{"id":118,"date":"2017-11-30T08:07:41","date_gmt":"2017-11-30T08:07:41","guid":{"rendered":"https:\/\/melanogaster.ibb-csic.info\/gonzalez_lab\/?page_id=118"},"modified":"2023-01-17T09:19:59","modified_gmt":"2023-01-17T09:19:59","slug":"publications","status":"publish","type":"page","link":"https:\/\/melanogaster.ibb-csic.info\/gonzalez_lab\/publications\/","title":{"rendered":"Publications"},"content":{"rendered":"
<\/a><\/form>
88 entries<\/span> «<\/a> ‹<\/a> 1 of 2 ›<\/a> »<\/a> <\/div><\/div>\r\n \r\n \r\n \r\n \r\n \r\n \r\n \r\n
\r\n

2024<\/h3>\r\n <\/td>\r\n <\/tr>

<\/td>

Orozco-Arias, Simon; Sierra, P\u00edo; Durbin, Richard; Gonz\u00e1lez, Josefa<\/p>

MCHelper automatically curates transposable element libraries across eukaryotic species<\/a> Journal Article<\/span> <\/p>

In: <\/span>Genome Research, <\/span>vol. 34, <\/span>no. 12, <\/span>pp. 2256\u20132268, <\/span>2024<\/span>, ISSN: 1549-5469<\/span>.<\/p>

Links<\/a><\/span> | BibTeX<\/a><\/span><\/p>

<\/td>

J, Nunez; M, Coronado-Zamora; M, Gautier; et al,<\/p>

Footprints of worldwide adaptation in structured populations of D. melanogaster through the expanded DEST 2.0 genomic resource<\/a> Online<\/span> <\/p>

2024<\/span>, visited: 11.11.2024<\/span>.<\/p>

Links<\/a><\/span> | BibTeX<\/a><\/span><\/p>

<\/td>

Bista, Basanta; Gonz\u00e1lez-Rodelas, Laura; \u00c1lvarez-Gonz\u00e1lez, Luc\u00eda; Wu, Zhi-qiang; Montiel, Eugenia E.; Lee, Ling Sze; Badenhorst, Daleen B.; Radhakrishnan, Srihari; Literman, Robert; Navarro-Dominguez, Beatriz; Iverson, John B.; Orozco-Arias, Simon; Gonz\u00e1lez, Josefa; Ruiz-Herrera, Aurora; Valenzuela, Nicole<\/p>

De novo genome assemblies of two cryptodiran turtles with ZZ\/ZW and XX\/XY sex chromosomes provide insights into patterns of genome reshuffling and uncover novel 3D genome folding in amniotes<\/a> Journal Article<\/span> <\/p>

In: <\/span>Genome Research, <\/span>vol. 34, <\/span>no. 10, <\/span>pp. 1553\u20131569, <\/span>2024<\/span>, ISSN: 1549-5469<\/span>.<\/p>

Links<\/a><\/span> | BibTeX<\/a><\/span><\/p>

<\/td>

Tahami, Mohadeseh S.; Vargas-Chavez, Carlos; Poikela, Noora; Coronado-Zamora, Marta; Gonz\u00e1lez, Josefa; Kankare, Maaria<\/p>

Transposable elements in Drosophila montana from harsh cold environments<\/a> Journal Article<\/span> <\/p>

In: <\/span>Mobile DNA, <\/span>vol. 15, <\/span>no. 1, <\/span>2024<\/span>, ISSN: 1759-8753<\/span>.<\/p>

Links<\/a><\/span> | BibTeX<\/a><\/span><\/p>

<\/td>

Coronado-Zamora, Marta; Gonz\u00e1lez, Josefa<\/p>

Transposable elements and adaptation<\/a> Book Chapter<\/span> <\/p>

In: <\/span>ISTE, <\/span>2024<\/span>, ISBN: 9781789451788<\/span>.<\/p>

Links<\/a><\/span> | BibTeX<\/a><\/span><\/p>

<\/td>

Cartney, Ann M Mc; Formenti, Giulio; Mouton, Alice; et al,<\/p>

The European Reference Genome Atlas: piloting a decentralised approach to equitable biodiversity genomics<\/a> Journal Article<\/span> <\/p>

In: <\/span>npj Biodiversity, <\/span>vol. 3, <\/span>no. 1, <\/span>2024<\/span>, ISSN: 2731-4243<\/span>.<\/p>

Links<\/a><\/span> | BibTeX<\/a><\/span><\/p>

<\/td>

Baduel, Pierre; Sammarco, Iris; Barrett, Rowan; Coronado\u2010Zamora, Marta; Crespel, Am\u00e9lie; D\u00edez\u2010Rodr\u00edguez, B\u00e1rbara; Fox, Janay; Galanti, Dario; Gonz\u00e1lez, Josefa; Jueterbock, Alexander; Wootton, Eric; Harney, Ewan<\/p>

The evolutionary consequences of interactions between the epigenome, the genome and the environment<\/a> Journal Article<\/span> <\/p>

In: <\/span>Evolutionary Applications, <\/span>vol. 17, <\/span>no. 7, <\/span>2024<\/span>, ISSN: 1752-4571<\/span>.<\/p>

Links<\/a><\/span> | BibTeX<\/a><\/span><\/p>

<\/td>

Hoedjes, Katja; Grath, Sonja; Posnien, Nico; Ritchie, Mike; Schl\u00f6tterer, Christian; Abbott, Jessica; Almudi, Isabel; Coronado-Zamora, Marta; Mitchell, Esra Durmaz; Flatt, Thomas; Fricke, Claudia; Glaser-Schmitt, Amanda; Gonzalez, Josefa; Holman, Luke; Kankare, Maaria; Lenhart, Adam; Orengo, Dorcas; Snook, Rhonda; Yilmaz, Vera; Yusuf, Leeban<\/p>

From whole bodies to single cells: a guide to transcriptomic approaches for ecology and evolutionary biology<\/a> Journal Article<\/span> <\/p>

In: <\/span>Molecular Ecology, <\/span>no. e17382, <\/span>2024<\/span>.<\/p>

Links<\/a><\/span> | BibTeX<\/a><\/span><\/p>

<\/td>

Sabar\u00eds, Gonzalo; Schuettengruber, Bernd; Papadopoulos, Giorgio L.; Coronado-Zamora, Marta; Fitz-James, Maximilian H.; Gonz\u00e1lez, Josefa; Cavalli, Giacomo<\/p>

The mechanistic basis of genetic assimilation in natural fly populations<\/a> Online<\/span> <\/p>

2024<\/span>, visited: 09.05.2024<\/span>.<\/p>

Links<\/a><\/span> | BibTeX<\/a><\/span><\/p>

<\/td>

Johnson, Marc T J; Arif, Irtaqa; Marchetti, Francesco; Munshi-South, Jason; Ness, Rob W; Szulkin, Marta; Verrelli, Brian C; Yauk, Carole L; Anstett, Daniel N; Booth, Warren; Caizergues, Aude E; Carlen, Elizabeth J; Dant, Anthony; Gonz\u00e1lez, Josefa; Lagos, C\u00e9sar Gonz\u00e1lez; Oman, Madeleine; Phifer-Rixey, Megan; Rennison, Diana J; Rosenberg, Michael S; Winchell, Kristin M<\/p>

Effects of urban-induced mutations on ecology, evolution and health Journal Article<\/span> <\/p>

In: <\/span>Nat. Ecol. Evol., <\/span>vol. 8, <\/span>pp. 1074\u20131086, <\/span>2024<\/span>.<\/p>

Abstract<\/a><\/span> | BibTeX<\/a><\/span><\/p>

@article{Johnson2024-ut,
\r\ntitle = {Effects of urban-induced mutations on ecology, evolution and  health},
\r\nauthor = {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 Gonz\u00e1lez and C\u00e9sar Gonz\u00e1lez Lagos and Madeleine Oman and Megan Phifer-Rixey and Diana J Rennison and Michael S Rosenberg and Kristin M Winchell},
\r\nyear  = {2024},
\r\ndate = {2024-04-19},
\r\nurldate = {2024-04-19},
\r\njournal = {Nat. Ecol. Evol.},
\r\nvolume = {8},
\r\npages = {1074\u20131086},
\r\npublisher = {Nature Publishing Group},
\r\nabstract = {Increasing evidence suggests that urbanization is associated 
\r\n with higher mutation rates, which can affect the health and 
\r\n evolution of organisms that inhabit cities. Elevated pollution 
\r\n levels in urban areas can induce DNA damage, leading to de novo 
\r\n mutations. Studies on mutations induced by urban pollution are 
\r\n most prevalent in humans and microorganisms, whereas studies of 
\r\n non-human eukaryotes are rare, even though increased mutation 
\r\n rates have the potential to affect organisms and their 
\r\n populations in contemporary time. Our Perspective explores how 
\r\n higher mutation rates in urban environments could impact the 
\r\n fitness, ecology and evolution of populations. Most mutations 
\r\n will be neutral or deleterious, and higher mutation rates 
\r\n associated with elevated pollution in urban populations can 
\r\n increase the risk of cancer in humans and potentially other 
\r\n species. We highlight the potential for urban-driven increased 
\r\n deleterious mutational loads in some organisms, which could lead 
\r\n to a decline in population growth of a wide diversity of 
\r\n organisms. Although beneficial mutations are expected to be 
\r\n rare, we argue that higher mutation rates in urban areas could 
\r\n influence adaptive evolution, especially in organisms with short 
\r\n generation times. Finally, we explore avenues for future 
\r\n research to better understand the effects of urban-induced 
\r\n mutations on the fitness, ecology and evolution of city-dwelling 
\r\n organisms. Pollution in urban areas causes higher rates of 
\r\n mutation than in unpolluted areas. This Perspective discusses 
\r\n the effects of these mutations on the health, evolutionary 
\r\n fitness and ecology of urban organisms.},
\r\nkeywords = {},
\r\npubstate = {published},
\r\ntppubtype = {article}
\r\n}
\r\n<\/pre><\/div>
Close<\/a><\/p><\/div>
Increasing evidence suggests that urbanization is associated 
\r\n with higher mutation rates, which can affect the health and 
\r\n evolution of organisms that inhabit cities. Elevated pollution 
\r\n levels in urban areas can induce DNA damage, leading to de novo 
\r\n mutations. Studies on mutations induced by urban pollution are 
\r\n most prevalent in humans and microorganisms, whereas studies of 
\r\n non-human eukaryotes are rare, even though increased mutation 
\r\n rates have the potential to affect organisms and their 
\r\n populations in contemporary time. Our Perspective explores how 
\r\n higher mutation rates in urban environments could impact the 
\r\n fitness, ecology and evolution of populations. Most mutations 
\r\n will be neutral or deleterious, and higher mutation rates 
\r\n associated with elevated pollution in urban populations can 
\r\n increase the risk of cancer in humans and potentially other 
\r\n species. We highlight the potential for urban-driven increased 
\r\n deleterious mutational loads in some organisms, which could lead 
\r\n to a decline in population growth of a wide diversity of 
\r\n organisms. Although beneficial mutations are expected to be 
\r\n rare, we argue that higher mutation rates in urban areas could 
\r\n influence adaptive evolution, especially in organisms with short 
\r\n generation times. Finally, we explore avenues for future 
\r\n research to better understand the effects of urban-induced 
\r\n mutations on the fitness, ecology and evolution of city-dwelling 
\r\n organisms. Pollution in urban areas causes higher rates of 
\r\n mutation than in unpolluted areas. This Perspective discusses 
\r\n the effects of these mutations on the health, evolutionary 
\r\n fitness and ecology of urban organisms.<\/div>
Close<\/a><\/p><\/div><\/td><\/tr>
<\/td>

Guirao-Rico, Sara; Gonz\u00e1lez, Josefa<\/p>

Transposable elements identify previously overlooked regions undergoing parallel evolution in response to diverse selective pressures<\/a> Online<\/span> <\/p>

2024<\/span>, visited: 06.04.2024<\/span>.<\/p>

Links<\/a><\/span> | BibTeX<\/a><\/span><\/p>

\r\n

2023<\/h3>\r\n <\/td>\r\n <\/tr>

<\/td>

Coronado-Zamora, Marta; Gonz\u00e1lez, Josefa<\/p>

The epigenetics effects of transposable elements are context dependent and not restricted to gene silencing<\/a> Online<\/span> <\/p>

2023<\/span>, visited: 28.11.2023<\/span>.<\/p>

Links<\/a><\/span> | BibTeX<\/a><\/span><\/p>

<\/td>

Merenciano, Miriam; Aguilera, Laura; Gonz\u00e1lez, Josefa<\/p>

Two-step CRISPR-Cas9 protocol for transposable element deletion in D. melanogaster natural populations <\/a> Journal Article<\/span> <\/p>

In: <\/span>Star Protocols , <\/span>2023<\/span>.<\/p>

Links<\/a><\/span> | BibTeX<\/a><\/span><\/p>

<\/td>

Coronado-Zamora, Marta; Gonz\u00e1lez, Josefa<\/p>

Transposons contribute to the functional diversification of the head, gut, and ovary transcriptomes across Drosophila natural strains<\/a> Journal Article<\/span> <\/p>

In: <\/span>Genome Research, <\/span>vol. 33, <\/span>no. 9, <\/span>pp. 1541\u20131553, <\/span>2023<\/span>.<\/p>

Links<\/a><\/span> | BibTeX<\/a><\/span><\/p>

<\/td>

Coronado-Zamora, Marta; Salces-Ortiz, Judit; Gonzalez, Josefa<\/p>

DrosOmics: the comparative genomics browser to explore omics data in natural strains of D. melanogaster<\/a> Journal Article<\/span> <\/p>

In: <\/span>Molecular Biology and Evolution, <\/span>2023<\/span>.<\/p>

Links<\/a><\/span> | BibTeX<\/a><\/span><\/p>

<\/td>

Merenciano, Miriam; Gonzalez, Josefa<\/p>

The interplay between developmental stage and environment determines the adaptive effect of a natural transposable element insertion<\/a> Journal Article<\/span> <\/p>

In: <\/span>Molecular Biology and Evolution, <\/span>2023<\/span>.<\/p>

Links<\/a><\/span> | BibTeX<\/a><\/span><\/p>

<\/td>

Horvath, Vivien; Guirao-Rico, Sara; Salces-Ortiz, Judit; Rech, Gabriel E; Green, Llewellyn; Aprea, Eugenio; Rodeghiero, Mirco; Anfora, Gianfranco; Gonzalez, Josefa<\/p>

Basal and stress-induced expression changes consistent with water loss reduction explain desiccation tolerance of natural Drosophila melanogaster populations<\/a> Journal Article<\/span> <\/p>

In: <\/span>BMC Biology, <\/span>vol. 31, <\/span>pp. 35, <\/span>2023<\/span>.<\/p>

Links<\/a><\/span> | BibTeX<\/a><\/span><\/p>

<\/td>

Merenciano, Miriam; Coronado-Zamora, Marta; Gonz\u00e1lez, Josefa<\/p>

Experimental Validation of Transposable Element Insertions Using the Polymerase Chain Reaction (PCR)<\/a> Book Chapter<\/span> <\/p>

In: <\/span> Branco, Miguel R; de Mendoza Soler, Alexandre (Ed.): Transposable Elements: Methods and Protocols, <\/span>pp. 95\u2013114, <\/span>Springer US, <\/span>New York, NY, <\/span>2023<\/span>, ISBN: 978-1-0716-2883-6<\/span>.<\/p>

Abstract<\/a><\/span> | Links<\/a><\/span> | BibTeX<\/a><\/span><\/p>

@inbook{Merenciano2023,
\r\ntitle = {Experimental Validation of Transposable Element Insertions Using the Polymerase Chain Reaction (PCR)},
\r\nauthor = {Miriam Merenciano and Marta Coronado-Zamora and Josefa Gonz\u00e1lez},
\r\neditor = {Miguel R Branco and Alexandre de Mendoza Soler},
\r\nurl = {https:\/\/doi.org\/10.1007\/978-1-0716-2883-6_6
\r\nhttps:\/\/ecoevorxiv.org\/g5xhz\/},
\r\ndoi = {10.1007\/978-1-0716-2883-6_6},
\r\nisbn = {978-1-0716-2883-6},
\r\nyear  = {2023},
\r\ndate = {2023-01-01},
\r\nurldate = {2023-01-01},
\r\nbooktitle = {Transposable Elements: Methods and Protocols},
\r\npages = {95--114},
\r\npublisher = {Springer US},
\r\naddress = {New York, NY},
\r\nabstract = {Transposable elements (TEs), also known as transposons, are repetitive DNA sequences, present in virtually all organisms, that can move from one genomic position to another. TEs can be a source of mutations with important consequences for organisms. Despite their interest, its repetitive nature has made their study very challenging. However, the emergence of new sequencing technologies that allow obtaining long-read sequences, has improved the in silico de novo detection and annotation of TEs. The de novo annotation of TEs has already been performed in several organisms including the fruit fly Drosophila melanogaster. Yet, experimental validation can be used to confirm the presence of TEs in specific D. melanogaster natural populations. Here, we present a step-by-step protocol to experimentally validate by polymerase chain reaction (PCR) the presence and\/or absence of TEs in natural populations of D. melanogaster. This detailed protocol has been implemented in the participant high schools of the Citizen Fly Lab activity that is part of the international citizen science project Melanogaster: Catch the Fly! (https:\/\/melanogaster.eu). Specifically, the students collaborate with the scientists of the European Drosophila Population Genomics Consortium (DrosEU) in the experimental validation of new genetic variants, previously identified using bioinformatic techniques.},
\r\nkeywords = {},
\r\npubstate = {published},
\r\ntppubtype = {inbook}
\r\n}
\r\n<\/pre><\/div>
Close<\/a><\/p><\/div>
Transposable elements (TEs), also known as transposons, are repetitive DNA sequences, present in virtually all organisms, that can move from one genomic position to another. TEs can be a source of mutations with important consequences for organisms. Despite their interest, its repetitive nature has made their study very challenging. However, the emergence of new sequencing technologies that allow obtaining long-read sequences, has improved the in silico de novo detection and annotation of TEs. The de novo annotation of TEs has already been performed in several organisms including the fruit fly Drosophila melanogaster. Yet, experimental validation can be used to confirm the presence of TEs in specific D. melanogaster natural populations. Here, we present a step-by-step protocol to experimentally validate by polymerase chain reaction (PCR) the presence and\/or absence of TEs in natural populations of D. melanogaster. This detailed protocol has been implemented in the participant high schools of the Citizen Fly Lab activity that is part of the international citizen science project Melanogaster: Catch the Fly! (https:\/\/melanogaster.eu). Specifically, the students collaborate with the scientists of the European Drosophila Population Genomics Consortium (DrosEU) in the experimental validation of new genetic variants, previously identified using bioinformatic techniques.<\/div>
Close<\/a><\/p><\/div>
\r\n

2022<\/h3>\r\n <\/td>\r\n <\/tr>

<\/td>

Green, Llewellyn; Coronado-Zamora, Marta; Rad\u00edo, Santiago; Rech, Gabriel E; Salces-Ortiz, Judit; Gonz\u00e1lez, Josefa<\/p>

The genomic basis of copper tolerance in Drosophila is shaped by a complex interplay of regulatory and environmental factors<\/a> Journal Article<\/span> <\/p>

In: <\/span>BMC Biology, <\/span>vol. 20, <\/span>no. 1, <\/span>2022<\/span>.<\/p>

Links<\/a><\/span> | BibTeX<\/a><\/span><\/p>

<\/td>

Brandt, Miriam; Groom, Quentin; Magro, Alexandra; Misevic, Dusan; Narraway, Claire L; Bruckermann, Till; Beniermann, Anna; B\u00f8rsen, Tom; Gonz\u00e1lez, Josefa; Meeus, Sofie; Roy, Helen E; S\u00e1-Pinto, Xana; Torres, Jorge Roberto; Jenkins, Tania<\/p>

Promoting scientific literacy in evolution through citizen science<\/a> Journal Article<\/span> <\/p>

In: <\/span>Proceedings of the Royal Society B: Biological Sciences, <\/span>vol. 289, <\/span>no. 1980, <\/span>2022<\/span>.<\/p>

Links<\/a><\/span> | BibTeX<\/a><\/span><\/p>

<\/td>

Rech, Gabriel E; Rad\u00edo, Santiago; Guirao-Rico, Sara; Aguilera, Laura; Horvath, Vivien; Green, Llewellyn; Lindstadt, Hannah; Jamilloux, V\u00e9ronique; Quesneville, Hadi; Gonz\u00e1lez, Josefa<\/p>

Population-scale long-read sequencing uncovers transposable elements associated with gene expression variation and adaptive signatures in Drosophila<\/a> Journal Article<\/span> <\/p>

In: <\/span>Nature Communications, <\/span>vol. 13, <\/span>no. 1, <\/span>2022<\/span>.<\/p>

Links<\/a><\/span> | BibTeX<\/a><\/span><\/p>

<\/td>

Vargas-Chavez, Carlos; Pendy, Neil Michel Longo; Nsango, Sandrine E; Aguilera, Laura; Ayala, Diego; Gonz\u00e1lez, Josefa<\/p>

Transposable element variants and their potential adaptive impact in urban populations of the malaria vector Anopheles coluzzii<\/a> Journal Article<\/span> <\/p>

In: <\/span>Genome Research, <\/span>2022<\/span>.<\/p>

Links<\/a><\/span> | BibTeX<\/a><\/span><\/p>

\r\n

2021<\/h3>\r\n <\/td>\r\n <\/tr>

<\/td>

Ullastres, Anna; Merenciano, Miriam; Gonz\u00e1lez, Josefa<\/p>

Regulatory regions in natural transposable element insertions drive interindividual differences in response to immune challenges in Drosophila<\/a> Journal Article<\/span> <\/p>

In: <\/span>Genome Biology, <\/span>vol. 22, <\/span>no. 1, <\/span>2021<\/span>.<\/p>

Links<\/a><\/span> | BibTeX<\/a><\/span><\/p>

\"Drosophila<\/td>

Kapun, Martin; Nunez, Joaquin C B; Bogaerts-M\u00e1rquez, Mar\u00eda; Murga-Moreno, Jes\u00fas; Paris, Margot; Outten, Joseph; Coronado-Zamora, Marta; Tern, Courtney; Rota-Stabelli, Omar; Garcia-Guerreiro, Maria P; Casillas, S\u00f2nia; Orengo, Dorcas J; Puerma, Eva; Kankare, Maaria; Ometto, Lino; Loeschcke, Volker; Onder, Banu S; Abbott, Jessica K; Schaeffer, Stephen W; Rajpurohit, Subhash; Behrman, Emily L; Schou, Mads F; Merritt, Thomas J S; Lazzaro, Brian P; Glaser-Schmitt, Amanda; Argyridou, Eliza; Staubach, Fabian; Wang, Yun; Tauber, Eran; Serga, Svitlana V; Fabian, Daniel K; Dyer, Kelly A; Wheat, Christopher W; Parsch, John; Grath, Sonja; Veselinovic, Marija Savic; Stamenkovic-Radak, Marina; Jelic, Mihailo; Buend\u00eda-Ru\u00edz, Antonio J; G\u00f3mez-Juli\u00e1n, Mar\u00eda Josefa; Espinosa-Jimenez, Luisa M; Gallardo-Jim\u00e9nez, Francisco D.; Patenkovic, Aleksandra; Eric, Katarina; Tanaskovic, Marija; Ullastres, Anna; Guio, Lain; Merenciano, Miriam; Guirao-Rico, Sara; Horv\u00e1th, Vivien; Obbard, Darren J; Pasyukova, Elena; Alatortsev, Vladimir E; Vieira, Cristina P; Vieira, Jorge; Torres, J Roberto; Kozeretska, Iryna; Maistrenko, Oleksandr M; Montchamp-Moreau, Catherine; Mukha, Dmitry V; Machado, Heather E; Lamb, Keric; Paulo, Tania; Yusuf, Leeban; Barbadilla, Antonio; Petrov, Dmitri; Schmidt, Paul; Gonzalez, Josefa; Flatt, Thomas; Bergland, Alan O<\/p>

Drosophila Evolution over Space and Time (DEST) - A New Population Genomics Resource<\/a> Journal Article<\/span> <\/p>

In: <\/span>Molecular Biology and Evolution, <\/span>vol. 38, <\/span>pp. 5782-5805, <\/span>2021<\/span>.<\/p>

Links<\/a><\/span> | BibTeX<\/a><\/span><\/p>

@article{Kapun2021,
\r\ntitle = {Drosophila Evolution over Space and Time (DEST) - A New Population Genomics Resource},
\r\nauthor = {Martin Kapun and Joaquin C B Nunez and Mar\u00eda Bogaerts-M\u00e1rquez and Jes\u00fas 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 S\u00f2nia 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 Buend\u00eda-Ru\u00edz and Mar\u00eda Josefa G\u00f3mez-Juli\u00e1n and Luisa M Espinosa-Jimenez and Francisco D. Gallardo-Jim\u00e9nez and Aleksandra Patenkovic and Katarina Eric and Marija Tanaskovic and Anna Ullastres and Lain Guio and Miriam Merenciano and Sara Guirao-Rico and Vivien Horv\u00e1th 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},
\r\neditor = {Rasmus Nielsen},
\r\nurl = {https:\/\/doi.org\/10.1093\/molbev\/msab259},
\r\ndoi = {10.1093\/molbev\/msab259},
\r\nyear  = {2021},
\r\ndate = {2021-09-01},
\r\njournal = {Molecular Biology and Evolution},
\r\nvolume = {38},
\r\npages = {5782-5805},
\r\npublisher = {Oxford University Press (OUP)},
\r\nkeywords = {},
\r\npubstate = {published},
\r\ntppubtype = {article}
\r\n}
\r\n<\/pre><\/div>
Close<\/a><\/p><\/div>
<\/td>

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

Broad geographic sampling reveals predictable and pervasive seasonal adaptation in Drosophila<\/a> Journal Article<\/span> <\/p>

In: <\/span>eLife, <\/span>2021<\/span>.<\/p>

Links<\/a><\/span> | BibTeX<\/a><\/span><\/p>

<\/td>

Hub, Consortium; Elliott, Tyler; Heitkam, Tony; Hubley, Robert; Quesneville, Hadi; Suh, Alexander; Wheeler, Travis<\/p>

TE Hub: A community-oriented space for sharing and connecting tools, data, resources, and methods for transposable element annotation<\/a> Journal Article<\/span> <\/p>

In: <\/span>Mobile DNA, <\/span>vol. 12, <\/span>no. 1, <\/span>2021<\/span>.<\/p>

Links<\/a><\/span> | BibTeX<\/a><\/span><\/p>

<\/td>

Wallace, Megan A; Coffman, Kelsey A; Gilbert, Cl\u00e9ment; Ravindran, Sanjana; Albery, Gregory F; Abbott, Jessica; Argyridou, Eliza; Bellosta, Paola; Betancourt, Andrea J; Colinet, Herv\u00e9; Eric, Katarina; Glaser-Schmitt, Amanda; Grath, Sonja; Jelic, Mihailo; Kankare, Maaria; Kozeretska, Iryna; Loeschcke, Volker; Montchamp-Moreau, Catherine; Ometto, Lino; Onder, Banu Sebnem; Orengo, Dorcas J; Parsch, John; Pascual, Marta; Patenkovic, Aleksandra; Puerma, Eva; Ritchie, Michael G; Rota-Stabelli, Omar; Schou, Mads Fristrup; Serga, Svitlana V; Stamenkovic-Radak, Marina; Tanaskovic, Marija; Veselinovic, Marija Savic; Vieira, Jorge; Vieira, Cristina P; Kapun, Martin; Flatt, Thomas; Gonz\u00e1lez, Josefa; Staubach, Fabian; Obbard, Darren J<\/p>

The discovery, distribution and diversity of DNA viruses associated with Drosophila melanogaster in Europe<\/a> Journal Article<\/span> <\/p>

In: <\/span>Virus Evolution, <\/span>2021<\/span>.<\/p>

Links<\/a><\/span> | BibTeX<\/a><\/span><\/p>

<\/td>

Casares, Fernando; Maeso, Ignacio; Gonz\u00e1lez, Josefa; G\u00f3mez-Mestre, Ivan; Nieto, Angela; Poyatos, Juan F.<\/p>

The Genesis of the Phenotype<\/a> Book Chapter<\/span> <\/p>

In: <\/span> Bovolenta, Paola; Manzanares, Miguel; Buceta, Javier (Ed.): Editorial CSIC, <\/span>2021<\/span>.<\/p>

Links<\/a><\/span> | BibTeX<\/a><\/span><\/p>

<\/td>

Guirao-Rico, Sara; Gonz\u00e1lez, Josefa<\/p>

Benchmarking the performance of Pool-seq SNP callers using simulated and real sequencing data<\/a> Journal Article<\/span> <\/p>

In: <\/span>Molecular Ecology Resources, <\/span>vol. 21, <\/span>pp. 1216\u20131229, <\/span>2021<\/span>.<\/p>

Links<\/a><\/span> | BibTeX<\/a><\/span><\/p>

<\/td>

Bogaerts-M\u00e1rquez, Mar\u00eda; Guirao-Rico, Sara; Gautier, Mathieu; Gonz\u00e1lez, Josefa<\/p>

Temperature, rainfall and wind variables underlie environmental adaptation in natural populations of Drosophila melanogaster<\/a> Journal Article<\/span> <\/p>

In: <\/span>Molecular Ecology, <\/span>vol. 30, <\/span>no. 4, <\/span>pp. 938\u2013954, <\/span>2021<\/span>.<\/p>

Links<\/a><\/span> | BibTeX<\/a><\/span><\/p>

\r\n

2020<\/h3>\r\n <\/td>\r\n <\/tr>

<\/td>

C. Ruiz-Arenas,; A. C\u00e1ceres,; M. L\u00f3pez,; D. Pelegr\u00ed-Sis\u00f3,; J. Gonz\u00e1lez,; Gonz\u00e1lez, J. R<\/p>

Identifying chromosomal subpopulations based on their recombination histories advances the study of the genetic basis of phenotypic traits<\/a> Journal Article<\/span> <\/p>

In: <\/span>Genome Research, <\/span>2020<\/span>.<\/p>

Links<\/a><\/span> | BibTeX<\/a><\/span><\/p>

<\/td>

Gonz\u00e1lez, Juan; Ruiz-Arenas, Carlos; C\u00e1ceres, Alejandro; Mor\u00e1n, Ignasi; L\u00f3pez-S\u00e1nchez, Marcos; Alonso, Lorena; Tolosana, Ignacio; Guindo-Mart\u00ednez, Marta; Mercader, Josep M; Esko, Tonu; Torrents, David; Gonz\u00e1lez, Josefa; P\u00e9rez-Jurado, Luis A<\/p>

Polymorphic Inversions Underlie the Shared Genetic Susceptibility of Obesity-Related Diseases<\/a> Journal Article<\/span> <\/p>

In: <\/span>The American Journal of Human Genetics, <\/span>2020<\/span>.<\/p>

Links<\/a><\/span> | BibTeX<\/a><\/span><\/p>

<\/td>

Almudi, Isabel; Vizueta, Joel; Wyatt, Christopher D R; de Mendoza, Alex; Marl\u00e9taz, Ferdinand; Firbas, Panos N; Feuda, Roberto; Masiero, Giulio; Medina, Patricia; Alcaina-Caro, Ana; Cruz, Fernando; G\u00f3mez-Garrido, Jessica; Gut, Marta; Alioto, Tyler S; Vargas-Chavez, Carlos; Davie, Kristofer; Misof, Bernhard; Gonz\u00e1lez, Josefa; Aerts, Stein; Lister, Ryan; Paps, Jordi; Rozas, Julio; S\u00e1nchez-Gracia, Alejandro; Irimia, Manuel; Maeso, Ignacio; Casares, Fernando<\/p>

Genomic adaptations to aquatic and aerial life in mayflies and the origin of insect wings<\/a> Journal Article<\/span> <\/p>

In: <\/span>Nature Communications, <\/span>vol. 11, <\/span>no. 1, <\/span>2020<\/span>.<\/p>

Links<\/a><\/span> | BibTeX<\/a><\/span><\/p>

<\/td>

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

Genomic analysis of European Drosophila populations reveals major longitudinal structure, continent-wide selection, and unknown DNA viruses<\/a> Journal Article<\/span> <\/p>

In: <\/span>Molecular Biology and Evolution, <\/span>vol. 37, <\/span>no. 9, <\/span>pp. 2661-2678, <\/span>2020<\/span>.<\/p>

Links<\/a><\/span> | BibTeX<\/a><\/span><\/p>

@article{Kapun2018,
\r\ntitle = {Genomic analysis of European Drosophila populations reveals major longitudinal structure, continent-wide selection, and unknown DNA viruses},
\r\nauthor = {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},
\r\nurl = {https:\/\/academic.oup.com\/mbe\/advance-article\/doi\/10.1093\/molbev\/msaa120\/5837682},
\r\ndoi = {https:\/\/doi.org\/10.1093\/molbev\/msaa120},
\r\nyear  = {2020},
\r\ndate = {2020-05-15},
\r\njournal = {Molecular Biology and Evolution},
\r\nvolume = {37},
\r\nnumber = {9},
\r\npages = {2661-2678},
\r\npublisher = {Cold Spring Harbor Laboratory},
\r\nkeywords = {},
\r\npubstate = {published},
\r\ntppubtype = {article}
\r\n}
\r\n<\/pre><\/div>
Close<\/a><\/p><\/div>
<\/td>

Bogaerts-Marquez, Mar\u00eda; Barr\u00f3n, Maite; Fiston-Lavier, Anna-Sophie; Vendrell-Mir, Pol; Castanera, Ra\u00fal; Casacuberta, Josep M; Gonz\u00e1lez, Josefa<\/p>

T-lex3: an accurate tool to genotype and estimate population frequencies of transposable elements using the latest short-read whole genome sequencing data<\/a> Journal Article<\/span> <\/p>

In: <\/span>Bioinformatics, <\/span>2020<\/span>.<\/p>

Links<\/a><\/span> | BibTeX<\/a><\/span><\/p>

<\/td>

Salces-Ortiz, Judit; Vargas-Chavez, Carlos; Guio, Lain; Rech, Gabriel E; Gonzalez, Josefa<\/p>

Transposable elements contribute to the genomic response to insecticides in Drosophila melanogaster<\/a> Journal Article<\/span> <\/p>

In: <\/span>Philosophical Transactions of the Royal Society B: Biological Sciences, <\/span>vol. 375, <\/span>no. 1795, <\/span>pp. 20190341, <\/span>2020<\/span>.<\/p>

Links<\/a><\/span> | BibTeX<\/a><\/span><\/p>

<\/td>

Vargas-Ch\u00e1vez, Carlos; Gonz\u00e1lez, Josefa<\/p>

Transposable Elements in Anopheles Species: Refining Annotation Strategies Towards Population Genomics Analyses<\/a> Book Chapter<\/span> <\/p>

In: <\/span>Population Genomics, <\/span>Springer International Publishing, <\/span>2020<\/span>.<\/p>

Links<\/a><\/span> | BibTeX<\/a><\/span><\/p>

<\/td>

Rota-Stabelli, Omar; Ometto, Lino; Tait, Gabriella; Ghirotto, Silvia; Kaur, Rupinder; Drago, Francesco; Gonz\u00e1lez, Josefa; Walton, Vaughn M; Anfora, Gianfranco; Rossi-Stacconi, Marco Valerio<\/p>

Distinct genotypes and phenotypes in European and American strains of Drosophila suzukii: implications for biology and management of an invasive organism<\/a> Journal Article<\/span> <\/p>

In: <\/span>Journal of Pest Science, <\/span>vol. 93, <\/span>no. 1, <\/span>pp. 77\u201389, <\/span>2020<\/span>.<\/p>

Links<\/a><\/span> | BibTeX<\/a><\/span><\/p>

\r\n

2019<\/h3>\r\n <\/td>\r\n <\/tr>

<\/td>

Vendrell-Mir, Pol; Barteri, Fabio; Merenciano, Miriam; Gonz\u00e1lez, Josefa; Casacuberta, Josep M; Castanera, Ra\u00fal<\/p>

A benchmark of transposon insertion detection tools using real data<\/a> Journal Article<\/span> <\/p>

In: <\/span>Mobile DNA, <\/span>vol. 10, <\/span>no. 1, <\/span>2019<\/span>.<\/p>

Links<\/a><\/span> | BibTeX<\/a><\/span><\/p>

<\/td>

Barr\u00f3n, Maite; Paupy, Christophe; Rahola, Nil; Akone-Ella, Ousman; Ngangue, Marc F; Wilson-Bahun, Theodel A; Pombi, Marco; Kengne, Pierre; Costantini, Carlo; Simard, Fr\u00e9d\u00e9ric; Gonz\u00e1lez, Josefa; Ayala, Diego<\/p>

A new species in the major malaria vector complex sheds light on reticulated species evolution<\/a> Journal Article<\/span> <\/p>

In: <\/span>Scientific Reports, <\/span>vol. 9, <\/span>no. 1, <\/span>2019<\/span>.<\/p>

Links<\/a><\/span> | BibTeX<\/a><\/span><\/p>

<\/td>

Guio, Lain; Gonz\u00e1lez, Josefa<\/p>

New Insights on the Evolution of Genome Content: Population Dynamics of Transposable Elements in Flies and Humans<\/a> Book Chapter<\/span> <\/p>

In: <\/span>Methods in Molecular Biology, <\/span>pp. 505\u2013530, <\/span>Springer New York, <\/span>2019<\/span>.<\/p>

Links<\/a><\/span> | BibTeX<\/a><\/span><\/p>

<\/td>

J.L. Villanueva-Ca\u00f1as, Horvath; Gonz\u00e1lez, J.<\/p>

Diverse families of transposable elements affect the transcriptional regulation of stress-response genes in Drosophila melanogaster <\/a> Journal Article<\/span> <\/p>

In: <\/span>Nucleic Acids Research, <\/span>2019<\/span>.<\/p>

Links<\/a><\/span> | BibTeX<\/a><\/span><\/p>

<\/td>

Merenciano, Miriam; Iacometti, Camillo; Gonz\u00e1lez, Josefa<\/p>

A unique cluster of roo insertions in the promoter region of a stress response gene in Drosophila melanogaster<\/a> Journal Article<\/span> <\/p>

In: <\/span>Mobile DNA, <\/span>vol. 10, <\/span>no. 1, <\/span>2019<\/span>.<\/p>

Links<\/a><\/span> | BibTeX<\/a><\/span><\/p>

\"Stress<\/td>

Rech, Gabriel E; Bogaerts-Marquez, Maria; Barron, Maite G; Merenciano, Miriam; Villanueva-Canas, Jose L; Horvath, Vivien; Fiston-Lavier, Anna-Sophie; Luyten, Isabelle; Venkataram, Sandeep; Quesneville, Hadi; Petrov, Dmitri A; Gonzalez, Josefa<\/p>

Stress response, behavior, and development are shaped by transposable element-induced mutations in Drosophila. <\/a> Journal Article<\/span> <\/p>

In: <\/span>PLoS Genetics, <\/span>vol. 15 , <\/span>no. 2, <\/span>pp. e1007900, <\/span>2019<\/span>.<\/p>

Links<\/a><\/span> | BibTeX<\/a><\/span><\/p>

<\/td>

Guirao-Rico, Sara; Gonz\u00e1lez, Josefa<\/p>

Evolutionary insights from large scale resequencing datasets in Drosophila melanogaster<\/a> Journal Article<\/span> <\/p>

In: <\/span>Current Opinion in Insect Science, <\/span>vol. 31, <\/span>pp. 70-76, <\/span>2019<\/span>.<\/p>

Links<\/a><\/span> | BibTeX<\/a><\/span><\/p>

<\/td>

Cl\u00e9ment Goubert Emmanuelle Lerat, Sara Guirao-Rico; Gonz\u00e1lez., Josefa<\/p>

Population specific dynamics and selection patterns of transposable element insertions in European natural populations<\/a> Journal Article<\/span> <\/p>

In: <\/span>Molecular Ecology, <\/span>2019<\/span>.<\/p>

Links<\/a><\/span> | BibTeX<\/a><\/span><\/p>

\r\n

2018<\/h3>\r\n <\/td>\r\n <\/tr>

<\/td>

Mateo, L; Rech, G; Gonzalez, J<\/p>

Genome-wide patterns of local adaptation in Western European Drosophila melanogaster natural populations<\/a> Journal Article<\/span> <\/p>

In: <\/span>Scientific Reports, <\/span>vol. 8, <\/span>pp. 16143, <\/span>2018<\/span>.<\/p>

Links<\/a><\/span> | BibTeX<\/a><\/span><\/p>

<\/td>

Guio, Lain; Vieira, Cristina; Gonz\u00e1lez, Josefa<\/p>

Stress affects the epigenetic marks added by natural transposable element insertions in Drosophila melanogaster<\/a> Journal Article<\/span> <\/p>

In: <\/span>Scientific Reports, <\/span>vol. 8, <\/span>pp. 12197, <\/span>2018<\/span>.<\/p>

Links<\/a><\/span> | BibTeX<\/a><\/span><\/p>

<\/td>

Li, Zi-Wen; Hou, Xing-Hui; Chen, Jia-Fu; Xu, Yong-Chao; Josefa Gonz\u00e1lez Qiong Wu,; Guo, Ya-Long<\/p>

Transposable elements contribute to the adaptation of Arabidopsis thaliana<\/a> Journal Article<\/span> <\/p>

In: <\/span>Genome Biology and Evolution, <\/span>2018<\/span>.<\/p>

Links<\/a><\/span> | BibTeX<\/a><\/span><\/p>

\r\n

2017<\/h3>\r\n <\/td>\r\n <\/tr>

<\/td>

Manh, H Le; Guio, L; Merenciano, M; Rovira, Q; Barron, M G; Gonzalez, J<\/p>

Natural and laboratory mutations in kuzbanian are associated with zinc stress phenotypes in Drosophila melanogaster<\/a> Journal Article<\/span> <\/p>

In: <\/span>Sci Rep, <\/span>vol. 7, <\/span>pp. 42663, <\/span>2017<\/span>.<\/p>

Links<\/a><\/span> | BibTeX<\/a><\/span><\/p>

@article{RN1n,
\r\ntitle = {Natural and laboratory mutations in kuzbanian are associated with zinc stress phenotypes in Drosophila melanogaster},
\r\nauthor = {H Le Manh and L Guio and M Merenciano and Q Rovira and M G Barron and J Gonzalez},
\r\nurl = {https:\/\/www.ncbi.nlm.nih.gov\/pubmed\/28218276},
\r\ndoi = {10.1038\/srep42663},
\r\nyear  = {2017},
\r\ndate = {2017-01-01},
\r\njournal = {Sci Rep},
\r\nvolume = {7},
\r\npages = {42663},
\r\nkeywords = {},
\r\npubstate = {published},
\r\ntppubtype = {article}
\r\n}
\r\n<\/pre><\/div>
Close<\/a><\/p><\/div>