Nos references scientifiques

Zinger L, Bonin A, Alsos I, Bálint M, Bik H, Boyer F, Chariton A, Creer S, Coissac E, Deagle B, De Barba M, Dickie I, Dumbrell A, Ficetola GF, Fierer N, Fumagalli L, Gilbert T, Jarman S, Jumpponen A, Kauserud H, Orlando L, Pansu J, Pawlowski J, Tedersoo L, Thomsen P, Willerslev E, Taberlet P (sous presse). DNA metabarcoding - need for robust experimental designs to draw sound ecological conclusions. Molecular Ecology.

Wallace RJ, Sasson G, Garnsworthy PC, Tapio I, Gregson E, Bani P, Huhtanen P, Bayat AR, Strozzi F, Biscarini F, Snelling TJ, Saunders N, Potterton SL, Craigon J, Minuti A, Trevisi E, Callegari ML, Piccioli Cappelli F, Cabezas Garcia EH, Vilkki J, Pinares-Patino C, Fliegerová KO, Mrázek J, Sechovcová H, Kopečný J, Bonin A, Boyer F, Taberlet P, Kokou F, Halperin E, Williams JL, Shingfield KJ, Mizrahi I. 2019. A heritable subset of the core rumen microbiome dictates dairy cow productivity and emissions. Science Advances, 5.

Zinger L, Taberlet P, Schimann H, Bonin A, Boyer F, de Barba M, Gaucher P, Gielly L, Giguet-Covex C, Iribar I, Réjou-Méchain M, Rayé G, Rioux D, Schilling V, Tymen B, Viers J, Zouiten C, Thuiller W, Coissac E, Chave J. 2019. Body size determines soil community assembly in a tropical forest. Molecular Ecology, 28: 528-543.


Kerley GIH, Landman M, Ficetola GF, Boyer F, Bonin A, Rioux D, Taberlet T, Coissac E. 2018. Diet shifts by adult flightless dung beetles Circellium bacchus, revealed using DNA metabarcoding, reflect complex life histories. Oecologia, 188: 107-115.


Taberlet P, Bonin A, Zinger L, Coissac E. 2018. Environmental DNA: for Biodiversity Research and Monitoring. Oxford University Press, Oxford, UK, 272 pages.

Bellemain E, Patricio H, Gray T, Guégan 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.


Valentini A, Taberlet P, Miaud C, Civade R, Herder J, Thomsen PF, Bellemain E, et al. 2016, Next-generation monitoring of aquatic biodiversity using environmental DNA metabarcoding. Molecular Ecology 25: 929–942. doi:10.1111/mec.13428

Civade R, Dejean T, Valentini A, Roset N, Raymond JC, 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: e0157366.


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.

Soininen E, Zinger L, Gielly L, Bellemain E, Bråthen KA, Brochmann C, Epp L, Gussarova G, Hassel C, Henden JA, Killengren ST, Rämä T, Stenøien HK, Yoccoz NG, Ims RA. 2015. Highly overlapping winter diet in two sympatric lemming species revealed by DNA metabarcoding. PlosOne 10(1) e0115335. doi:10.1371/journal.pone.0115335.

Bonin A, Paris M, Frérot H, Bianco E, Tetreau G, Després L. 2015. The genetic architecture of a complex trait: resistance to multiple toxins produced by Bacillus thuringiensis israelensis in the dengue and yellow fever vector, the mosquito Aedes aegypti. Infection, Genetics and Evolution 35: 204-213.


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.

Herder JE, Valentini A, Bellemain E, Dejean T, van Delft JJCW, Thomsen PF, Taberlet P. 2014. Environmental DNA - a review of the possible applications for the detection of (invasive) species. Stichting RAVON, Nijmegen. Rapport 2013-104.

Kuduk K, Babik W, Bellemain E, Valentini A, Zedrosser A, Taberlet P, Kindberg J, Swenson JE, Radwan J. 2014. No Evidence for the Effect of MHC on Male Mating Success in the Brown Bear. PlosOne 9(12): e113414.

Willerslev E et al. 2014. Fifty thousand years of Arctic vegetation and megafaunal diet. Nature 506, 47–51; doi: 10.1038/nature12921.

Després L, Stalinski R, Faucon F, Navratil V, Viari A, Paris M, Tetreau G, Poupardin R, Riaz MA, Bonin A, Reynaud S, David JP. 2014. Chemical and biological insecticides select distinct gene expression patterns in Aedes aegypti mosquito. Biology Letters 10: 20140716.


Després L, Stalinski R, Tetreau G, Paris M, Bonin A, Navratil V, Reynaud S, David JP. 2014. Gene expression patterns and sequence polymorphisms associated with mosquito resistance to Bacillus thuringiensis israelensis toxins. BMC Genomics 15:926.


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.


Regnault C, Worms IAM, Oger-Desfeux C, MelodeLima C, Veyrenc S, Bayle ML, Combourieu B, Bonin A, Renaud J, Raveton M, Reynaud S. 2014. Impaired liver function in Xenopus tropicalis exposed to benzo[a]pyrene: transcriptomic and metabolic evidence. BMC Genomics 15: 666.


David JP, Faucon F, Chandor-Proust A, Poupardin R, Riaz MA, Bonin A, Navatril V, Reynaud S. 2014. Comparative analysis of response to selection with three insecticides in the dengue mosquito Aedes aegypti using mRNA sequencing. BMC Genomics 15: 174.

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.


Dlugosch KM, Lai Z, Bonin A, Hierro J, Rieseberg LH. 2013. Allele identification for transcriptome-based population genomics in the invasive plant Centaurea solstitialis. G3: Genes, Genomes, Genetics, 3: 359-367.

Soininen EM, Zinger L, Gielly L, Bellemain E, Bråthen KA, 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

Bellemain E, Kauserud H, Boessenkool S, Epp L, Brochmann C. 2012. Fungal paleodiversity revealed using high-throughput metabarcoding of ancient DNA from arctic permafrost. Environmental Microbiology doi: 10.1111/1462-2920.12020

Epp LS, 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.

Boessenkool S, Epp LS, 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. 

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.


Dlugosch KM, Bonin A. 2012. Allele identification in assembled genomic sequence datasets. In: Data Production and Analysis in Population Genomics, Methods in Molecular Biology Series (eds. Pompanon F, Bonin A), pp 197-211. Humana Press, Totowa, New Jersey.


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.

Kindberg J, Swenson JE, 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. doi: 10.2981/10-100 

Joost S, Colli L, Bonin A, Biebach I, Allendorf F, Hoffmann I, Hanotte O, Taberlet P, Bruford M, The GlobalDiv Consortium. 2011. Promoting collaboration between livestock and wildlife conservation genetics communities. Conservation Genetics Resources, 3: 785-788.


Ficetola GF, Bonin A. 2011. Conserving adaptive genetic diversity in dynamic landscapes. Molecular Ecology, 20: 1569-1571.


Strasburg JL, Kane NC, Raduski AR, Bonin A, Michelmore R, Rieseberg LH. 2011. Effective population size is positively correlated with levels of adaptive divergence among annual sunflowers. Molecular Biology and Evolution, 28: 1569-1580.

Swenson JE, Taberlet P, Bellemain E. Genetics and conservation of European brown bears. 2011. Mammal Review 41(2) 87-97.

Manel S, Joost S, Epperson B, Holdergger R, Storfer A, Rosenberg M, Scribner K, Bonin A, Fortin MJ. 2010. Perspectives on the use of landscape genetics to detect genetic adaptive variation in the field. Molecular Ecology, 19: 3760-3772.


Paris M, Boyer S, Bonin A, Collado A, David JP, Despres L. 2010. Genome scan in the mosquito Aedes rusticus: population structure and detection of positive selection after insecticide treatments. Molecular Ecology, 19: 325-337.

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

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.

Pages M, Maudet C, Bellemain E, Taberlet P, Hugues S, Hänni C. 2009. Sex your Ursid free. Conservation Genetics doi 10.1007/s10592-008-9650-x

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.


Mir C, Jarne P, Sarda V, Bonin A, Lumaret R. 2009. Contrasted nuclear and cytoplasmic reciprocal exchanges between two phylogenetically distant oak species (Quercus suber L. and Q. ilex L.) in Southern France. Plant Biology, 11: 213-226.


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.


Joost S, Kalbermatten M, Bonin A. 2008. Spatial analysis method (SAM): a software to detect signatures of natural selection within the genome. Molecular Ecology Resources 8: 957-960.

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.


Valentini A, Miquel C, Nawaz MA, Bellemain E, Coissac E, Pompanon F, Gielly L, Cruaud C, Nascetti G, Winker P, Swenson JE, Taberlet P. New perspectives in diet analysis based on DNA barcoding and parallel pyrosequencing: the trnL approach. 2008. Molecular Ecology doi: 10.1111/j.1755-0998.2008.02352.x

Manel S, Berthoud F, Bellemain E, Gaudeul, M, Swenson JE, Luikart G, Waits LP. Intrabiodiv consortium, Taberlet, P. 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.

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

Joost S, Bonin A, Bruford MW, Despres L, Conord C, Ehrardt G, Taberlet P. 2007. A Spatial Analysis Method (SAM) to detect candidate loci for selection: towards a landscape genomics approach of adaptation. Molecular Ecology 16: 3965-3969.


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.


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

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.


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.

Solberg H, Bellemain E, Drageset OM, Taberlet P, Swenson JE. 2006. An evaluation of field and genetic methods to estimate brown bear (Ursus arctos) population size. Biological conservation128,158-168.

Pompanon F, Bonin ABellemain E, Taberlet P. 2005 Genotyping errors: causes, consequences and solutions. Nature Review Genetics 6, 847-856.

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, New York.


Bellemain E, Swenson JE, Tallmon DA, 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.

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 Ecology13, 3261-3273.

Piggott MP, Bellemain E, Taberlet P, Taylor AC. 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.


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

Staudt M, Mir C, Joffre R, Rambal S, Bonin A, Landais D, Lumaret R. 2004. Isoprenoid emissions of Quercus spp. (Q. suber and Q. ilex) in mixed stands contrasting in interspecific genetic introgression. New Phytologist 163: 573-584.



soil sampling

diet analysis