2012, Combined mitochondrial and nuclear markers revealed a deep vicariant history for Leopoldamys neilli, a cave-dwelling rodent of Thailand: PLoS ONE, v. 7, no. 10, article e47670, 17 p. doi:10.1371/journal.pone.0047670.
Latinne, A., Waengsothorn, S., Rojanadilok, P., Eiamampai, K., Sribuarod, K., and Michaux, J.R., 2013b, Diversity and endemism of Murinae rodents in Thai limestone karsts: Systematics and Biodiversity, v. 11, no. 3, p. 323-344. doi:10.1080/14772000.2013.818587.
Lim, Boo-Liat, 1970, Distribution, relative abundance, food habits, and parasite patterns of giant rats (Rattus) in West Malaysia: Journal of Mammalogy, v. 51, no. 4, p. 730-740.
Marshall, J.D., 1977, Rats and mice of Thailand, in Lekagul, B., and McNeely, J.A., eds., Mammals of Thailand, Bangkok, Thailand, Saha Karn Bhaet, p. 395-490.
Meglécz, E., Piry, S., Desmarais, E., Galan, M., Gilles, A., Guivier, E., Pech, N., and Martin, J.-F., 2011, SESAME (SEquence Sorter & AMplicon Explorer): Genotyping based on high-throughput multiplex amplicon sequencing: Bioinformatics, v. 27, no. 2, p. 277-278. doi:10.1093/bioinformatics/btq641.
Musser, G.G., Smith, A.L., Robinson, M.F., and Lunde, D.P., 2005, Description of a New Genus and Species of Rodent (Murinae, Muridae, Rodentia) from Khammouan Limestone National Biodiversity Conservation Area in Lao PDR, American Museum Novitates, no. 3497, 31 p.
Musser, G.G., Lunde, D.P., and Son, N.T., 2006, Description of a New Genus and Species of Rodent (Murinae, Muridae, Rodentia) from the Tower Karst Region of Northeastern Vietnam, American Museum Novitates, no. 3517, 41 p.
Soininen, E.M., Valentini, A., Coissac, E., Miquel, C., Gielly, L., Brochmann, C., Brysting, A.K., Sønstebø, J.H., Ims, R.A., Yoccoz, N.G., and Taberlet, P., 2009, Analysing diet of small herbivores: the efficiency of DNA barcoding coupled with high-throughput pyrosequencing for deciphering the composition of complex plant mixtures: Frontiers in Zoology, v. 6, article 16, 9 p. doi:10.1186/1742-9994-6-16.
Taberlet, P., Coissac, E., Pompanon, F., Gielly, L., Miquel, C., Valentini, A., Vermat, T., Corthier, G., Brochmann, C., and Willerslev, E., 2007, Power and limitations of the chloroplast trnL (UAA) intron for plant barcoding: Nucleic Acids Research, v. 35, no. 3, article e14, 8 p. doi:10.1093/nar/gkl938.
Valentini, A., Miquel, C., Nawaz, M.A., Bellemain, E., Coissac, E., Pompanon, F., Gielly, L., Cruaud, C., Nascetti, G., Wincker, P., Swenson, J.E., and Taberlet, P., 2009, New perspectives in diet analysis based on DNA barcoding and parallel pyrosequencing: the trnL approach: Molecular Ecology Resources, v. 9, no. 1, p. 51-60. doi:10.1111/j.1755-0998.2008.02352.x.
Wells,K., Corlett, R.T., Lakim,M.B.,Kalko, E.K.V., and Pfeiffer, M., 2009, Seed consumption by small mammals from Borneo: Journal of Tropical Ecology, v. 25, no. 5, p. 555-558. doi:10.1017/S0266467409990058.
Zhang, Hongmao, Cheng, Jinrui, Xiao, Zhishu, and Zhang, Zhibin, 2008, Effects of seed abundance on seed scatter-hoarding of Edward's rat (Leopoldamys edwardsi Muridae) at the individual level: Oecologia, v. 158, no. 1, p. 57-63. doi:10.1007/s00442-008-1114-y.
Zhang, Zheng, Schwartz, S., Wagner, L., and Miller, W., 2000, A greedy algorithm for aligning DNA sequences: Journal of Computational Biology, v. 7, no. 1-2, p. 203-214. doi:10.1089/10665270050081478.
