​- 2024 -​

​

• Ficetola GF, Guerrieri A, Cantera I, Bonin A (in press). In silico assessment of 18S rDNA metabarcoding markers for the characterization of nematode communities. PLoS ONE.

​

• Carteron A, Cantera I, Guerrieri A, Marta S, Bonin A, Ambrosini R, Anthelme F, Azzoni RS, Almond P, Alviz Gazitúa P, Cauvy-Fraunié S, Ceballos Lievano JL, Chand P, Chand Sharma M, Clague J, Cochachín Rapre JA, Compostella C, Cruz Encarnación R, Dangles O, Eger A, Erokhin S, Franzetti A, Gielly L, Gili F, Gobbi M, Hågvar S, Khedim N, Meneses RI, Peyre G, Pittino F, Rabatel A, Urseitova N, Yang Y, Zaginaev V, Zerboni A, Zimmer A, Taberlet P, Diolaiuti GA, Poulenard J, Thuiller W, Caccianiga M, Ficetola GF (in press). Dynamics and drivers of mycorrhizal fungi after glacier retreat. New Phytologist.

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• Cantera I, Carteron  A, Guerrieri A, Marta S, Bonin  A, Ambrosini R, Anthelme F, Azzoni RS, Almond P, Alviz Gazitúa P, Cauvy-Fraunié S, Ceballos Lievano JL, Chand P, Chand Sharma M, Clague J, Cochachín Rapre JA, Compostella C, Cruz Encarnación R, Dangles O, Eger A, Erokhin S, Franzetti A, Gielly L, Gili F, Gobbi M, Hågvar S, Khedim N, Meneses, RI, Peyre G, Pittino F, Rabatel A, Urseitova N, Yang Y, Zaginaev V, Zerboni, A, Zimmer A, Taberlet P, Diolaiuti AG, Poulenard J, Thuiller W, Caccianiga M, Ficetola GF (in press). The importance of species addition versus replacement varies over succession in plant communities after glacial retreat. Nature Plants. 

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• Pfendler S, Ciadamidaro L, Ozaki S, Bonin A, Taberlet P, Zappelini C, Maillard F, Blaudez D, Chalot M (2024). Differential effects of tree species identity on rhizospheric bacterial and fungal community richness and composition across multiple trace element-contaminated sites. Science of the Total Environment, 912: 168600.

​

​- 2023 -

​

• Nikolic N, Desbonnes O, Bonin A, Corse E, Mulochau T, Inçaby L, Gustavo Cardoso L, Clua E, Planes S, Archambeau H, Pierron M, Sessegolo C, Bellemain E, Crochelet E (2023). Inventaire des requins autour de La Réunion à partir d’analyses d’ADN environnemental avec une approche écosystémique (élasmobranches et poissons osseux). Rapport projet IRRAE.​

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• Giachello S, Cantera I, Carteron A, Marta S, Cipriano C, Guerrieri A, Bonin A, Thuiller W, Ficetola GF (2023). Toward a common set of functional traits for soil protists. Soil Biology and Biochemistry, 187, 109​

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• Ficetola GF, Marta S, Guerrieri A, Cantera I, Bonin A, Cauvy-Fraunié S, Ambrosini R, Caccianiga M, Anthelme F, Azzoni RS, Almond P, Alviz Gazitúa P, Ceballos Lievano JL, Chand P, Chand Sharma M, Clague J, Cochachín Rapre JA, Compostella C, Cruz Encarnación R, Dangles O, Deline P, Eger P, Erokhin S, Franzetti A, Gielly L, Gili F, Gobbi M, Hågvar S, Kaufmann R, Khedim N, Meneses RI, Morales-Martínez MA, Peyre G, Pittino F, Proietto A, Rabatel A, Sieron K, Tielidze L, Urseitova N, Yang Y, Zaginaev V, Zerboni A, Zimmer A, Diolaiuti GA, Taberlet P, Poulenard J, Fontaneto D, Thuiller W, Carteron A (under revision). The development of terrestrial ecosystems emerging after glacier retreats. Nature.​

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• Guerrieri A, Cantera I, Marta S, Bonin A, Carteron A, Ambrosini R, Caccianiga M, Anthelme F, Azzoni RS, Almond P, Alviz Gazitúa P, Cauvy-Fraunié S, Ceballos Lievano JL, Chand P, Chand Sharma M, Clague J, Cochachín Rapre JA, Compostella C, Cruz Encarnación R, Dangles O, Deline P, Eger A, Erokhin S, Franzetti A, Gielly L, Gili F, Gobbi M, Hågvar S, Khedim N, Meneses RI, Peyre G, Pittino F, Proietto A, Rabatel A, Urseitova N, Yang Y, Zaginaev V, Zerboni A, Zimmer A, Taberlet P, Diolaiuti GA, Poulenard J, Fontaneto D, Thuiller W, Ficetola GF (2023). Local climate modulates the development of soil nematode communities after glacier retreat. Global Change Biology, 30, e17057.​

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• Guerrieri A, Carteron A, Bonin A, Marta S, Ambrosini R, Caccianiga M, Cantera I, Compostella C, Diolaiuti G, Fontaneto D, Gielly L, Gili F, Gobbi M, Poulenard J, Taberlet P, Zerboni A, Thuiller W, Ficetola GF (2023). Metabarcoding data reveal vertical multi-taxa variation in topsoil communities during the colonization of deglaciated forelands. Molecular Ecology, 32: 6304-6319.

 

• Bonin A, Guerrieri A, Ficetola GF (2023) Optimal sequence similarity thresholds for clustering of molecular operational taxonomic units in DNA metabarcoding studies. Molecular Ecology Resources, 23: 368-381. ​

​

- 2022 - ​​

​

• Pansu J, Hutchinson MC, Anderson TM, te Beest M, Begg CM, Begg KS, Bonin A, Chama L, Chamaillé-Jammes S, Coissac E, Cromsigt JPGM, Demmel MY, Donaldson JE, Guyton JA, Hansen CB, Imakando CI, Iqbal A, Kalima DF, Kerley GIH, Kurukura S, Landman M, Long RA, Munuo IN, Nutter CM, Parr CL, Potter AB, Siachoono S, Taberlet P, Waiti E, Kartzinel TR, Pringle RM (2022). The generality of cryptic dietary niche differentiation in diverse large-herbivore assemblages. Proceedings of the National Academy of Sciences, 119: e2204400119. 

 

• Lunghi E, Valle B, Guerrieri A, Bonin A, Cianferoni F, Manenti R, Ficetola GF (2022). Environmental DNA of insects and springtails from caves reveals complex processes of eDNA transfer in soils. Science of The Total Environment, 826, 154022.

​

- 2021 - 

​

• Ficetola GF, Marta S, Guerrieri A, Gobbi M, Ambrosini R, Fontaneto D, Zerboni A, Poulenard J, Caccianiga M, Thuiller W (2021). Dynamics of Ecological Communities Following Current Retreat of Glaciers. Annual Review of Ecology, Evolution, and Systematics, 52(1): 1-51. ​

​​

• Marta S, Azzoni RS, Fugazza D, Tielidze L, Sieron K, Chand P, Almond P, Ambrosini R, Anthelme F, Alviz Gazitúa P, Bhambri R, Bonin A, Caccianiga M, Cauvy-Fraunié S, Ceballos Lievano JL, Clague J, Cochachín Rapre JA, Dangles O, Deline P, Eger A, Encarnación RC, Erokhin S, Franzetti A, Gielly L, Gili F, Gobbi M, Guerrieri A, Hågvar S, Khedim N, Kinyanjui R, Messager E, Morales-Martínez MA, Peyre G, Pittino F, Poulenard J, Seppi R, Sharma MC, Urseitova N, Weissling BP, Yang Y, Zaginaev V, Zimmer A, Diolaiuti GA, Rabatel A, Ficetola GF (2021). The retreat of mountain glaciers since the Little Ice Age: a spatially explicit database. Data, 6: 107. 

 

• Pawlowski J, Bonin A, Boyer F, Cordier T, Taberlet T (2021). Environmental DNA for biomonitoring. Molecular Ecology, 30: 2931-2936. 

 

• Martins FMS, Feio MJ, Porto M, Filipe AF, Bonin A, Serra SRQ, Alves PC, Taberlet P, Beja P (2021). Assessing changes in stream macroinvertebrate communities across ecological gradients using morphological versus DNA metabarcoding approaches. Science of the Total Environment, 797: 149030. 

 

• Rodriguez-Ezpeleta N, Zinger L, Kinziger A Bik H, Bonin A, Coissac E, Emerson B, Lopes C, Pelletier T, Narum S (2021). Biodiversity monitoring using environmental DNA. Molecular Ecology Resources, 21: 1405-1409. 

 

• Guerrieri A, Bonin A, Münkemüller T, Gielly L, Thuiller W, Ficetola GF (2021). Effects of soil preservation for biodiversity monitoring using environmental DNA. Molecular Ecology, 30: 3313–3325. 

 

• Valle B, Cucini C, Nardi F, Caccianiga M, Gobbi M, Di Musciano M, Carapelli A, Ficetola GF, Guerrieri A, Fanciulli PP (2021). Desoria calderonis sp. nov., a new species of alpine cryophilic springtail (Collembola: Isotomidae) from the Apennines (Italy), with phylogenetic and ecological considerations. European Journal of Taxonomy, 787:32-52.

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• Cumer T, Pouchon C, Boyer F, Yannic G, Rioux D, Bonin A, Capblancq T (2021). Double-digest RAD-sequencing: do wet and dry protocol parameters impact biological results? Molecular Genetics and Genomics, 296: 457-471. 

 

• Marden E, Abbott RJ, Austerlitz F, Ortiz‐Barrientos D, Baucom RS, Pim Bongaerts, Bonin A, Bonneaud C, Browne L, CA Buerkle, Caicedo AL, Coltman DW, Cruzan MB, Davison A, DeWoody JA, Dumbrell AJ, Emerson BC, Fountain‐Jones NM, Gillespie R, Giraud T, Hansen MM, Hodgins KA, Heuertz M, Hirase S, Hooper R, Hohenlohe P, Kane NC, Kelley JL, Kinziger AP, McKenzie VJ, Moreau CS Nazareno AG, Pelletier TA, Pemberton JM, Qu Y, Renaut S, Riginos C, Rodríguez‐Ezpeleta N, Rogers SM, Russell JA, Schoville SD, Shi S, Smith M, Sork VL, Stone GN, Taberlet P, Videvall E, Waits L, Warschefsky E, Wayne RK, Whibley A, Willoughby J, Yoder JB, Zinger L, Sibbett B, Narum S, Rieseberg LH (2021). Sharing and reporting benefits from biodiversity research. Molecular Ecology, 30: 1103-1107. 

 

• Meyer A, Boyer F, Valentini A, Bonin A, Ficetola GF, Beisel J-N, Bouquerel J, Wagner P, Gaboriaud C, Leese F, Dejean T, Taberlet P, Usseglio-Polatera P (2021). Morphological vs. DNA metabarcoding approaches for the evaluation of stream ecological status with benthic invertebrates: Testing different combinations of markers and strategies of data filtering. Molecular Ecology, 30: 3203–3220. 

 

• Menaa JL, Yagui H, Tejeda V, Bonifaz E, Bellemain E, Valentini A, Tobler MW, Sánchez-Vendizú P & Lyet A (2021). Environmental DNA metabarcoding as a useful tool for evaluating terrestrial mammal diversity in tropical forests. Ecological Applications, 31: e02335.

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• Samaké A, Martins JMF, Bonin A, Uzu G, Taberlet P, Conil S, Favez O, Thomasson A, Chazeau B, Marchand N, Jaffrezo J-L (2021). Variability of the atmospheric PM10 microbiome in several climatic regions of France. Frontiers in Microbiology, 11: 576750.

​

• ​Pawlowski J, Bonin A, Boyer F, Cordier T, Taberlet T (2021). Environmental DNA for biomonitoring. Molecular Ecology, 30:2931–2936.

 

• Ficetola GF, Boyer F, Valentini A, Bonin A, Meyer A, Dejean T, Gaboriaud C, Usseglio-Polatera P, Taberlet P (2021). Comparison of markers for the monitoring of freshwater benthic biodiversity through DNA metabarcoding. Molecular Ecology, 30: 3189–3202.

​

- 2020 - 

​

• Rota N, Canedoli C, Ferrè C, Ficetola GF, Guerrieri A, Padoa-Schioppa E (2020). Evaluation of soil biodiversity in alpine habitats through eDNA metabarcoding and relationships with environmental features. Forests, 11: 738.

​​

• Samaké A, Bonin A, Jaffrezo J-L, Taberlet P, Weber S, Uzu G, Jacob V, Conil S, Martins JMF (2020). High levels of primary biogenic organic aerosols are driven by only a few plant-associated microbial taxa. Atmospheric Chemistry and Physics, 20: 5609–5628.

​

• Kitchener AC, Bellemain E, Kopatz A, Ruiz-García M, Mano T,  Tsuruga H, Hou W, Ding X, Hou Y, Kutschera VE, Janke A, Salomaskina V, Ruiz-García M (2020). Systematic, evolution and genetic of bears. In: Bears of the World: Ecology, Conservation and Management. Chapitre: 1.  Cambridge University Press.  

​

- 2019 - 

​

• 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 (2019). DNA metabarcoding - need for robust experimental designs to draw sound ecological conclusions. Molecular Ecology, 28: 1857-1852.

 

• Sessegolo C, Cruaud C, Da Silva C, Cologne A, Dubarry M, Derrien T, Lacroix V, Aury JM (2019). Transcriptome profiling of mouse samples using nanopore sequencing of cDNA and RNA molecules. Scientific Reports, 9(1): 12.

​

• 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(7): eaav8391.

 

• 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.

​

- 2018 - 

 

• 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.

​

- 2016 - 

 

• Sessegolo C, Burlet N, Haudry A (2016). Strong phylogenetic inertia on genome size and transposable element content among 26 species of flies. Biology Letters, 12(8): 8.

​

• 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, Besnard A, Coissac E, Boyer F, Gaboriaud C, Jean P, Poulet N, Roset N, Copp GH, Geniez P, Pont D, Argillier C, Baudoin JM, Peroux T, Crivelli AJ, Olivier A, Acqueberge M, Le Brun M, Møller PR, Willerslev E, Dejean T (2016). Next-generation monitoring of aquatic biodiversity using environmental DNA metabarcoding. Molecular Ecology, 25: 929–942.

 

• 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.

​

- 2015 - 

 

• Soininen EM, Gauthier G, Bilodeau F, Berteaux D, Gielly L, Taberlet P, Gussarova G, Bellemain E, Hassel C, Stenøien HK, Epp L, Schrøder-Nielsen A, Brochmann C, Yoccoz NG (2015). Highly overlapping winter diet in two sympatric lemming species revealed by DNA metabarcoding. PLoS ONE, 10: e0115335.

 

• 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.

​

- 2014 - ​

 

• 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. PLoS ONE, 9: e113414.

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• Willerslev E, Davison J, Moora M, Zobel M, Coissac E, Edwards ME, Lorenzen ED, Vestergård M, Gussarova G, Haile J, Craine J, Gielly L, Boessenkool S, Epp LS, Pearman PB, Cheddadi R, Murray D, Bråthen KA, Yoccoz N, Binney H, Cruaud C, Wincker P, Goslar T, Alsos IG, Bellemain E, Brysting AK, Elven R, Sønstebø JH, Murton J, Sher A, Rasmussen M, Rønn R, Mourier T, Cooper A, Austin J, Möller P, Froese D, Zazula G, Pompanon F, Rioux D, Niderkorn V, Tikhonov A, Savvinov G, Roberts RG, MacPhee RDE, P. Gilbert MT, Kjær KH, Orlando L, Brochmann C & Taberlet P (2014). Fifty thousand years of Arctic vegetation and megafaunal diet. Nature, 506: 47–51.

 

• 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.

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- 2013 - 

 

• 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 LS, Gussarova G, Hassel K, Henden JA, Killengreen ST, Rämä T, Stenøien HK, Yoccoz NG, Ims RA (2013). Shedding new light on the diet of Norwegian lemmings: DNA metabarcoding of stomach content. Polar Biology, 36: 1069-1076

 

• Bellemain E, Davey ML, Kauserud H, Epp LS, Boessenkool S, Coissac E, Geml J, Edwards M, Willerslev E, Gussarova G, Taberlet P, Haile J, Brochmann C (2013). Fungal paleodiversity revealed using high-throughput metabarcoding of ancient DNA from arctic permafrost. Environmental Microbiology, 15: 1176-1189.

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- 2012 - 

 

• Epp LS, Boessenkool S, Bellemain E, Haile J, Esposito A, Riaz T, Erséus C, Gusarov VI, Edwards ME, Johnsen A, Stenøien HK, Hassel K, Kauserud H, Yoccoz NG, Bråthen KA, 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: 1821-1833.

 

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

 

• Pompanon F, Bonin A (2012). Data Production and Analysis in Population Genomics. In: 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.

​

- 2011 - 

 

• 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: 114-123.

 

• 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 (2011). Genetics and conservation of European brown bears Ursus arctos. Mammal Review, 41: 87-97.

​

- 2010 - 

 

• 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, Després 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.

​

- 2009 - 

 

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

 

• Bonin A, Paris M, Tetreau G, David JP, Després 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.

​

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

​

- 2008 - 

 

• Bonin A, Paris M, Després 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.​

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- 2007 - 

 

• Manel S, Berthoud F, Bellemain E, Gaudeul M, Luikart G, Swenson JE, Waits LP, Taberlet P, the Intrabiodiv Consortium (2007). A new individual-based spatial approach for identifying genetic discontinuities in natural populations. 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, Després 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.

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- 2006 - 

 

• 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, Bessière J, Durand A, 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 KH, Bellemain E, Drageset O-M, Taberlet P, Swenson JE (2006). An evaluation of field and genetic methods to estimate brown bear (Ursus arctos) population size. Biological Conservation, 128: 158-168.

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- 2005 - 

 

• Pompanon F, Bonin A, Bellemain 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: 150-161.

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- 2004 - 

 

• 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.

 

• 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: 417-420.

 

• Bellemain E, Taberlet P (2004). Improved noninvasive genotyping method: application to brown bear (Ursus arctos) faeces. 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.