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Unlocking biodiversity and conservation studies in high diversity environments using environmental DNA (eDNA): a test with Guianese freshwater fishes.

Cilleros K, Valentini A, Allard L, Dejean T, Etienne R, Grenouillet G, Iribar A, Taberlet P, Vigouroux R, Brosse S.

Mol Ecol Resour. 2018 May 16. doi: 10.1111/1755-0998.12900. [Epub ahead of print]


DNA from lake sediments reveals long-term ecosystem changes after a biological invasion.

Ficetola GF, Poulenard J, Sabatier P, Messager E, Gielly L, Leloup A, Etienne D, Bakke J, Malet E, Fanget B, Støren E, Reyss JL, Taberlet P, Arnaud F.

Sci Adv. 2018 May 9;4(5):eaar4292. doi: 10.1126/sciadv.aar4292. eCollection 2018 May.


Convergent genomic signatures of domestication in sheep and goats.

Alberto FJ, Boyer F, Orozco-terWengel P, Streeter I, Servin B, de Villemereuil P, Benjelloun B, Librado P, Biscarini F, Colli L, Barbato M, Zamani W, Alberti A, Engelen S, Stella A, Joost S, Ajmone-Marsan P, Negrini R, Orlando L, Rezaei HR, Naderi S, Clarke L, Flicek P, Wincker P, Coissac E, Kijas J, Tosser-Klopp G, Chikhi A, Bruford MW, Taberlet P, Pompanon F.

Nat Commun. 2018 Mar 6;9(1):813. doi: 10.1038/s41467-018-03206-y.


Sheep genome functional annotation reveals proximal regulatory elements contributed to the evolution of modern breeds.

Naval-Sanchez M, Nguyen Q, McWilliam S, Porto-Neto LR, Tellam R, Vuocolo T, Reverter A, Perez-Enciso M, Brauning R, Clarke S, McCulloch A, Zamani W, Naderi S, Rezaei HR, Pompanon F, Taberlet P, Worley KC, Gibbs RA, Muzny DM, Jhangiani SN, Cockett N, Daetwyler H, Kijas J.

Nat Commun. 2018 Feb 28;9(1):859. doi: 10.1038/s41467-017-02809-1.


Lack of evidence for selection favouring MHC haplotypes that combine high functional diversity.

Gaigher A, Roulin A, Gharib WH, Taberlet P, Burri R, Fumagalli L.

Heredity (Edinb). 2018 May;120(5):396-406. doi: 10.1038/s41437-017-0047-9. Epub 2018 Jan 24.


Ancient environmental DNA reveals shifts in dominant mutualisms during the late Quaternary.

Zobel M, Davison J, Edwards ME, Brochmann C, Coissac E, Taberlet P, Willerslev E, Moora M.

Nat Commun. 2018 Jan 10;9(1):139. doi: 10.1038/s41467-017-02421-3.


Evaluating the impact of domestication and captivity on the horse gut microbiome.

Metcalf JL, Song SJ, Morton JT, Weiss S, Seguin-Orlando A, Joly F, Feh C, Taberlet P, Coissac E, Amir A, Willerslev E, Knight R, McKenzie V, Orlando L.

Sci Rep. 2017 Nov 14;7(1):15497. doi: 10.1038/s41598-017-15375-9.


Spatio-temporal monitoring of deep-sea communities using metabarcoding of sediment DNA and RNA.

Guardiola M, Wangensteen OS, Taberlet P, Coissac E, Uriz MJ, Turon X.

PeerJ. 2016 Dec 21;4:e2807. doi: 10.7717/peerj.2807. eCollection 2016.


Corrigendum to "Evolution and taxonomy of the wild species of the genus Ovis (Mammalia, Artiodactyla, Bovidae)" [Mol. Phylogenet. Evol. 54(2) (2010) 315-326].

Rezaei HR, Naderi S, Chintauan-Marquier IC, Jordan S, Taberlet P, Virk AT, Naghash HR, Rioux D, Kaboli M, Luikart G, Pompanon F.

Mol Phylogenet Evol. 2017 Apr;109:465. doi: 10.1016/j.ympev.2016.11.011. Epub 2016 Nov 27. No abstract available.


High performance computation of landscape genomic models including local indicators of spatial association.

Stucki S, Orozco-terWengel P, Forester BR, Duruz S, Colli L, Masembe C, Negrini R, Landguth E, Jones MR; NEXTGEN Consortium, Bruford MW, Taberlet P, Joost S.

Mol Ecol Resour. 2017 Sep;17(5):1072-1089. doi: 10.1111/1755-0998.12629. Epub 2016 Nov 28.


Inferring neutral biodiversity parameters using environmental DNA data sets.

Sommeria-Klein G, Zinger L, Taberlet P, Coissac E, Chave J.

Sci Rep. 2016 Oct 20;6:35644. doi: 10.1038/srep35644.


Detection of Invasive Mosquito Vectors Using Environmental DNA (eDNA) from Water Samples.

Schneider J, Valentini A, Dejean T, Montarsi F, Taberlet P, Glaizot O, Fumagalli L.

PLoS One. 2016 Sep 14;11(9):e0162493. doi: 10.1371/journal.pone.0162493. eCollection 2016.


High-throughput microsatellite genotyping in ecology: improved accuracy, efficiency, standardization and success with low-quantity and degraded DNA.

De Barba M, Miquel C, Lobréaux S, Quenette PY, Swenson JE, Taberlet P.

Mol Ecol Resour. 2017 May;17(3):492-507. doi: 10.1111/1755-0998.12594. Epub 2016 Aug 29.


Understanding the evolution of holoparasitic plants: the complete plastid genome of the holoparasite Cytinus hypocistis (Cytinaceae).

Roquet C, Coissac É, Cruaud C, Boleda M, Boyer F, Alberti A, Gielly L, Taberlet P, Thuiller W, Van Es J, Lavergne S.

Ann Bot. 2016 Jul 21. pii: mcw135. [Epub ahead of print]


Spatial Representativeness of Environmental DNA Metabarcoding Signal for Fish Biodiversity Assessment in a Natural Freshwater System.

Civade R, Dejean T, Valentini A, Roset N, Raymond JC, Bonin A, Taberlet P, Pont D.

PLoS One. 2016 Jun 30;11(6):e0157366. doi: 10.1371/journal.pone.0157366. eCollection 2016.


Using metabarcoding to reveal and quantify plant-pollinator interactions.

Pornon A, Escaravage N, Burrus M, Holota H, Khimoun A, Mariette J, Pellizzari C, Iribar A, Etienne R, Taberlet P, Vidal M, Winterton P, Zinger L, Andalo C.

Sci Rep. 2016 Jun 3;6:27282. doi: 10.1038/srep27282.


Family-assisted inference of the genetic architecture of major histocompatibility complex variation.

Gaigher A, Burri R, Gharib WH, Taberlet P, Roulin A, Fumagalli L.

Mol Ecol Resour. 2016 Nov;16(6):1353-1364. doi: 10.1111/1755-0998.12537. Epub 2016 Jun 4.


Testing the potential of a ribosomal 16S marker for DNA metabarcoding of insects.

Elbrecht V, Taberlet P, Dejean T, Valentini A, Usseglio-Polatera P, Beisel JN, Coissac E, Boyer F, Leese F.

PeerJ. 2016 Apr 19;4:e1966. doi: 10.7717/peerj.1966. eCollection 2016.


Correction: Deep-Sea, Deep-Sequencing: Metabarcoding Extracellular DNA from Sediments of Marine Canyons.

Guardiola M, Uriz MJ, Taberlet P, Coissac E, Wangensteen OS, Turon X.

PLoS One. 2016 Apr 13;11(4):e0153836. doi: 10.1371/journal.pone.0153836. eCollection 2016. No abstract available.


How to limit false positives in environmental DNA and metabarcoding?

Ficetola GF, Taberlet P, Coissac E.

Mol Ecol Resour. 2016 May;16(3):604-7. doi: 10.1111/1755-0998.12508.


Oral Samples as Non-Invasive Proxies for Assessing the Composition of the Rumen Microbial Community.

Tapio I, Shingfield KJ, McKain N, Bonin A, Fischer D, Bayat AR, Vilkki J, Taberlet P, Snelling TJ, Wallace RJ.

PLoS One. 2016 Mar 17;11(3):e0151220. doi: 10.1371/journal.pone.0151220. eCollection 2016.


From barcodes to genomes: extending the concept of DNA barcoding.

Coissac E, Hollingsworth PM, Lavergne S, Taberlet P.

Mol Ecol. 2016 Apr;25(7):1423-8. doi: 10.1111/mec.13549. Epub 2016 Mar 14.


Whole mitochondrial genomes unveil the impact of domestication on goat matrilineal variability.

Colli L, Lancioni H, Cardinali I, Olivieri A, Capodiferro MR, Pellecchia M, Rzepus M, Zamani W, Naderi S, Gandini F, Vahidi SM, Agha S, Randi E, Battaglia V, Sardina MT, Portolano B, Rezaei HR, Lymberakis P, Boyer F, Coissac E, Pompanon F, Taberlet P, Ajmone Marsan P, Achilli A.

BMC Genomics. 2015 Dec 29;16:1115. doi: 10.1186/s12864-015-2342-2.


Next-generation monitoring of aquatic biodiversity using environmental DNA metabarcoding.

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.

Mol Ecol. 2016 Feb;25(4):929-42. doi: 10.1111/mec.13428. Epub 2016 Jan 18.


Deep-Sea, Deep-Sequencing: Metabarcoding Extracellular DNA from Sediments of Marine Canyons.

Guardiola M, Uriz MJ, Taberlet P, Coissac E, Wangensteen OS, Turon X.

PLoS One. 2015 Oct 5;10(10):e0139633. doi: 10.1371/journal.pone.0139633. eCollection 2015. Erratum in: PLoS One. 2016;11(4):e0153836.


Long-lasting modification of soil fungal diversity associated with the introduction of rabbits to a remote sub-Antarctic archipelago.

Pansu J, Winkworth RC, Hennion F, Gielly L, Taberlet P, Choler P.

Biol Lett. 2015 Sep;11(9):20150408. doi: 10.1098/rsbl.2015.0408.


Upscaling the niche variation hypothesis from the intra- to the inter-specific level.

Bison M, Ibanez S, Redjadj C, Boyer F, Coissac E, Miquel C, Rioux D, Said S, Maillard D, Taberlet P, Yoccoz NG, Loison A.

Oecologia. 2015 Nov;179(3):835-42. doi: 10.1007/s00442-015-3390-7. Epub 2015 Jul 22.


Metagenome skimming for phylogenetic community ecology: a new era in biodiversity research.

Papadopoulou A, Taberlet P, Zinger L.

Mol Ecol. 2015 Jul;24(14):3515-7. doi: 10.1111/mec.13263.


obitools: a unix-inspired software package for DNA metabarcoding.

Boyer F, Mercier C, Bonin A, Le Bras Y, Taberlet P, Coissac E.

Mol Ecol Resour. 2016 Jan;16(1):176-82. doi: 10.1111/1755-0998.12428. Epub 2015 May 26.


Characterizing neutral genomic diversity and selection signatures in indigenous populations of Moroccan goats (Capra hircus) using WGS data.

Benjelloun B, Alberto FJ, Streeter I, Boyer F, Coissac E, Stucki S, BenBati M, Ibnelbachyr M, Chentouf M, Bechchari A, Leempoel K, Alberti A, Engelen S, Chikhi A, Clarke L, Flicek P, Joost S, Taberlet P, Pompanon F; NextGen Consortium.

Front Genet. 2015 Apr 7;6:107. doi: 10.3389/fgene.2015.00107. eCollection 2015.


Reconstructing long-term human impacts on plant communities: an ecological approach based on lake sediment DNA.

Pansu J, Giguet-Covex C, Ficetola GF, Gielly L, Boyer F, Zinger L, Arnaud F, Poulenard J, Taberlet P, Choler P.

Mol Ecol. 2015 Apr;24(7):1485-98. doi: 10.1111/mec.13136. Epub 2015 Mar 23.


DNA metabarcoding diet analysis for species with parapatric vs sympatric distribution: a case study on subterranean rodents.

Lopes CM, De Barba M, Boyer F, Mercier C, da Silva Filho PJ, Heidtmann LM, Galiano D, Kubiak BB, Langone P, Garcias FM, Gielly L, Coissac E, de Freitas TR, Taberlet P.

Heredity (Edinb). 2015 May;114(5):525-36. doi: 10.1038/hdy.2014.109. Epub 2015 Feb 4.


Highly overlapping winter diet in two sympatric lemming species revealed by DNA metabarcoding.

Soininen EM, Gauthier G, Bilodeau F, Berteaux D, Gielly L, Taberlet P, Gussarova G, Bellemain E, Hassel K, Stenøien HK, Epp L, Schrøder-Nielsen A, Brochmann C, Yoccoz NG.

PLoS One. 2015 Jan 30;10(1):e0115335. doi: 10.1371/journal.pone.0115335. eCollection 2015.


No evidence for the effect of MHC on male mating success in the brown bear.

Kuduk K, Babik W, Bellemain E, Valentini A, Zedrosser A, Taberlet P, Kindberg J, Swenson JE, Radwan J.

PLoS One. 2014 Dec 3;9(12):e113414. doi: 10.1371/journal.pone.0113414. eCollection 2014.


Replication levels, false presences and the estimation of the presence/absence from eDNA metabarcoding data.

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.

Mol Ecol Resour. 2015 May;15(3):543-56. doi: 10.1111/1755-0998.12338. Epub 2014 Nov 10.


DNA metabarcoding and the cytochrome c oxidase subunit I marker: not a perfect match.

Deagle BE, Jarman SN, Coissac E, Pompanon F, Taberlet P.

Biol Lett. 2014 Sep;10(9). pii: 20140562. doi: 10.1098/rsbl.2014.0562.


Fifty thousand years of Arctic vegetation and megafaunal diet.

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 RD, Gilbert MT, Kjær KH, Orlando L, Brochmann C, Taberlet P.

Nature. 2014 Feb 6;506(7486):47-51. doi: 10.1038/nature12921.


Long livestock farming history and human landscape shaping revealed by lake sediment DNA.

Giguet-Covex C, Pansu J, Arnaud F, Rey PJ, Griggo C, Gielly L, Domaizon I, Coissac E, David F, Choler P, Poulenard J, Taberlet P.

Nat Commun. 2014;5:3211. doi: 10.1038/ncomms4211.


Fast and efficient DNA-based method for winter diet analysis from stools of three cervids: moose, red deer, and roe deer.

Czernik M, Taberlet P, Swisłocka M, Czajkowska M, Duda N, Ratkiewicz M.

Acta Theriol (Warsz). 2013;58:379-386. Epub 2013 May 17.


DNA metabarcoding multiplexing and validation of data accuracy for diet assessment: application to omnivorous diet.

De Barba M, Miquel C, Boyer F, Mercier C, Rioux D, Coissac E, Taberlet P.

Mol Ecol Resour. 2014 Mar;14(2):306-23. doi: 10.1111/1755-0998.12188. Epub 2013 Nov 16.


Effect of DNA extraction and sample preservation method on rumen bacterial population.

Fliegerova K, Tapio I, Bonin A, Mrazek J, Callegari ML, Bani P, Bayat A, Vilkki J, Kopečný J, Shingfield KJ, Boyer F, Coissac E, Taberlet P, Wallace RJ.

Anaerobe. 2014 Oct;29:80-4. doi: 10.1016/j.anaerobe.2013.09.015. Epub 2013 Oct 12.


Plant functional traits reveal the relative contribution of habitat and food preferences to the diet of grasshoppers.

Ibanez S, Manneville O, Miquel C, Taberlet P, Valentini A, Aubert S, Coissac E, Colace MP, Duparc Q, Lavorel S, Moretti M.

Oecologia. 2013 Dec;173(4):1459-70. doi: 10.1007/s00442-013-2738-0. Epub 2013 Oct 6.


Genetic roadmap of the Arctic: plant dispersal highways, traffic barriers and capitals of diversity.

Eidesen PB, Ehrich D, Bakkestuen V, Alsos IG, Gilg O, Taberlet P, Brochmann C.

New Phytol. 2013 Nov;200(3):898-910. doi: 10.1111/nph.12412. Epub 2013 Jul 22.


Unveiling the diet of elusive rainforest herbivores in next generation sequencing era? The tapir as a case study.

Hibert F, Taberlet P, Chave J, Scotti-Saintagne C, Sabatier D, Richard-Hansen C.

PLoS One. 2013;8(4):e60799. doi: 10.1371/journal.pone.0060799. Epub 2013 Apr 1.


A DNA metabarcoding study of a primate dietary diversity and plasticity across its entire fragmented range.

Quéméré E, Hibert F, Miquel C, Lhuillier E, Rasolondraibe E, Champeau J, Rabarivola C, Nusbaumer L, Chatelain C, Gautier L, Ranirison P, Crouau-Roy B, Taberlet P, Chikhi L.

PLoS One. 2013;8(3):e58971. doi: 10.1371/journal.pone.0058971. Epub 2013 Mar 19.


Fungal palaeodiversity revealed using high-throughput metabarcoding of ancient DNA from arctic permafrost.

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.

Environ Microbiol. 2013 Apr;15(4):1176-89. doi: 10.1111/1462-2920.12020. Epub 2012 Nov 22. Erratum in: Environ Microbiol. 2013 Jul;15(7):2146. Haile, James [added].


Evolution of major histocompatibility complex class I and class II genes in the brown bear.

Kuduk K, Babik W, Bojarska K, Sliwińska EB, Kindberg J, Taberlet P, Swenson JE, Radwan J.

BMC Evol Biol. 2012 Oct 2;12:197. doi: 10.1186/1471-2148-12-197.


Genetic diversity in widespread species is not congruent with species richness in alpine plant communities.

Taberlet P, Zimmermann NE, Englisch T, Tribsch A, Holderegger R, Alvarez N, Niklfeld H, Coldea G, Mirek Z, Moilanen A, Ahlmer W, Marsan PA, Bona E, Bovio M, Choler P, Cieślak E, Colli L, Cristea V, Dalmas JP, Frajman B, Garraud L, Gaudeul M, Gielly L, Gutermann W, Jogan N, Kagalo AA, Korbecka G, Küpfer P, Lequette B, Letz DR, Manel S, Mansion G, Marhold K, Martini F, Negrini R, Niño F, Paun O, Pellecchia M, Perico G, Piękoś-Mirkowa H, Prosser F, Puşcaş M, Ronikier M, Scheuerer M, Schneeweiss GM, Schönswetter P, Schratt-Ehrendorfer L, Schüpfer F, Selvaggi A, Steinmann K, Thiel-Egenter C, van Loo M, Winkler M, Wohlgemuth T, Wraber T, Gugerli F; IntraBioDiv Consortium, Vellend M.

Ecol Lett. 2012 Dec;15(12):1439-48. doi: 10.1111/ele.12004. Epub 2012 Sep 25.


Major histocompatibility complex class II compatibility, but not class I, predicts mate choice in a bird with highly developed olfaction.

Strandh M, Westerdahl H, Pontarp M, Canbäck B, Dubois MP, Miquel C, Taberlet P, Bonadonna F.

Proc Biol Sci. 2012 Nov 7;279(1746):4457-63. Epub 2012 Sep 5.


Broad-scale adaptive genetic variation in alpine plants is driven by temperature and precipitation.

Manel S, Gugerli F, Thuiller W, Alvarez N, Legendre P, Holderegger R, Gielly L, Taberlet P; IntraBioDiv Consortium.

Mol Ecol. 2012 Aug;21(15):3729-38. doi: 10.1111/j.1365-294X.2012.05656.x. Epub 2012 Jun 10.

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