The key question in genomics is how genomes vary and evolve at both large and fine scales. The Evolutionary and Functional Genomics lab is particularly interested in understanding the molecular processes underlying adaptive evolution and the functional consequences of adaptive mutations. Towards this end, -omics strategies with detailed molecular and functional analyses of the candidate adaptive mutations are combined in order to arrive at a comprehensive picture of adaptation. This lab studies both transposable element (TE)-induced adaptations and point mutations in the model organism Drosophila melanogaster. It is also interested in the population dynamics of TEs. TEs are the most active, diverse, and ancient components in a broad range of genomes. As such, a complete understanding of genome function and evolution cannot be achieved without a thorough understanding of TE impact and TE biology.

Lab website: González Lab

Principal Investigator

Josefa González Pérez

González Pérez, Josefa
CSIC Tenured Scientist
Evolutionary and Functional Genomics Lab

Current members


Scientific Support Personnel
Evolutionary and Functional Genomics

Francesca Destefanis

Destefanis, Francesca
Scientific Support Personnel
Evolutionary and Functional Genomics Lab

Michael Willam Nachman

Nachman, Michael Willam
Visiting Sabbatical Professor from California University
Evolution and Developmental Biology Lab

Simón Orozco Arias

Orozco Arias, Simón
Scientific Support Personnel
Evolutionary and Functional Genomics

Eduard Solà Vázquez

Solà Vázquez, Eduard
Scientific Support Personnel
Evolutionary and Functional Genomics Lab

Ongoing projects


Merenciano M, Aguilera L, González J. 2023. Two-step CRISPR-Cas9 protocol for transposable element deletion in D. melanogaster natural populations. STAR Protocols, 4(3):102501. DOI:10.1016/j.xpro.2023.102501

Merenciano M, González J. 2023. The Interplay Between Developmental Stage and Environment Underlies the Adaptive Effect of a Natural Transposable Element Insertion. Molecular Biology and Evolution, 40(3). DOI:10.1093/molbev/msad044

Horváth V, Guirao-Rico S, Salces-Ortiz J, Rech GE, Green L, Aprea E, Rodeghiero M, Anfora G, González J. 2023. Gene expression differences consistent with water loss reduction underlie desiccation tolerance of natural Drosophila populations. BMC Biology, 21(1):35. DOI:10.1186/s12915-023-01530-4

Coronado-Zamora M, Salces-Ortiz J, González J. 2023. DrosOmics: A Browser to Explore -omics Variation Across High-Quality Reference Genomes From Natural Populations of Drosophila melanogaster.  Molecular Biology and Evolution, 40(4). DOI:10.1093/molbev/msad075

Coronado-Zamora M, González J. 2023. Transposons contribute to the functional diversification of the head, gut, and ovary transcriptomes across Drosophila natural strains. Genome Research, 33(9):1541-1553. DOI:10.1101/gr.277565.122

Vargas-Chavez C, Longo Pendy NM, Nsango SE, Aguilera L, Ayala D, González J. 2022. Transposable element variants and their potential adaptive impact in urban populations of the malaria vector Anopheles coluzzii. Genome Research, 32(1):189-202. DOI:10.1101/gr.275761.121

Rech GE, Radío S, Guirao-Rico S, Aguilera L, Horvath V, Green L, Lindstadt H, Jamilloux V, Quesneville H, González J. 2022. Population-scale long-read sequencing uncovers transposable elements associated with gene expression variation and adaptive signatures in Drosophila. Nature Communications, 13(1):1948. DOI:10.1038/s41467-022-29518-8

Green L, Coronado-Zamora M, Radío S, Rech GE, Salces-Ortiz J, González J. 2022. The genomic basis of copper tolerance in Drosophila is shaped by a complex interplay of regulatory and environmental factors. BMC Biology, 20(1):275. DOI:10.1186/s12915-022-01479-w

Brandt M, Groom Q, Magro A, Misevic D, Narraway CL, Bruckermann T, Beniermann A, Børsen T, González J, Meeus S, Roy HE, Sá-Pinto X, Torres JR, Jenkins T. 2022. Promoting scientific literacy in evolution through citizen science. Proceedings of the Royal Society B: Biological Sciences, 289(1980):46-82. DOI:10.1098/rspb.2022.1077

Wallace MA, Coffman KA, Gilbert C, Ravindran S, Albery GF, Abbott J, Argyridou E, Bellosta P, Betancourt AJ, Colinet H, Eric K, Glaser-Schmitt A, Grath S, Jelic M, Kankare M, Kozeretska I, Loeschcke V, Montchamp-Moreau C, Ometto L, Onder BS, Orengo DJ, Parsch J, Pascual M, Patenkovic A, Puerma E, Ritchie MG, Rota-Stabelli O, Schou MF, Serga SV, Stamenkovic-Radak M, Tanaskovic M, Veselinovic MS, Vieira J, Vieira CP, Kapun M, Flatt T, González J, Staubach F, Obbard DJ. 2021. The discovery, distribution and diversity of DNA viruses associated with Drosophila melanogaster in Europe. Virus Evolution, 7(1). DOI:10.1093/ve/veab031

Ullastres A, Merenciano M, González J. 2021. Regulatory regions in natural transposable element insertions drive interindividual differences in response to immune challenges in Drosophila. Genome Biology, 22(1):265. DOI:10.1186/s13059-021-02471-3

Machado HE, Bergland A, Taylor RW, Tilk S, Behrman E, Dyer K, Fabian DK, Flatt T, González J, Karasov TL, Kim BY, Kozeretska I, Lazzaro BP, Merritt T, Pool JE, O'Brien K, Rajpurohit S, Roy PR, Schaeffer SW, Serga S, Schmidt P, Petrov DA. 2021. Broad geographic sampling reveals the shared basis and environmental correlates of seasonal adaptation in Drosophila. eLife, 10. DOI:10.7554/eLife.67577

Kapun M, Nunez JCB, Bogaerts-Márquez M, Murga-Moreno J, Paris M, Outten J, Coronado-Zamora M, Tern C, Rota-Stabelli O, García Guerreiro MP, Casillas S, Orengo DJ, Puerma E, Kankare M, Ometto L, Loeschcke V, Onder BS, Abbott JK, Schaeffer SW, Rajpurohit S, Behrman EL, Schou MF, Merritt TJS, Lazzaro BP, Glaser-Schmitt A, Argyridou E, Staubach F, Wang Y, Tauber E, Serga SV, Fabian DK, Dyer KA, Wheat CW, Parsch J, Grath S, Veselinovic MS, Stamenkovic-Radak M, Jelic M, Buendía-Ruíz AJ, Gómez-Julián MJ, Espinosa-Jimenez ML, Gallardo-Jiménez FD, Patenkovic A, Eric K, Tanaskovic M, Ullastres A, Guio L, Merenciano M, Guirao-Rico S, Horváth V, Obbard DJ, Pasyukova E, Alatortsev VE, Vieira CP, Vieira J, Torres JR, Kozeretska I, Maistrenko OM, Montchamp-Moreau C, Mukha DV, Machado HE, Lamb K, Paulo T, Yusuf L, Barbadilla A, Petrov D, Schmidt P, Gonzalez J, Flatt T, Bergland AO. 2021. Drosophila Evolution over Space and Time (DEST) - A New Population Genomics Resource. Molecular Biology and Evolution, 38(12):5782-5805. DOI: 10.1093/molbev/msab259

Guirao-Rico S, González J. 2021. Benchmarking the performance of Pool-seq SNP callers using simulated and real sequencing data. Molecular Ecology Resources, 21: 1216-1229. DOI: 10.1111/1755-0998.13343. 

Bogaerts-Márquez M, Guirao-Rico S, Gautier M, González J. 2021. Temperature, rainfall and wind variables underlie environmental adaptation in natural populations of Drosophila melanogaster. Molecular Ecology, 30(4): 938-954. DOI: 10.1111/mec.15783

Salces-Ortiz J, Vargas-Chavez C, Guio L, Rech GE, González J. 2020. Transposable elements contribute to the genomic response to insecticides in Drosophila melanogaster. Philosophical Transactions of the Royal Society B: Biological Sciences, 375(1795):20190341. DOI:10.1098/rstb.2019.0341

Ruiz-Arenas C, Cáceres A, López M, Pelegrí-Sisó D, González J, González JR.2020. Identifying chromosomal subpopulations based on their recombination histories advances the study of the genetic basis of phenotypic traits. Genome Research, 30(12):1802-1814. DOI:10.1101/gr.258301.119

Kapun M, Barrón MG, Staubach F, Obbard DJ, Wiberg RAW, Vieira J, Goubert C, Rota-Stabelli O, Kankare M, Bogaerts-Márquez M, Haudry A, Waidele L, Kozeretska I, Pasyukova EG, Loeschcke V, Pascual M, Vieira CP, Serga S, Montchamp-Moreau C, Abbott J, Gibert P, Porcelli D, Posnien N, Sánchez-Gracia A, Grath S, Sucena É, Bergland AO, Guerreiro MPG, Onder BS, Argyridou E, Guio L, Schou MF, Deplancke B, Vieira C, Ritchie MG, Zwaan BJ, Tauber E, Orengo DJ, Puerma E, Aguadé M, Schmidt P, Parsch J, Betancourt AJ, Flatt T, González J. 2020. Genomic Analysis of European Drosophila melanogaster Populations Reveals Longitudinal Structure, Continent-Wide Selection, and Previously Unknown DNA Viruses. Molecular Biology and Evolution, 37(9):2661–2678. DOI: 10.1093/molbev/msaa120

González JR, Ruiz-Arenas C, Cáceres A, Morán I, López-Sánchez M, Alonso L, Tolosana I, Guindo-Martínez M, Mercader JM, Esko T, Torrents D, González J, Pérez-Jurado LA. 2020. Polymorphic Inversions Underlie the Shared Genetic Susceptibility of Obesity-Related Diseases. The American Journal of Human Genetics, 106(6):846–858. DOI: 10.1016/j.ajhg.2020.04.017

Bogaerts-Márquez M, Barrón MG, Fiston-Lavier AS, Vendrell-Mir P, Castanera R, Casacuberta JM, González J. 2020. T-lex3: An accurate tool to genotype and estimate population frequencies of transposable elements using the latest short-read whole genome sequencing data. Bioinformatics, 36(4):1191-1197. DOI:10.1093/bioinformatics/btz727

Almudi I, Vizueta J, Wyatt CDR, de Mendoza A, Marlétaz F, Firbas PN, Feuda R, Masiero G, Medina P, Alcaina-Caro A, Cruz F, Gómez-Garrido J, Gut M, Alioto TS, Vargas-Chavez C, Davie K, Misof B, González J, Aerts S, Lister R, Paps J, Rozas J, Sánchez-Gracia A, Irimia M, Maeso I, Casares F. 2020. Genomic adaptations to aquatic and aerial life in mayflies and the origin of insect wings. Nature Communications, 11(1):1–11. DOI:10.1038/s41467-020-16284-8

Villanueva-Cañas JL, Horvath V, Aguilera L, González J. 2019. Diverse families of transposable elements affect the transcriptional regulation of stress-response genes in Drosophila melanogaster. Nucleic Acids Research, 47(13):6842-6857. DOI:10.1093/nar/gkz490

Rech GE, Bogaerts-Márquez M, Barrón MG, Merenciano M, Villanueva-Cañas JL, Horváth V, Fiston-Lavier AS, Luyten I, Venkataram S, Quesneville H, Petrov DA, González J. 2019. Stress response, behavior, and development are shaped by transposable element-induced mutations in Drosophila. PLOS Genetics, 15(2). DOI:10.1371/journal.pgen.1007900

Merenciano M, Iacometti C, González J. 2019. A unique cluster of roo insertions in the promoter region of a stress response gene in Drosophila melanogaster. Mobile DNA, 10(1):1-11. doi:10.1186/s13100-019-0152-9

Lerat E, Goubert C, Guirao-Rico S, Merenciano M, Dufour AB, Vieira C, González J. 2019. Population-specific dynamics and selection patterns of transposable element insertions in European natural populations. Molecular Ecology, 28(6):1506-1522. DOI:10.1111/mec.14963

Guirao-Rico S, González J. 2019. Evolutionary insights from large scale resequencing datasets in Drosophila melanogaster. Current Opinion in Insect Science, 31:70-76. DOI:10.1016/j.cois.2018.11.002

Guio L, González J. 2019. New insights on the evolution of genome content: Population dynamics of transposable elements in flies and humans. Methods in Molecular Biology, 1910:505-530. DOI:10.1007/978-1-4939-9074-0_16

Fablet M, Jacquet A, Rebollo R, Haudry A, Rey C, Salces-Ortiz J, Bajad P, Burlet N, Jantsch MF, Guerreiro MPG, Vieira C. 2019. Dynamic interactions between the genome and an endogenous retrovirus: Tirant in Drosophila simulans wild-type strains. G3: Genes, Genomes, Genetics, 9(3):855-865. DOI:10.1534/g3.118.200789

Barrón MG, Paupy C, Rahola N, Akone-Ella O, Ngangue MF, Wilson-Bahun TA, Pombi M, Kengne P, Costantini C, Simard F, González J, Ayala D. 2019. A new species in the major malaria vector complex sheds light on reticulated species evolution. Scientific Reports, 9(1):1-13. DOI:10.1038/s41598-019-49065-5.

Agostini RB, Postigo A, Rius SP, Rech GE, Campos-Bermudez VA, Vargas WA.2019. Long-lasting primed state in maize plants: Salicylic acid and steroid signaling pathways as key players in the early activation of immune responses in silks. Molecular Plant-Microbe Interactions, 32(1):90-106. DOI:10.1094/MPMI-07-18-0208-R

Mateo L, Rech GE, González J. 2018. Genome-wide patterns of local adaptation in Western European Drosophila melanogaster natural populations. Scientific Reports, 8(1):37-49. DOI:10.1038/s41598-018-34267-0

Li ZW, Hou XH, Chen JF, Xu YC, Wu Q, González J, Guo YL. Transposable elements contribute to the adaptation of arabidopsis thaliana. Genome Biology and Evolution. 2018;10(8):2140-2150. doi:10.1093/gbe/evy171

Guio L, Vieira C, González J. 2018. Stress affects the epigenetic marks added by natural transposable element insertions in Drosophila melanogaster. Scientific Reports, 8(1):1-10. DOI:10.1038/s41598-018-30491-w.

Villanueva-Cañas JL, Rech GE, de Cara MAR, González J. 2017. Beyond SNPs: how to detect selection on transposable element insertions. Methods in Ecology and Evolution, 8(6):728-737. DOI:10.1111/2041-210X.12781

Villanueva-Cañas JL, Ruiz-Orera J, Agea MI, Gallo M, Andreu D, Albà MM. 2017. New genes and functional innovation in mammals. Genome Biology and Evolution, 9(7):1886-1900. DOI:10.1093/gbe/evx136

Le Manh H, Guio L, Merenciano M, Rovira Q, Barrón MG, González J. 2017. Natural and laboratory mutations in kuzbanian are associated with zinc stress phenotypes in Drosophila melanogaster. Scientific Reports, 7:1-12. DOI:10.1038/srep42663

Horváth V, Merenciano M, González J. 2017. Revisiting the Relationship between Transposable Elements and the Eukaryotic Stress Response. Trends in Genetics, 33(11):832-841. DOI:10.1016/j.tig.2017.08.007

Merenciano M, Ullastres A, de Cara MAR, Barrón MG, González J. 2016. Multiple Independent Retroelement Insertions in the Promoter of a Stress Response Gene Have Variable Molecular and Functional Effects in Drosophila. PLoS Genetics, 12(8):1-24. DOI:10.1371/journal.pgen.1006249

Bergland AO, Tobler R, González J, Schmidt P, Petrov D. 2016. Secondary contact and local adaptation contribute to genome-wide patterns of clinal variation in Drosophila melanogaster. Molecular Ecology, 25(5):1157-1174. DOI:10.1111/mec.13455

Ullastres A, Petit N, González J. 2015. Exploring the phenotypic space and the evolutionary history of a natural mutation in drosophila melanogaster. Molecular Biology and Evolution, 32(7):1800-1814. DOI:10.1093/molbev/msv061

Guio L, González J. 2015. The dominance effect of the adaptive transposable element insertion Bari-Jheh depends on the genetic background. Genome Biology and Evolution, 7(5):1260-1266. DOI:10.1093/gbe/evv071

González J, Martínez J, Makalowski W. 2015. Lack of population differentiation patterns of previously identified putatively adaptive transposable element insertions at microgeographic scales. Biology Direct, 10(1):1-6. DOI:10.1186/s13062-015-0075-4

Fiston-Lavier AS, Barrón MG, Petrov DA, González J. 2015. T-lex2: Genotyping, frequency estimation and re-annotation of transposable elements using single or pooled next-generation sequencing data. Nucleic Acids Research, 43(4). DOI:10.1093/nar/gku1250

Ullastres A, Farré M, Capilla L, Ruiz-Herrera A. 2014. Unraveling the effect of genomic structural changes in the rhesus macaque - implications for the adaptive role of inversions. BMC Genomics, 15(1):1-13. DOI:10.1186/1471-2164-15-530

Mateo L, Ullastres A, González J. 2014. A Transposable Element Insertion Confers Xenobiotic Resistance in Drosophila. PLoS Genetics, 10(8). DOI:10.1371/journal.pgen.1004560

Mateo L, González J. 2014. Pogo-Like transposases have been repeatedly domesticated into CENP-B-Related Proteins. Genome Biology and Evolution, 6(8):2008-2016. DOI:10.1093/gbe/evu153

Guio L, Barrõn MG, González J. 2014. The transposable element Bari-Jheh mediates oxidative stress response in Drosophila. Molecular Ecology, 23(8):2020-2030. DOI:10.1111/mec.12711

Barrón MG, Fiston-Lavier AS, Petrov DA, González J. 2014. Population genomics of transposable elements in drosophila. Annual Review of Genetics, 48:561-581. DOI:10.1146/annurev-genet-120213-092359

Ayala D, Ullastres A, González J. 2014. Adaptation through chromosomal inversions in Anopheles. Frontiers in Genetics, 5(MAY):1-10. DOI:10.3389/fgene.2014.00129

Casacuberta E, González J. 2013. The impact of transposable elements in environmental adaptation. Molecular Ecology, 22(6):1503-1517. DOI:10.1111/mec.12170

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