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New approaches to long-standing questions: adaptation in Drosophila

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

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, Issue 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, Issue 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, Issue 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, Issue 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, Issue 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, Issue 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, Issue 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, Issue 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, Issue 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, Issue 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, Issue 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, Issue 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, Issue 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, Issue 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, Issue 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, Issue 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, Issue 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

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