Publications

@article{Harney2026-yi,

title = {Transgenerational effects of heat shock on gene regulation and 

 fitness-related traits in natural Drosophila populations},

author = {Ewan Harney and Josefa González},

year  = {2026},

date = {2026-04-01},

journal = {Mol. Biol. Evol.},

volume = {43},

number = {4},

publisher = {Oxford University Press (OUP)},

abstract = {Heat stress will increasingly affect populations as climate 

 change leads to higher temperatures and more frequent heat 

 waves. Recent work suggests that interactions between the 

 epigenome and transposable elements (TEs) could link 

 environmental acclimation with rapid evolution. Yet little is 

 known about how these processes interact in natural genetic 

 backgrounds or shape evolutionarily relevant phenotypes. To 

 investigate these interactions, we carried out laboratory 

 experiments measuring gene expression and chromatin 

 accessibility responses to heat shock in female D. melanogaster 

 from arid and cold climates, their associations with population 

 variation in TEs, and fitness-related phenotypes including 

 viability and development time in the offspring. We also 

 measured expression, accessibility and phenotypic traits three 

 generations later to explore transgenerational inheritance. 

 Expression and accessibility responses to heat shock varied 

 between populations and were influenced by TE presence, with 

 more upregulated responses in the arid population. Effects of 

 heat shock on transcription were detected three generations 

 later, especially in the arid population, although this was not 

 driven by chromatin accessibility. Among offspring of heat 

 shocked flies, phenotypes of the initial cohort (eggs laid 

 within 2 d of heat shock) were negatively affected in both 

 populations, but later cohorts (eggs laid more than 2 d after 

 heat shock) from the arid population developed quicker than 

 controls, indicating hormesis. This effect was still present 

 four generations after the heat shock in the 

 great-great-grandoffspring, demonstrating transgenerational 

 inheritance of potentially beneficial phenotypes and gene 

 expression in a natural insect population.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid38856653,

title = {From whole bodies to single cells: A guide to transcriptomic approaches for ecology and evolutionary biology},

author = {Katja M Hoedjes and Sonja Grath and Nico Posnien and Michael G Ritchie and Christian Schlötterer and Jessica K Abbott and Isabel Almudi and Marta Coronado-Zamora and Esra Durmaz Mitchell and Thomas Flatt and Claudia Fricke and Amanda Glaser-Schmitt and Josefa González and Luke Holman and Maaria Kankare and Benedict Lenhart and Dorcas J Orengo and Rhonda R Snook and Vera M Yılmaz and Leeban Yusuf},

doi = {10.1111/mec.17382},

issn = {1365-294X},

year  = {2025},

date = {2025-08-01},

journal = {Mol Ecol},

volume = {34},

number = {15},

pages = {e17382},

abstract = {RNA sequencing (RNAseq) methodology has experienced a burst of technological developments in the last decade, which has opened up opportunities for studying the mechanisms of adaptation to environmental factors at both the organismal and cellular level. Selecting the most suitable experimental approach for specific research questions and model systems can, however, be a challenge and researchers in ecology and evolution are commonly faced with the choice of whether to study gene expression variation in whole bodies, specific tissues, and/or single cells. A wide range of sometimes polarised opinions exists over which approach is best. Here, we highlight the advantages and disadvantages of each of these approaches to provide a guide to help researchers make informed decisions and maximise the power of their study. Using illustrative examples of various ecological and evolutionary research questions, we guide the readers through the different RNAseq approaches and help them identify the most suitable design for their own projects.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid40980703,

title = {Continent-wide differentiation of fitness traits and patterns of climate adaptation among European populations of },

author = {Esra Durmaz Mitchell and Envel Kerdaffrec and Ewan Harney and Tânia F Paulo and Marija Savic Veselinovic and Marija Tanaskovic and Venera Tyukmaeva and Teresa Abaurrea Fernandez de Arcaya and Cansu Aksoy and Eliza Argyridou and Tiphaine P M Bailly and Dogus Can and Ezgi Cobanoglu and Nicola Cook and Seda Coşkun and Slobodan Davidovic and Ekin Demir and Tânia Dias and Somayeh Rasouli-Dogaheh and Pedro Duque and Katarina Eric and Pavle Eric and Priscilla Erickson and Filip Filipovski and Bettina Fishman and Amanda Glaser-Schmitt and August Goldfischer and Llewellyn Green and Sonia Janillon and Mihailo Jelic and Hristina Kostic and Lucas E Kreiman and Natacha Kremer and Manolis Lyrakis and Oleksandr M Maistrenko and Sapho-Lou Marti and Megan McGunnigle and Miriam Merenciano and Mário S Mira and Vincent Montbel and Laurence Mouton and Dmitry V Mukha and Siddharth Murali and Aleksandra Patenkovic and Oleksandra Protsenko and Florencia A Putero and Micael Reis and Natalia V Roshina and Olga Y Rybina and Mads F Schou and Thibault Schowing and Senel Selin Senkal and Svitlana Serga and Virginie Trieu and Alexander V Symonenko and Mikhail V Trostnikov and Evgenia A Tsybul'ko and Joost van den Heuvel and David van Waarde and Ekaterina R Veselkina and Cristina P Vieira and Xiaocui Wang and Jelle Zandveld and Jessica Abbott and Jean-Christophe Billeter and Hervé Colinet and Mehregan Ebrahimi and Patricia Gibert and Jan Hrcek and Maaria Kankare and Iryna Kozeretska and Volker Loeschcke and Julián Mensch and Banu Sebnem Onder and John Parsch and Elena G Pasyukova and Marina Stamenkovic-Radak and Eran Tauber and Cristina Vieira and Christian Wegener and Katja M Hoedjes and Bas J Zwaan and Andrea J Betancourt and Claudia Fricke and Sonja Grath and Nico Posnien and Jorge Vieira and Martin Kapun and Christian Schlötterer and Paul Schmidt and Élio Sucena and Josefa González and Alan Bergland and Michael G Ritchie and Thomas Flatt},

doi = {10.1093/evlett/qraf014},

issn = {2056-3744},

year  = {2025},

date = {2025-08-01},

journal = {Evol Lett},

volume = {9},

number = {4},

pages = {473--490},

abstract = {A particularly well-studied evolutionary model is the vinegar fly , a cosmopolitan insect of ancestral southern-central African origin. Recent work suggests that it expanded out of Africa ∼9,000 years ago, and spread from the Middle East into Europe ∼1,800 years ago. During its global expansion, this human commensal adapted to novel climate zones and habitats. Despite much work on phenotypic differentiation and adaptation on several continents (especially North America and Australia), typically in the context of latitudinal clines, little is known about phenotypic divergence among European populations. Here, we sought to provide a continent-wide study of phenotypic differentiation among European populations of . In a consortium-wide phenomics effort, we assayed 16 fitness-related traits on a panel of 173 isofemale lines from 9 European populations, with the majority of traits measured by several groups using semi-standardized protocols. For most fitness-related traits, we found significant differentiation among populations on a continental scale. Despite inevitable differences in assay conditions among labs, the reproducibility and hence robustness of our measurements were overall remarkably good. Several fitness components (e.g., viability, development time) exhibited significant latitudinal or longitudinal clines, and populations differed markedly in multivariate trait structure. Notably, populations experiencing higher humidity/rainfall and lower maximum temperature showed higher viability, fertility, starvation resistance, and lifespan at the expense of lower heat-shock survival, suggesting a pattern of local adaptation. Our results indicate that derived populations of this tropical fly have been shaped by pervasive spatially varying multivariate selection and adaptation to different climates on the European continent.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid40826096,

title = {The epigenetics effects of transposable elements are genomic context dependent and not restricted to gene silencing in Drosophila},

author = {Marta Coronado-Zamora and Josefa González},

doi = {10.1186/s13059-025-03705-4},

issn = {1474-760X},

year  = {2025},

date = {2025-08-01},

journal = {Genome Biol},

volume = {26},

number = {1},

pages = {251},

abstract = {BACKGROUND: Transposable elements (TEs) represent a threat to genome integrity due to their proliferative capacity. Eukaryotic cells silence TEs through different molecular mechanisms, including the deposition of repressive histone marks. Previous studies have shown that TE repressive marks can spread to neighboring sequences. However, evidence for this spreading leading to nearby gene silencing remains limited. Similarly, whether TEs induce changes in the enrichment of active histone marks genome-wide, and the potential impact on gene expression have not been widely studied.nnRESULTS: In this work, we perform a comprehensive study of the epigenetic effects of 2235 TEs and their potential effects on nearby gene expression on Drosophila melanogaster head, gut, and ovary. While most TEs (816) induce the enrichment of the H3K9me3 repressive mark, with stronger epigenetic effects in the ovary, a substantial number (345 TEs) induce the enrichment of the H3K27ac active mark, particularly in the gut. We find that 70% of the H3K9me3 enriched TEs associated with expression changes downregulate the nearby gene, and 50% of the H3K27ac enriched TEs associated with expression changes lead to gene upregulation. These changes in expression affect specific regulatory networks only in the head. Furthermore, TE epigenetic effects on gene expression are genomic context dependent. Finally, we find that 221 TEs also affect gene expression by disrupting regions enriched for histone marks.  CONCLUSIONS: Overall, our results show that TEs contribute to the generation of regulatory novelty through epigenetic changes, with these epigenetic effects not restricted to gene silencing and being genomic context dependent.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid40824865,

title = {Footprints of Worldwide Adaptation in Structured Populations of Drosophila melanogaster Through the Expanded DEST 2.0 Genomic Resource},

author = {Joaquin C B Nunez and Marta Coronado-Zamora and Mathieu Gautier and Martin Kapun and Sonja Steindl and Lino Ometto and Katja Hoedjes and Julia Beets and R Axel W Wiberg and Giovanni R Mazzeo and David J Bass and Denys Radionov and Iryna Kozeretska and Mariia Zinchenko and Oleksandra Protsenko and Svitlana V Serga and Cristina Amor-Jimenez and Sònia Casillas and Alejandro Sánchez-Gracia and Aleksandra Patenkovic and Amanda Glaser-Schmitt and Antonio Barbadilla and Antonio J Buendia-Ruíz and Astra Clelia Bertelli and Balázs Kiss and Banu Sebnem Önder and Bélen Roldán Matrín and Bregje Wertheim and Candice Deschamps and Carlos E Arboleda-Bustos and Carlos Tinedo and Christian Feller and Christian Schlötterer and Clancy Lawler and Claudia Fricke and Cristina P Vieira and Cristina Vieira and Darren J Obbard and Dorcas Juana Orengo and Doris Vela and Eduardo Amat and Elgion Loreto and Envel Kerdaffrec and Esra Durmaz Mitchell and Eva Puerma and Fabian Staubach and M Florencia Camus and Hervé Colinet and Jan Hrcek and Jesper Givskov Sørensen and Jessica Abbott and Joan Torro and John Parsch and Jorge Vieira and Jose Luis Olmo and Khalid Khfif and Krzysztof Wojciechowski and Lilian Madi-Ravazzi and Maaria Kankare and Mads F Schou and Emmanuel D Ladoukakis and M Josefa Gómez-Julián and M Luisa Espinosa-Jimenez and Maria Pilar Garcia Guerreiro and Maria-Eleni Parakatselaki and Marija Savic Veselinovic and Marija Tanaskovic and Marina Stamenkovic-Radak and Margot Paris and Marta Pascual and Michael G Ritchie and Michel Rera and Mihailo Jelić and Mina Hojat Ansari and Mina Rakic and Miriam Merenciano and Natalia Hernandes and Nazar Gora and Nicolas Rode and Omar Rota-Stabelli and Paloma Sepulveda and Patricia Gibert and Pau Carazo and Pinar Kohlmeier and Priscilla A Erickson and Renaud Vitalis and Jorge Roberto Torres and Sara Guirao-Rico and Sebastian E Ramos-Onsins and Silvana Castillo and Tânia F Paulo and Venera Tyukmaeva and Zahara Alonso and Vladimir E Alatortsev and Elena Pasyukova and Dmitry V Mukha and Dmitri A Petrov and Paul Schmidt and Thomas Flatt and Alan O Bergland and Josefa Gonzalez},

doi = {10.1093/molbev/msaf132},

issn = {1537-1719},

year  = {2025},

date = {2025-07-01},

journal = {Mol Biol Evol},

volume = {42},

number = {8},

abstract = {Large-scale genomic resources can place genetic variation into an ecologically informed context. To advance our understanding of the population genetics of the fruit fly Drosophila melanogaster, we present an expanded release of the community-generated population genomics resource Drosophila Evolution over Space and Time (DEST 2.0; https://dest.bio/). This release includes 530 high-quality pooled libraries from flies collected across six continents over more than a decade (2009 to 2021), most at multiple time points per year; 211 of these libraries are sequenced and shared here for the first time. We used this enhanced resource to elucidate several aspects of the species' demographic history and identify novel signs of adaptation across spatial and temporal dimensions. For example, we showed that the spatial genetic structure of populations is stable over time, but that drift due to seasonal contractions of population size causes populations to diverge over time. We identified signals of adaptation that vary between continents in genomic regions associated with xenobiotic resistance, consistent with independent adaptation to common pesticides. Moreover, by analyzing samples collected during spring and fall across Europe, we provide new evidence for seasonal adaptation related to loci associated with pathogen response. Furthermore, we have also released an updated version of the DEST genome browser. This is a useful tool for studying spatiotemporal patterns of genetic variation in this classic model system.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{nokey,

title = {The evolutionary consequences of interactions between the epigenome, the genome, and the environment},

author = {Pierre Baduel and Marta Coronado-Zamora and Amélie Crespel and Bárbara Díez Rodríguez and Janay Fox and Dario Galanti and Josefa González and Alexander Jueterbock and Iris Sammarco and Eric Wootton and Ewan Harney

},

year  = {2024},

date = {2024-05-31},

keywords = {},

pubstate = {forthcoming},

tppubtype = {article}

}

@article{Johnson2024-ut,

title = {Effects of urban-induced mutations on ecology, evolution and  health},

author = {Marc T J Johnson and Irtaqa Arif and Francesco Marchetti and Jason Munshi-South and Rob W Ness and Marta Szulkin and Brian C Verrelli and Carole L Yauk and Daniel N Anstett and Warren Booth and Aude E Caizergues and Elizabeth J Carlen and Anthony Dant and Josefa González and César González Lagos and Madeleine Oman and Megan Phifer-Rixey and Diana J Rennison and Michael S Rosenberg and Kristin M Winchell},

year  = {2024},

date = {2024-04-19},

urldate = {2024-04-19},

journal = {Nat. Ecol. Evol.},

volume = {8},

pages = {1074–1086},

publisher = {Nature Publishing Group},

abstract = {Increasing evidence suggests that urbanization is associated 

 with higher mutation rates, which can affect the health and 

 evolution of organisms that inhabit cities. Elevated pollution 

 levels in urban areas can induce DNA damage, leading to de novo 

 mutations. Studies on mutations induced by urban pollution are 

 most prevalent in humans and microorganisms, whereas studies of 

 non-human eukaryotes are rare, even though increased mutation 

 rates have the potential to affect organisms and their 

 populations in contemporary time. Our Perspective explores how 

 higher mutation rates in urban environments could impact the 

 fitness, ecology and evolution of populations. Most mutations 

 will be neutral or deleterious, and higher mutation rates 

 associated with elevated pollution in urban populations can 

 increase the risk of cancer in humans and potentially other 

 species. We highlight the potential for urban-driven increased 

 deleterious mutational loads in some organisms, which could lead 

 to a decline in population growth of a wide diversity of 

 organisms. Although beneficial mutations are expected to be 

 rare, we argue that higher mutation rates in urban areas could 

 influence adaptive evolution, especially in organisms with short 

 generation times. Finally, we explore avenues for future 

 research to better understand the effects of urban-induced 

 mutations on the fitness, ecology and evolution of city-dwelling 

 organisms. Pollution in urban areas causes higher rates of 

 mutation than in unpolluted areas. This Perspective discusses 

 the effects of these mutations on the health, evolutionary 

 fitness and ecology of urban organisms.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{nokey,

title = {Two-step CRISPR-Cas9 protocol for transposable element deletion in D. melanogaster natural populations },

author = {Miriam Merenciano and Laura Aguilera and Josefa González},

url = {http://www.sciencedirect.com/science/article/pii/S2666166723004689?via%3Dihub},

year  = {2023},

date = {2023-09-15},

urldate = {2023-06-14},

journal = {Star Protocols },

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{CoronadoZamora2023,

title = {Transposons contribute to the functional diversification of the head, gut, and ovary transcriptomes across Drosophila natural strains},

author = {Marta Coronado-Zamora and Josefa González},

url = {http://doi.org/10.1101/gr.277565.122},

doi = {10.1101/gr.277565.122},

year  = {2023},

date = {2023-09-01},

urldate = {2023-09-01},

journal = {Genome Research},

volume = {33},

number = {9},

pages = {1541--1553},

publisher = {Cold Spring Harbor Laboratory},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{CoronadoZamora2022,

title = {DrosOmics: the comparative genomics browser to explore omics data in natural strains of D. melanogaster},

author = {Marta Coronado-Zamora and Judit Salces-Ortiz and Josefa Gonzalez},

doi = {http://doi.org/10.1093/molbev/msad075},

year  = {2023},

date = {2023-03-28},

urldate = {2023-03-24},

journal = {Molecular Biology and Evolution},

publisher = {Cold Spring Harbor Laboratory},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Merenciano2022,

title = {The interplay between developmental stage and environment determines the adaptive effect of a natural transposable element insertion},

author = {Miriam Merenciano and Josefa Gonzalez},

url = {http://doi.org/10.1093/molbev/msad044},

doi = {http://doi.org/10.1093/molbev/msad044},

year  = {2023},

date = {2023-02-22},

urldate = {2023-02-10},

journal = {Molecular Biology and Evolution},

publisher = {Cold Spring Harbor Laboratory},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{des,

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

author = {Vivien Horvath and Sara Guirao-Rico and Judit Salces-Ortiz and Gabriel E Rech and Llewellyn Green and Eugenio Aprea and Mirco Rodeghiero and Gianfranco Anfora and Josefa Gonzalez},

doi = {http://doi.org/10.1186/s12915-023-01530-4},

year  = {2023},

date = {2023-02-16},

urldate = {2023-02-16},

journal = {BMC Biology},

volume = {31},

pages = {35},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Green2022b,

title = {The genomic basis of copper tolerance in Drosophila is shaped by a complex interplay of regulatory and environmental factors},

author = {Llewellyn Green and Marta Coronado-Zamora and Santiago Radío and Gabriel E Rech and Judit Salces-Ortiz and Josefa González},

url = {http://doi.org/10.1186/s12915-022-01479-w},

doi = {10.1186/s12915-022-01479-w},

year  = {2022},

date = {2022-12-08},

journal = {BMC Biology},

volume = {20},

number = {1},

publisher = {Springer Science and Business Media LLC},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Brandt2022,

title = {Promoting scientific literacy in evolution through citizen science},

author = {Miriam Brandt and Quentin Groom and Alexandra Magro and Dusan Misevic and Claire L Narraway and Till Bruckermann and Anna Beniermann and Tom Børsen and Josefa González and Sofie Meeus and Helen E Roy and Xana Sá-Pinto and Jorge Roberto Torres and Tania Jenkins},

url = {http://doi.org/10.1098/rspb.2022.1077},

doi = {10.1098/rspb.2022.1077},

year  = {2022},

date = {2022-08-10},

journal = {Proceedings of the Royal Society B: Biological Sciences},

volume = {289},

number = {1980},

publisher = {The Royal Society},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Rech2022b,

title = {Population-scale long-read sequencing uncovers transposable elements associated with gene expression variation and adaptive signatures in Drosophila},

author = {Gabriel E Rech and Santiago Radío and Sara Guirao-Rico and Laura Aguilera and Vivien Horvath and Llewellyn Green and Hannah Lindstadt and Véronique Jamilloux and Hadi Quesneville and Josefa González},

url = {http://doi.org/10.1038/s41467-022-29518-8},

doi = {10.1038/s41467-022-29518-8},

year  = {2022},

date = {2022-04-12},

journal = {Nature Communications},

volume = {13},

number = {1},

publisher = {Springer Science and Business Media LLC},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{VargasChavez2021,

title = {Transposable element variants and their potential adaptive impact in urban populations of the malaria vector Anopheles coluzzii},

author = {Carlos Vargas-Chavez and Neil Michel Longo Pendy and Sandrine E Nsango and Laura Aguilera and Diego Ayala and Josefa González},

url = {http://doi.org/10.1101/gr.275761.121},

doi = {10.1101/gr.275761.121},

year  = {2022},

date = {2022-01-31},

journal = {Genome Research},

publisher = {Cold Spring Harbor Laboratory},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Ullastres2021c,

title = {Regulatory regions in natural transposable element insertions drive interindividual differences in response to immune challenges in Drosophila},

author = {Anna Ullastres and Miriam Merenciano and Josefa González},

url = {http://doi.org/10.1186/s13059-021-02471-3},

doi = {10.1186/s13059-021-02471-3},

year  = {2021},

date = {2021-09-14},

journal = {Genome Biology},

volume = {22},

number = {1},

publisher = {Springer Science and Business Media LLC},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Kapun2021,

title = {Drosophila Evolution over Space and Time (DEST) - A New Population Genomics Resource},

author = {Martin Kapun and Joaquin C B Nunez and María Bogaerts-Márquez and Jesús Murga-Moreno and Margot Paris and Joseph Outten and Marta Coronado-Zamora and Courtney Tern and Omar Rota-Stabelli and Maria P Garcia-Guerreiro and Sònia Casillas and Dorcas J Orengo and Eva Puerma and Maaria Kankare and Lino Ometto and Volker Loeschcke and Banu S Onder and Jessica K Abbott and Stephen W Schaeffer and Subhash Rajpurohit and Emily L Behrman and Mads F Schou and Thomas J S Merritt and Brian P Lazzaro and Amanda Glaser-Schmitt and Eliza Argyridou and Fabian Staubach and Yun Wang and Eran Tauber and Svitlana V Serga and Daniel K Fabian and Kelly A Dyer and Christopher W Wheat and John Parsch and Sonja Grath and Marija Savic Veselinovic and Marina Stamenkovic-Radak and Mihailo Jelic and Antonio J Buendía-Ruíz and María Josefa Gómez-Julián and Luisa M Espinosa-Jimenez and Francisco D. Gallardo-Jiménez and Aleksandra Patenkovic and Katarina Eric and Marija Tanaskovic and Anna Ullastres and Lain Guio and Miriam Merenciano and Sara Guirao-Rico and Vivien Horváth and Darren J Obbard and Elena Pasyukova and Vladimir E Alatortsev and Cristina P Vieira and Jorge Vieira and J Roberto Torres and Iryna Kozeretska and Oleksandr M Maistrenko and Catherine Montchamp-Moreau and Dmitry V Mukha and Heather E Machado and Keric Lamb and Tania Paulo and Leeban Yusuf and Antonio Barbadilla and Dmitri Petrov and Paul Schmidt and Josefa Gonzalez and Thomas Flatt and Alan O Bergland},

editor = {Rasmus Nielsen},

url = {http://doi.org/10.1093/molbev/msab259},

doi = {10.1093/molbev/msab259},

year  = {2021},

date = {2021-09-01},

journal = {Molecular Biology and Evolution},

volume = {38},

pages = {5782-5805},

publisher = {Oxford University Press (OUP)},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Machado2018,

title = {Broad geographic sampling reveals predictable and pervasive seasonal adaptation in Drosophila},

author = {Heather Machado and Alan O Bergland and Ryan Taylor and Susanne Tilk and Emily Behrman and Kelly Dyer and Daniel Fabian and Thomas Flatt and Josefa Gonzalez and Talia Karasov and Iryna Kozeretska and Brian P Lazzaro and Thomas Merritt and John Pool and Katherine O textquotesingle and Subhash Rajpurohit and Paula Roy and Stephen Schaeffer and Svitlana Serga and Paul Schmidt and Dmitri Petrov},

url = {http://elifesciences.org/articles/67577},

doi = {10.7554/eLife.67577},

year  = {2021},

date = {2021-06-22},

journal = {eLife},

publisher = {Cold Spring Harbor Laboratory},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2021c,

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

author = {Consortium Hub and Tyler Elliott and Tony Heitkam and Robert Hubley and Hadi Quesneville and Alexander Suh and Travis Wheeler},

url = {http://doi.org/10.1186/s13100-021-00244-0

http://blogs.biomedcentral.com/on-biology/2021/06/15/introducing-the-te-hub-a-platform-for-researchers-in-transposable-elements/},

doi = {10.1186/s13100-021-00244-0},

year  = {2021},

date = {2021-06-21},

journal = {Mobile DNA},

volume = {12},

number = {1},

publisher = {Springer Science and Business Media LLC},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Wallace2021,

title = {The discovery, distribution and diversity of DNA viruses associated with Drosophila melanogaster in Europe},

author = {Megan A Wallace and Kelsey A Coffman and Clément Gilbert and Sanjana Ravindran and Gregory F Albery and Jessica Abbott and Eliza Argyridou and Paola Bellosta and Andrea J Betancourt and Hervé Colinet and Katarina Eric and Amanda Glaser-Schmitt and Sonja Grath and Mihailo Jelic and Maaria Kankare and Iryna Kozeretska and Volker Loeschcke and Catherine Montchamp-Moreau and Lino Ometto and Banu Sebnem Onder and Dorcas J Orengo and John Parsch and Marta Pascual and Aleksandra Patenkovic and Eva Puerma and Michael G Ritchie and Omar Rota-Stabelli and Mads Fristrup Schou and Svitlana V Serga and Marina Stamenkovic-Radak and Marija Tanaskovic and Marija Savic Veselinovic and Jorge Vieira and Cristina P Vieira and Martin Kapun and Thomas Flatt and Josefa González and Fabian Staubach and Darren J Obbard},

url = {http://doi.org/10.1093/ve/veab031},

doi = {10.1093/ve/veab031},

year  = {2021},

date = {2021-04-01},

journal = {Virus Evolution},

publisher = {Oxford University Press (OUP)},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{bib,

title = {Benchmarking the performance of Pool-seq SNP callers using simulated and real sequencing data},

author = {Sara Guirao-Rico and Josefa González},

url = {http://onlinelibrary.wiley.com/doi/abs/10.1111/1755-0998.13343},

year  = {2021},

date = {2021-02-19},

journal = {Molecular Ecology Resources},

volume = {21},

pages = {1216–1229},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{BogaertsMrquez2021,

title = {Temperature, rainfall and wind variables underlie environmental adaptation in natural populations of  Drosophila  melanogaster},

author = {María Bogaerts-Márquez and Sara Guirao-Rico and Mathieu Gautier and Josefa González},

url = {http://doi.org/10.1111/mec.15783},

doi = {10.1111/mec.15783},

year  = {2021},

date = {2021-01-01},

journal = {Molecular Ecology},

volume = {30},

number = {4},

pages = {938--954},

publisher = {Wiley},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{bioRxivb,

title = {Identifying chromosomal subpopulations based on their recombination histories advances the study of the genetic basis of phenotypic traits},

author = {Ruiz-Arenas, C., and Cáceres, A., and López, M., and Pelegrí-Sisó, D., and González, J., and González, J.R},

url = {http://genome.cshlp.org/content/early/2020/11/17/gr.258301.119},

year  = {2020},

date = {2020-11-18},

journal = {Genome Research},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Gonzlez2020,

title = {Polymorphic Inversions Underlie the Shared Genetic Susceptibility of Obesity-Related Diseases},

author = {Juan González and Carlos Ruiz-Arenas and Alejandro Cáceres and Ignasi Morán and Marcos López-Sánchez and Lorena Alonso and Ignacio Tolosana and Marta Guindo-Martínez and Josep M Mercader and Tonu Esko and David Torrents and Josefa González and Luis A Pérez-Jurado},

url = {http://doi.org/10.1016/j.ajhg.2020.04.017

http://bit.ly/2B8TGCt},

doi = {10.1016/j.ajhg.2020.04.017},

year  = {2020},

date = {2020-05-28},

journal = {The American Journal of Human Genetics},

publisher = {Elsevier BV},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Almudi2020,

title = {Genomic adaptations to aquatic and aerial life in mayflies and the origin of insect wings},

author = {Isabel Almudi and Joel Vizueta and Christopher D R Wyatt and Alex de Mendoza and Ferdinand Marlétaz and Panos N Firbas and Roberto Feuda and Giulio Masiero and Patricia Medina and Ana Alcaina-Caro and Fernando Cruz and Jessica Gómez-Garrido and Marta Gut and Tyler S Alioto and Carlos Vargas-Chavez and Kristofer Davie and Bernhard Misof and Josefa González and Stein Aerts and Ryan Lister and Jordi Paps and Julio Rozas and Alejandro Sánchez-Gracia and Manuel Irimia and Ignacio Maeso and Fernando Casares},

url = {http://doi.org/10.1038/s41467-020-16284-8},

doi = {10.1038/s41467-020-16284-8},

year  = {2020},

date = {2020-05-26},

journal = {Nature Communications},

volume = {11},

number = {1},

publisher = {Springer Science and Business Media LLC},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Kapun2018,

title = {Genomic analysis of European Drosophila populations reveals major longitudinal structure, continent-wide selection, and unknown DNA viruses},

author = {Martin Kapun and Maite Barron and Fabian Staubach and Jorge Vieira and Darren Obbard and Axel R W Wiberg and Clement Goubert and Omar Rota Stabelli and Maaria Kankare and Annabelle Haudry and Maria Bogaerts-Marquez and Lena Waidele and Iryna Kozeretska and Elena Pasyukova and Volker Loeschcke and Marta Pascual and Cristina P Vieira and Svitlana Serga and Catherine Montchamp-Moreau and Jessica Abbott and Patricia Gibert and Damiano Porcelli and Nico Posnien and Alejandro Sanchez-Gracia and Sonja Grath and Elio Sucena and Alan Bergland and Maria Pilar Garcia Guerreiro and Banu Sebnem Onder and Eliza Argyridou and Lain Guio and Mads Fristrup Schou and Bart Deplancke and Cristina Vieira and Michael G Ritchie and Bas Zwaan and Eran Tauber and Dorcas Orengo and Eva Puerma and Montserrat Aguade and Paul Schmidt and John Parsch and Andrea Betancourt and Thomas Flatt and Josefa Gonzalez},

url = {http://academic.oup.com/mbe/advance-article/doi/10.1093/molbev/msaa120/5837682},

doi = {http://doi.org/10.1093/molbev/msaa120},

year  = {2020},

date = {2020-05-15},

journal = {Molecular Biology and Evolution},

volume = {37},

number = {9},

pages = {2661-2678},

publisher = {Cold Spring Harbor Laboratory},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{BogaertsMrquez2019,

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

author = {María Bogaerts-Marquez and Maite Barrón and Anna-Sophie Fiston-Lavier and Pol Vendrell-Mir and Raúl Castanera and Josep M Casacuberta and Josefa González},

editor = {Russell Schwartz},

url = {http://doi.org/10.1093/bioinformatics/btz727},

doi = {10.1093/bioinformatics/btz727},

year  = {2020},

date = {2020-02-15},

journal = {Bioinformatics},

publisher = {Oxford University Press (OUP)},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{SalcesOrtiz2020,

title = {Transposable elements contribute to the genomic response to insecticides in  Drosophila melanogaster},

author = {Judit Salces-Ortiz and Carlos Vargas-Chavez and Lain Guio and Gabriel E Rech and Josefa Gonzalez},

url = {http://doi.org/10.1098/rstb.2019.0341},

doi = {10.1098/rstb.2019.0341},

year  = {2020},

date = {2020-02-10},

journal = {Philosophical Transactions of the Royal Society B: Biological Sciences},

volume = {375},

number = {1795},

pages = {20190341},

publisher = {The Royal Society},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{RotaStabelli2019b,

title = {Distinct genotypes and phenotypes in European and American strains of Drosophila suzukii: implications for biology and management of an invasive organism},

author = {Omar Rota-Stabelli and Lino Ometto and Gabriella Tait and Silvia Ghirotto and Rupinder Kaur and Francesco Drago and Josefa González and Vaughn M Walton and Gianfranco Anfora and Marco Valerio Rossi-Stacconi},

url = {http://doi.org/10.1007/s10340-019-01172-y},

doi = {10.1007/s10340-019-01172-y},

year  = {2020},

date = {2020-01-01},

journal = {Journal of Pest Science},

volume = {93},

number = {1},

pages = {77--89},

publisher = {Springer Science and Business Media LLC},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{VendrellMir2019,

title = {A benchmark of transposon insertion detection tools using real data},

author = {Pol Vendrell-Mir and Fabio Barteri and Miriam Merenciano and Josefa González and Josep M Casacuberta and Raúl Castanera},

url = {http://doi.org/10.1186/s13100-019-0197-9},

doi = {10.1186/s13100-019-0197-9},

year  = {2019},

date = {2019-12-30},

journal = {Mobile DNA},

volume = {10},

number = {1},

publisher = {Springer Science and Business Media LLC},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Barrn2019,

title = {A new species in the major malaria vector complex sheds light on reticulated species evolution},

author = {Maite Barrón and Christophe Paupy and Nil Rahola and Ousman Akone-Ella and Marc F Ngangue and Theodel A Wilson-Bahun and Marco Pombi and Pierre Kengne and Carlo Costantini and Frédéric Simard and Josefa González and Diego Ayala},

url = {http://doi.org/10.1038/s41598-019-49065-5},

doi = {10.1038/s41598-019-49065-5},

year  = {2019},

date = {2019-10-14},

journal = {Scientific Reports},

volume = {9},

number = {1},

publisher = {Springer Science and Business Media LLC},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2019d,

title = {Diverse families of transposable elements affect the transcriptional regulation of stress-response genes in Drosophila melanogaster },

author = {Villanueva-Cañas, J.L., Horvath, V., Aguilera;L., and González, J.},

url = {http://doi.org/10.1093/nar/gkz490},

doi = {10.1093/nar/gkz490},

year  = {2019},

date = {2019-06-08},

journal = {Nucleic Acids Research},

publisher = {Oxford University Press (OUP)},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Merenciano2019,

title = {A unique cluster of roo insertions in the promoter region of a stress response gene in Drosophila melanogaster},

author = {Miriam Merenciano and Camillo Iacometti and Josefa González},

url = {http://doi.org/10.1186/s13100-019-0152-9},

doi = {10.1186/s13100-019-0152-9},

year  = {2019},

date = {2019-03-14},

journal = {Mobile DNA},

volume = {10},

number = {1},

publisher = {Springer Nature},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Rech2018,

title = {Stress response, behavior, and development are shaped by transposable element-induced mutations in Drosophila. },

author = {Gabriel E Rech and Maria Bogaerts-Marquez and Maite G Barron and Miriam Merenciano and Jose L Villanueva-Canas and Vivien Horvath and Anna-Sophie Fiston-Lavier and Isabelle Luyten and Sandeep Venkataram and Hadi Quesneville and Dmitri A Petrov and Josefa Gonzalez},

url = {http://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1007900

http://www.ncbi.nlm.nih.gov/pubmed/30753202},

year  = {2019},

date = {2019-02-13},

urldate = {2019-02-12},

journal = {PLoS Genetics},

volume = {15 },

number = {2},

pages = {e1007900},

publisher = {Cold Spring Harbor Laboratory},

organization = {PLoS Genetics},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{COIS,

title = {Evolutionary insights from large scale resequencing datasets in Drosophila melanogaster},

author = {Sara Guirao-Rico and Josefa González},

url = {http://hdl.handle.net/10261/172876},

doi = {10.1016/j.cois.2018.11.002},

year  = {2019},

date = {2019-02-01},

journal = {Current Opinion in Insect Science},

volume = {31},

pages = {70-76},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{MolEcol,

title = {Population specific dynamics and selection patterns of transposable element insertions in European natural populations},

author = {Emmanuelle Lerat, Clément Goubert, Sara Guirao-Rico, Miriam Merenciano, Anne-Béatrice Dufour, Cristina Vieira, and Josefa González.},

doi = {10.1111/mec.14963},

year  = {2019},

date = {2019-01-31},

journal = {Molecular Ecology},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{,

title = {Genome-wide patterns of local adaptation in Western European Drosophila melanogaster natural populations},

author = {L Mateo and G Rech and J Gonzalez},

doi = {10.1038/s41598-018-34267-0},

year  = {2018},

date = {2018-11-01},

journal = {Scientific Reports},

volume = {8},

pages = {16143},

publisher = {Cold Spring Harbor Laboratory},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Guio2018,

title = {Stress affects the epigenetic marks added by natural transposable element insertions in Drosophila melanogaster},

author = {Lain Guio and Cristina Vieira and Josefa González},

url = {http://doi.org/10.1038/s41598-018-30491-w},

doi = {10.1038/s41598-018-30491-w},

year  = {2018},

date = {2018-08-15},

journal = {Scientific Reports},

volume = {8},

pages = {12197},

publisher = {Springer Nature America, Inc},

keywords = {},

pubstate = {published},

tppubtype = {article}

}