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New approaches to long-standing questions: adaptation in Drosophila

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Publications

The interplay between developmental stage and environment determines the adaptive effect of a natural transposable element insertion

Author(s): Miriam Merenciano, Josefa Gonzalez
Published in: bioRxiv, 2022
Publisher: CSHL
DOI: 10.1101/2022.02.09.479730

Basal and stress-induced expression changes consistent with water loss reduction explain desiccation tolerance of natural Drosophila melanogaster populations

Author(s): Vivien Horváth, Sara Guirao-Rico, Judit Salces-Ortiz, Gabriel E. Rech, Llewellyn Green, Eugenio Aprea, Mirco Rodeghiero, Gianfranco Anfora, Josefa González
Published in: 2022
Publisher: Cold Spring Harbour Laboratory
DOI: 10.1101/2022.03.21.485105

Population-scale long-read sequencing uncovers transposable elements contributing to gene expression variation and associated with adaptive signatures in Drosophila melanogaster

Author(s): Gabriel E. Rech, Santiago Radío, Sara Guirao-Rico, Laura Aguilera, Vivien Horvath, Llewellyn Green, Hannah Lindstadt, Véronique Jamilloux, Hadi Quesneville, Josefa González
Published in: bioRxiv, 2021
Publisher: CSHL
DOI: 10.1101/2021.10.08.463646

Genomic analysis of European Drosophila populations reveals longitudinal structure and continent-wide selection

Author(s): Martin Kapun, Maite Garazi Barron Aduriz, Fabian Staubach, Jorge Vieira, Darren Obbard, Clement Goubert, Omar Rota Stabelli, Maaria Kankare, Annabelle Haudry, R. Axel W. Wiberg, Lena Waidele, Iryna Kozeretska, Elena Pasyukova, Volker Loeschcke, Marta Pascual, Cristina P Vieira, Svitlana Serga, Catherine Montchamp-Moreau, Jessica Abbott, Patricia Gibert, Damiano Porcelli, Nico
Published in: bioRxiv, 2018
Publisher: Cold Spring Harbor Laboratory
DOI: 10.1101/313759

Broad geographic sampling reveals predictable and pervasive seasonal adaptation in Drosophila

Author(s): Heather Machado, Alan O. Bergland, Ryan Taylor, Susanne Tilk, Emily Behrman, Kelly Dyer, Daniel Fabian, Thomas Flatt, Josefa Gonzalez, Talia Karasov, Iryna Kozeretska, Brian P. Lazzaro, Thomas Merritt, John Pool, Katherine O'Brien, Subhash Rajpurohit, Paula Roy, Stephen Schaeffer, Svitlana Serga, Paul Schmidt, Dmitri Petrov
Published in: bioRxiv, 2018
Publisher: Cold Spring Harbor Laboratory
DOI: 10.1101/337543

Natural variation in copper tolerance in Drosophila melanogaster is shaped by transcriptional and physiological changes in the gut

Author(s): Llewellyn Green, Santiago Radio, Gabriel E. Rech, Judit Salces-Ortiz, Josefa González
Published in: bioRxiv, 2021
Publisher: CSHL
DOI: 10.1101/2021.07.12.452058

Deciphering the molecular and phenotypic effects of a Drosophila melanogaster transposable element located in a unique insertional cluster

Author(s): Miriam Merenciano
Published in: 2020
Publisher: Universitat de Barcelona

Identification of environmental variables in Drosophila melanogaster natural populations

Author(s): María Bogaerts Márquez
Published in: 2021
Publisher: Universitat Pompeu Fabra

Unravelling the role of transposable elements in the eukaryotic stress response

Author(s): Vivien Horvath
Published in: 2020
Publisher: Universitat Pompeu Fabra

T-lex3: an accurate tool to genotype and estimate population frequencies of transposable elements using the latest short-read whole genome sequencing data

Author(s): María Bogaerts-Márquez, Maite G Barrón, Anna-Sophie Fiston-Lavier, Pol Vendrell-Mir, Raúl Castanera, Josep M Casacuberta, Josefa González
Published in: Bioinformatics, 2019, ISSN 1367-4803
Publisher: Oxford University Press
DOI: 10.1093/bioinformatics/btz727

Temperature, rainfall and wind variables underlie environmental adaptation in natural populations of Drosophila melanogaster

Author(s): María Bogaerts‐Márquez, Sara Guirao‐Rico, Mathieu Gautier, Josefa González
Published in: Molecular Ecology, 30/4, 2021, Page(s) 938-954, ISSN 0962-1083
Publisher: Blackwell Publishing Inc.
DOI: 10.1111/mec.15783

A benchmark of transposon insertion detection tools using real data

Author(s): Pol Vendrell-Mir, Fabio Barteri, Miriam Merenciano, Josefa González, Josep M. Casacuberta, Raúl Castanera
Published in: Mobile DNA, 10/1, 2019, ISSN 1759-8753
Publisher: BioMed Central
DOI: 10.1186/s13100-019-0197-9

Benchmarking the performance of Pool-seq SNP callers using simulated and real sequencing data

Author(s): Sara Guirao-Rico, Josefa González
Published in: Molecular Ecology Resources, 2021, ISSN 1755-0998
Publisher: Wiley Online
DOI: 10.1111/1755-0998.13343

Diverse families of transposable elements affect the transcriptional regulation of stress-response genes in Drosophila melanogaster

Author(s): José Luis Villanueva-Cañas, Vivien Horvath, Laura Aguilera, Josefa González
Published in: Nucleic Acids Research, 2019, ISSN 0305-1048
Publisher: Oxford University Press
DOI: 10.1093/nar/gkz490

Genomic Analysis of European Drosophila melanogaster Populations Reveals Longitudinal Structure, Continent-Wide Selection, and Previously Unknown DNA Viruses

Author(s): Martin Kapun, Maite G Barrón, Fabian Staubach, Darren J Obbard, R Axel W Wiberg, Jorge Vieira, Clément Goubert, Omar Rota-Stabelli, Maaria Kankare, María Bogaerts-Márquez, Annabelle Haudry, Lena Waidele, Iryna Kozeretska, Elena G Pasyukova, Volker Loeschcke, Marta Pascual, Cristina P Vieira, Svitlana Serga, Catherine Montchamp-Moreau, Jessica Abbott, Patricia Gibert, Damiano Porcelli, Nico Pos
Published in: Molecular Biology and Evolution, 37/9, 2020, Page(s) 2661-2678, ISSN 0737-4038
Publisher: Oxford University Press
DOI: 10.1093/molbev/msaa120

Drosophila Evolution over Space and Time (DEST) - A New Population Genomics Resource

Author(s): Martin Kapun, Joaquin C B Nunez, María Bogaerts-Márquez, Jesús Murga-Moreno, Margot Paris, Joseph Outten, Marta Coronado-Zamora, Courtney Tern, Omar Rota-Stabelli, Maria P García Guerreiro, Sònia Casillas, Dorcas J Orengo, Eva Puerma, Maaria Kankare, Lino Ometto, Volker Loeschcke, Banu S Onder, Jessica K Abbott, Stephen W Schaeffer, Subhash Rajpurohit, Emily L Behrman, Mads
Published in: Molecular Biology and Evolution, 2021, ISSN 1537-1719
Publisher: Oxford University Press
DOI: 10.1093/molbev/msab259

The discovery, distribution and diversity of DNA viruses associated with Drosophila melanogaster in Europe

Author(s): Megan A. Wallace; Kelsey A. Coffman; Clément Gilbert; Sanjana Ravindran; Gregory F. Albery; Jessica K. Abbott; Eliza Argyridou; Paola Bellosta; Paola Bellosta; Andrea J. Betancourt; Hervé Colinet; Katarina Eric; Amanda Glaser-Schmitt; Sonja Grath; Mihailo Jelić; Maaria Kankare; Iryna Kozeretska; Volker Loeschcke; Catherine Montchamp-Moreau; Lino Ometto; Banu Sebnem Onder; Dorcas J. Orengo; John
Published in: Virus Evolution, 8, 2021, ISSN 2057-1577
Publisher: Oxford University Press
DOI: 10.1093/ve/veab031

Identifying chromosomal subpopulations based on their recombination histories advances the study of the genetic basis of phenotypic traits.

Author(s): Carlos Ruiz-Arenas; Alejandro Cáceres; Marcos Lamelas López; Dolors Pelegrí-Sisó; Josefa González; Juan R. González
Published in: Genome Research, 5, 2020, ISSN 1549-5469
Publisher: CSHLP
DOI: 10.1101/gr.258301.119

Revisiting the Relationship between Transposable Elements and the Eukaryotic Stress Response

Author(s): Vivien Horváth, Miriam Merenciano, Josefa González
Published in: Trends in Genetics, 33/11, 2017, Page(s) 832-841, ISSN 0168-9525
Publisher: Elsevier BV
DOI: 10.1016/j.tig.2017.08.007

Beyond SNPs: how to detect selection on transposable element insertions

Author(s): José Luis Villanueva-Cañas, Gabriel E. Rech, Maria Angeles Rodriguez de Cara, Josefa González
Published in: Methods in Ecology and Evolution, 8/6, 2017, Page(s) 728-737, ISSN 2041-210X
Publisher: John Wiley and Sons Inc.
DOI: 10.1111/2041-210X.12781

Stress affects the epigenetic marks added by natural transposable element insertions in Drosophila melanogaster

Author(s): Lain Guio, Cristina Vieira, Josefa González
Published in: Scientific Reports, 8/1, 2018, ISSN 2045-2322
Publisher: Nature Publishing Group
DOI: 10.1038/s41598-018-30491-w

Genome-wide patterns of local adaptation in Western European Drosophila melanogaster natural populations

Author(s): Lidia Mateo, Gabriel E. Rech, Josefa González
Published in: Scientific Reports, 8/1, 2018, ISSN 2045-2322
Publisher: Nature Publishing Group
DOI: 10.1038/s41598-018-34267-0

Evolutionary insights from large scale resequencing datasets in Drosophila melanogaster

Author(s): Sara Guirao-Rico, Josefa González
Published in: Current Opinion in Insect Science, 31, 2019, Page(s) 70-76, ISSN 2214-5745
Publisher: Elsevier BV
DOI: 10.1016/j.cois.2018.11.002

Stress response, behavior, and development are shaped by transposable element-induced mutations in Drosophila

Author(s): Gabriel E. Rech, María Bogaerts-Márquez, Maite G. Barrón, Miriam Merenciano, José Luis Villanueva-Cañas, Vivien Horváth, Anna-Sophie Fiston-Lavier, Isabelle Luyten, Sandeep Venkataram, Hadi Quesneville, Dmitri A. Petrov, Josefa González
Published in: PLOS Genetics, 15/2, 2019, Page(s) e1007900, ISSN 1553-7404
Publisher: Public Library of Sciences
DOI: 10.1371/journal.pgen.1007900

Population-specific dynamics and selection patterns of transposable element insertions in European natural populations

Author(s): Emmanuelle Lerat, Clément Goubert, Sara Guirao-Rico, Miriam Merenciano, Anne-Béatrice Dufour, Cristina Vieira, Josefa González
Published in: Molecular Ecology, 2019, ISSN 0962-1083
Publisher: Blackwell Publishing Inc.
DOI: 10.1111/mec.14963

Transposable Elements Contribute to the Adaptation of Arabidopsis thaliana

Author(s): Zi-Wen Li, Xing-Hui Hou, Jia-Fu Chen, Yong-Chao Xu, Qiong Wu, Josefa González, Ya-Long Guo
Published in: Genome Biology and Evolution, 10/8, 2018, Page(s) 2140-2150, ISSN 1759-6653
Publisher: Oxford University Press
DOI: 10.1093/gbe/evy171

A unique cluster of roo insertions in the promoter region of a stress response gene in Drosophila melanogaster

Author(s): Miriam Merenciano, Camillo Iacometti, Josefa González
Published in: Mobile DNA, 10/1, 2019, ISSN 1759-8753
Publisher: BioMed Central
DOI: 10.1186/s13100-019-0152-9

Transposable elements contribute to the genomic response to insecticides in Drosophila melanogaster

Author(s): Judit Salces-Ortiz, Carlos Vargas-Chavez, Lain Guio, Gabriel E. Rech, Josefa González
Published in: Philosophical Transactions of the Royal Society B: Biological Sciences, 375/1795, 2020, Page(s) 20190341, ISSN 0962-8436
Publisher: Royal Society of London
DOI: 10.1098/rstb.2019.0341

TE Hub: A community-oriented space for sharing and connecting tools, data, resources, and methods for transposable element annotation.

Author(s): The TE Hub Consortium; Tyler A. Elliott; Tony Heitkam; Robert Hubley; Hadi Quesneville; Alexander Suh; Travis J. Wheeler
Published in: Mobile DNA, 7, 2021, ISSN 1759-8753
Publisher: BioMed Central
DOI: 10.1186/s13100-021-00244-0

Regulatory regions in natural transposable element insertions drive interindividual differences in response to immune challenges in Drosophila

Author(s): Anna Ullastres, Miriam Merenciano, Josefa González
Published in: Genome Biology, 2021, ISSN 1465-6906
Publisher: Biomed Central
DOI: 10.1186/s13059-021-02471-3

Broad geographic sampling reveals the shared basis and environmental correlates of seasonal adaptation in Drosophila .

Author(s): Heather E. Machado; Alan O. Bergland; Ryan W. Taylor; Susanne Tilk; Emily L. Behrman; Kelly A. Dyer; Daniel K. Fabian; Thomas Flatt; Josefa González; Talia L. Karasov; Bernard Y. Kim; Iryna Kozeretska; Brian P. Lazzaro; Thomas J.S. Merritt; John E. Pool; Katherine R. O'Brien; Subhash Rajpurohit; Paula R. Roy; Stephen W. Schaeffer; Svitlana Serga; Paul S. Schmidt; Dmitri A. Petrov
Published in: eLife, 10, 2021, ISSN 2050-084X
Publisher: eLife Sciences Publications
DOI: 10.17863/cam.73315

Polymorphic Inversions Underlie the Shared Genetic Susceptibility of Obesity-Related Diseases

Author(s): Juan R. González; Carlos Ruiz-Arenas; Alejandro Cáceres; Ignasi Moran; Marcos López-Sánchez; Lorena Alonso; Ignacio Tolosana; Marta Guindo-Martínez; Josep M. Mercader; Tõnu Esko; David Torrents; David Torrents; Josefa González; Luis A. Pérez-Jurado
Published in: The American Journal of Human Genetics, 3, 2020, ISSN 0002-9297
Publisher: University of Chicago Press
DOI: 10.1016/j.ajhg.2020.04.017

New Insights on the Evolution of Genome Content: Population Dynamics of Transposable Elements in Flies and Humans

Author(s): Lain Guio, Josefa González
Published in: Methods in Molecular Biology, 2019
Publisher: Springer Nature
DOI: 10.1007/978-1-4939-9074-0_16