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1.
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18 p, 5.3 MB |
Genomic analysis of European Drosophila melanogaster populations reveals longitudinal structure, continent-wide selection, and previously unknown DNA viruses
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Kapun, Martin (The European Drosophila Population Genomics Consortium) ;
Barrón Aduriz, Maite Garazi (Institut de Biologia Evolutiva (UPF-CSIC) (Barcelona)) ;
Staubach, Fabian (University of Freiburg. Department of Evolutionary Biology and Ecology) ;
Obbard, Darren J. (University of Edinburgh. Institute of Evolutionary Biology) ;
Wiberg, R. Axel W. (University of Basel. Department of Environmental Sciences) ;
Vieira, Jorge (Instituto de Investigação e Inovação em Saúde (Porto, Portugal)) ;
Goubert, Clément (Cornell University. Department of Molecular Biology and Genetics) ;
Rota-Stabelli, Omar (The European Drosophila Population Genomics Consortium) ;
Kankare, Maaria (University of Jyväskylä. Department of Biological and Environmental Science) ;
Bogaerts-Márquez, María (Institut de Biologia Evolutiva (UPF-CSIC) (Barcelona)) ;
Haudry, Annabelle (Université Lyon 1. Laboratoire de Biométrie et Biologie Evolutive) ;
Waidele, Lena (University of Freiburg. Department of Evolutionary Biology and Ecology) ;
Kozeretska, Iryna (The European Drosophila Population Genomics Consortium) ;
Pasyukova, Elena G. (The European Drosophila Population Genomics Consortium) ;
Loeschcke, Volker (Aarhus University. Department of Bioscience-Genetics, Ecology and Evolution) ;
Pascual, Marta (Universitat de Barcelona. Departament de Genètica, Microbiologia i Estadística) ;
Vieira, Cristina P. (The European Drosophila Population Genomics Consortium) ;
Serga, Svitlana (Taras Shevchenko National University of Kyiv. General and Medical Genetics Department) ;
Montchamp-Moreau, Catherine (The European Drosophila Population Genomics Consortium) ;
Abbott, Jessica (Lund University. Department of Biology) ;
Gibert, Patricia (Université Lyon 1. Laboratoire de Biométrie et Biologie Evolutive) ;
Porcelli, Damiano (The European Drosophila Population Genomics Consortium) ;
Posnien, Nico (Universität Göttingen. Johann-Friedrich-Blumenbach-Institut für Zoologie und Anthropologie) ;
Sánchez-Gracia, Alejandro (Universitat de Barcelona. Departament de Genètica, Microbiologia i Estadística) ;
Grath, Sonja (The European Drosophila Population Genomics Consortium) ;
Sucena, Élio (Universidade de Lisboa. Departamento de Biologia Animal) ;
Bergland, Alan O. (University of Virginia. Department of Biology) ;
García Guerreiro, María Pilar (Universitat Autònoma de Barcelona. Departament de Genètica i de Microbiologia) ;
Onder, Banu Sebnem (Hacettepe University. Department of Biology) ;
Argyridou, Eliza (The European Drosophila Population Genomics Consortium) ;
Guio, Lain (Institut de Biologia Evolutiva (UPF-CSIC) (Barcelona)) ;
Schou, Mads Fristrup (Lund University. Department of Biology) ;
Deplancke, Bart (The European Drosophila Population Genomics Consortium) ;
Vieira, Cristina (Université Lyon 1. Laboratoire de Biométrie et Biologie Evolutive) ;
Ritchie, Michael G. (University of St. Andrews. Centre for Biological Diversity) ;
Zwaan, Bas J. (Wageningen University. Department of Plant Sciences) ;
Tauber, Eran (University of Haifa. Department of Evolutionary and Environmental Biology) ;
Orengo, Dorcas J. (Universitat de Barcelona. Departament de Genètica, Microbiologia i Estadística) ;
Puerma, Eva (Universitat de Barcelona. Departament de Genètica, Microbiologia i Estadística) ;
Aguadé, Montserrat (Universitat de Barcelona. Departament de Genètica, Microbiologia i Estadística) ;
Schmidt, Paul (University of Pennsylvania. Department of Biology) ;
Parsch, John (Ludwig-Maximilians-Universität München. Division of Evolutionary Biology) ;
Betancourt, Andrea J. (University of Liverpool. Department of Evolution, Ecology, and Behaviour) ;
Flatt, Thomas (University of Fribourg. Department of Biology) ;
González, Josefa (Institut de Biologia Evolutiva (UPF-CSIC) (Barcelona))
Genetic variation is the fuel of evolution, with standing genetic variation especially important for short-term evolution and local adaptation. To date, studies of spatiotemporal patterns of genetic variation in natural populations have been challenging, as comprehensive sampling is logistically difficult, and sequencing of entire populations costly. [...]
2020 -  10.1093/molbev/msaa120
Molecular biology and evolution, Vol. 37, issue 9 (Sep. 2020) , p. 2661-2678
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2.
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6 p, 807.2 KB |
The Drosophila melanogaster Genetic Reference Panel
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MacKay, Trudy F. C. (Department of Genetics. North Carolina State University) ;
Richards, Stephen (Human Genome Sequencing Center. Baylor College of Medicine) ;
Stone, Eric A. (Department of Genetics. North Carolina State University) ;
Barbadilla Prados, Antonio (Universitat Autònoma de Barcelona. Departament de Genètica i de Microbiologia) ;
Ayroles, Julien F. (Harvard University) ;
Zhu, Dianhui (Human Genome Sequencing Center. Baylor College of Medicine) ;
Casillas Viladerrams, Sònia (Universitat Autònoma de Barcelona. Institut de Biotecnologia i de Biomedicina "Vicent Villar Palasí") ;
Han, Yi (Human Genome Sequencing Center. Baylor College of Medicine) ;
Magwire, Michael M. (Department of Genetics. North Carolina State University) ;
Cridland, Julie M. (Department of Ecology and Evolutionary Biology. University of California-Irvine) ;
Richardson, Mark F. (Faculty of Life Sciences. University of Manchester) ;
Anholt, Robert R. H. (Department of Biology. North Carolina State University) ;
Barrón Aduriz, Maite Garazi (Universitat Autònoma de Barcelona. Institut de Biotecnologia i de Biomedicina "Vicent Villar Palasí") ;
Bess, Crystal (Human Genome Sequencing Center. Baylor College of Medicine) ;
Blankenburg, Kerstin Petra (Human Genome Sequencing Center. Baylor College of Medicine) ;
Carbone, Mary Anna (Department of Genetics. North Carolina State University) ;
Castellano Esteve, David (Universitat Autònoma de Barcelona. Institut de Biotecnologia i de Biomedicina "Vicent Villar Palasí") ;
Chaboub, Lesley (Human Genome Sequencing Center. Baylor College of Medicine) ;
Duncan, Laura (Department of Genetics. North Carolina State University) ;
Harris, Zeke (Department of Genetics. North Carolina State University) ;
Javaid, Mehwish (Human Genome Sequencing Center. Baylor College of Medicine) ;
Jayaseelan, Joy Christina (Human Genome Sequencing Center. Baylor College of Medicine) ;
Jhangiani, Shalini N. (Human Genome Sequencing Center. Baylor College of Medicine) ;
Jordan, Katherine W. (Department of Genetics. North Carolina State University) ;
Lara, Fremiet (Human Genome Sequencing Center. Baylor College of Medicine) ;
Lawrence, Faye (Department of Genetics. North Carolina State University) ;
Lee, Sandra L. (Human Genome Sequencing Center. Baylor College of Medicine) ;
Librado, Pablo (Universitat de Barcelona. Departament de Genètica) ;
Linheiro, Raquel S. (Faculty of Life Sciences. University of Manchester) ;
Lyman, Richard F. (Department of Genetics. North Carolina State University) ;
MacKey, Aaron J. (Center for Public Health Genomics. University of Virginia) ;
Munidasa, Mala (Human Genome Sequencing Center. Baylor College of Medicine) ;
Muzny, Donna Marie (Human Genome Sequencing Center. Baylor College of Medicine) ;
Nazareth, Lynne (Human Genome Sequencing Center. Baylor College of Medicine) ;
Newsham, Irene (Human Genome Sequencing Center. Baylor College of Medicine) ;
Perales, Lora (Human Genome Sequencing Center. Baylor College of Medicine) ;
Pu, Ling-Ling (Human Genome Sequencing Center. Baylor College of Medicine) ;
Qu, Carson (Human Genome Sequencing Center. Baylor College of Medicine) ;
Ràmia Jesús, Miquel (Universitat Autònoma de Barcelona. Institut de Biotecnologia i de Biomedicina "Vicent Villar Palasí") ;
Reid, Jeffrey G. (Human Genome Sequencing Center. Baylor College of Medicine) ;
Rollmann, Stephanie M. (Department of Biological Sciences. University of Cincinnati) ;
Rozas, Julio (Universitat de Barcelona. Departament de Genètica) ;
Saada, Nehad (Human Genome Sequencing Center. Baylor College of Medicine) ;
Turlapati, Lavanya (Department of Genetics. North Carolina State University) ;
Worley, Kim C. (Human Genome Sequencing Center. Baylor College of Medicine) ;
Wu, Yuan-Qing (Human Genome Sequencing Center. Baylor College of Medicine) ;
Yamamoto, Akihiko (Department of Genetics. North Carolina State University) ;
Zhu, Yiming (Human Genome Sequencing Center. Baylor College of Medicine) ;
Bergman, Casey M. (Faculty of Life Sciences. University of Manchester) ;
Thornton, Kevin R. (Department of Ecology and Evolutionary Biology. University of California-Irvine) ;
Mittelman, David (Virginia Bioinformatics Institute. Department of Biological Sciences. Virginia Tech) ;
Gibbs, Richard A. (Human Genome Sequencing Center. Baylor College of Medicine)
A major challenge of biology is understanding the relationship between molecular genetic variation and variation in quantitative traits, including fitness. This relationship determines our ability to predict phenotypes from genotypes and to understand how evolutionary forces shape variation within and between species. [...]
2012 - 10.1038/nature10811
Nature, Vol. 482, issue 7384 (Feb. 2012) , p. 173-178
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3.
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7 p, 1.9 MB |
T-lex3 : An accurate tool to genotype and estimate population frequencies of transposable elements using the latest short-read whole genome sequencing data
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Bogaerts-Márquez, María (Institut de Biologia Evolutiva (UPF-CSIC) (Barcelona)) ;
Barrón Aduriz, Maite Garazi (Institut de Biologia Evolutiva (UPF-CSIC) (Barcelona)) ;
Fiston-Lavier, Anna-Sophie (Institut des Sciences de l'Evolution de Montpellier) ;
Vendrell Mir, Pol (Centre de Recerca en Agrigenòmica) ;
Castanera, Raúl (Centre de Recerca en Agrigenòmica) ;
Casacuberta i Suñer, Josep M. 1962- (Centre de Recerca en Agrigenòmica) ;
González, Josefa (Institut de Biologia Evolutiva (UPF-CSIC) (Barcelona))
Motivation: Transposable elements (TEs) constitute a significant proportion of the majority of genomes sequenced to date. TEs are responsible for a considerable fraction of the genetic variation within and among species. [...]
2020 - 10.1093/bioinformatics/btz727
Bioinformatics, Vol. 36, Issue 4 (February 2020) , p. 1191-1197
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4.
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16 p, 3.7 MB |
T-lex2 : genotyping, frequency estimation and re-annotation of transposable elements using single or pooled next-generation sequencing data
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Fiston-Lavier, Anna-Sophie (Institut des Sciences de l'Evolution de Montpellier) ;
Barrón Aduriz, Maite Garazi (Universitat Autònoma de Barcelona. Institut de Biotecnologia i de Biomedicina "Vicent Villar Palasí") ;
Petrov, Dmitri A. (Department of Biology, Stanford University) ;
González, Josefa (Institut de Biologia Evolutiva (UPF-CSIC) (Barcelona))
Transposable elements (TEs) constitute the most active, diverse and ancient component in a broad range of genomes. Complete understanding of genome function and evolution cannot be achieved without a thorough understanding of TE impact and biology. [...]
2014 - 10.1093/nar/gku1250
Nucleic acids research, Vol. 43 (december 2014) , p. e22
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