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Items: 48

1.

An evaluation of sequencing coverage and genotyping strategies to assess neutral and adaptive diversity.

Benjelloun B, Boyer F, Streeter I, Zamani W, Engelen S, Alberti A, Alberto FJ, BenBati M, Ibnelbachyr M, Chentouf M, Bechchari A, Rezaei HR, Naderi S, Stella A, Chikhi A, Clarke L, Kijas J, Flicek P, Taberlet P, Pompanon F.

Mol Ecol Resour. 2019 Nov;19(6):1497-1515. doi: 10.1111/1755-0998.13070. Epub 2019 Sep 9.

PMID:
31359622
2.

Genetic homogenization of indigenous sheep breeds in Northwest Africa.

Belabdi I, Ouhrouch A, Lafri M, Gaouar SBS, Ciani E, Benali AR, Ould Ouelhadj H, Haddioui A, Pompanon F, Blanquet V, Taurisson-Mouret D, Harkat S, Lenstra JA, Benjelloun B, Da Silva A.

Sci Rep. 2019 May 28;9(1):7920. doi: 10.1038/s41598-019-44137-y.

3.

[Homologous genomic signatures of domestication in goat and sheep].

Pompanon F.

Med Sci (Paris). 2018 Nov;34(11):916-919. doi: 10.1051/medsci/2018229. Epub 2018 Dec 10. French. No abstract available.

4.

Genetic homogeneity of North-African goats.

Ouchene-Khelifi NA, Lafri M, Pompanon F, Ouhrouch A, Ouchene N, Blanquet V, Lenstra JA, Benjelloun B, Da Silva A.

PLoS One. 2018 Aug 16;13(8):e0202196. doi: 10.1371/journal.pone.0202196. eCollection 2018.

5.

Old origin of a protective endogenous retrovirus (enJSRV) in the Ovis genus.

Cumer T, Pompanon F, Boyer F.

Heredity (Edinb). 2019 Feb;122(2):187-194. doi: 10.1038/s41437-018-0112-z. Epub 2018 Jul 5.

PMID:
29976957
6.

Ancient goat genomes reveal mosaic domestication in the Fertile Crescent.

Daly KG, Maisano Delser P, Mullin VE, Scheu A, Mattiangeli V, Teasdale MD, Hare AJ, Burger J, Verdugo MP, Collins MJ, Kehati R, Erek CM, Bar-Oz G, Pompanon F, Cumer T, Çakırlar C, Mohaseb AF, Decruyenaere D, Davoudi H, Çevik Ö, Rollefson G, Vigne JD, Khazaeli R, Fathi H, Doost SB, Rahimi Sorkhani R, Vahdati AA, Sauer EW, Azizi Kharanaghi H, Maziar S, Gasparian B, Pinhasi R, Martin L, Orton D, Arbuckle BS, Benecke N, Manica A, Horwitz LK, Mashkour M, Bradley DG.

Science. 2018 Jul 6;361(6397):85-88. doi: 10.1126/science.aas9411.

PMID:
29976826
7.

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.

8.

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.

9.

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.

PMID:
27899018
10.

Microsatellite diversity of the Nordic type of goats in relation to breed conservation: how relevant is pure ancestry?

Lenstra JA, Tigchelaar J, Biebach I; Econogene Consortium, Hallsson JH, Kantanen J, Nielsen VH, Pompanon F, Naderi S, Rezaei HR, Saether N, Ertugrul O, Grossen C, Camenisch G, Vos-Loohuis M, van Straten M, de Poel EA, Windig J, Oldenbroek K.

J Anim Breed Genet. 2017 Feb;134(1):78-84. doi: 10.1111/jbg.12226. Epub 2016 Jun 24.

PMID:
27339108
11.

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.

12.

Prospects and challenges for the conservation of farm animal genomic resources, 2015-2025.

Bruford MW, Ginja C, Hoffmann I, Joost S, Orozco-terWengel P, Alberto FJ, Amaral AJ, Barbato M, Biscarini F, Colli L, Costa M, Curik I, Duruz S, Ferenčaković M, Fischer D, Fitak R, Groeneveld LF, Hall SJ, Hanotte O, Hassan FU, Helsen P, Iacolina L, Kantanen J, Leempoel K, Lenstra JA, Ajmone-Marsan P, Masembe C, Megens HJ, Miele M, Neuditschko M, Nicolazzi EL, Pompanon F, Roosen J, Sevane N, Smetko A, Štambuk A, Streeter I, Stucki S, Supakorn C, Telo Da Gama L, Tixier-Boichard M, Wegmann D, Zhan X.

Front Genet. 2015 Oct 21;6:314. doi: 10.3389/fgene.2015.00314. eCollection 2015.

13.

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.

14.

Next generation sequencing for characterizing biodiversity: promises and challenges.

Pompanon F, Samadi S.

Genetica. 2015 Apr;143(2):133-8. doi: 10.1007/s10709-015-9816-7. Epub 2015 Jan 23.

PMID:
25613325
15.

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.

PMID:
25327646
16.

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.

17.

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.

PMID:
24499916
18.

Optimizing the trade-off between spatial and genetic sampling efforts in patchy populations: towards a better assessment of functional connectivity using an individual-based sampling scheme.

Prunier JG, Kaufmann B, Fenet S, Picard D, Pompanon F, Joly P, Lena JP.

Mol Ecol. 2013 Nov;22(22):5516-30. doi: 10.1111/mec.12499. Epub 2013 Oct 7.

PMID:
24118539
19.

Inside the Melanoplinae: new molecular evidence for the evolutionary history of the Eurasian Podismini (Orthoptera: Acrididae).

Chintauan-Marquier IC, Amédégnato C, Nichols RA, Pompanon F, Grandcolas P, Desutter-Grandcolas L.

Mol Phylogenet Evol. 2014 Feb;71:224-33. doi: 10.1016/j.ympev.2013.09.009. Epub 2013 Sep 23.

PMID:
24071559
20.

DNA from soil mirrors plant taxonomic and growth form diversity.

Yoccoz NG, Bråthen KA, Gielly L, Haile J, Edwards ME, Goslar T, Von Stedingk H, Brysting AK, Coissac E, Pompanon F, Sønstebø JH, Miquel C, Valentini A, De Bello F, Chave J, Thuiller W, Wincker P, Cruaud C, Gavory F, Rasmussen M, Gilbert MT, Orlando L, Brochmann C, Willerslev E, Taberlet P.

Mol Ecol. 2012 Aug;21(15):3647-55. doi: 10.1111/j.1365-294X.2012.05545.x. Epub 2012 Apr 16.

PMID:
22507540
21.

Towards next-generation biodiversity assessment using DNA metabarcoding.

Taberlet P, Coissac E, Pompanon F, Brochmann C, Willerslev E.

Mol Ecol. 2012 Apr;21(8):2045-50. doi: 10.1111/j.1365-294X.2012.05470.x.

PMID:
22486824
22.

Prey preference of snow leopard (Panthera uncia) in South Gobi, Mongolia.

Shehzad W, McCarthy TM, Pompanon F, Purevjav L, Coissac E, Riaz T, Taberlet P.

PLoS One. 2012;7(2):e32104. doi: 10.1371/journal.pone.0032104. Epub 2012 Feb 29.

23.

Soil sampling and isolation of extracellular DNA from large amount of starting material suitable for metabarcoding studies.

Taberlet P, Prud'Homme SM, Campione E, Roy J, Miquel C, Shehzad W, Gielly L, Rioux D, Choler P, Clément JC, Melodelima C, Pompanon F, Coissac E.

Mol Ecol. 2012 Apr;21(8):1816-20. doi: 10.1111/j.1365-294X.2011.05317.x. Epub 2012 Feb 2.

PMID:
22300434
24.

A dig into the past mitochondrial diversity of Corsican goats reveals the influence of secular herding practices.

Hughes S, Fernández H, Cucchi T, Duffraisse M, Casabianca F, Istria D, Pompanon F, Vigne JD, Hänni C, Taberlet P.

PLoS One. 2012;7(1):e30272. doi: 10.1371/journal.pone.0030272. Epub 2012 Jan 27.

25.

Carnivore diet analysis based on next-generation sequencing: application to the leopard cat (Prionailurus bengalensis) in Pakistan.

Shehzad W, Riaz T, Nawaz MA, Miquel C, Poillot C, Shah SA, Pompanon F, Coissac E, Taberlet P.

Mol Ecol. 2012 Apr;21(8):1951-65. doi: 10.1111/j.1365-294X.2011.05424.x. Epub 2012 Jan 17.

PMID:
22250784
26.

Skin swabbing as a new efficient DNA sampling technique in amphibians, and 14 new microsatellite markers in the alpine newt (Ichthyosaura alpestris).

Prunier J, Kaufmann B, Grolet O, Picard D, Pompanon F, Joly P.

Mol Ecol Resour. 2012 May;12(3):524-31. doi: 10.1111/j.1755-0998.2012.03116.x. Epub 2012 Jan 17.

PMID:
22248363
27.

Who is eating what: diet assessment using next generation sequencing.

Pompanon F, Deagle BE, Symondson WO, Brown DS, Jarman SN, Taberlet P.

Mol Ecol. 2012 Apr;21(8):1931-50. doi: 10.1111/j.1365-294X.2011.05403.x. Epub 2011 Dec 15. Review.

PMID:
22171763
28.

ecoPrimers: inference of new DNA barcode markers from whole genome sequence analysis.

Riaz T, Shehzad W, Viari A, Pompanon F, Taberlet P, Coissac E.

Nucleic Acids Res. 2011 Nov;39(21):e145. doi: 10.1093/nar/gkr732. Epub 2011 Sep 19.

29.

Persistence of environmental DNA in freshwater ecosystems.

Dejean T, Valentini A, Duparc A, Pellier-Cuit S, Pompanon F, Taberlet P, Miaud C.

PLoS One. 2011;6(8):e23398. doi: 10.1371/journal.pone.0023398. Epub 2011 Aug 8.

30.

Conservation genetics of cattle, sheep, and goats.

Taberlet P, Coissac E, Pansu J, Pompanon F.

C R Biol. 2011 Mar;334(3):247-54. doi: 10.1016/j.crvi.2010.12.007. Epub 2011 Feb 1. Review.

PMID:
21377620
31.

Evolutionary history and taxonomy of a short-horned grasshopper subfamily: the Melanoplinae (Orthoptera: Acrididae).

Chintauan-Marquier IC, Jordan S, Berthier P, Amédégnato C, Pompanon F.

Mol Phylogenet Evol. 2011 Jan;58(1):22-32. doi: 10.1016/j.ympev.2010.07.003. Epub 2010 Jul 17.

PMID:
20643218
32.

An in silico approach for the evaluation of DNA barcodes.

Ficetola GF, Coissac E, Zundel S, Riaz T, Shehzad W, Bessière J, Taberlet P, Pompanon F.

BMC Genomics. 2010 Jul 16;11:434. doi: 10.1186/1471-2164-11-434.

33.

Evolution and taxonomy of the wild species of the genus Ovis (Mammalia, Artiodactyla, Bovidae).

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. 2010 Feb;54(2):315-26. doi: 10.1016/j.ympev.2009.10.037. Epub 2009 Nov 6. Erratum in: Mol Phylogenet Evol. 2017 Apr;109 :465.

PMID:
19897045
34.

Universal DNA-based methods for assessing the diet of grazing livestock and wildlife from feces.

Pegard A, Miquel C, Valentini A, Coissac E, Bouvier F, François D, Taberlet P, Engel E, Pompanon F.

J Agric Food Chem. 2009 Jul 8;57(13):5700-6. doi: 10.1021/jf803680c.

PMID:
19566081
35.

New perspectives in diet analysis based on DNA barcoding and parallel pyrosequencing: the trnL approach.

Valentini A, Miquel C, Nawaz MA, Bellemain E, Coissac E, Pompanon F, Gielly L, Cruaud C, Nascetti G, Wincker P, Swenson JE, Taberlet P.

Mol Ecol Resour. 2009 Jan;9(1):51-60. doi: 10.1111/j.1755-0998.2008.02352.x. Epub 2008 Oct 22.

PMID:
21564566
36.

DNA barcoding for ecologists.

Valentini A, Pompanon F, Taberlet P.

Trends Ecol Evol. 2009 Feb;24(2):110-7. doi: 10.1016/j.tree.2008.09.011. Epub 2008 Dec 25. Review.

PMID:
19100655
37.

The goat domestication process inferred from large-scale mitochondrial DNA analysis of wild and domestic individuals.

Naderi S, Rezaei HR, Pompanon F, Blum MG, Negrini R, Naghash HR, Balkiz O, Mashkour M, Gaggiotti OE, Ajmone-Marsan P, Kence A, Vigne JD, Taberlet P.

Proc Natl Acad Sci U S A. 2008 Nov 18;105(46):17659-64. doi: 10.1073/pnas.0804782105. Epub 2008 Nov 12.

38.

Species detection using environmental DNA from water samples.

Ficetola GF, Miaud C, Pompanon F, Taberlet P.

Biol Lett. 2008 Aug 23;4(4):423-5. doi: 10.1098/rsbl.2008.0118.

39.

CE-SSCP and CE-FLA, simple and high-throughput alternatives for fungal diversity studies.

Zinger L, Gury J, Alibeu O, Rioux D, Gielly L, Sage L, Pompanon F, Geremia RA.

J Microbiol Methods. 2008 Jan;72(1):42-53. Epub 2007 Oct 18. Erratum in: J Microbiol Methods. 2008 May;73(2):209.

PMID:
18054096
40.

Are cattle, sheep, and goats endangered species?

Taberlet P, Valentini A, Rezaei HR, Naderi S, Pompanon F, Negrini R, Ajmone-Marsan P.

Mol Ecol. 2008 Jan;17(1):275-84. Epub 2007 Oct 8.

PMID:
17927711
41.

Large-scale mitochondrial DNA analysis of the domestic goat reveals six haplogroups with high diversity.

Naderi S, Rezaei HR, Taberlet P, Zundel S, Rafat SA, Naghash HR, el-Barody MA, Ertugrul O, Pompanon F; Econogene Consortium.

PLoS One. 2007 Oct 10;2(10):e1012.

42.

Population adaptive index: a new method to help measure intraspecific genetic diversity and prioritize populations for conservation.

Bonin A, Nicole F, Pompanon F, Miaud C, Taberlet P.

Conserv Biol. 2007 Jun;21(3):697-708.

PMID:
17531048
43.

Power and limitations of the chloroplast trnL (UAA) intron for plant DNA barcoding.

Taberlet P, Coissac E, Pompanon F, Gielly L, Miquel C, Valentini A, Vermat T, Corthier G, Brochmann C, Willerslev E.

Nucleic Acids Res. 2007;35(3):e14. Epub 2006 Dec 14.

44.

Explorative genome scan to detect candidate loci for adaptation along a gradient of altitude in the common frog (Rana temporaria).

Bonin A, Taberlet P, Miaud C, Pompanon F.

Mol Biol Evol. 2006 Apr;23(4):773-83. Epub 2006 Jan 5.

PMID:
16396915
45.

Genotyping errors: causes, consequences and solutions.

Pompanon F, Bonin A, Bellemain E, Taberlet P.

Nat Rev Genet. 2005 Nov;6(11):847-59. Review.

PMID:
16304600
46.

Use of amplified fragment length polymorphism (AFLP) markers in surveys of vertebrate diversity.

Bonin A, Pompanon F, Taberlet P.

Methods Enzymol. 2005;395:145-61.

PMID:
15865966
47.

How to track and assess genotyping errors in population genetics studies.

Bonin A, Bellemain E, Bronken Eidesen P, Pompanon F, Brochmann C, Taberlet P.

Mol Ecol. 2004 Nov;13(11):3261-73.

PMID:
15487987
48.

Speciation in the globeflower fly Chiastocheta spp. (Diptera: Anthomyiidae) in relation to host plant species, biogeography, and morphology.

Després L, Pettex E, Plaisance V, Pompanon F.

Mol Phylogenet Evol. 2002 Feb;22(2):258-68.

PMID:
11820846

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