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1. Normal force and displacement amplitude influences on silver-plated electrical contacts subjected to fretting wear: A basic friction energy – contact compliance formulation

Author: Pompanon, F., Laporte, J., Fouvry, S., and Alquier, O.
Published: 2019
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2. Effects of isothermal crystallization on the mechanical properties of a elastomeric medium chain length polyhydroxyalkanoate

Author: Larrañaga, A., Pompanon, F., Gruffat, N., Palomares, T., Alonso-Varona, A., Larrañaga Varga, A., Fernandez-Yague, M.A., Biggs, M.J.P., and Sarasua, J.R.
Published: 2016
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3. Y-chromosomal haplogroups from wild and domestic goats reveal ancient migrations and recent introgressions

Author: Lenstra, J.A., Consortium, VarGoats, Nijman, I.J., Rosen, B.D., Bardou, P., Faraut, T., Cumer, T., Daly, K.G., Zheng, Z., Cai, Y., Asadollahpour, H., Kul, Çınar B., Zhang, W.-Y., E, G., Ayin, A., Bakhtin, M., Balteanu, V.A., Barfield, D., Baird, H., Berger, B., Blichfeldt, T., Boink, G., Bugiwati, S.R.A., Cai, Z., Carolan, S., Clark, E., Cubric-Curik, V., Dagong, M.I.A., Dorji, T., Drew, L., Guo, J., Hallsson, J., Horvat, S., Kantanen, J., Kawaguchi, F., Kazymbet, P., Khayatzadeh, N., Kim, N., Kumar Shah, M., Liao, Y., Martínez, A., Masangkay, J.S., Masaoka, M., Mazza, R., McEwan, J., Milanesi, M., Omar, F.Md., Nomura, Y., Ouchene-Khelifi, N.-A., Pereira, F., Sahana, G., Sasazaki, S., Da Silva, A., Simčič, M., Sölkner, J., Sutherland, A., Tigchelaar, J., Zhang, H., Consortium, Econogene, Ajmone-Marsan, P., Bradley, D.G., Colli, L., Drögemüller, C., Lei, C., Mannen, H., Pompanon, F., Tosser-Klopp, G., Jiang, Y., Veerkamp, R. F., and de Haas, Y.
Subjects: 630 Agriculture, 590 Animals (Zoology), 570 Life sciences, biology
Abstract: By its paternal transmission, Y-chromosomal haplotypes are sensitive markers of population history and male-mediated introgression. We used whole-genome sequences (WGSs) of 386 domestic goats from 75 modern breeds and 7 wild goat species generated by the VarGoats goat genome project. Phylogenetic analyses indicated five domestic haplogroups Y1AA, Y1AB, Y1B, Y2A and Y2B. Haplogroup distributions for 180 domestic breeds indicate ancient paternal population bottlenecks during the migration into northern Europe, southern Asia and Africa. Sharing of haplogroups reveals male-mediated introgressions: from Asia into Madagascar and, more recently, into the South-African Boer goat; then from this breed into other southeastern African goats; and from Europe into native Korean and Ugandan goats. This study illustrates the power of the Y-chromosomal variation for the reconstructing the history of domestic species with a wide geographic range.
Published: 2023

4. Influence of the relative humidity and H2S - SO2 polluted air on the fretting wear behavior of silver-plated electrical contacts

Author: Pompanon, F., primary, Fouvry, S., additional, and Alquier, O., additional
Published: 2022
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5. Geographical contrasts of Y-chromosomal haplogroups from wild and domestic goats reveal ancient migrations and recent introgressions

Author: Nijman, I. J., Rosen, B. D., Bardou, P., Faraut, T., Cumer, T., Daly, K. G., Zheng, Z., Cai, Y., Asadollahpour, H., Kul, B. C., Zhang, W. -Y., Guangxin, E., Ayin, A., Baird, H., Bakhtin, M., Balteanu, V. A., Barfield, D., Berger, B., Blichfeldt, T., Boink, G., Bugiwati, S. R. A., Cai, Z., Carolan, S., Clark, E., Cubric-Curik, V., Dagong, M. I. A., Dorji, T., Drew, L., Guo, J., Hallsson, J., Horvat, S., Kantanen, J., Kawaguchi, F., Kazymbet, P., Khayatzadeh, N., Kim, N., Shah, M. K., Liao, Y., Martinez, A., Masangkay, J., Masaoka, M., Mazza, R., Mcewan, J., Milanesi, M., Omar, F. M., Nomura, Y., Ouchene-Khelifi, N. -A., Pereira, F., Sahana, G., Salavati, M., Sasazaki, S., Da Silva, A., Simcic, M., Solkner, J., Sutherland, A., Tigchelaar, J., Zhang, H., Ajmone-Marsan, P., Bradley, D. G., Colli, L., Drogemuller, C., Jiang, Y., Lei, C., Mannen, H., Pompanon, F., Tosser-Klopp, G., Lenstra, J. A., Kijas, J., Guldbrandtsen, B., Denoyelle, L., Sarry, J., le Talouarn, E., Alberti, A., Orvain, C., Engelen, S., Duby, D., Martin, P., Danchin, C., Duclos, D., Allain, D., Arquet, R., Mandonnet, N., Naves, M., Palhiere, I., Rupp, R., Rezaei, H. R., Foran, M., Stella, A., Del Corvo, M., Crisa, A., Marletta, D., Crepaldi, P., Ottino, M., Randi, E., Mujibi, D. F., Gondwe, T., Benjelloun, B., Taela, M. D. G., Nash, O., Moaeen-ud-Din, M., Visser, C., Goyache, F., Alvarez, I., Amills, M., Sanchez, A., Capote, J., Jordana, J., Pons, A., Balears, I., Molina, A., Mruttu, H. A., Masiga, C. W., Van Tassell, C. P., Reecy, J., Luikart, G., Sikosana, J., Anila, H., Petrit, D., Roswitha, B., Philippe, B., Aziz, F., Christos, P., El-Barody, M. A. A., Pierre, T., Phillip, E., Gordon, L., Albano, B. -P., Stephanie, Z., Michel, T., Georg, E., Horst, B., Eveline, I. -A., Luhken, G., Krugmann, D., Eva-Maria, P., Shirin, L., Katja, G., Christina, P., Jutta, R., Marco, B., Andreas, G., Al Tarrayrah, J., Georgios, K., Olga, K., Katerina, K., Christina, L., Anton, I., Lazlo, F., Gabriele, C., Elisabetta, M., Marco, P., Antonello, C., Tiziana, S., Mario, C., Francesca, F., Stefano, G., Marta, M., Bordonaro, S., Giuseppe, D. U., Fabio, P., Mariasilvia, D. A., Alessio, V., Irene, C., Lorraine, P., Mahamoud, A. -S., Van Cann, L. M., Roman, N., Popielarczyk, D., Ewa, S., Augustin, V., Susana, D., Javier, C., Oscar, C., David, G., Regis, C., Gabriela, O. -R., Glowatzki, M. -L., Okan, E., Inci, T., Evren, K., Mike, B., Trinidad, P., Gabriela, J., Godfrey, H., Stella, D., Louise, W., Martin, T., Sam, J., and Riccardo, S.
Subjects: haplogroup, introgresija, domestication, goat, introgression, migration, phylogeography, Y-chromosome, Evolution, MITOCHONDRIAL-DNA, FLOW, Haplotypes/genetics, divje koze, DNA, Mitochondrial, DNA, Mitochondrial/genetics, Behavior and Systematics, BREEDS, Y Chromosome, Goats/genetics, Genetics, Animals, domače koze, Ecology, Evolution, Behavior and Systematics, Phylogeny, udc:575:636.39, kozorogi, Ecology, 630 Agriculture, Goats, Genetic Variation, NETWORKS, DIFFERENTIATION, genetika, Haplotypes, ORIGINS, GENETIC DIVERSITY, 590 Animals (Zoology), 570 Life sciences, biology, Y Chromosome/genetics
Abstract: By their paternal transmission, Y-chromosomal haplotypes are sensitive markers of population history and male-mediated introgression. Previous studies identified biallelic single-nucleotide variants in the SRY, ZFY and DDX3Y genes, which in domestic goats identified four major Y-chromosomal haplotypes, Y1A, Y1B, Y2A and Y2B, with a marked geographical partitioning. Here, we extracted goat Y-chromosomal variants from whole-genome sequences of 386 domestic goats (75 breeds) and seven wild goat species, which were generated by the VarGoats goat genome project. Phylogenetic analyses indicated domestic haplogroups corresponding to Y1B, Y2A and Y2B, respectively, whereas Y1A is split into Y1AA and Y1AB. All five haplogroups were detected in 26 ancient DNA samples from southeast Europe or Asia. Haplotypes from present-day bezoars are not shared with domestic goats and are attached to deep nodes of the trees and networks. Haplogroup distributions for 186 domestic breeds indicate ancient paternal population bottlenecks and expansions during migrations into northern Europe, eastern and southern Asia, and Africa south of the Sahara. In addition, sharing of haplogroups indicates male-mediated introgressions, most notably an early gene flow from Asian goats into Madagascar and the crossbreeding that in the 19th century resulted in the popular Boer and Anglo-Nubian breeds. More recent introgressions are those from European goats into the native Korean goat population and from Boer goat into Uganda, Kenya, Tanzania, Malawi and Zimbabwe. This study illustrates the power of the Y-chromosomal variants for reconstructing the history of domestic species with a wide geographical range.
Published: 2022

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

Author: Lenstra, J.A., Tigchelaar, J., Biebach, I., Hallsson, J.H., Kantanen, J., Nielsen, V.H., Pompanon, F., Naderi, S., Rezaei, H.R., Sæther, N., Ertugrul, O., Grossen, C., Camenisch, G., VosLoohuis, M., van Straten, M., de Poel, E.A., Windig, J., Oldenbroek, K., AboShehada, Mahamoud, Marsan, Paolo Ajmone, Tarrayrah, Jamil Al, Angiolillo, Antonella, Baret, Philip, Baumung, Roswitha, BejaPereira, Albano, Bertaglia, Marco, Bordonaro, Salvatore, Brandt, Horst, Bruford, Mike, Caloz, Régis, Canali, Gabriele, Canon, Javier, Cappuccio, Irene, Carta, Antonello, Cicogna, Mario, Crepaldi, Paola, Dalamitra, Stella, Dobi, Petrit, Dunner, Susana, DʼUrso, Giuseppe, El Barody, M. A. A., England, Phillip, Erhardt, Georg, Ertuğrul, Okan, Glowatzki, MarieLouise, IbeaghaAwemu, Eveline, Strzelec, Ewa, Fadlaoui, Aziz, Fornarelli, Francesca, Garcia, David, Georgoudis, Andreas, Giovenzana, Stefano, Gutscher, Katja, Hewitt, Godfrey, Hoda, Anila, Istvan, Anton, Jones, Sam, Joost, Stéphane, Juma, Gabriela, Karetsou, Katerina, Kliambas, Georgios, Koban, Evren, Krugmann, Daniela, Kutita, Olga, Lazlo, Fesus, Ligda, Christina, Lipsky, Shirin, Luikart, Gordon, Lühken, Gesine, Marilli, Marta, Marletta, Donata, Milanesi, Elisabetta, Negrini, Riccardo, Nijman, Isaäc J., Niznikowski, Roman, ObexerRuff, Gabriela, Papachristoforou, Christos, Pariset, Lorraine, Peter, Marco Pellecchia, Christina, Perez, Trinidad, Pietrolà, Emilio, Pilla, Fabio, Popielarczyk, Dominik, Prinzenberg, MariaEva, Roosen, Jutta, Scarpa, Riccardo, Sechi, Tiziana, Taberlet, Pierre, Taylor, Martin, Togan, Inci, Trommetter, Michel, Valentini, Alessio, Van Cann, Lisette M., Vlaic, Augustin, Wiskin, Louise, and Zundel, Stéphanie
Published: 2017
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7. Y-chromosomal haplogroups from wild and domestic goats reveal ancient migrations and recent introgressions

Author: Lenstra, J.A., VarGoats Consortium, Nijman, I.J., Rosen, B.D., Bardou, P., Faraut, T., Cumer, T., Daly, K.G., Zheng, Z., Cai, Y., Asadollahpour, H., Kul, B., Zhang, W.-Y., E, G., Ayin, A., Bakhtin, M., Bâlteanu, V.A., Barfield, D., Baird, H., Berger, B., Blichfeldt, T., Boink, G., Bugiwati, S.R.A., Cai, Z., Carolan, S., Clark, E., Cubric-Curik, Vlatka, Dagong, M.I.A., Dorji, T., Drew, L., Guo, J., Hallsson, J., Horvat, S., Kantanen, J., Kawaguchi, F., Kazymbet, P., Khayatzadeh, N., Kim, N., Kumar Shah, M., Liao, Y., Martínez, A., Masangkay, J. S., Masaoka, M., Mazza, R., McEwan, J., Milanesi, M., Omar, F. Md., Nomura, Y., Ouchene-Khelifi, N.-A., Pereira, F., Sahana, G., Sasazaki, S., Da Silva, A., Simčič, M., Sölkner, J., Sutherland, A., Tigchelaar, J., Zhang, H., Econogene Consortium, Ajmone- Marsan, P., Bradley, D. G., Colli, L., Drögemüller, C., Lei, C., Mannen, H., Pompanon, F., Tosser-Klopp, G., and Jiang, Y.
Subjects: wild and domestic goats, Y-chromosome, haplogroups, migrations, introgressions
Abstract: By its paternal transmission, Y-chromosomal haplotypes are sensitive markers of population history and male-mediated introgression. We used whole-genome sequences (WGSs) of 386 domestic goats from 75 modern breeds and 7 wild goat species generated by the VarGoats goat genome project. Phylogenetic analyses indicated five domestic haplogroups Y1AA, Y1AB, Y1B, Y2A and Y2B. Haplogroup distributions for 180 domestic breeds indicate ancient paternal population bottlenecks during the migration into northern Europe, southern Asia and Africa. Sharing of haplogroups reveals male-mediated introgressions: from Asia into Madagascar and, more recently, into the South-African Boer goat ; then from this breed into other southeastern African goats ; and from Europe into native Korean and Ugandan goats. This study illustrates the power of the Y-chromosomal variation for the reconstructing the history of domestic species with a wide geographic range.
Published: 2022

8. VarGoats project : a dataset of 1159 whole-genome sequences to dissect Capra hircus global diversity

Author: Denoyelle, L., Talouarn, E., Bardou, P., Colli, L., Alberti, A., Danchin, C., Del Corvo, M., Engelen, S., Orvain, C., Palhiere, I., Rupp, R., Sarry, J., Salavati, M., Amills, M., Clark, E., Crepaldi, P., Faraut, T., Masiga, C. W., Pompanon, F., Rosen, B. D., Stella, A., Van Tassell, C. P., Tosser-Klopp, G., Kijas, J., Guldbrandtsen, B., Kantanen, J., Duby, D., Martin, P., Duclos, D., Allain, D., Arquet, R., Mandonnet, N., Naves, M., Carolan, S., Foran, M., Crisa, A., Marletta, D., Ottino, M., Randi, E., Benjelloun, B., Lenstra, H., Moaeen-ud-Din, M., Reecy, J., Goyache, F., Alvarez, I., Capote, J., Jordana, J., Pons, A., Martinez, A., Molina, A., Rosen, B., Drogemuller, C., Luikart, G., Mruttu, H. A., Gondwe, T., Sikosana, J., Taela, M. D. G., Nash, O., Agence Nationale de la Recherche (France), Région Occitanie / Pyrénées-Méditerranée, Ministère de l’Enseignement supérieur et de la Recherche (France), Biotechnology and Biological Sciences Research Council (UK), Bill & Melinda Gates Foundation, Department for International Development (UK), Center for Tropical Studies and Conservation (US), University of Edinburgh, Scottish Government's Rural and Environment Science and Analytical Services, Laboratoire d'Ecologie Alpine (LECA ), Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry])-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes (UGA), Génétique Physiologie et Systèmes d'Elevage (GenPhySE ), Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Université de Toulouse (UT)-École nationale supérieure agronomique de Toulouse (ENSAT), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Système d'Information des GENomes des Animaux d'Elevage (SIGENAE), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Università cattolica del Sacro Cuore [Piacenza e Cremona] (Unicatt), Génomique métabolique (UMR 8030), Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), Institut de l'élevage (IDELE), Università cattolica del Sacro Cuore [Milano] (Unicatt), The Roslin Institute, Biotechnology and Biological Sciences Research Council (BBSRC), Centre for Tropical Livestock Genetics and Health [Edimburgh] (CTLGH), Centre for Research in Agricultural Genomics (CRAG), Università degli Studi di Milano = University of Milan (UNIMI), Tropical Institute of Development Innovations (TRIDI), USDA Agricultural Research Service [Beltsville, Maryland], USDA-ARS : Agricultural Research Service, Consiglio Nazionale delle Ricerche [Milano] (CNR), CSIRO Agriculture and Food (CSIRO), Unité de Recherches Zootechniques (URZ), APIS-GENE, Occitanie region, Ministere de l'Enseignement superieur, de la Recherche et de l'Innovation, United States Agency for International Development (USAID), CGIAR:OPP1127286, ACTIVEGOAT & CAPRISNP projects, UK Research & Innovation (UKRI) : BBS/OS/GC/000012F, ANR-10-INBS-0009,France-Génomique,Organisation et montée en puissance d'une Infrastructure Nationale de Génomique(2010), ANR-11-INBS-0003,CRB-Anim,Réseau de Centres de Ressources Biologiques pour les animaux domestiques(2011), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-École nationale supérieure agronomique de Toulouse [ENSAT]-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université d'Évry-Val-d'Essonne (UEVE), University of Milan, and Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)-Université d'Évry-Val-d'Essonne (UEVE)
Subjects: [SDV.BIO]Life Sciences [q-bio]/Biotechnology, [SDV]Life Sciences [q-bio], Short Communication, Single-nucleotide polymorphism, 610 Medicine & health, Biology, QH426-470, Genome, SF1-1100, Domestication, Animals, Domestication, Genetic Variation, Genomics, Goats, Genome, Genome-Wide Association Study, 03 medical and health sciences, Capra hircus, Genetics, Animals, Indel, Ecology, Evolution, Behavior and Systematics, 030304 developmental biology, Genetic association, 2. Zero hunger, 0303 health sciences, Genetic diversity, [SDV.BA.MVSA]Life Sciences [q-bio]/Animal biology/Veterinary medicine and animal Health, Settore AGR/17 - ZOOTECNICA GENERALE E MIGLIORAMENTO GENETICO, 630 Agriculture, Goats, 0402 animal and dairy science, Genetic Variation, 04 agricultural and veterinary sciences, General Medicine, Genomics, 15. Life on land, 040201 dairy & animal science, Animal culture, Evolutionary biology, 570 Life sciences, biology, 590 Animals (Zoology), Animal Science and Zoology, Reference genome, Genome-Wide Association Study
Abstract: [Background]: Since their domestication 10,500 years ago, goat populations with distinctive genetic backgrounds have adapted to a broad variety of environments and breeding conditions. The VarGoats project is an international 1000-genome resequencing program designed to understand the consequences of domestication and breeding on the genetic diversity of domestic goats and to elucidate how speciation and hybridization have modeled the genomes of a set of species representative of the genus Capra., [Findings]: A dataset comprising 652 sequenced goats and 507 public goat sequences, including 35 animals representing eight wild species, has been collected worldwide. We identified 74,274,427 single nucleotide polymorphisms (SNPs) and 13,607,850 insertion-deletions (InDels) by aligning these sequences to the latest version of the goat reference genome (ARS1). A Neighbor-joining tree based on Reynolds genetic distances showed that goats from Africa, Asia and Europe tend to group into independent clusters. Because goat breeds from Oceania and Caribbean (Creole) all derive from imported animals, they are distributed along the tree according to their ancestral geographic origin., [Conclusions]: We report on an unprecedented international effort to characterize the genome-wide diversity of domestic goats. This large range of sequenced individuals represents a unique opportunity to ascertain how the demographic and selection processes associated with post-domestication history have shaped the diversity of this species. Data generated for the project will also be extremely useful to identify deleterious mutations and polymorphisms with causal effects on complex traits, and thus will contribute to new knowledge that could be used in genomic prediction and genome-wide association studies., We are grateful to France Génomique “Call for high impact projects” (ANR‐10‐INBS‐09‐08) for selecting our project and providing us the resources to sequence 400 goats. We would like to mention that APIS-GENE funded some WGS sequences through ACTIVEGOAT & CAPRISNP projects. We thank the Occitanie region and the Animal Genetics Division of the French National Institute for Agriculture, Food and Environment (INRAE-GA) for financing the PhD of ET. We thank the Ministère de l'Enseignement supérieur, de la Recherche et de l'Innovation for financing LD. We thank André Eggen (Illumina) for providing chips to genotype 192 animals. We thank the Animal Genetics Division of the French National Institute for Agriculture, Food and Environment (INRAE-GA) for funding VarGoats2 grant, which allowed DNA extraction and genotyping of 384 animals and CRB-Anim, Grant Agreement ANR-11-INBS-0003, (https://crb-anim.fr/) for funding French local breeds sampling. We thank the Italian Goat and Sheep Breeders Association (AssoNaPa) for supporting in sampling. Whole-genome sequencing libraries for the African goats were prepared and sequenced by Edinburgh Genomics and funded via Biotechnology and Biological Sciences Research Council research grant (BBS/OS/GC/000012F) ‘Reference genome and population sequencing of African goats’ awarded to The Roslin Institute. USDA-ARS with funding from USAID funded the collection of samples from Uganda, Tanzania, Malawi, Mozambique and Zimbabwe. EC and MS were partially supported by the Bill & Melinda Gates Foundation and with UK aid from the UK Government’s Department for International Development (Grant Agreement OPP1127286) under the auspices of the Centre for Tropical Livestock Genetics and Health (CTLGH), established jointly by the University of Edinburgh, SRUC (Scotland’s Rural College), and the International Livestock Research Institute. The findings and conclusions contained within are those of the authors and do not necessarily reflect positions or policies of the Bill & Melinda Gates Foundation nor the UK Government.
Published: 2021

9. Influence of humidity on the endurance of silver-plated electrical contacts subjected to fretting wear

Author: Pompanon, F., primary, Fouvry, S., additional, and Alquier, O., additional
Published: 2018
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10. Microsatellite diversity of the Nordic type of goats in relation to breed conservation: how relevant is pure ancestry?

Author: Lenstra, J A, Tigchelaar, J, Biebach, Iris, Econogene Consortium, Hallsson, J H, Kantanen, J, Nielsen, V H, Pompanon, F, Naderi, S, Rezaei, H R, Saether, N, Ertugrul, O, Grossen, Christine, Camenisch, Glauco, Vos-Loohuis, M, van Straten, M, de Poel, E A, Windig, J, Oldenbroek, K, University of Zurich, and Lenstra, J A
Subjects: 10127 Institute of Evolutionary Biology and Environmental Studies, 570 Life sciences, biology, 590 Animals (Zoology), 1103 Animal Science and Zoology, 3403 Food Animals
Published: 2017

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

Author: Lenstra, J. A., Biebach, I., Hallsson, J. H., Kantanen, J., Nielsen, V. H., Pompanon, F., Naderi, S., Rezaei, H. R., Sæther, N., Ertugrul, O., Grossen, C., Camenisch, G., Vos-Loohuis, M., van Straten, M., de Poel, E. A., Windig, J., Oldenbroek, K., LS IRAS Tox Algemeen, Biochemisch laboratorium, dIRAS RA-1, and dCSCA AVR
Subjects: Diversity, Goats, Microsatellite, Conservation
Abstract: In the last decades, several endangered breeds of livestock species have been re-established effectively. However, the successful revival of the Dutch and Danish Landrace goats involved crossing with exotic breeds and the ancestry of the current populations is therefore not clear. We have generated genotypes for 27 FAO-recommended microsatellites of these landraces and three phenotypically similar Nordic-type landraces and compared these breeds with central European, Mediterranean and south-west Asian goats. We found decreasing levels of genetic diversity with increasing distance from the south-west Asian domestication site with a south-east-to-north-west cline that is clearly steeper than the Mediterranean east-to-west cline. In terms of genetic diversity, the Dutch Landrace comes next to the isolated Icelandic breed, which has an extremely low diversity. The Norwegian coastal goat and the Finnish and Icelandic landraces are clearly related. It appears that by a combination of mixed origin and a population bottleneck, the Dutch and Danish Land-races are separated from the other breeds. However, the current Dutch and Danish populations with the multicoloured and long-horned appearance effectively substitute for the original breed, illustrating that for conservation of cultural heritage, the phenotype of a breed is more relevant than pure ancestry and the genetic diversity of the original breed. More in general, we propose that for conservation, the retention of genetic diversity of an original breed and of the visual phenotype by which the breed is recognized and defined needs to be considered separately.
Published: 2017

12. The Effects of Relative Humidity on the Fretting Wear Behavior of Silver-plated Electrical Contacts

Author: Pompanon, F., primary, Fouvry, S., additional, and Alquier, O., additional
Published: 2018
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13. Microsatellite diversity of the Nordic type of goats in relation to breed conservation: How relevant is pure ancestry?

Author: LS IRAS Tox Algemeen, Biochemisch laboratorium, dIRAS RA-1, dCSCA AVR, Lenstra, J. A., Biebach, I., Hallsson, J. H., Kantanen, J., Nielsen, V. H., Pompanon, F., Naderi, S., Rezaei, H. R., Sæther, N., Ertugrul, O., Grossen, C., Camenisch, G., Vos-Loohuis, M., van Straten, M., de Poel, E. A., Windig, J., Oldenbroek, K., LS IRAS Tox Algemeen, Biochemisch laboratorium, dIRAS RA-1, dCSCA AVR, Lenstra, J. A., Biebach, I., Hallsson, J. H., Kantanen, J., Nielsen, V. H., Pompanon, F., Naderi, S., Rezaei, H. R., Sæther, N., Ertugrul, O., Grossen, C., Camenisch, G., Vos-Loohuis, M., van Straten, M., de Poel, E. A., Windig, J., and Oldenbroek, K.
Published: 2017

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

Author: Lenstra, J. A, Tigchelaar, J., Biebach, I., Hallsson, J. H., Kantanen, J., Nielsen, V. H., Pompanon, F., Naderi, S., Rezaei, H. R., Sæther, N., Ertugrul, O., Grossen, C., Camenisch, G., Vos Loohuis, M., van Straten, M., de Poel, E. A., Windig, J., Oldenbroek, K., Abo Shehada, Mahamoud, Ajmone Marsan, Paolo, Tarrayrah, Jamil Al, Angiolillo, Antonella, Baret, Philip, Baumung, Roswitha, Beja Pereira, Albano, Bertaglia, Marco, Bordonaro, Salvatore, Brandt, Horst, Bruford, Mike, Caloz, Régi, Canali, Gabriele, Canon, Javier, Cappuccio, Irene, Carta, Antonello, Cicogna, Mario, Crepaldi, Paola, Dalamitra, Stella, Dobi, Petrit, Dunner, Susana, D'Urso, Giuseppe, El Barody, M. A. A., England, Phillip, Erhardt, Georg, Ertuğrul, Okan, Glowatzki, Marie Louise, Ibeagha Awemu, Eveline, Strzelec, Ewa, Fadlaoui, Aziz, Fornarelli, Francesca, Garcia, David, Georgoudis, Andrea, Giovenzana, Stefano, Gutscher, Katja, Hewitt, Godfrey, Hoda, Anila, Istvan, Anton, Jones, Sam, Joost, Stephane, Juma, Gabriela, Karetsou, Katerina, Kliambas, Georgio, Koban, Evren, Krugmann, Daniela, Kutita, Olga, Lazlo, Fesu, Ligda, Christina, Lipsky, Shirin, Luikart, Gordon, Lühken, Gesine, Marilli, Marta, Marletta, Donata, Milanesi, Elisabetta, Negrini, Riccardo, Nijman, Isaäc J., Niznikowski, Roman, Obexer Ruff, Gabriela, Papachristoforou, Christo, Pariset, Lorraine, Peter, Marco Pellecchia, Christina, Null, Perez, Trinidad, Pietrolà, Emilio, Pilla, Fabio, Popielarczyk, Dominik, Prinzenberg, Maria Eva, Roosen, Jutta, Scarpa, Riccardo, Sechi, Tiziana, Taberlet, Pierre, Taylor, Martin, Togan, Inci, Trommetter, Michel, Valentini, Alessio, Van Cann, Lisette M., Vlaic, Augustin, Wiskin, Louise, Zundel, Stéphanie, Ajmone Marsan, Paolo (ORCID:0000-0003-3165-4579), Canali, Gabriele (ORCID:0000-0001-9244-8184), Negrini, Riccardo (ORCID:0000-0002-8735-0286), Lenstra, J. A, Tigchelaar, J., Biebach, I., Hallsson, J. H., Kantanen, J., Nielsen, V. H., Pompanon, F., Naderi, S., Rezaei, H. R., Sæther, N., Ertugrul, O., Grossen, C., Camenisch, G., Vos Loohuis, M., van Straten, M., de Poel, E. A., Windig, J., Oldenbroek, K., Abo Shehada, Mahamoud, Ajmone Marsan, Paolo, Tarrayrah, Jamil Al, Angiolillo, Antonella, Baret, Philip, Baumung, Roswitha, Beja Pereira, Albano, Bertaglia, Marco, Bordonaro, Salvatore, Brandt, Horst, Bruford, Mike, Caloz, Régi, Canali, Gabriele, Canon, Javier, Cappuccio, Irene, Carta, Antonello, Cicogna, Mario, Crepaldi, Paola, Dalamitra, Stella, Dobi, Petrit, Dunner, Susana, D'Urso, Giuseppe, El Barody, M. A. A., England, Phillip, Erhardt, Georg, Ertuğrul, Okan, Glowatzki, Marie Louise, Ibeagha Awemu, Eveline, Strzelec, Ewa, Fadlaoui, Aziz, Fornarelli, Francesca, Garcia, David, Georgoudis, Andrea, Giovenzana, Stefano, Gutscher, Katja, Hewitt, Godfrey, Hoda, Anila, Istvan, Anton, Jones, Sam, Joost, Stephane, Juma, Gabriela, Karetsou, Katerina, Kliambas, Georgio, Koban, Evren, Krugmann, Daniela, Kutita, Olga, Lazlo, Fesu, Ligda, Christina, Lipsky, Shirin, Luikart, Gordon, Lühken, Gesine, Marilli, Marta, Marletta, Donata, Milanesi, Elisabetta, Negrini, Riccardo, Nijman, Isaäc J., Niznikowski, Roman, Obexer Ruff, Gabriela, Papachristoforou, Christo, Pariset, Lorraine, Peter, Marco Pellecchia, Christina, Null, Perez, Trinidad, Pietrolà, Emilio, Pilla, Fabio, Popielarczyk, Dominik, Prinzenberg, Maria Eva, Roosen, Jutta, Scarpa, Riccardo, Sechi, Tiziana, Taberlet, Pierre, Taylor, Martin, Togan, Inci, Trommetter, Michel, Valentini, Alessio, Van Cann, Lisette M., Vlaic, Augustin, Wiskin, Louise, Zundel, Stéphanie, Ajmone Marsan, Paolo (ORCID:0000-0003-3165-4579), Canali, Gabriele (ORCID:0000-0001-9244-8184), and Negrini, Riccardo (ORCID:0000-0002-8735-0286)
Abstract: In the last decades, several endangered breeds of livestock species have been re-established effectively. However, the successful revival of the Dutch and Danish Landrace goats involved crossing with exotic breeds and the ancestry of the current populations is therefore not clear. We have generated genotypes for 27 FAO-recommended microsatellites of these landraces and three phenotypically similar Nordic-type landraces and compared these breeds with central European, Mediterranean and south-west Asian goats. We found decreasing levels of genetic diversity with increasing distance from the south-west Asian domestication site with a south-east-to-north-west cline that is clearly steeper than the Mediterranean east-to-west cline. In terms of genetic diversity, the Dutch Landrace comes next to the isolated Icelandic breed, which has an extremely low diversity. The Norwegian coastal goat and the Finnish and Icelandic landraces are clearly related. It appears that by a combination of mixed origin and a population bottleneck, the Dutch and Danish Land-races are separated from the other breeds. However, the current Dutch and Danish populations with the multicoloured and long-horned appearance effectively substitute for the original breed, illustrating that for conservation of cultural heritage, the phenotype of a breed is more relevant than pure ancestry and the genetic diversity of the original breed. More in general, we propose that for conservation, the retention of genetic diversity of an original breed and of the visual phenotype by which the breed is recognized and defined needs to be considered separately.
Published: 2017

15. Environmental DNA for the detection of alien (and native) species in freshwaters

Author: FICETOLA, GENTILE FRANCESCO, Dejean, T, Pompanon, F, Taberlet, P, Miaud, C., Ficetola, G, Dejean, T, Pompanon, F, Taberlet, P, and Miaud, C
Subjects: Invasive species, Environmental DNA
Published: 2013

16. Do habitat and pollution disturbances affect the diet of the wood mouse Apodemus syvaticus? a DNA metabarcoding approach

Author: Drouhot, S., Tougard, C., Pompanon, F., Faure, Olivier, Rioux, D., Boyer, F., Scheifler, R., Raoul, F., Environnement Ville Société (EVS), École normale supérieure - Lyon (ENS Lyon)-École des Mines de Saint-Étienne (Mines Saint-Étienne MSE), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-Université Lumière - Lyon 2 (UL2)-Université Jean Moulin - Lyon 3 (UJML), Université de Lyon-Université de Lyon-Institut National des Sciences Appliquées de Lyon (INSA Lyon), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université Jean Monnet [Saint-Étienne] (UJM)-École Nationale des Travaux Publics de l'État (ENTPE)-École nationale supérieure d'architecture de Lyon (ENSAL)-Centre National de la Recherche Scientifique (CNRS), Environnement, Ville, Société (EVS), École normale supérieure de Lyon (ENS de Lyon)-École des Mines de Saint-Étienne (Mines Saint-Étienne MSE), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université Jean Monnet - Saint-Étienne (UJM)-École Nationale des Travaux Publics de l'État (ENTPE)-École nationale supérieure d'architecture de Lyon (ENSAL)-Centre National de la Recherche Scientifique (CNRS), Institut National des Sciences Appliquées de Lyon (INSA Lyon), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Université de Lyon-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS)-École nationale supérieure d'architecture de Lyon (ENSAL)-École des Mines de Saint-Étienne (Mines Saint-Étienne MSE), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-École Nationale des Travaux Publics de l'État (ENTPE)-Université Jean Monnet [Saint-Étienne] (UJM)-Université Jean Moulin - Lyon 3 (UJML), Université de Lyon-Université Lumière - Lyon 2 (UL2)-École normale supérieure - Lyon (ENS Lyon), and TROUFLEAU, Pascal
Subjects: habitat and pollution disturbances, [SHS] Humanities and Social Sciences, DNA metabarcoding approach, ComputingMilieux_MISCELLANEOUS, diet of the wood mouse Apodemus syvaticus, [SHS]Humanities and Social Sciences
Abstract: International audience
Published: 2013

17. Coupler isotopes stables et métabarcoding alimentaire pour l’analyse des réseaux trophiques

Author: Launey, S., Quéméré, Erwan, Tréguier, Anne, Paillisson, Jean-Marc, Besnard, A.L., Huteau, D., Pompanon, F., Taberlet, Pierre, Roussel, Jean-Marie, Evolution et Diversité Biologique (EDB), Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Ecosystèmes, biodiversité, évolution [Rennes] (ECOBIO), Centre National de la Recherche Scientifique (CNRS)-Observatoire des Sciences de l'Univers de Rennes (OSUR)-Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES), Écologie et santé des écosystèmes (ESE), Institut National de la Recherche Agronomique (INRA)-AGROCAMPUS OUEST, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Laboratoire d'Ecologie Alpine (LECA), Université Joseph Fourier - Grenoble 1 (UJF)-Centre National de la Recherche Scientifique (CNRS)-Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry]), Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), Université de Rennes (UR)-Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Observatoire des Sciences de l'Univers de Rennes (OSUR), Université de Rennes (UR)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Centre National de la Recherche Scientifique (CNRS), Université Joseph Fourier - Grenoble 1 (UJF)-Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry])-Centre National de la Recherche Scientifique (CNRS), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS), Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Observatoire des Sciences de l'Univers de Rennes (OSUR)-Centre National de la Recherche Scientifique (CNRS), and Centre National de la Recherche Scientifique (CNRS)-Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry])-Université Joseph Fourier - Grenoble 1 (UJF)-Université Grenoble Alpes (UGA)
Subjects: [SDE.BE]Environmental Sciences/Biodiversity and Ecology
Published: 2013

18. S0125 Changing patterns of genomic variability following domestication of sheep

Author: Sanchez, M. Naval, primary, Brauning, R., additional, Clarke, S. M., additional, Nguyen, Q., additional, McCulloch, A., additional, Cockett, N. E., additional, Zamani, W., additional, Pompanon, F., additional, Taberlet, P., additional, McWilliam, S., additional, Daetwyler, H., additional, and Kijas, J., additional
Published: 2016
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19. Whole mitochondrial genomes unveil the impact of domestication on goat matrilineal variability

Author: Colli, Licia, Lancioni, H., Cardinali, I., Olivieri, A., Capodiferro, M. R., Pellecchia, Marco, Rzepus, Marcin, Zamani, W., Naderi, S., Gandini, F., Vahidi, S. M. F., Agha, S., Randi, E., Battaglia, V., Sardina, M. T., Portolano, B., Rezaei, H. R., Lymberakis, P., Boyer, F., Coissac, E., Pompanon, F., Taberlet, P., Ajmone Marsan, Paolo, Achilli, A., Colli L. (ORCID:0000-0002-7221-2905), Pellecchia M., Rzepus M., Ajmone Marsan P. (ORCID:0000-0003-3165-4579), Colli, Licia, Lancioni, H., Cardinali, I., Olivieri, A., Capodiferro, M. R., Pellecchia, Marco, Rzepus, Marcin, Zamani, W., Naderi, S., Gandini, F., Vahidi, S. M. F., Agha, S., Randi, E., Battaglia, V., Sardina, M. T., Portolano, B., Rezaei, H. R., Lymberakis, P., Boyer, F., Coissac, E., Pompanon, F., Taberlet, P., Ajmone Marsan, Paolo, Achilli, A., Colli L. (ORCID:0000-0002-7221-2905), Pellecchia M., Rzepus M., and Ajmone Marsan P. (ORCID:0000-0003-3165-4579)
Abstract: Background: The current extensive use of the domestic goat (Capra hircus) is the result of its medium size and high adaptability as multiple breeds. The extent to which its genetic variability was influenced by early domestication practices is largely unknown. A common standard by which to analyze maternally-inherited variability of livestock species is through complete sequencing of the entire mitogenome (mitochondrial DNA, mtDNA). Results: We present the first extensive survey of goat mitogenomic variability based on 84 complete sequences selected from an initial collection of 758 samples that represent 60 different breeds of C. hircus, as well as its wild sister species, bezoar (Capra aegagrus) from Iran. Our phylogenetic analyses dated the most recent common ancestor of C. hircus to ∼460,000 years (ka) ago and identified five distinctive domestic haplogroups (A, B1, C1a, D1 and G). More than 90 % of goats examined were in haplogroup A. These domestic lineages are predominantly nested within C. aegagrus branches, diverged concomitantly at the interface between the Epipaleolithic and early Neolithic periods, and underwent a dramatic expansion starting from ∼12-10 ka ago. Conclusions: Domestic goat mitogenomes descended from a small number of founding haplotypes that underwent domestication after surviving the last glacial maximum in the Near Eastern refuges. All modern haplotypes A probably descended from a single (or at most a few closely related) female C. aegagrus. Zooarchaelogical data indicate that domestication first occurred in Southeastern Anatolia. Goats accompanying the first Neolithic migration waves into the Mediterranean were already characterized by two ancestral A and C variants. The ancient separation of the C branch (∼130 ka ago) suggests a genetically distinct population that could have been involved in a second event of domestication. The novel diagnostic mutational motifs defined here, which distinguish wild and domestic haplogroups, could be u
Published: 2015

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

Author: Bruford, Mw, Ginja, C, Hoffmann, I, Joost, S, Orozco Terwengel, P, Alberto, Fj, Amaral, Aj, Barbato, Mario, Biscarini, F, Colli, Licia, Costa, M, Curik, I, Duruz, S, Ferenčaković, M, Fischer, D, Fitak, R, Groeneveld, Lf, Hall, Sjg, Hanotte, O, Hassan, F, Helsen, P, Iacolina, L, Kantanen, J, Leempoel, K, Lenstra, Ja, Ajmone Marsan, Paolo, Masembe, C, Megens, H, 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., Barbato, M (ORCID:0000-0002-7203-1549), Colli, Licia (ORCID:0000-0002-7221-2905), Ajmone Marsan, Paolo (ORCID:0000-0003-3165-4579), Bruford, Mw, Ginja, C, Hoffmann, I, Joost, S, Orozco Terwengel, P, Alberto, Fj, Amaral, Aj, Barbato, Mario, Biscarini, F, Colli, Licia, Costa, M, Curik, I, Duruz, S, Ferenčaković, M, Fischer, D, Fitak, R, Groeneveld, Lf, Hall, Sjg, Hanotte, O, Hassan, F, Helsen, P, Iacolina, L, Kantanen, J, Leempoel, K, Lenstra, Ja, Ajmone Marsan, Paolo, Masembe, C, Megens, H, 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., Barbato, M (ORCID:0000-0002-7203-1549), Colli, Licia (ORCID:0000-0002-7221-2905), and Ajmone Marsan, Paolo (ORCID:0000-0003-3165-4579)
Abstract: Livestock conservation practice is changing rapidly in light of policy developments, climate change and diversifying market demands. The last decade has seen a step change in technology and analytical approaches available to define, manage and conserve Farm Animal Genomic Resources (FAnGR). However, these rapid changes pose challenges for FAnGR conservation in terms of technological continuity, analytical capacity and integrative methodologies needed to fully exploit new, multidimensional data. The final conference of the ESF Genomic Resources program aimed to address these interdisciplinary problems in an attempt to contribute to the agenda for research and policy development directions during the coming decade. By 2020, according to the Convention on Biodiversity's Aichi Target 13, signatories should ensure that "...the genetic diversity of ...farmed and domesticated animals and of wild relatives ...is maintained, and strategies have been developed and implemented for minimizing genetic erosion and safeguarding their genetic diversity." However, the real extent of genetic erosion is very difficult to measure using current data. Therefore, this challenging target demands better coverage, understanding and utilization of genomic and environmental data, the development of optimized ways to integrate these data with social and other sciences and policy analysis to enable more flexible, evidence-based models to underpin FAnGR conservation. At the conference, we attempted to identify the most important problems for effective livestock genomic resource conservation during the next decade. Twenty priority questions were identified that could be broadly categorized into challenges related to methodology, analytical approaches, data management and conservation. It should be acknowledged here that while the focus of our meeting was predominantly around genetics, genomics and animal science, many of the practical challenges facing conservation of genomic resources are societa
Published: 2015

21. A DNA metabarcoding approach to understand trophic transfers of pollutants

Author: Drouhot , Séverine, Tougard , C., Pompanon , F., Faure , Olivier, Druart , Coline, Rioux , D., Boyer , F., Prudent , Anne-Sophie, Goydadin , A.-C., Capelli , Nicolas, Giraudoux , Patrick, Scheifler , Renaud, Raoul , Francis, Laboratoire Chrono-environnement (UMR 6249) (LCE), Centre National de la Recherche Scientifique (CNRS)-Université de Franche-Comté (UFC), Université Bourgogne Franche-Comté [COMUE] (UBFC)-Université Bourgogne Franche-Comté [COMUE] (UBFC), Environnement, Ville, Société (EVS), École normale supérieure de Lyon (ENS de Lyon)-École des Mines de Saint-Étienne (Mines Saint-Étienne MSE), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-Université Lumière - Lyon 2 (UL2)-Université Jean Moulin - Lyon 3 (UJML), Université de Lyon-Université de Lyon-Institut National des Sciences Appliquées de Lyon (INSA Lyon), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université Jean Monnet - Saint-Étienne (UJM)-École Nationale des Travaux Publics de l'État (ENTPE)-École nationale supérieure d'architecture de Lyon (ENSAL)-Centre National de la Recherche Scientifique (CNRS), Département GéoSciences et Environnement (GSE-ENSMSE), École des Mines de Saint-Étienne (Mines Saint-Étienne MSE), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-SPIN, Centre Sciences des Processus Industriels et Naturels (SPIN-ENSMSE), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT), Laboratoire d'Ecologie Alpine (LECA), Université Joseph Fourier - Grenoble 1 (UJF)-Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry])-Centre National de la Recherche Scientifique (CNRS), Institut Universitaire de France (IUF), Ministère de l'Education nationale, de l’Enseignement supérieur et de la Recherche (M.E.N.E.S.R.), Laboratoire Chrono-environnement - CNRS - UBFC (UMR 6249) (LCE), Environnement Ville Société (EVS), Institut National des Sciences Appliquées de Lyon (INSA Lyon), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Université de Lyon-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS)-École nationale supérieure d'architecture de Lyon (ENSAL)-École des Mines de Saint-Étienne (Mines Saint-Étienne MSE), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-École Nationale des Travaux Publics de l'État (ENTPE)-Université Jean Monnet [Saint-Étienne] (UJM)-Université Jean Moulin - Lyon 3 (UJML), Université de Lyon-Université Lumière - Lyon 2 (UL2)-École normale supérieure - Lyon (ENS Lyon), Laboratoire Chrono-environnement ( LCE ), Université Bourgogne Franche-Comté ( UBFC ) -Centre National de la Recherche Scientifique ( CNRS ) -Université de Franche-Comté ( UFC ), Environnement Ville Société ( EVS ), École normale supérieure - Lyon ( ENS Lyon ) -Université Lumière - Lyon 2 ( UL2 ) -Université Jean Moulin - Lyon III-Université Jean Monnet [Saint-Étienne] ( UJM ) -École Nationale des Travaux Publics de l'État ( ENTPE ) -Ecole Nationale Supérieure des Mines de Saint-Etienne-École nationale supérieure d'architecture de Lyon ( ENSAL ) -Centre National de la Recherche Scientifique ( CNRS ) -Institut National des Sciences Appliquées de Lyon ( INSA Lyon ), Université de Lyon-Institut National des Sciences Appliquées ( INSA ) -Université de Lyon-Institut National des Sciences Appliquées ( INSA ), Département GéoSciences et Environnement ( GSE-ENSMSE ), École des Mines de Saint-Étienne ( Mines Saint-Étienne MSE ), Institut Mines-Télécom [Paris]-Institut Mines-Télécom [Paris]-SPIN, Centre Sciences des Processus Industriels et Naturels ( SPIN-ENSMSE ), Institut Mines-Télécom [Paris]-Institut Mines-Télécom [Paris], Laboratoire d'Ecologie Alpine ( LECA ), Université Joseph Fourier - Grenoble 1 ( UJF ) -Université Savoie Mont Blanc ( USMB [Université de Savoie] [Université de Chambéry] ) -Centre National de la Recherche Scientifique ( CNRS ), Institut Universitaire de France ( IUF ), Ministère de l'Éducation nationale, de l’Enseignement supérieur et de la Recherche ( M.E.N.E.S.R. ), Université de Franche-Comté (UFC), Université Bourgogne Franche-Comté [COMUE] (UBFC)-Université Bourgogne Franche-Comté [COMUE] (UBFC)-Centre National de la Recherche Scientifique (CNRS), École normale supérieure - Lyon (ENS Lyon)-École des Mines de Saint-Étienne (Mines Saint-Étienne MSE), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université Jean Monnet [Saint-Étienne] (UJM)-École Nationale des Travaux Publics de l'État (ENTPE)-École nationale supérieure d'architecture de Lyon (ENSAL)-Centre National de la Recherche Scientifique (CNRS), and Université Joseph Fourier - Grenoble 1 (UJF)-Centre National de la Recherche Scientifique (CNRS)-Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry])
Subjects: trophic transferts, pollutants, [ SHS ] Humanities and Social Sciences, pollutants tranferts, DNA barcoding, ComputingMilieux_MISCELLANEOUS, [SHS]Humanities and Social Sciences
Abstract: International audience
Published: 2013

22. Fifty thousand years of Arctic vegetation and megafaunal diet

Author: Willerslev, E., Davison, J., Moora, M., Zobel, M., Coissac, E., Edwards, M.E., Lorenzen, E.D., Vestergård, M., Gussarova, G., Haile, J., Craine, J., Gielly, L., Boessenkool, S., Epp, L.S., Pearman, P.B., Cheddadi, R., Murray, D., Bråthen, K.A., Yoccoz, N., Binney, H., Cruaud, C., Wincker, P., Goslar, T., Alsos, I.G., Bellemain, E., Brysting, A.K., Elven, R., Sønstebø, J.H., 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, R.G., MacPhee, R.D.E., Gilbert, M.T.P., Kjær, K.H., Orlando, L., Brochmann, C., Taberlet, P., Willerslev, E., Davison, J., Moora, M., Zobel, M., Coissac, E., Edwards, M.E., Lorenzen, E.D., Vestergård, M., Gussarova, G., Haile, J., Craine, J., Gielly, L., Boessenkool, S., Epp, L.S., Pearman, P.B., Cheddadi, R., Murray, D., Bråthen, K.A., Yoccoz, N., Binney, H., Cruaud, C., Wincker, P., Goslar, T., Alsos, I.G., Bellemain, E., Brysting, A.K., Elven, R., Sønstebø, J.H., 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, R.G., MacPhee, R.D.E., Gilbert, M.T.P., Kjær, K.H., Orlando, L., Brochmann, C., and Taberlet, P.
Abstract: Although it is generally agreed that the Arctic flora is among the youngest and least diverse on Earth, the processes that shaped it are poorly understood. Here we present 50 thousand years (kyr) of Arctic vegetation history, derived from the first large-scale ancient DNA metabarcoding study of circumpolar plant diversity. For this interval we also explore nematode diversity as a proxy for modelling vegetation cover and soil quality, and diets of herbivorous megafaunal mammals, many of which became extinct around 10 kyr bp (before present). For much of the period investigated, Arctic vegetation consisted of dry steppe-tundra dominated by forbs (non-graminoid herbaceous vascular plants). During the Last Glacial Maximum (25-15 kyr bp), diversity declined markedly, although forbs remained dominant. Much changed after 10 kyr bp, with the appearance of moist tundra dominated by woody plants and graminoids. Our analyses indicate that both graminoids and forbs would have featured in megafaunal diets. As such, our findings question the predominance of a Late Quaternary graminoid-dominated Arctic mammoth steppe.
Published: 2014

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

Author: Deagle, B., Jarman, Simon, Coissac, E., Pompanon, F., Taberlet, P., Deagle, B., Jarman, Simon, Coissac, E., Pompanon, F., and Taberlet, P.
Abstract: © 2014 The Author(s) Published by the Royal Society. DNA metabarcoding enables efficient characterization of species composition in environmental DNA or bulk biodiversity samples, and this approach is making significant and unique contributions in the field of ecology. In metabarcoding of animals, the cytochrome c oxidase subunit I (COI) gene is frequently used as the marker of choice because no other genetic region can be found in taxonomically verified databases with sequences covering so many taxa. However, the accuracy of metabarcoding datasets is dependent on recovery of the targeted taxa using conserved amplification primers.We argue that COI does not contain suitably conserved regions for most amplicon-based metabarcoding applications. Marker selection deserves increased scrutiny and available marker choices should be broadened in order to maximize potential in this exciting field of research.
Published: 2014

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

Author: Valentini, A., Miquel, C., Nawaz, M. A., Bellemain, E., Coissac, Eric, Pompanon, F., Gielly, L., Cruaud, Corinne, Nascetti, G., Wincker, P., Swenson, J. E., Taberlet, P., Laboratoire d'Ecologie Alpine (LECA), Université Joseph Fourier - Grenoble 1 (UJF)-Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry])-Centre National de la Recherche Scientifique (CNRS), Dipartimento di Ecologia e Sviluppo Economico Sostenibile (DECOS), Università degli studi della Tuscia [Viterbo], Department of Ecology and Natural Resource Management, Norwegian University of Life Sciences (NMBU), Himalayan Wildlife Foundation, Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), and Norwegian Institute for Nature Research (NINA)
Subjects: [SDV.EE]Life Sciences [q-bio]/Ecology, environment, spectroscopy, [SDE.MCG]Environmental Sciences/Global Changes, conservation, Extinct ground sloth, [SDV.BID]Life Sciences [q-bio]/Biodiversity, amplification, herbivores, chain-reaction, pyrosequencing, chloroplast DNA, pcr, universal primers, diet analysis, identification, DNA barcoding, molecular analysis, faeces, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, trnL (UAA) intron, land plants
Abstract: International audience; The development of DNA barcoding (species identification using a standardized DNA sequence), and the availability of recent DNA sequencing techniques offer new possibilities in diet analysis. DNA fragments shorter than 100-150 bp remain in a much higher proportion in degraded DNA samples and can be recovered from faeces. As a consequence, by using universal primers that amplify a very short but informative DNA fragment, it is possible to reliably identify the plant taxon that has been eaten. According to our experience and using this identification system, about 50% of the taxa can be identified to species using the trnL approach, that is, using the P6 loop of the chloroplast trnL (UAA) intron. We demonstrated that this new method is fast, simple to implement, and very robust. It can be applied for diet analyses of a wide range of phytophagous species at large scales. We also demonstrated that our approach is efficient for mammals, birds, insects and molluscs. This method opens new perspectives in ecology, not only by allowing large-scale studies on diet, but also by enhancing studies on resource partitioning among competing species, and describing food webs in ecosystems.
Published: 2009

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

Author: Bonin, A., Bellemain, E., Eidesen, P. B., Pompanon, F., Brochmann, C., Taberlet, P., Laboratoire d'Ecologie Alpine (LECA), Université Joseph Fourier - Grenoble 1 (UJF)-Centre National de la Recherche Scientifique (CNRS)-Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry]), Department of Ecology and Natural Resource Management, Norwegian University of Life Sciences (NMBU), National Centre for Biosystematics (NCB), and University of Oslo (UiO)
Subjects: [SDV.EE]Life Sciences [q-bio]/Ecology, environment, [SDV.BID]Life Sciences [q-bio]/Biodiversity, [SDE.BE]Environmental Sciences/Biodiversity and Ecology
Abstract: Times Cited: 124; International audience; Genotyping errors occur when the genotype determined after molecular analysis does not correspond to the real genotype of the individual under consideration. Virtually every genetic data set includes some erroneous genotypes, but genotyping errors remain a taboo subject in population genetics, even though they might greatly bias the final conclusions, especially for studies based on individual identification. Here, we consider four case studies representing a large variety of population genetics investigations differing in their sampling strategies (noninvasive or traditional), in the type of organism studied (plant or animal) and the molecular markers used [microsatellites or amplified fragment length polymorphisms (AFLPs)]. In these data sets, the estimated genotyping error rate ranges from 0.8% for microsatellite loci from bear tissues to 2.6% for AFLP loci from dwarf birch leaves. Main sources of errors were allelic dropouts for microsatellites and differences in peak intensities for AFLPs, but in both cases human factors were non-negligible error generators. Therefore, tracking genotyping errors and identifying their causes are necessary to clean up the data sets and validate the final results according to the precision required. In addition, we propose the outline of a protocol designed to limit and quantify genotyping errors at each step of the genotyping process. In particular, we recommend (i) several efficient precautions to prevent contaminations and technical artefacts; (ii) systematic use of blind samples and automation; (iii) experience and rigor for laboratory work and scoring; and (iv) systematic reporting of the error rate in population genetics studies.
Published: 2004

26. Next generation sequencing as a novel tool for diagnostics of apicomplexan pathogen in ticks and mammalian hosts

Author: Qablan, MA, primary, Boyer, F, additional, Miquel, C, additional, D'Amico, G, additional, Mihalca, AD, additional, Pompanon, F, additional, and Modrý, D, additional
Published: 2014
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27. Isolation and caractérisation of microsatellites in European alpine marmots (Marmota marmota)

Author: Da Silva, A., Luikart, G., Allainé, Dominique, Gautier, P., Taberlet, P., Pompanon, F., Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS), Evolution, adaptation et comportement, Département écologie évolutive [LBBE], Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), and Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE)
Subjects: [SDV.OT]Life Sciences [q-bio]/Other [q-bio.OT]
Published: 2003

28. Environmental DNA for the detection of alien (and native) species in freshwaters

Author: Ficetola, G, Dejean, T, Pompanon, F, Taberlet, P, Miaud, C, FICETOLA, GENTILE FRANCESCO, Miaud, C., Ficetola, G, Dejean, T, Pompanon, F, Taberlet, P, Miaud, C, FICETOLA, GENTILE FRANCESCO, and Miaud, C.
Published: 2013

29. Isolation and characterization of microsatellites in a perennial Apiaceae, Eryngium alpinum L

Author: Gaudeul, M., Naciri-Graven, Y., Gauthier, P., Pompanon, F., Laboratoire d'Ecologie Alpine (LECA), Université Joseph Fourier - Grenoble 1 (UJF)-Centre National de la Recherche Scientifique (CNRS)-Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry]), Conservatoire et Jardin Botaniques, and Pla, Kim
Subjects: [SDE.BE] Environmental Sciences/Biodiversity and Ecology, [SDV.EE]Life Sciences [q-bio]/Ecology, environment, [SDV.EE] Life Sciences [q-bio]/Ecology, environment, enrichment, microsatellite, nonradioactive probes, plants, genetic structure, [SDV.BID]Life Sciences [q-bio]/Biodiversity, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, [SDV.BID] Life Sciences [q-bio]/Biodiversity
Abstract: International audience; In order to investigate the genetic structure in an endangered Alpine plant (Eryngium alpinum L.), we developed microsatellites. Two different approaches were used: an enrichment protocol and the classical technique of hybridization on nylon membranes. We identified 25 loci, 13 of which revealed to be polymorphic. The polymorphism was rather low (2-6 alleles; H-E = 0.49 +/- 0.16), probably due to the short size of microsatellites (6-10 dinucleotide repeats) and to the fine spatial scale investigated. However, these markers are expected to provide a new insight about the genetic processes at work within and among E. alpinum populations.
Published: 2002

30. Variation in predation costs with Chiastocheta egg number on Trollius europaeus: how many seeds to pay for pollination?

Author: Jaeger, N., Pompanon, F., Despres, L., Laboratoire d'Ecologie Alpine (LECA), Université Joseph Fourier - Grenoble 1 (UJF)-Centre National de la Recherche Scientifique (CNRS)-Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry]), and Pla, Kim
Subjects: [SDV.EE]Life Sciences [q-bio]/Ecology, environment, pollination, mutualism, fungi, food and beverages, plant, [SDV.BID]Life Sciences [q-bio]/Biodiversity, Chiastocheta, stability, diptera, Trollius europaeus, anthomyiidae, [SDE.BE] Environmental Sciences/Biodiversity and Ecology, [SDV.EE] Life Sciences [q-bio]/Ecology, environment, seed predation, evolution, flies, Yucca moths, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, competition, [SDV.BID] Life Sciences [q-bio]/Biodiversity
Abstract: 1. In obligate plant/seed parasite-pollinator mutualisms, the plant is exclusively pollinated by an insect whose larvae are specific seed predators. Hence, outcomes of the interaction for the plant can vary with the number of eggs laid and the number of seeds eaten per larva. 2. In the work reported here, predation by Chiastocheta larvae on seeds of Trollius europaeus was analysed as a function of the number of eggs laid on the flower. Flowers with an increasing number of eggs were bagged in three populations and seeds were counted after the end of larval predation, in order to assess whether there was competition among larvae. 3. Seed predation on single-egg flowers was high and variable (mean per population ranging from 15 to 40% of the developed seeds). Seed predation increased weakly with increasing egg load and was lower than gross seed production (always
Published: 2001

31. DNA from soil mirrors plant taxonomic and growth form diversity

Author: Yoccoz, N. G., Bråthen, K. A., Gielly, L., Haile, James Seymour, Edwards, M. E., Goslar, T., von Stedingk, H., Brysting, A. K., Coissac, E., Pompanon, F., Sønstebo, J. H., Miquel, C., Valentini, A., de Bello, F., Chave, J., Thuiller, W., Wincker, P., Cruaud, C., Gavory, F., Rasmussen, Morten, Gilbert, Tom, Orlando, Ludovic Antoine Alexandre, Brochmann, C., Willerslev, Eske, Taberlet, P., Yoccoz, N. G., Bråthen, K. A., Gielly, L., Haile, James Seymour, Edwards, M. E., Goslar, T., von Stedingk, H., Brysting, A. K., Coissac, E., Pompanon, F., Sønstebo, J. H., Miquel, C., Valentini, A., de Bello, F., Chave, J., Thuiller, W., Wincker, P., Cruaud, C., Gavory, F., Rasmussen, Morten, Gilbert, Tom, Orlando, Ludovic Antoine Alexandre, Brochmann, C., Willerslev, Eske, and Taberlet, P.
Abstract: Ecosystems across the globe are threatened by climate change and human activities. New rapid survey approaches for monitoring biodiversity would greatly advance assessment and understanding of these threats. Taking advantage of next-generation DNA sequencing, we tested an approach we call metabarcoding: high-throughput and simultaneous taxa identification based on a very short (usually
Published: 2012

32. DNA from soil mirrors plant taxonomic and growth form diversity

Author: Yoccoz, N., Brathen, K., Gielly, L., Haile, James, Edwards, M., Goslar, T., Von Stedingk, H., Brysting, A., Coissac, E., Pompanon, F., Sonstebo, J., Miquel, C., Valentini, A., De Bello, F., Chave, J., Thuiller, W., Wincker, P., Cruaud, C., Gavory, F., Rasmussen, M., Gilbert, Thomas, Orlando, L., Brochmann, C., Willerslev, E., Taberlet, P., Yoccoz, N., Brathen, K., Gielly, L., Haile, James, Edwards, M., Goslar, T., Von Stedingk, H., Brysting, A., Coissac, E., Pompanon, F., Sonstebo, J., Miquel, C., Valentini, A., De Bello, F., Chave, J., Thuiller, W., Wincker, P., Cruaud, C., Gavory, F., Rasmussen, M., Gilbert, Thomas, Orlando, L., Brochmann, C., Willerslev, E., and Taberlet, P.
Abstract: Ecosystems across the globe are threatened by climate change and human activities. New rapid survey approaches for monitoring biodiversity would greatly advance assessment and understanding of these threats. Taking advantage of next-generation DNA sequencing, we tested an approach we call metabarcoding: high-throughput and simultaneous taxa identification based on a very short (usually <100 base pairs) but informative DNA fragment. Short DNA fragments allow the use of degraded DNA from environmental samples. All analyses included amplification using plant-specific versatile primers, sequencing and estimation of taxonomic diversity. We tested in three steps whether degraded DNA from dead material in soil has the potential of efficiently assessing biodiversity in different biomes. First, soil DNA from eight boreal plant communities located in two different vegetation types (meadow and heath) was amplified. Plant diversity detected from boreal soil was highly consistent with planttaxonomic and growth form diversity estimated from conventional above-ground surveys. Second, we assessed DNA persistence using samples from formerly cultivated soils in temperate environments. We found that the number of crop DNA sequences retrieved strongly varied with years since last cultivation, and crop sequences were absent from nearby, uncultivated plots. Third, we assessed the universal applicability of DNA metabarcoding using soil samples from tropical environments: a large proportion of species and families from the study site were efficiently recovered. The results openunprecedented opportunities for large-scale DNA-based biodiversity studies across a range of taxonomic groups using standardized metabarcoding approaches.
Published: 2012

33. Comparacion de los caracteres biologicos y etologicos de Trichogramma pretiosum y de T.Exiguum (Hymenoptera: Trichogrammatidae)

Author: Basso, Cesar, Grille, G., Pompanon, F., Allemand, Roland, Pintureau, Bernard, ProdInra, Migration, Laboratoire de biologie appliquée, and Institut National de la Recherche Agronomique (INRA)
Subjects: RELATION HOTE PARASITE, [SDV] Life Sciences [q-bio], [SDV]Life Sciences [q-bio]
Published: 1998

34. Inhibition of sex pheromone communications of Trichogramma Brassicae (Hymenoptera) by the insecticide chlorpyrifos

Author: Delpuech, Jean-Marie, Froment, B., Fouillet, P., Pompanon, F., Janillon, S., Boulétreau, P., Génétique et évolution des interactions hôtes-parasites, Département génétique, interactions et évolution des génomes [LBBE] (GINSENG), Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), and Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)
Subjects: [SDV.OT]Life Sciences [q-bio]/Other [q-bio.OT]
Published: 1998

35. 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

Author: Prunier, J. G., primary, Kaufmann, B., additional, Fenet, S., additional, Picard, D., additional, Pompanon, F., additional, Joly, P., additional, and Lena, J. P., additional
Published: 2013
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36. DNA from soil mirrors plant taxonomic and growth form diversity

Author: YOCCOZ, N. G., primary, BRÅTHEN, K. A., additional, GIELLY, L., additional, HAILE, J., additional, EDWARDS, M. E., additional, GOSLAR, T., additional, Von STEDINGK, H., additional, BRYSTING, A. K., additional, COISSAC, E., additional, POMPANON, F., additional, SØNSTEBØ, J. H., additional, MIQUEL, C., additional, VALENTINI, A., additional, De BELLO, F., additional, CHAVE, J., additional, THUILLER, W., additional, WINCKER, P., additional, CRUAUD, C., additional, GAVORY, F., additional, RASMUSSEN, M., additional, GILBERT, M. T. P., additional, ORLANDO, L., additional, BROCHMANN, C., additional, WILLERSLEV, E., additional, and TABERLET, P., additional
Published: 2012
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37. Skin swabbing as a new efficient DNA sampling technique in amphibians, and 14 new microsatellite markers in the alpine newt ( Ichthyosaura alpestris )

Author: PRUNIER, J., primary, KAUFMANN, B., additional, GROLET, O., additional, PICARD, D., additional, POMPANON, F., additional, and JOLY, P., additional
Published: 2012
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38. Mitochondrial DNA polymorphism in Moroccan goats

Author: Benjelloun, B., primary, Pompanon, F., additional, Ben Bati, M., additional, Chentouf, M., additional, Ibnelbachyr, M., additional, El Amiri, B., additional, Rioux, D., additional, Boulanouar, B., additional, and Taberlet, P., additional
Published: 2011
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39. Are cattle, sheep, and goats endangered species?

Author: TABERLET, P., primary, VALENTINI, A., additional, REZAEI, H. R., additional, NADERI, S., additional, POMPANON, F., additional, NEGRINI, R., additional, and AJMONE‐MARSAN, P., additional
Published: 2007
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40. Power and limitations of the chloroplast trnL (UAA) intron for plant DNA barcoding

Author: Taberlet, P., primary, Coissac, E., additional, Pompanon, F., additional, Gielly, L., additional, Miquel, C., additional, Valentini, A., additional, Vermat, T., additional, Corthier, G., additional, Brochmann, C., additional, and Willerslev, E., additional
Published: 2007
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41. Polymorphic microsatellite DNA loci identified in the common frog (Rana temporaria, Amphibia, Ranidae)

Author: Pidancier, N., primary, Gauthier, P., additional, Miquel, C., additional, and Pompanon, F., additional
Published: 2002
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42. Are cattle, sheep, and goats endangered species?

Author: TABERLET, P., VALENTINI, A., REZAEI, H. R., NADERI, S., POMPANON, F., NEGRINI, R., and AJMONE-MARSAN, P.
Subjects: MOLECULAR ecology, BIODIVERSITY, SPECIES diversity, ECOLOGICAL heterogeneity, PATHOGENIC microorganisms, CONSERVATION biology, WILDLIFE conservation, ENDANGERED species, GERMPLASM
Abstract: For about 10 000 years, farmers have been managing cattle, sheep, and goats in a sustainable way, leading to animals that are well adapted to the local conditions. About 200 years ago, the situation started to change dramatically, with the rise of the concept of breed. All animals from the same breed began to be selected for the same phenotypic characteristics, and reproduction among breeds was seriously reduced. This corresponded to a strong fragmentation of the initial populations. A few decades ago, the selection pressures were increased again in order to further improve productivity, without enough emphasis on the preservation of the overall genetic diversity. The efficiency of modern selection methods successfully increased the production, but with a dramatic loss of genetic variability. Many industrial breeds now suffer from inbreeding, with effective population sizes falling below 50. With the development of these industrial breeds came economic pressure on farmers to abandon their traditional breeds, and many of these have recently become extinct as a result. This means that genetic resources in cattle, sheep, and goats are highly endangered, particularly in developed countries. It is therefore important to take measures that promote a sustainable management of these genetic resources; first, by in situ preservation of endangered breeds; second, by using selection programmes to restore the genetic diversity of industrial breeds; and finally, by protecting the wild relatives that might provide useful genetic resources. [ABSTRACT FROM AUTHOR]
Published: 2008
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43. PRIMER NOTE Isolation and characterization of microsatellites in a perennial Apiaceae, Eryngium alpinum L.

Author: Gaudeul, M., Naciri-Graven, Y., Gauthier, P., and Pompanon, F.
Abstract: In order to investigate the genetic structure in an endangered Alpine plant (Eryngium alpinum L.), we developed microsatellites. Two different approaches were used: an enrichment protocol and the classical technique of hybridization on nylon membranes. We identified 25 loci, 13 of which revealed to be polymorphic. The polymorphism was rather low (2–6 alleles; HE = 0.49 ± 0.16), probably due to the short size of microsatellites (6–10 dinucleotide repeats) and to the fine spatial scale investigated. However, these markers are expected to provide a new insight about the genetic processes at work within and among E. alpinum populations.
Published: 2002
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44. EVOSHEEP Project. First zootechnical innovations in Southwest Asian societies (6th–1rst millennia B.C.): Origin and development of sheep breeds

Author: Emmanuelle Vila, Philippe Abrahami, Moussab Al Besso, Rémy Berthon, Frédéric Boyer, Catherine Breniquet, Dan Bradley, Jwana Chahoud, Thomas CUCCHI, Gilles Escarguel, Lionel Gourichon, Huangfu, W., Daniel Helmer, Jamet, H., Joséphine Lesur, Marjan Mashkour, Xavier Matta, Cécile Michel, Azadeh Mohaseb, Bruno Morandière, Ludovic Orlando, Stéphanie Pompanon F., Laure Tonasso-Calvière, Catherine Thèves, Manon Vuillien, ARCHEORIENT - Environnements et sociétés de l'Orient ancien (Archéorient), Université Lumière - Lyon 2 (UL2)-Centre National de la Recherche Scientifique (CNRS), Archéologie des Sociétés Méditerranéennes (ASM), Université Paul-Valéry - Montpellier 3 (UPVM)-Centre National de la Recherche Scientifique (CNRS)-Ministère de la Culture (MC), Département Automatique, Productique et Informatique (IMT Atlantique - DAPI), IMT Atlantique (IMT Atlantique), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT), Centre d'Histoire 'Espaces et Cultures' (CHEC), Université Blaise Pascal - Clermont-Ferrand 2 (UBP), Lebanese University [Beirut] (LU), Archéozoologie, archéobotanique : sociétés, pratiques et environnements (AASPE), Muséum national d'Histoire naturelle (MNHN)-Centre National de la Recherche Scientifique (CNRS), Laboratoire d'Ecologie des Hydrosystèmes Naturels et Anthropisés (LEHNA), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-École Nationale des Travaux Publics de l'État (ENTPE)-Centre National de la Recherche Scientifique (CNRS), Gestion des ressources naturelles , environnements et sociétés (GReNES), Culture et Environnements, Préhistoire, Antiquité, Moyen-Age (CEPAM), Université Nice Sophia Antipolis (1965 - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Centre National de la Recherche Scientifique (CNRS)-Université Côte d'Azur (UCA)-Université Nice Sophia Antipolis (1965 - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Centre National de la Recherche Scientifique (CNRS)-Université Côte d'Azur (UCA), Département de Chimie Moléculaire - Chimie Inorganique Redox (DCM - CIRE ), Département de Chimie Moléculaire (DCM), Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019]), Archéologies et Sciences de l'Antiquité (ArScAn), Université Paris 1 Panthéon-Sorbonne (UP1)-Université Paris 8 Vincennes-Saint-Denis (UP8)-Université Paris Nanterre (UPN)-Ministère de la Culture et de la Communication (MCC)-Centre National de la Recherche Scientifique (CNRS), Histoire et Archéologie de l'Orient Cunéiforme (HAROC), Université Paris 1 Panthéon-Sorbonne (UP1)-Université Paris 8 Vincennes-Saint-Denis (UP8)-Université Paris Nanterre (UPN)-Ministère de la Culture et de la Communication (MCC)-Centre National de la Recherche Scientifique (CNRS)-Université Paris 1 Panthéon-Sorbonne (UP1)-Université Paris 8 Vincennes-Saint-Denis (UP8)-Université Paris Nanterre (UPN)-Ministère de la Culture et de la Communication (MCC)-Centre National de la Recherche Scientifique (CNRS), Section for GeoGenetics, Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen = Københavns Universitet (UCPH)-University of Copenhagen = Københavns Universitet (UCPH)-Faculty of Health and Medical Sciences, University of Copenhagen = Københavns Universitet (UCPH)-University of Copenhagen = Københavns Universitet (UCPH), Anthropologie Moléculaire et Imagerie de Synthèse (AMIS), Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), ANR-17-CE27-0004,EVOSHEEP,Exploration des premières innovations zootechniques dans les sociétés du sud-ouest asiatique (5e-1er millénaires av. J.-C.)(2017), Centre National de la Recherche Scientifique (CNRS)-Université Paul-Valéry - Montpellier 3 (UPVM)-Ministère de la Culture (MC), IMT Atlantique Bretagne-Pays de la Loire (IMT Atlantique), Centre National de la Recherche Scientifique (CNRS)-Muséum national d'Histoire naturelle (MNHN), Université Côte d'Azur (UCA)-Centre National de la Recherche Scientifique (CNRS)-Université Nice Sophia Antipolis (... - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Université Côte d'Azur (UCA)-Centre National de la Recherche Scientifique (CNRS)-Université Nice Sophia Antipolis (... - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA), Département de Chimie Moléculaire - Chimie Inorganique Redox Biomimétique (DCM - CIRE ), Université Paris 1 Panthéon-Sorbonne (UP1)-Université Paris Nanterre (UPN)-Ministère de la Culture et de la Communication (MCC)-Centre National de la Recherche Scientifique (CNRS), University of Copenhagen = Københavns Universitet (KU)-University of Copenhagen = Københavns Universitet (KU)-Faculty of Health and Medical Sciences, University of Copenhagen = Københavns Universitet (KU)-University of Copenhagen = Københavns Universitet (KU), Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Université Paris 1 Panthéon-Sorbonne (UP1)-Université Paris 8 Vincennes-Saint-Denis (UP8)-Université Paris Nanterre (UPN)-Ministère de la Culture et de la Communication (MCC)-Institut national de recherches archéologiques préventives (Inrap)-Centre National de la Recherche Scientifique (CNRS), Université Paris 1 Panthéon-Sorbonne (UP1)-Université Paris 8 Vincennes-Saint-Denis (UP8)-Université Paris Nanterre (UPN)-Ministère de la Culture et de la Communication (MCC)-Institut national de recherches archéologiques préventives (Inrap)-Centre National de la Recherche Scientifique (CNRS)-Université Paris 1 Panthéon-Sorbonne (UP1)-Université Paris 8 Vincennes-Saint-Denis (UP8)-Université Paris Nanterre (UPN)-Ministère de la Culture et de la Communication (MCC)-Institut national de recherches archéologiques préventives (Inrap)-Centre National de la Recherche Scientifique (CNRS), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS), Archéologie des Sociétés Méditerranéennes, Université Paul-Valéry - Montpellier 3 (UM3)-Ministère de la Culture et de la Communication (MCC)-Centre National de la Recherche Scientifique (CNRS)-Université Paul-Valéry - Montpellier 3 (UM3)-Ministère de la Culture et de la Communication (MCC)-Centre National de la Recherche Scientifique (CNRS), Université Paul-Valéry - Montpellier 3 (UM3)-Ministère de la Culture et de la Communication (MCC)-Centre National de la Recherche Scientifique (CNRS), Robotique Et Vivant (ReV), Laboratoire des Sciences du Numérique de Nantes (LS2N), Université de Nantes - Faculté des Sciences et des Techniques, Université de Nantes (UN)-Université de Nantes (UN)-École Centrale de Nantes (ECN)-Centre National de la Recherche Scientifique (CNRS)-IMT Atlantique Bretagne-Pays de la Loire (IMT Atlantique), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-Université de Nantes - Faculté des Sciences et des Techniques, Lebanese University [Beirut], Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-École Nationale des Travaux Publics de l'État (ENTPE), GRENES, Université Nice Sophia Antipolis (... - 2019) (UNS), Université Côte d'Azur (UCA)-Université Côte d'Azur (UCA)-Centre National de la Recherche Scientifique (CNRS)-Université Nice Sophia Antipolis (... - 2019) (UNS), Université Côte d'Azur (UCA)-Université Côte d'Azur (UCA)-Centre National de la Recherche Scientifique (CNRS), Département de Chimie Moléculaire - Chimie Inorganique Redox Biomimétique (DCM - CIRE), Université Joseph Fourier - Grenoble 1 (UJF)-Institut de Chimie Moléculaire de Grenoble (ICMG)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes (UGA), and Université Panthéon-Sorbonne (UP1)-Université Paris Nanterre (UPN)-Institut national de recherches archéologiques préventives (Inrap)-Ministère de la Culture et de la Communication (MCC)-Centre National de la Recherche Scientifique (CNRS)
Subjects: breeds, 1rst, sheep, Asian, [SHS.ARCHEO]Humanities and Social Sciences/Archaeology and Prehistory, 6th, Southwend, B-C, innovations, Origin, societies, millennia, EVOSHEEP, zootechnical, First, development, ComputingMilieux_MISCELLANEOUS
Abstract: International audience

45. Analysis of B. taurus and B. indicus admixture in Uganda as revealed by the Illumina BovineSNP50 Genotyping BeadChip

Author: Bomba, L., Colli, L., Milanesi, M., Kabi, F., Muwanika, V., Masembe, C., Joost, Stéphane, Stucki, Sylvie, Taberlet, Pierre, Pompanon, F., Mazza, R., Stella, A., Ajmone-Marsan, Paolo, Negrini, R., Nextgen, C., and Taberlet, Pierre
Subjects: Ankole, Illumina BovineSNP50 Genotyping BeadChip, Nextgen, Uganda, Cattle, Admixture
Abstract: The NextGen project investigates disease resistance in indigenous Ugandan cattle. Since population structure and stratification may produce biased results, We have investigated the genomic structure of sampled animals genotyped with the BovineSNP50 Genotyping Beadchip. A total of 788 animals from 9 populations belonging to Ankole (crossbred between B. indicus and B. taurus), Zebu and Ankole-Zebu crosses have been sampled in 52 grid cells throughout the country (Table 1). We merged this data whit other 400 Italian Holstein Cattle, genotyped in the framework of SELMOL project to seek for a likely introgression of European B. taurus. The data were filtered with the following exclusion criteria: MAF < 0.01, genotype call rate (SNPs) < 0.95, genotype call rate (Animals) < 0.95. The resulting working dataset were composed of 43494 SNPs and 1188 animals. Hidden genetic structures were investigated by a Bayesian clustering approach with the ADMIXTURE software (Novembre et al. 2010). The software Admixture identified four ancestral genomic components. Three of them likely correspond to European taurine, African indicine and African taurine components (Figure 2). The fourth has a still unidentified origin (Yellow, Figure 2d). Most Ugandan individuals investigated have a remarkable level of admixture. Overall, about 20% of the Zebu genome is of African taurine origin, confirming previous data on the foundation of African Zebu. The European taurine (Blue, Figure 2) is a minor component of African genomes, rare in Zebu and evenly distributed in Ankole, other taurine subgroups and Ankole- Zebu crosses. Indicine and taurine components show a clear geographical structure, the former being predominant in north-eastern Uganda, and the latter in the south-west. Holstein Fresian introgression is spread mostly in south-western Uganda, while the fourth component is located in restricted geographical area in the East (Figure 3). The Ugandan cattle population is a complex admixture of African taurine (green in Figure 2) and zebuine (red) genomes, with a minor component of European origin (blue) and a rare but relevant contribution (yellow) from a still unidentified source. This complexity is to be accounted for in the following GWAS and selection signatures analyses planned within the NextGen project.

46. An In silico approach for the evaluation of DNA barcodes

Author: Shehzad Wasim, Riaz Tiayyba, Zundel Stéphanie, Coissac Eric, Ficetola Gentile, Bessière Julien, Taberlet Pierre, and Pompanon François
Subjects: Biotechnology, TP248.13-248.65, Genetics, QH426-470
Abstract: Abstract Background DNA barcoding is a key tool for assessing biodiversity in both taxonomic and environmental studies. Essential features of barcodes include their applicability to a wide spectrum of taxa and their ability to identify even closely related species. Several DNA regions have been proposed as barcodes and the region selected strongly influences the output of a study. However, formal comparisons between barcodes remained limited until now. Here we present a standard method for evaluating barcode quality, based on the use of a new bioinformatic tool that performs in silico PCR over large databases. We illustrate this approach by comparing the taxonomic coverage and the resolution of several DNA regions already proposed for the barcoding of vertebrates. To assess the relationship between in silico and in vitro PCR, we also developed specific primers amplifying different species of Felidae, and we tested them using both kinds of PCR Results Tests on specific primers confirmed the correspondence between in silico and in vitro PCR. Nevertheless, results of in silico and in vitro PCRs can be somehow different, also because tuning PCR conditions can increase the performance of primers with limited taxonomic coverage. The in silico evaluation of DNA barcodes showed a strong variation of taxonomic coverage (i.e., universality): barcodes based on highly degenerated primers and those corresponding to the conserved region of the Cyt-b showed the highest coverage. As expected, longer barcodes had a better resolution than shorter ones, which are however more convenient for ecological studies analysing environmental samples. Conclusions In silico PCR could be used to improve the performance of a study, by allowing the preliminary comparison of several DNA regions in order to identify the most appropriate barcode depending on the study aims.
Published: 2010
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47. PRIMER NOTE Isolation and characterization of microsatellites in European alpine marmots (Marmota marmota)

Author: Da Silva, A., Luikart, G., Allainé, D., Gautier, P., Taberlet, P., and Pompanon, F.
Abstract: For future investigations of the mating system of a highly social mammal (Marmota marmota), we identified 16 new microsatellites using an enrichment protocol. Five loci were revealed to be polymorphic. The polymorphism was rather low (two to six alleles among 24 individuals). However, these markers, added to the other six published microsatellites for M. marmota and Spermophilus citellus, will help to assess dispersal patterns and test for genetic monogamy in alpine marmots from the European Alps.
Published: 2003
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48. PRIMER NOTE Polymorphic microsatellite DNA loci identified in the common frog (Rana temporaria, Amphibia, Ranidae)

Author: Pidancier, N., Gauthier, P., Miquel, C., and Pompanon, F.
Abstract: We developed seven microsatellite loci in the common frog, Rana temporaria. There were between 2 and 27 alleles per locus and the expected heterozygosities ranged from 0.28 to 0.96 in a sample of frogs collected in the French Alps. Adding these seven markers to the 15 previously available microsatellite loci for this species should facilitate studies of genetic structure of Rana temporaria populations at a fine geographical scale.
Published: 2002
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49. Inhibition of sex pheromone communications of Trichogramma brassicae(Hymenoptera) by the insecticide chlorpyrifos

Author: Fouillet, P., Delpuech, J.-M., Bouletreau, M., Froment, B., Janillon, S., and Pompanon, F.
Subjects: PHYSIOLOGICAL control systems, INSECTICIDES, POLLUTION
Abstract: Biological control agents such as entomophagus insects (e.g., Trichogramma sp.) are important components of integrated pest management (IPM) programs. Because pesticides are also an important component of IPM programs, it is essential to understand how biological control agents are affected by pesticides and how these effects may affect the effectiveness of the biological control agents. Contrary to most insect species that use volatile pheromones for mate location, T. brassicae is one of the few species using a s substrate -borne sex pheromonefor mating. In this work we determined the effects of an organophosphorus insecticide, chlorpyrifos, on sex pheromone reception by males and emission by virgin females. The insects used in the pheromone tests were survivors 11-0111 an acute toxicity test in which individualswere exposed to a dose of chlorpyrifos equivalent to a 20% lethal dose. Males that survived the insecticide exposure spent much less timeon the area marked with the female pheromone than control males (mean choice indexes, 0.46 [0.34 SDI vs 0.70 (0.25 SD], p < 0.001). The kinetics of the response of males to marking by control and treated females indicated that chlorpyrifos decreased the emission of sex pheromone by females surviving the insecticide. Therefore, chlorpyrifos inhibited, pheromone reception by males and decreased pheromone emission by virgin females. These results are interpreted in the context of-sex pheromone regulation by the nervous system of insects and according to the mode of action of chlorpyrifos. Extensions of these results on actual work on sex pheromone, the use of pheromone traps, and the population biology of Trichogramma sp. are discussed. [ABSTRACT FROM AUTHOR]
Published: 1998

50. Emergence rhythms and protandry in relation to daily patterns of locomotor activity in Trichogramma species

Author: Fouillet, P., Bouletreau, M., and Pompanon, F.
Subjects: EVOLUTIONARY theories
Published: 1995

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