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Nos références

Depuis 2004, les scientifiques de SPYGEN participent activement au développement des méthodes d’inventaire de la biodiversité par l’ADNe et sont co-auteurs de nombreuses publications dans ce domaine.


Bellemain, E., Patricio, H., Gray, T., Guegan, F., Valentini, A., Miaud, C., Dejean, T. 2016. Trails of river monsters: Detecting critically endangered Mekong giant catfish Pangasianodon gigas using environmental DNA. Global Ecology and Conservation 7, 148–156 (PDF).

Civade, R., Dejean, T., Valentini, A., Roset, N., Raymond, J-C., Bonin, A., Taberlet, P., Pont, D. 2016. Spatial Representativeness of Environmental DNA Metabarcoding Signal for Fish Biodiversity Assessment in a Natural Freshwater System. PLoS ONE 11(6):e0157366. (PDF)

Miaud, C., Dejean, T., Savard, K., Millery-Vigues, A., Valentini, A., Curt Grand Gaudin, N., Garner, T.W.J. 2016. Invasive North American bullfrogs transmit lethal fungus Batrachochytrium dendrobatidis infections to native amphibian host species. Biological Invasions, DOI 10.1007/s10530-016-1161-y.

Elbrecht, V., Taberlet, P., Dejean, T., Valentini, A., Usseglio-Polatera, P., Beisel, J-N., Coissac, E., Boyer, F., Leese, F. 2016. Testing the potential of a ribosomal 16S marker for DNA metabarcoding of insects. PeerJ 4:e1966; DOI 10.7717/peerj.1966. (PDF)

Valentini, A., Taberlet, P., Miaud, C., Civade,  R., Herder, J., Thomsen, P. , Bellemain, E., Besnard, A.,  Croissac, E., Boyer, F., Gaboriaud, C., Jean, P., Poulet, N., Roset, N., Copp, G., Geniez, P., Pont, D., Argillier, C., Baudoin, J.-M., Peroux, T., Crivelli, A., Olivier, A., Acqueberge, M., Le Brun, M., Møller, P. R., Willerslev, E., Dejean, T. 2016. Next-generation monitoring of aquatic biodiversity using environmental DNA metabarcoding. Molecular Ecology 25, 929-942. (PDF)

Tapio, I., Shingfield, KJ., McKain, N., Bonin, A., Fischer, D., Bayat, AR., Vilkki, J., Taberlet, P., Snelling, TJ., Wallace, RJ. 2016. Oral samples as non-invasive proxies for assessing the composition of the rumen microbial community. PLoS ONE, 11:e0151220.

Boyer, F., Mercier, C., Bonin, A., Le Bras, Y., Taberlet, P., Coissac, E. 2016. Obitools: a unix-inspired software package for DNA metabarcoding. Molecular Ecology Resources 16: 176-182.


Biggs, J., Ewald, N., Valentini, A., Gaboriaud, C., Dejean, T., Griffiths, R.A., Foster, J., Wilkinson, J.W., Arnell, A., Brotherton, P., Williams, P., Dunn, F. 2015. Using eDNA to develop a national citizen science-based monitoring programme for the great crested newt. Special Issue: Environmental DNA: A powerful new tool for biological conservation, Biological Conservation 183, 19-28. (PDF)

Soininen, E., Zinger, L., Gielly, L., Bellemain, E., Bråthen, K.A., Brochmann, C., Epp, L., Gussarova, G., Hassel, C., Henden, J.A., Killengren, S.T., Rämä, T., Stenøien, H.K., Yoccoz, N.G., Ims, R.A. 2015. Highly overlapping winter diet in two sympatric lemming species revealed by DNA metabarcoding. PlosOne 10(1) e0115335. doi:10.1371/journal.pone.0115335. (PDF)

Ficetola, GF., Pansu, J., Bonin, A., Coissac, E., Giguet-Covex, C., de Barba, M., Gielly, L., Lopes, CM., Boyer, F., Pompanon, F., Rayé, G., Taberlet, P. 2015. Replication levels, false presences, and the estimation of presence / absence from eDNA metabarcoding data. Molecular Ecology Resources 15: 543-556.


Tréguier, A., Paillisson, J.M., Dejean, T., Valentini, A., Schlaepfer, M., Roussel, J.M. 2014. Environmental DNA surveillance for invertebrate species: advantages and technical limitations to detect invasive crayfish Procambarus clarkii in freshwater ponds. Journal of Applied Ecology 51(4), 871-879. (Abstract)

Giampaoli, S., Berti, A., Di Maggio, R.M., Pilli, E., Valentini, A., Valeriani, F., Gianfranceschi, G., Barni, F., Ripani, L., Romano Spica, V. 2014.  The environmental biological signature: NGS profiling for forensic comparison of soils. Forensic Science International 240:41-7. doi: 10.1016/j.forsciint.2014.02.028. (Abstract)

Willerslev, E, Davison, J., Moora, M., Zobel, M., Coissac, E., Edwards, M., Lorenzen, E., Vestergård, M., Gussarova, G., Haile, J., Craine, J., Gielly, L., Boessenkool, S., Epp, L., Pearman, P., Cheddadi, R., Murray, D, Bråthen, K.A., Yoccoz, N., Binney, H., Cruaud, C., Wincker, P., Goslar, T., Alsos, I.G., Bellemain, E. et al., 2014. Fifty thousand years of Arctic vegetation and megafaunal diet. Nature 506, 47-51 doi: 10.1038. (Abstract)

Herder, J.E., Valentini, A., Bellemain, E., Dejean, T., van Delft, J.J.C.W., Thomsen P.F., Taberlet, P., 2014. Environmental DNA – a review of the possible applications for the detection of (invasive) species. Stichting RAVON, Nijmegen. Report-104. (PDF)

Fliegerova, K., Tapio, I., Bonin, A., Mrazek, J., Callegari, ML., Bani, P., Bayat, A., Vilkki, J., Kopecny, J., Shingfield, K., Boyer, F., Coissac, E., Taberlet, P., Wallace, RJ. 2014. Effect of DNA extraction and sample preservation method on rumen bacterial population. Anaerobe 29: 80-84.


Bellemain, E., Kauserud, H., Boessenkool, S., Epp, L., Brochmann, C. 2013. Fungal paleodiversity revealed using high-throughput metabarcoding of ancient DNA from arctic permafrost. Environmental Microbiology DOI: 10.1111/1462-2920.12020. (Abstract)

Ibanez, S., Manneville, O., Miquel, C., Taberlet, P., Valentini, A., Aubert, S., Coissac, E., Colace, M.P., Duparc, Q., Lavorel, S., Moretti, M. 2013. Plant functional traits reveal the relative contribution of habitat and food preferences to the diet of grasshoppers. Oecologia 173(4), 1459-1470. (Abstract)

Soininen, E.M., Zinger, L., Gielly, L., Bellemain, E., Bråthen, K.A., Brochmann, C., Epp, L., Gussarova, G. et al. 2013. Shedding new light on the diet of Norwegian lemmings: DNA metabarcoding of stomach content.  Polar Biology 36 (7), 1069-1076. (Abstract)

Andrew, RL., Bernatchez, L., Bonin, A., Buerkle, CA., Carstens, BC., Emerson, BC., Garant, D., Giraud, T., Kane, NC., Rogers, SM., Slate, J., Smith, H., Sork, VL., Stone, GN., Vines, TH., Waits, L., Widmer, A., Rieserberg, LH. 2013. A roadmap for molecular ecology. Molecular Ecology 22: 2605-2626.


Boessenkool, S., Epp L. S., Haile J., Bellemain, E., Coissac E., Willerslev, E., Brochmann, C. 2012. Blocking human contaminant DNA during PCR allows amplification of rare mammal species in sedimentary ancient DNA. 2012. Molecular Ecology 21(8): 1806-1815. (Abstract)

Dejean, T., Valentini, A., Miquel, C., Taberlet, P., Bellemain, E., Miaud, C. 2012. Improved detection of an alien invasive species through environmental DNA barcoding: the example of the American bullfrog Lithobates catesbeianus. Journal of Applied Ecology 49 (4), 953-960. (PDF)

Epp L. S., Boessenkool, S., Bellemain, E., Haile, J., Esposito, A., Gusarov, V., Johnsen, A., Willerslev, E., Taberlet, P., Coissac E., Brochmann, C. 2012. New environmental metabarcodes for analysing soil DNA: potential for studying past and present ecosystems. Molecular Ecology 21(8): 1821-1833. (Abstract)

Yoccoz, N.G., Brathen, K.A., Gielly, L., Haile, J., Edwards, M.E., Goslar, T., Von Stedingk, H., Brysting, A.K., Coissac, E., Pompanon, F., Sonstebo,  J.H., Miquel, C., Valentini, A., De Bello, F., Chave, J., Thuiller, W., Wincker, P., Cruaud, C., Gavory, F., Rasmussen, M. 2012. DNA from soil mirrors plant taxonomic and growth form diversity. Molecular Ecology 21(15), 3647-3656. (Abstract)

Schoville, SD., Bonin, A., François, O., Lobreaux, S., Melodelima, C., Manel, S. 2012. Adaptive genetic variation on the landscape: methods and cases. Annual Review of Ecology, Evolution and Systematics, 43: 23-43.

Pompanon, F., Bonin, A. 2012. Data Production and Analysis in Population Genomics, Methods in Molecular Biology Series Vol. 888. Humana Press, Totowa, New Jersey, 337 pages.


Dejean, T., Valentini, A., Duparc, A., Pellier-Cuit, S., Pompanon, F., Taberlet, P., Miaud, C. 2011. Persistence of Environmental DNA in Freshwater Ecosystems. PLoSOne 6 (8), 1-4. (PDF)

Kindberg, J., Swenson, J.E., Ericsson, G., Bellemain, E., Miquel, C., Taberlet, P. 2011. Estimating population size and trends of the Swedish brown bear Ursus arctos population. Wildlife Biology 17 (2), 114-123. (Abstract)

Kowalczyk, R., Taberlet, P., Coissac, E.,  Valentini, A., Miquel, C., Kaminski, T., Wojcik,  J.M. 2011. Influence of management practices on large herbivore diet—Case of European bison in Białowieża Primeval Forest. Forest Ecology and Management 261(4), 821-828. (Abstract)


Bellemain, E., Carlsen, T., Coissac, E., Taberlet, P., Brochmann, C., Kauserud, H. 2010. ITS as a DNA barcode in fungi: An in silico approach reveals potential PCR biases. BMC Microbiology 10:189. (PDF)

Valentini, A., Miquel, C., Taberlet, P. 2010. DNA Barcoding for Honey Biodiversity. Diversity 2(4), 610-617. (PDF)


Pages, M., Maudet, C., Bellemain, E., Taberlet, P., Hughes, S., Hanni, C. 2009. A system for sex determination from degraded DNA: a useful tool for palaeogenetics and conservation genetics of ursids. Conservation Genetics 10(4), 897-907. (Abstract)

Pegard, A., Miquel, C., Valentini, A., Coissac, E., Bouvier, F., Francois, D., Taberlet, P., Engel, E., Pompanon, F., 2009. Universal DNA-Based Methods for Assessing the Diet of Grazing Livestock and Wildlife from Feces. Journal of Agricultural and Food Chemistry 57(13), 5700-5706. (Abstract)

Soininen, E.M., Valentini, A., Coissac, E., Miquel, C., Gielly, L., Brochmann, C., Brysting, A.K., Sonstebo, J.H., Ims, R.A., Yoccoz, N.G., 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 6(16) doi:10.1186/1742-9994-6-16. (PDF)

Valentini, A., Pompanon, F., Taberlet, P., 2009. DNA barcoding for ecologists. Trends in Ecology & Evolution  24(2), 110-117. (Abstract)

Valentini, A., Miquel, C., Nawaz, M.A., Bellemain, E., Coissac, E., Pompanon, F., Gielly, L., Cruaud, C., Nascetti, G., Winker, P., Swenson, J.E., Taberlet, P. 2009. New perspectives in diet analysis based on DNA barcoding and parallel pyrosequencing: the trnL approach. Molecular Ecology Resources 9(1), 51-60. (Abstract)

Bonin, A., Paris, M., Tetreau, G., David, JP., Despres, L. 2009. Candidate genes revealed by a genome scan for mosquito resistance to a bacterial insecticide: sequence and gene expression variations. BMC Genomics 10: 551.

Bonin, A., Bernatchez, L. 2009. Challenges in assessing adaptive genetic diversity: overview of methods and empirical illustrations. In: Population genetics for animal conservation (eds. Bertorelle G, Bruford MW, Hauffe HC, Rizzoli A, Vernesi C), pp. 123-147. Cambridge University Press, Cambridge, UK.


Bonin, A., Paris, M., Despres, L., Tetreau, G., David, JP., Kilian, A. 2008. A MITE-based genotyping method to reveal hundreds of DNA polymorphisms in an animal genome after a few generations of artificial selection. BMC Genomics 9: 459.

Bonin, A. 2008. Population genomics: a new generation of genome scans to bridge the gap with functional genomics. Molecular Ecology 18: 3583-3584.

Ficetola, GF., Bonin, A., Miaud, C. 2008. Population genetics reveals origin and number of founders in a biological invasion. Molecular Ecology 17: 773-782.


Bellemain, E., Nawaz, A., Valentini, A., Swenson, J.E, Taberlet, P. 2007. Genetic tracking of the brown bear in northern Pakistan and implications for conservation. Biological Conservation 134, 537-547. (Abstract)

Manel, S., Berthoud, F., Bellemain, E., Gaudeul, M., Swenson, J.E., Luikart, G., Waits, L.P., Taberlet, P., Intrabiodiv consortium. A new individual-based geographic approach (based on assignment test and moving window) for identifying genetic discontinuities in natural populations. 2007. Molecular Ecology 16, 2031–2043. (Abstract)

Taberlet, P., Coissac, E., Pompanon, F., Gielly, L., Miquel, C., Valentini, A., Vermat, T., Corthier, G., Brochmann, C., Willerslev, E. 2007. Power and limitations of the chloroplast trnL (UAA) intron for plant DNA barcoding. Nucleic Acids Research 35(3) doi: 10.1093/nar/gkl938. (PDF)

Zedrosser, A., Bellemain, E., Taberlet, P., Swenson, J.E. Genetic estimates of annual reproductive success in male brown bears: the effects of body size, age, heterozygosity and population density. 2007. Journal of Animal Ecology 76(2), 368-75. (PDF)

Bonin, A., Ehrich, D., Manel, S. 2007. Statistical analysis of AFLP data: a toolbox for molecular ecologists and evolutionists. Molecular Ecology 16: 3737-3758.

Bonin, A., Nicole, F., Pompanon, F., Miaud, C., Taberlet, P. 2007. Population Adaptive Index: a new index to help measure intraspecific genetic diversity and prioritize populations for conservation. Conservation Biology 21: 697-708.


Miquel, C., Bellemain, E., Poillot, C., Taberlet, P. 2006. Quality indexes to assess genotypes reliability for studies using non-invasive sampling and multiple-tube approach. Molecular Ecology Notes 6, 985-988. (Abstract)

Solberg, H., Bellemain, E., Drageset, O.M., Taberlet, P., Swenson, J.E. 2006. An evaluation of field and genetic methods to estimate brown bear (Ursus arctos) population size. Biological Conservation 128, 158-168. (Abstract)

Bonin, A., Taberlet, P., Miaud, C., Pompanon, F. 2006. Explorative genome scan to detect candidate loci for adaptation along a gradient of altitude in the common frog (Rana temporaria). Molecular Biology and Evolution 23: 773-783.


Bellemain, E., Swenson, J.E., Tallmon, D.A, Brunberg, S., Taberlet, P. 2005. Estimating population size of elusive animals using DNA from hunter-collected feces: comparing four methods for brown bears. Conservation Biology 19(1), 150-161. (Abstract)

Pompanon, F., Bonin, A., Bellemain, E., Taberlet, P. 2005 Genotyping errors: causes, consequences and solutions. Nature Review Genetics 6, 847-856. (Abstract)

Bonin, A., Pompanon, F., Taberlet, P. 2005. Use of Amplified Fragment Length Polymorphism (AFLP) markers in surveys of vertebrate diversity. In: Methods in Enzymology, Molecular Evolution: Producing the Biochemical Data, Part B (eds. Zimmer EA, Roalson E), pp. 145-161. Academic Press, New York City.


Bellemain, E., Taberlet, P. 2004. Improved non invasive genotyping method: application to brown bear (Ursus arctos) feces. Molecular Ecology Notes 4, 519-522. (Abstract)

Bonin, A., Bellemain, E., Bronken Eidesen, P., Pompanon, F., Brochmann, C., Taberlet, P. 2004. How to track and deal with genotyping errors in population genetics studies. Molecular Ecology 13, 3261-3273. (Abstract)

Piggott, M.P., Bellemain, E., Taberlet, P., Taylor, A.C. 2004. A multiplex pre-amplification method that significantly improves microsatellite amplification and error rates for faecal DNA in limiting conditions. Conservation Genetics 5(2), 417-420. (PDF)

Tallmon, D.A, Bellemain, E., Swenson, J.E., Taberlet, P. 2004. Genetic monitoring of Scandinavian brown bear effective population size and immigration. Journal of Wildlife Management 68(4), 960-965. (Abstract)