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A new method to identify the endangered Pyrenean desman (Galemys pyrenaicus) and to study its diet, using next generation sequencing from faeces

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Abstract

The Pyrenean desman (Galemys pyrenaicus) is a small endangered semi-aquatic mammal endemic to the Pyrenean Mountains and to the northern half of the Iberian Peninsula whose ecology and biology are still poorly known. The aim of this study was to identify Pyrenean desman faeces and to analyze its diet from this material using next-generation sequencing methods. We amplified and sequenced a small DNA minibarcode (133 bp) of the COI gene in twenty-four putative faeces samples of Pyrenean desman and successfully identified the species in 16 samples. Other identified species were mammals, birds and amphibians, evidencing the potential application of our methods to a larger panel of taxa.

In the Pyrenean desman faeces, we were able to identify nineteen prey species with a positive match (more than 98% of identity with a reference sequence) and eleven putative prey species with lower identity scores (90–96%). The nineteen species belonged to four orders and eleven families among which Trichoptera and Hydropsychidae were the most frequent, respectively. Future improvements could be obtained by extending the reference DNA sequence collection to reach precise identifications over the Desman’s range and by increasing the sampling to gain a better knowledge of the local diet of this endangered species. Such information is of great importance to propose the best management measures for its conservation.

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References

  • Bertrand, A., 1993. Découvrir le Desman des Pyrénées. Ed. A.N.A., pp. 32.

  • Bertrand, A., 1994. Répartition géographique et écologie alimentaire de desman des pyrénées G. pyrenaicus dans les Pyrénées francaises. Diplôme Universitaire de Recherche, Toulouse, pp. 217.

    Google Scholar 

  • Castién, E., Gosálbez, J., 1995. Diet of Galemyspyrenaicus (Geoffroy, 1811) inthe North of the Iberian peninsula. Netherlands J. Zool. 45 (3–4), 422–430.

    Google Scholar 

  • Charbonnel, A., (Thèse de doctorat) 2015. Influence multi-échelle des facteurs environnementaux dans la répartition du Desman des Pyrénées (Galemys pyrenaicus) en France. l’Université de Toulouse, pp. 245.

  • Fernandes, M., et al., 2008. Galemys pyrenaicus. IUCN Red List of Threatened Species. Version 2013.2, Available at: https://doi.org/www.iucnredlist.org

  • Fernández-Salvador, R., et al., 1998. Feeding habits of the Iberian desman, Galemys pyrenaicus. Euro-American Mammal Congress, Santiago de Compostela (Spain).

    Google Scholar 

  • Galan, M., Pagès, M., Cosson, J.F., 2012. Next-generation sequencing for rodent barcoding: species identification from fresh, degraded and environmental samples. PLoS ONE 7 (11).

    Article  CAS  Google Scholar 

  • Gillet, F., et al., 2015. PCR-RFLP identification of the endangered Pyrenean desman, Galemys pyrenaicus (Soricomorpha, Talpidae), based on faecal DNA. Mammalia, Available at: https://doi.org/www.degruyter.com/view/j/mamm.ahead-of-print/mammalia-2014-0093/mammalia-2014-0093.xml (accessed 01.11.14).

  • Gisbert, J., Garciá-Perea, R., 2014. Historiade la regresióndel desmán ibérico Galemys pyrenaicus (É. Geoffroy Saint-Hilaire, 1811) en el Sistema Central (Península Ibérica). Munibe Monographs Nature Series.

  • Hajibabaei, M., et al., 2011. Environmental barcoding: a next-generation sequencing approach forbiomonitoring applications using river benthos. PLoS ONE 6 (4), e17497, Available at: https://doi.org/www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3076369&tool=pmcentrez&rendertype=abstract (accessed 07.11.13).

    Article  CAS  Google Scholar 

  • Hebert, P.D.N., et al., 2004. Ten species in one: DNA barcoding reveals cryptic species inthe neotropical skipper butterfly Astraptes fulgerator. PNAS 101 (41).

  • Latinne, A., et al., 2014. Diet analysis of Leopoldamys neilli, a cave-dwelling rodent in southeast asia, using next-generation sequencing from feces. J. Cave Karst Stud. 76 (2), 139–145, Available at: https://doi.org/caves.org/pub/journal/PDF/v76/cave-76-02-139.pdf (accessed 25.02.15).

    Article  Google Scholar 

  • Lees, D.C., et al., 2010. DNA mini-barcodes in taxonomic assignment: a morphologically unique new homoneurous moth clade from the Indian Himalayas described in Micropterix (Lepidoptera, Micropterigidae). Zool. Scr. 39 (6), 642–661, Available at: https://doi.org/doi.wiley.com/10.1111/j.1463-6409.2010.00447.x (accessed 14.11.13).

    Article  Google Scholar 

  • Meusnier, I., et al., 2008. A universal DNA mini-barcode for biodiversity analysis. BMC Genomics 9, 214, Available at: https://doi.org/www.ncbi.nlm.nih.gov/pubmed/18474098 (accessed 07.11.13).

    Article  Google Scholar 

  • Némoz, M., Bertrand, A., 2008. Plan National d’Actions en faveurdu Desman des Pyrénéés (Galemys pyrenaicus), 2009–2014. Société Francaise pour l’Etude et la Protection des Mammifères/Ministère de l’Ecologie, de l’Energie, du Développement Durable et de l’Aménagement du Territoire, 1.

  • Nores, C, Queiroz, A.I., Gisbert, J., 2007. Galemys pyrenaicus, (E. Geoffroy Saint-Hilaire, 1811). In: Palomo, L, Gisbert, J., Blanco, J. (Eds.), Atlas y libro rojo de los mamíferos terrestres de Espan˜a. Dirección General para la Biodiversidad – SECEM – SECEMU, Madrid, pp. 92–98.

    Google Scholar 

  • Palmeirim, J.M., Hoffmann, S.H., 1983. Galemys pyrenaicus. Mamm. Species 207, 1–5.

    Article  Google Scholar 

  • Piñol, J., et al., 2014. A pragmatic approach to the analysis of diets of generalist predators: the use of next-generation sequencing with no blocking probes. Mol. Ecol. Resour. 14 (1), 18–26, Available at: https://doi.org/www.ncbi.nlm.nih.gov/pubmed/23957910 (accessed 10.02.15).

    Article  Google Scholar 

  • Piry, S., et al., 2012. |SE|S|AM|E| Barcode: NGS-oriented software foramplicon characterization – application to species and environmental barcoding. Mol. Ecol. Resour. 12 (6), 1151–1157, Available at: https://doi.org/www.ncbi.nlm.nih.gov/pubmed/22823139 (accessed 30.03.15).

    Article  CAS  Google Scholar 

  • Puisségur, C, 1935. Recherches sur le Desman des Pyrénées. Bull. Soc. Hist. Nat. Toulouse 67, 163–227.

    Google Scholar 

  • Ratnasingham, S., Hebert, P.D.N., 2007. BOLD: The Barcode of Life Data System (https://doi.org/www.barcodinglife.org). Mol. Ecol. Notes 7, 355–364.

    Article  CAS  Google Scholar 

  • Richard, P.B., 1986. Les Desman des Pyrénées, un mammifère inconnu à découvrir. Science et Découvertes, Ed., Le Rocher, Monaco, 118 pp.

    Google Scholar 

  • Richard, P.B., Vallette Vialard, A., 1969. Le Desman des Pyrénées (Galemys pyrenaicus): premières notes sursabiologie. LaTerre et la Vie 116 (3), 225–245.

    Google Scholar 

  • Santamarina, J., 1993. Feeding ecology of a vertebrate assemblage inhabiting a stream of NW Spain (Riobo; Ulla basin). Hydrobiologia 252 (2), 175–191, Available at: https://doi.org/link.springer.com/10.1007/BF00008154

    Article  Google Scholar 

  • Santamarina, J., Guitian, J., 1988. Quelques données sur le régime alimentaire du desman (Galemys pyrenaicus) dans le nord-ouest de l’Espagne. Mammalia 52 (3).

  • Shehzad, W., et al., 2012. Carnivore diet analysis based on next-generation sequencing: application to the leopard cat (Prionailurus bengalensis) in Pakistan. Mol. Ecol. 21 (8), 1951–1965, Available at: https://doi.org/www.ncbi.nlm.nih.gov/pubmed/22250784 (accessed 28.03.14).

    Article  CAS  Google Scholar 

  • Soininen, E.M., et al., 2009. Analysing diet of small herbivores: the efficiency of DNA barcoding coupled with high-throughput pyrosequencing for deciphering the composition of complex plant mixtures. Front. Zool. 6,16, Available at: https://doi.org/www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2736939&tool=pmcentrez&rendertype=abstract (accessed 17.12.14).

    Article  Google Scholar 

  • Stone, R.D., 1987. The activity pattern of the Pyrenean desman (Galemys pyrenaicus) (Insectivora: Talpidae), as determined under natural condition. J. Zool. Lond. 213, 95–106.

    Article  Google Scholar 

  • Trutat, E., 1891. Essai sur l’histoire naturelle du Desman des Pyrénées. Douladoure-Privat, Toulouse, pp. 107.

    Google Scholar 

  • Virgilio, M., et al., 2010. Comparative performances of DNA barcoding across insect orders. BMC Bioinformatics 11, 206, Available at: https://doi.org/www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2885370&tool=pmcentrez&rendertype=abstract

    Article  Google Scholar 

  • Zeale, M.R.K., et al., 2011. Taxon-specific PCR for DNA barcoding arthropod prey in bat faeces. Mol. Ecol. Resour. 11 (2), 236–244, Available at: https://doi.org/www.ncbi.nlm.nih.gov/pubmed/21429129 (accessed 09.03.15).

    Article  CAS  Google Scholar 

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Authors and Affiliations

  1. Department of Life Sciences, Conservation Genetics Unit, University of Liège, 4000, Liège, Belgium

    François Gillet & Johan R. Michaux

  2. Comportement et Ecologie de la Faune Sauvage (CEFS), Institut National de la Recherche Agronomique, 24 Chemin de Borde Rouge, Auzeville, CS 52627, 31326, Castanet-Tolosan Cedex, France

    François Gillet & Stéphane Aulagnier

  3. Conservatoire d’Espaces Naturels de Midi-Pyrénées, 75 voie du Toec, BP 57611, 31076, Toulouse Cedex 3, France

    François Gillet, Frédéric Blan & Mélanie Némoz

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

    Marie-Laure Tiouchichine & Maxime Galan

  5. CIRAD, Agirs Unit, TA C-22/E-Campus international de Baillarguet, 34398, Montpellier Cedex 5, France

    Johan R. Michaux

Authors
  1. François Gillet
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  2. Marie-Laure Tiouchichine
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  3. Maxime Galan
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  4. Frédéric Blan
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  5. Mélanie Némoz
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  6. Stéphane Aulagnier
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  7. Johan R. Michaux
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Correspondence to François Gillet.

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Gillet, F., Tiouchichine, ML., Galan, M. et al. A new method to identify the endangered Pyrenean desman (Galemys pyrenaicus) and to study its diet, using next generation sequencing from faeces. Mamm Biol 80, 505–509 (2015). https://doi.org/10.1016/j.mambio.2015.08.002

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