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297 results on '"Obbard, Darren J."'

1. Single-fly genome assemblies fill major phylogenomic gaps across the Drosophilidae Tree of Life

Author

Kim, Bernard Y, Gellert, Hannah R, Church, Samuel H, Suvorov, Anton, Anderson, Sean S, Barmina, Olga, Beskid, Sofia G, Comeault, Aaron A, Crown, K Nicole, Diamond, Sarah E, Dorus, Steve, Fujichika, Takako, Hemker, James A, Hrcek, Jan, Kankare, Maaria, Katoh, Toru, Magnacca, Karl N, Martin, Ryan A, Matsunaga, Teruyuki, Medeiros, Matthew J, Miller, Danny E, Pitnick, Scott, Schiffer, Michele, Simoni, Sara, Steenwinkel, Tessa E, Syed, Zeeshan A, Takahashi, Aya, Wei, Kevin H-C, Yokoyama, Tsuya, Eisen, Michael B, Kopp, Artyom, Matute, Daniel, Obbard, Darren J, O’Grady, Patrick M, Price, Donald K, Toda, Masanori J, Werner, Thomas, and Petrov, Dmitri A

Subjects
Biological Sciences, Bioinformatics and Computational Biology, Evolutionary Biology, Genetics, Bioengineering, Human Genome, Biotechnology, Generic health relevance, Animals, Phylogeny, Drosophilidae, Genome, Insect, Genomics, Sequence Analysis, DNA, High-Throughput Nucleotide Sequencing, Agricultural and Veterinary Sciences, Medical and Health Sciences, Developmental Biology, Agricultural, veterinary and food sciences, Biological sciences, Biomedical and clinical sciences
Abstract

Long-read sequencing is driving rapid progress in genome assembly across all major groups of life, including species of the family Drosophilidae, a longtime model system for genetics, genomics, and evolution. We previously developed a cost-effective hybrid Oxford Nanopore (ONT) long-read and Illumina short-read sequencing approach and used it to assemble 101 drosophilid genomes from laboratory cultures, greatly increasing the number of genome assemblies for this taxonomic group. The next major challenge is to address the laboratory culture bias in taxon sampling by sequencing genomes of species that cannot easily be reared in the lab. Here, we build upon our previous methods to perform amplification-free ONT sequencing of single wild flies obtained either directly from the field or from ethanol-preserved specimens in museum collections, greatly improving the representation of lesser studied drosophilid taxa in whole-genome data. Using Illumina Novaseq X Plus and ONT P2 sequencers with R10.4.1 chemistry, we set a new benchmark for inexpensive hybrid genome assembly at US $150 per genome while assembling genomes from as little as 35 ng of genomic DNA from a single fly. We present 183 new genome assemblies for 179 species as a resource for drosophilid systematics, phylogenetics, and comparative genomics. Of these genomes, 62 are from pooled lab strains and 121 from single adult flies. Despite the sample limitations of working with small insects, most single-fly diploid assemblies are comparable in contiguity (>1 Mb contig N50), completeness (>98% complete dipteran BUSCOs), and accuracy (>QV40 genome-wide with ONT R10.4.1) to assemblies from inbred lines. We present a well-resolved multi-locus phylogeny for 360 drosophilid and 4 outgroup species encompassing all publicly available (as of August 2023) genomes for this group. Finally, we present a Progressive Cactus whole-genome, reference-free alignment built from a subset of 298 suitably high-quality drosophilid genomes. The new assemblies and alignment, along with updated laboratory protocols and computational pipelines, are released as an open resource and as a tool for studying evolution at the scale of an entire insect family.

Published
2024

3. Single-fly assemblies fill major phylogenomic gaps across the Drosophilidae Tree of Life

Author

Kim, Bernard Y., primary, Gellert, Hannah R., additional, Church, Samuel H., additional, Suvorov, Anton, additional, Anderson, Sean S., additional, Barmina, Olga, additional, Beskid, Sofia G., additional, Comeault, Aaron A., additional, Nicole Crown, K., additional, Diamond, Sarah E., additional, Dorus, Steve, additional, Fujichika, Takako, additional, Hemker, James A., additional, Hrcek, Jan, additional, Kankare, Maaria, additional, Katoh, Toru, additional, Magnacca, Karl N., additional, Martin, Ryan A., additional, Matsunaga, Teruyuki, additional, Medeiros, Matthew J., additional, Miller, Danny E., additional, Pitnick, Scott, additional, Simoni, Sara, additional, Steenwinkel, Tessa E., additional, Schiffer, Michele, additional, Syed, Zeeshan A., additional, Takahashi, Aya, additional, Wei, Kevin H-C., additional, Yokoyama, Tsuya, additional, Eisen, Michael B., additional, Kopp, Artyom, additional, Matute, Daniel, additional, Obbard, Darren J., additional, O’Grady, Patrick M., additional, Price, Donald K., additional, Toda, Masanori J., additional, Werner, Thomas, additional, and Petrov, Dmitri A., additional

Published
2023
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5. Estimating divergence dates and substitution rates in the Drosophila phylogeny.

Author

Obbard, Darren J, Maclennan, John, Kim, Kang-Wook, Rambaut, Andrew, O'Grady, Patrick M, and Jiggins, Francis M

Subjects
Animals, Drosophila, Drosophila melanogaster, Calibration, Uncertainty, Phylogeny, Base Sequence, Models, Genetic, Time Factors, Molecular Sequence Data, Hawaii, Genome, Insect, Genetic Speciation, Genetic Variation, Volcanic Eruptions, Mutation Rate, Evolutionary Biology, Genetics, Biochemistry and Cell Biology
Abstract

An absolute timescale for evolution is essential if we are to associate evolutionary phenomena, such as adaptation or speciation, with potential causes, such as geological activity or climatic change. Timescales in most phylogenetic studies use geologically dated fossils or phylogeographic events as calibration points, but more recently, it has also become possible to use experimentally derived estimates of the mutation rate as a proxy for substitution rates. The large radiation of drosophilid taxa endemic to the Hawaiian islands has provided multiple calibration points for the Drosophila phylogeny, thanks to the "conveyor belt" process by which this archipelago forms and is colonized by species. However, published date estimates for key nodes in the Drosophila phylogeny vary widely, and many are based on simplistic models of colonization and coalescence or on estimates of island age that are not current. In this study, we use new sequence data from seven species of Hawaiian Drosophila to examine a range of explicit coalescent models and estimate substitution rates. We use these rates, along with a published experimentally determined mutation rate, to date key events in drosophilid evolution. Surprisingly, our estimate for the date for the most recent common ancestor of the genus Drosophila based on mutation rate (25-40 Ma) is closer to being compatible with independent fossil-derived dates (20-50 Ma) than are most of the Hawaiian-calibration models and also has smaller uncertainty. We find that Hawaiian-calibrated dates are extremely sensitive to model choice and give rise to point estimates that range between 26 and 192 Ma, depending on the details of the model. Potential problems with the Hawaiian calibration may arise from systematic variation in the molecular clock due to the long generation time of Hawaiian Drosophila compared with other Drosophila and/or uncertainty in linking island formation dates with colonization dates. As either source of error will bias estimates of divergence time, we suggest mutation rate estimates be used until better models are available.

Published
2012

7. Alternative splicing of the Anopheles gambiae Dscam gene in diverse Plasmodium falciparum infections

Author

Smith, Paul H, Mwangi, Jonathan M, Afrane, Yaw A, Yan, Guiyun, Obbard, Darren J, Ranford-Cartwright, Lisa C, and Little, Tom J

Abstract

Abstract Background In insects, including Anopheles mosquitoes, Dscam (Down syndrome cell adhesion molecule) appears to be involved in phagocytosis of pathogens, and shows pathogen-specific splice-form expression between divergent pathogen (or parasite) types (e.g. between bacteria and Plasmodium or between Plasmodium berghei and Plasmodium falciparum). Here, data are presented from the first study of Dscam expression in response to genetic diversity within a parasite species. Methods In independent field and laboratory studies, a measure of Dscam splice-form diversity was compared between mosquitoes fed on blood that was free of P. falciparum to mosquitoes exposed to either single or mixed genotype infections of P. falciparum. Results Significant increases in Anopheles gambiae Dscam (AgDscam) receptor diversity were observed in parasite-exposed mosquitoes, but only weak evidence that AgDscam diversity rises further upon exposure to mixed genotype parasite infections was found. Finally, a cluster of AgDscam exon 4 variants that become especially common during Plasmodium invasion was identified. Conclusions While the data clearly indicate that AgDscam diversity increases with P. falciparum exposure, they do not suggest that AgDscam diversity rises further in response to increased parasite diversity.

Published
2011

8. Vertically transmitted rhabdoviruses are found across three insect families and have dynamic interactions with their hosts

Author

Longdon, Ben, Day, Jonathan P., Schulz, Nora, Leftwich, Philip T., de Jong, Maaike A., Breuker, Casper J., Gibbs, Melanie, Obbard, Darren J., Wilfert, Lena, Smith, Sophia C. L., McGonigle, John E., Houslay, Thomas M., Wright, Lucy I., Livraghi, Luca, Evans, Luke C., Friend, Lucy A., Chapman, Tracey, Vontas, John, Kambouraki, Natasa, and Jiggins, Francis M.

Published
2017

12. The evolution of TEP1, an exceptionally polymorphic immunity gene in Anopheles gambiae

Author

Obbard, Darren J, Callister, Deborah M, Jiggins, Francis M, Soares, Dinesh C, Yan, Guiyun, and Little, Tom J

Subjects
complement-like protein, molecular evolution, natural-selection, statistical tests, dna polymorphism, mosquito, sequence, resistance, diversity, dynamics
Abstract

BackgroundHost-parasite coevolution can result in balancing selection, which maintains genetic variation in the susceptibility of hosts to parasites. It has been suggested that variation in a thioester-containing protein called TEP1 (AGAP010815) may alter the ability of Anopheles mosquitoes to transmit Plasmodium parasites, and high divergence between alleles of this gene suggests the possible action of long-term balancing selection. We studied whether TEP1 is a case of an ancient balanced polymorphism in an animal immune system.ResultsWe found evidence that the high divergence between TEP1 alleles is the product of genetic exchange between TEP1 and other TEP loci, i.e. gene conversion. Additionally, some TEP1 alleles showed unexpectedly low variability.ConclusionThe TEP1 gene appears to be a chimera produced from at least two other TEP loci, and the divergence between TEP1 alleles is probably not caused by long-term balancing selection, but is instead due to two independent gene conversion events from one of these other genes. Nevertheless, TEP1 still shows evidence of natural selection, in particular there appears to have been recent changes in the frequency of alleles that has diminished polymorphism within each allelic class. Although the selective force driving this dynamic was not identified, given that susceptibility to Plasmodium parasites is known to be associated with allelic variation in TEP1, these changes in allele frequencies could alter the vectoring capacity of populations.

Published
2008

13. Genetic variation and sexual system evolution in the annual mercuries

Author

Obbard, Darren J., Pannell, John R., and Harris, Stephen A.

Subjects
583.69135, Biology, Genetics (life sciences), Evolution,ecology and systematics, Evolution (zoology), Mercurialis annua, phylogeny, population genetics, androdioecy, mating-system
Abstract

The Mercurialis annua L. (Euphorbiaceae) species complex comprises a group of closely related lineages that present a wide range of sexual-systems, making it a valuable model for the study of plant sexual-system evolution. Within this polyploid complex, diploid populations are dioecious, and polyploid populations either monoecious or androdioecious (males coexist with functional hermaphrodites). The primary aim of this thesis was to use patterns of genetic diversity to elucidate the evolutionary origin and maintenance of the sexual-system diversity in M. annua. The phylogeny of the M. annua complex was reconstructed using chloroplast and ITS DNA sequence. This, in conjunction with morphometric analysis, showed that both hexaploid M. annua, and a novel species from the Canary Islands (newly described here as Mercurialis canariensis), were allopolyploid in origin. Such an origin for hexaploid M. annua suggests that androdioecy may have been able to arise in this group as a consequence of hybridisation between a monoecious lineage, tetraploid M. annua, and a dioecious lineage, M. huetii. Artificial crosses were used to show that hexaploid M. annua has disomic marker inheritance, and a statistical approach was developed to quantify genetic diversity and differentiation in polyploids with disomic inheritance. Strong gradients in genetic (allozyme) diversity at a pan-European scale were used to infer the existence of separate glacial refugia for dioecious and monoecious races of M. annua, at the eastern and western ends of the Mediterranean basin, respectively. A metapopulation model had previously been proposed to explain the ecological maintenance of androdioecy in M. annua. Here, population-level patterns of genetic diversity were used as an indirect test of this model. The discovery of lower within-population diversity, and of greater genetic differentiation between populations, for monoecious populations than for androdioecious populations was consistent with the metapopulation model, and suggests that androdioecy is maintained by the occurrence of regular local extinction.

Published
2004

20. Population-genomic analysis identifies a low rate of global adaptive fixation in the proteins of the cyclical parthenogen Daphnia magna

Author

Fields, Peter D, Mctaggart, Seanna, Reisser, Celine, Haag, Christoph, Palmer, William H, Little, Tom J, Ebert, Dieter, Obbard, Darren J, Lu, Jian, and Lu, Jian

Subjects
Male, McDonald-Kreitman, adaptive evolution, immune genes, fungi, Daphnia magna, Genomics, McDonald Kreitman, Drosophila melanogaster, RNA interference, Daphnia, arms race, Reproduction, Asexual, Genetics, DNA Transposable Elements, Animals, distribution of fitness effects, Molecular Biology, Ecology, Evolution, Behavior and Systematics
Abstract

Daphnia are well-established ecological and evolutionary models, and the interaction between D. magna and its microparasites is widely considered a paragon of the host-parasite coevolutionary process. Like other well-studied arthropods such as Drosophila melanogaster and Anopheles gambiae, D. magna is a small, widespread, and abundant species that is therefore expected to display a large long-term population size and high rates of adaptive protein evolution. However, unlike these other species, D. magna is cyclically asexual and lives in a highly structured environment (ponds and lakes) with moderate levels of dispersal, both of which are predicted to impact upon long-term effective population size and adaptive protein evolution. To investigate patterns of adaptive protein fixation, we produced the complete coding genomes of 36 D. magna clones sampled from across the European range (Western Palaearctic), along with draft sequences for the close relatives D. similis and D. lumholtzi, used as outgroups. We analyzed genome-wide patterns of adaptive fixation, with a particular focus on genes that have an a priori expectation of high rates, such as those likely to mediate immune responses, RNA interference against viruses and transposable elements, and those with a strongly male-biased expression pattern. We find that, as expected, D. magna displays high levels of diversity and that this is highly structured among populations. However, compared with Drosophila, we find that D. magna proteins appear to have a high proportion of weakly deleterious variants and do not show evidence of pervasive adaptive fixation across its entire range. This is true of the genome as a whole, and also of putative ‘arms race’ genes that often show elevated levels of adaptive substitution in other species. In addition to the likely impact of extensive, and previously documented, local adaptation, we speculate that these findings may reflect reduced efficacy of selection associated with cyclical asexual reproduction.

Published
2022

21. Corrigendum to: Drosophila Evolution over Space and Time (DEST): a New Population Genomics Resource

Author

European Society for Evolutionary Biology, Austrian Science Fund, European Research Council, Ministerio de Ciencia e Innovación (España), Swiss National Science Foundation, German Research Foundation, National Institutes of Health (US), Academy of Finland, Danish Natural Science Research Council, Israel Science Foundation, Ministry of Education, Science and Technological Development (Serbia), Natural Sciences and Engineering Research Council of Canada, Kapun, Martin, Nunez, Joaquin C. B., Bogaerts-Márquez, María, Murga-Moreno, Jesús, Paris, Margot, Outten, Joseph, Coronado, Marta, Tern, Courtney, Rota-Stabelli, Omar, Garcia Guerreiro, Maria Pilar, Casillas, Sònia, Orengo, Dorcas J., Puerma, Eva, Kankare, Maaria, Ometto, Lino, Loeschcke, Volker, Onder, Banu Sebnem, Abbott, Jessica, Schaeffer, Stephen W., Rajpurohit, Subhash, Behrman, Emily L., Schou, Mads Fristrup, Merritt, Thomas J. S., Lazzaro, Brian P., Glaser-Schmitt, Amanda, Argyridou, Eliza, Staubach, Fabian, Wang, Yun, Tauber, Eran, Serga, Svitlana, Fabian, Daniel K., Dyer, Kelly A., Wheat, Christopher, Parsch, John, Grath, Sonja, Savic Veselinovic, Marija, Stamenkovic-Radak, Marina, Jelic, Mihailo, Buendía-Ruíz, Antonio J., Gómez-Julián, M. Josefa, Espinosa-Jimenez, M. Luisa, Gallardo-Jiménez, Francisco D., Patenkovic, Aleksandra, Eric, Katarina, Tanaskovic, Marija, Ullastres, Ana, Guio, Lain, Merenciano, Miriam, Guirao-Rico, Sara, Horváth, Vivien, Obbard, Darren, J., Pasyukova, Elena G., 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, Tânia, Yusuf, Leeban, Barbadilla, Antonio, Petrov, Dmitri A., Schmidt, Paul S., González Pérez, Josefa, Flatt, Thomas, Bergland, Alan O., European Society for Evolutionary Biology, Austrian Science Fund, European Research Council, Ministerio de Ciencia e Innovación (España), Swiss National Science Foundation, German Research Foundation, National Institutes of Health (US), Academy of Finland, Danish Natural Science Research Council, Israel Science Foundation, Ministry of Education, Science and Technological Development (Serbia), Natural Sciences and Engineering Research Council of Canada, Kapun, Martin, Nunez, Joaquin C. B., Bogaerts-Márquez, María, Murga-Moreno, Jesús, Paris, Margot, Outten, Joseph, Coronado, Marta, Tern, Courtney, Rota-Stabelli, Omar, Garcia Guerreiro, Maria Pilar, Casillas, Sònia, Orengo, Dorcas J., Puerma, Eva, Kankare, Maaria, Ometto, Lino, Loeschcke, Volker, Onder, Banu Sebnem, Abbott, Jessica, Schaeffer, Stephen W., Rajpurohit, Subhash, Behrman, Emily L., Schou, Mads Fristrup, Merritt, Thomas J. S., Lazzaro, Brian P., Glaser-Schmitt, Amanda, Argyridou, Eliza, Staubach, Fabian, Wang, Yun, Tauber, Eran, Serga, Svitlana, Fabian, Daniel K., Dyer, Kelly A., Wheat, Christopher, Parsch, John, Grath, Sonja, Savic Veselinovic, Marija, Stamenkovic-Radak, Marina, Jelic, Mihailo, Buendía-Ruíz, Antonio J., Gómez-Julián, M. Josefa, Espinosa-Jimenez, M. Luisa, Gallardo-Jiménez, Francisco D., Patenkovic, Aleksandra, Eric, Katarina, Tanaskovic, Marija, Ullastres, Ana, Guio, Lain, Merenciano, Miriam, Guirao-Rico, Sara, Horváth, Vivien, Obbard, Darren, J., Pasyukova, Elena G., 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, Tânia, Yusuf, Leeban, Barbadilla, Antonio, Petrov, Dmitri A., Schmidt, Paul S., González Pérez, Josefa, Flatt, Thomas, and Bergland, Alan O.

Abstract

Drosophila melanogaster is a leading model in population genetics and genomics, and a growing number of whole-genome datasets from natural populations of this species have been published over the last years. A major challenge is the integration of disparate datasets, often generated using different sequencing technologies and bioinformatic pipelines, which hampers our ability to address questions about the evolution of this species. Here we address these issues by developing a bioinformatics pipeline that maps pooled sequencing (Pool-Seq) reads from D. melanogaster to a hologenome consisting of fly and symbiont genomes and estimates allele frequencies using either a heuristic (PoolSNP) or a probabilistic variant caller (SNAPE-pooled). We use this pipeline to generate the largest data repository of genomic data available for D. melanogaster to date, encompassing 271 previously published and unpublished population samples from over 100 locations in > 20 countries on four continents. Several of these locations have been sampled at different seasons across multiple years. This dataset, which we call Drosophila Evolution over Space and Time (DEST), is coupled with sampling and environmental meta-data. A web-based genome browser and web portal provide easy access to the SNP dataset. We further provide guidelines on how to use Pool-Seq data for model-based demographic inference. Our aim is to provide this scalable platform as a community resource which can be easily extended via future efforts for an even more extensive cosmopolitan dataset. Our resource will enable population geneticists to analyze spatio-temporal genetic patterns and evolutionary dynamics of D. melanogaster populations in unprecedented detail.

Published
2022

28. Pool-seq DrosEU 2014 samples VCF file

Author

Agencia Estatal de Investigación (España), University of Freiburg, Academy of Finland, Russian Foundation for Basic Research, Danish Natural Science Research Council, Ministerio de Economía y Competitividad (España), European Commission, Centre National de la Recherche Scientifique (France), Swedish Research Council, German Research Foundation, National Institutes of Health (US), Ministerio de Ciencia, Innovación y Universidades (España), The Scientific and Technological Research Council of Turkey, Agence Nationale de la Recherche (France), Israel Science Foundation, Austrian Science Fund, Biotechnology and Biological Sciences Research Council (UK), Swiss National Science Foundation, Kapun, Martin [0000-0002-3810-0504], Barrón, Maite G. [0000-0001-6146-6259], Staubach, Fabian [0000-0002-8097-2349], Vieira, Jorge [0000-0001-7032-5220], Obbard, Darren, J. [0000-0001-5392-8142], Rota-Stabelli, Omar [0000-0002-0030-7788], Kankare, Maaria [0000-0003-1541-9050], Haudry, Annabelle [0000-0001-6088-0909], Wiberg, R. Axel W. [0000-0002-8074-8670], Waidele, Lena [0000-0002-6323-6438], Kozeretska, Iryna [0000-0002-6485-1408], Pasyukova, Elena G. [0000-0002-6491-8561], Loeschcke, Volker [0000-0003-1450-0754], Pascual, Marta [0000-0002-6189-0612], Vieira, Cristina P. [0000-0002-7139-2107], Serga, Svitlana [0000-0003-1875-3185], Montchamp-Moreau, Catherine [0000-0002-5044-9709], Abbott, Jessica [0000-0002-8743-2089], Gibert, Patricia [0000-0002-9461-6820], Porcelli, Damiano [0000-0002-9019-5758], Posnien, Nico [0000-0003-0700-5595], Grath, Sonja [0000-0003-3621-736X], Sucena, Élio [0000-0001-8810-870X], Bergland, Alan O. [0000-0001-7145-7575], Onder, Banu Sebnem [0000-0002-3003-248X], Argyridou, Eliza [0000-0002-6890-4642], Guio, Lain [0000-0002-5481-5200], Schou, Mads Fristrup [0000-0001-5521-5269], Deplancke, Bart [0000-0001-9935-843X], Vieira, Cristina [0000-0003-3414-3993], Ritchie, Michael G. [0000-0001-7913-8675], Zwaan, Blas J. [0000-0002-8221-4998], Tauber, Eran [0000-0003-4018-6535], Orengo, Dorcas J. [0000-0001-7911-3224], Puerma, Eva [0000-0001-7261-187X], Aguadé i Porres, Montserrat [0000-0002-3884-7800], Schmidt, Paul S. [0000-0002-8076-6705], Parsch, John [0000-0001-9068-5549], Betancourt, Andrea J. [0000-0001-9351-1413], Flatt, Thomas [0000-0002-5990-1503], González Pérez, Josefa [0000-0001-9824-027X], González Pérez, Josefa [josefa.gonzalez@ibe.upf-csic.es], Kapun, Martin, Barrón, Maite G., Staubach, Fabian, Vieira, Jorge, Obbard, Darren, J., Rota-Stabelli, Omar, Kankare, Maaria, Haudry, Annabelle, Wiberg, R. Axel W., Waidele, Lena, Kozeretska, Iryna, Pasyukova, Elena G., Loeschcke, Volker, Pascual, Marta, Vieira, Cristina P., Serga, Svitlana, Montchamp-Moreau, Catherine, Abbott, Jessica, Gibert, Patricia, Porcelli, Damiano, Posnien, Nico, Grath, Sonja, Sucena, Élio, Bergland, Alan O., Garcia Guerreiro, Maria Pilar, Onder, Banu Sebnem, Argyridou, Eliza, Guio, Lain, Schou, Mads Fristrup, Deplancke, Bart, Vieira, Cristina, Ritchie, Michael G., Zwaan, Blas J., Tauber, Eran, Orengo, Dorcas J., Puerma, Eva, Aguadé i Porres, Montserrat, Schmidt, Paul S., Parsch, John, Betancourt, Andrea J., Flatt, Thomas, González Pérez, Josefa, Agencia Estatal de Investigación (España), University of Freiburg, Academy of Finland, Russian Foundation for Basic Research, Danish Natural Science Research Council, Ministerio de Economía y Competitividad (España), European Commission, Centre National de la Recherche Scientifique (France), Swedish Research Council, German Research Foundation, National Institutes of Health (US), Ministerio de Ciencia, Innovación y Universidades (España), The Scientific and Technological Research Council of Turkey, Agence Nationale de la Recherche (France), Israel Science Foundation, Austrian Science Fund, Biotechnology and Biological Sciences Research Council (UK), Swiss National Science Foundation, Kapun, Martin [0000-0002-3810-0504], Barrón, Maite G. [0000-0001-6146-6259], Staubach, Fabian [0000-0002-8097-2349], Vieira, Jorge [0000-0001-7032-5220], Obbard, Darren, J. [0000-0001-5392-8142], Rota-Stabelli, Omar [0000-0002-0030-7788], Kankare, Maaria [0000-0003-1541-9050], Haudry, Annabelle [0000-0001-6088-0909], Wiberg, R. Axel W. [0000-0002-8074-8670], Waidele, Lena [0000-0002-6323-6438], Kozeretska, Iryna [0000-0002-6485-1408], Pasyukova, Elena G. [0000-0002-6491-8561], Loeschcke, Volker [0000-0003-1450-0754], Pascual, Marta [0000-0002-6189-0612], Vieira, Cristina P. [0000-0002-7139-2107], Serga, Svitlana [0000-0003-1875-3185], Montchamp-Moreau, Catherine [0000-0002-5044-9709], Abbott, Jessica [0000-0002-8743-2089], Gibert, Patricia [0000-0002-9461-6820], Porcelli, Damiano [0000-0002-9019-5758], Posnien, Nico [0000-0003-0700-5595], Grath, Sonja [0000-0003-3621-736X], Sucena, Élio [0000-0001-8810-870X], Bergland, Alan O. [0000-0001-7145-7575], Onder, Banu Sebnem [0000-0002-3003-248X], Argyridou, Eliza [0000-0002-6890-4642], Guio, Lain [0000-0002-5481-5200], Schou, Mads Fristrup [0000-0001-5521-5269], Deplancke, Bart [0000-0001-9935-843X], Vieira, Cristina [0000-0003-3414-3993], Ritchie, Michael G. [0000-0001-7913-8675], Zwaan, Blas J. [0000-0002-8221-4998], Tauber, Eran [0000-0003-4018-6535], Orengo, Dorcas J. [0000-0001-7911-3224], Puerma, Eva [0000-0001-7261-187X], Aguadé i Porres, Montserrat [0000-0002-3884-7800], Schmidt, Paul S. [0000-0002-8076-6705], Parsch, John [0000-0001-9068-5549], Betancourt, Andrea J. [0000-0001-9351-1413], Flatt, Thomas [0000-0002-5990-1503], González Pérez, Josefa [0000-0001-9824-027X], González Pérez, Josefa [josefa.gonzalez@ibe.upf-csic.es], Kapun, Martin, Barrón, Maite G., Staubach, Fabian, Vieira, Jorge, Obbard, Darren, J., Rota-Stabelli, Omar, Kankare, Maaria, Haudry, Annabelle, Wiberg, R. Axel W., Waidele, Lena, Kozeretska, Iryna, Pasyukova, Elena G., Loeschcke, Volker, Pascual, Marta, Vieira, Cristina P., Serga, Svitlana, Montchamp-Moreau, Catherine, Abbott, Jessica, Gibert, Patricia, Porcelli, Damiano, Posnien, Nico, Grath, Sonja, Sucena, Élio, Bergland, Alan O., Garcia Guerreiro, Maria Pilar, Onder, Banu Sebnem, Argyridou, Eliza, Guio, Lain, Schou, Mads Fristrup, Deplancke, Bart, Vieira, Cristina, Ritchie, Michael G., Zwaan, Blas J., Tauber, Eran, Orengo, Dorcas J., Puerma, Eva, Aguadé i Porres, Montserrat, Schmidt, Paul S., Parsch, John, Betancourt, Andrea J., Flatt, Thomas, and González Pérez, Josefa

Published
2019

29. Drosophila Evolution over Space and Time (DEST): A New Population Genomics Resource

Author

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

Published
2021
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30. Virus prevalence and genetic diversity across a wild bumblebee community

Author

Pascall, David J, Tinsley, Matthew C, Clark, Bethany L, Obbard, Darren J, Wilfert, Lena, Pascall, David [0000-0002-7543-0860], and Apollo - University of Cambridge Repository

Subjects
Microbiology (medical), Host-pathogen interactions, Viren, viruses, virus diversity, Biotic communities, Microbiology, bumblebees (Bombus), Animal ecology, Viruses, disease ecology, wildlife epidemiology, ddc:610, pollinators, DDC 610 / Medicine & health, virus community ecology, Wildlife epidemiology, Original Research
Abstract

Viruses are key population regulators, but we have limited knowledge of the diversity and ecology of viruses. This is even the case in wild host populations that provide ecosystem services, where small fitness effects may have major ecological impacts in aggregate. One such group of hosts are the bumblebees, which have a major role in the pollination of food crops and have suffered population declines and range contractions in recent decades. In this study, we investigate the diversity of four recently discovered bumblebee viruses (Mayfield virus 1, Mayfield virus 2, River Liunaeg virus, and Loch Morlich virus), and two previously known viruses that infect both wild bumblebees and managed honeybees (Acute bee paralysis virus and Slow bee paralysis virus) from isolates in Scotland. We investigate the ecological and environmental factors that determine viral presence and absence. We show that the recently discovered bumblebee viruses were more genetically diverse than the viruses shared with honeybees. Coinfection is potentially important in shaping prevalence: we found a strong positive association between River Liunaeg virus and Loch Morlich virus presence after controlling for host species, location and other relevant ecological variables. We tested for a relationship between environmental variables (temperature, UV radiation, wind speed, and prevalence), but as we had few sampling sites, and thus low power for site-level analyses, we could not conclude anything regarding these variables. We also describe the relationship between the bumblebee communities at our sampling sites. This study represents a first step in the description of predictors of bumblebee infection in the wild., publishedVersion

Published
2021

31. Drosophila Evolution over Space and Time (DEST) : A New Population Genomics Resource

Author

Kapun, Martin, Nunez, Joaquin C. B., Bogaerts-Marquez, Maria, Murga-Moreno, Jesus, Paris, Margot, Outten, Joseph, Coronado-Zamora, Marta, Tern, Courtney, Rota-Stabelli, Omar, Guerreiro, Maria P. Garcia, Casillas, Sonia, 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, Fabian, Daniel K., Dyer, Kelly A., Wheat, Christopher W., Parsch, John, Grath, Sonja, Veselinovic, Marija Savic, Stamenkovic-Radak, Marina, Jelic, Mihailo, Buendia-Ruiz, Antonio J., Gomez-Julian, Maria Josefa, Espinosa-Jimenez, Maria Luisa, Gallardo-Jimenez, Francisco D., Patenkovic, Aleksandra, Eric, Katarina, Tanaskovic, Marija, Ullastres, Anna, Guio, Lain, Merenciano, Miriam, Guirao-Rico, Sara, Horvath, Vivien, Obbard, Darren J., Pasyukova, Elena, Alatortsev, Vladimir E., Vieira, Cristina P., Vieira, Jorge, Torres, Jorge Roberto, Kozeretska, Iryna, Maistrenko, Oleksandr M., Montchamp-Moreau, Catherine, Mukha, Dmitry, Machado, Heather E., Lamb, Keric, Paulo, Tania, Yusuf, Leeban, Barbadilla, Antonio, Petrov, Dmitri, Schmidt, Paul, Gonzalez, Josefa, Flatt, Thomas, Bergland, Alan O., Kapun, Martin, Nunez, Joaquin C. B., Bogaerts-Marquez, Maria, Murga-Moreno, Jesus, Paris, Margot, Outten, Joseph, Coronado-Zamora, Marta, Tern, Courtney, Rota-Stabelli, Omar, Guerreiro, Maria P. Garcia, Casillas, Sonia, 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, Fabian, Daniel K., Dyer, Kelly A., Wheat, Christopher W., Parsch, John, Grath, Sonja, Veselinovic, Marija Savic, Stamenkovic-Radak, Marina, Jelic, Mihailo, Buendia-Ruiz, Antonio J., Gomez-Julian, Maria Josefa, Espinosa-Jimenez, Maria Luisa, Gallardo-Jimenez, Francisco D., Patenkovic, Aleksandra, Eric, Katarina, Tanaskovic, Marija, Ullastres, Anna, Guio, Lain, Merenciano, Miriam, Guirao-Rico, Sara, Horvath, Vivien, Obbard, Darren J., Pasyukova, Elena, Alatortsev, Vladimir E., Vieira, Cristina P., Vieira, Jorge, Torres, Jorge Roberto, Kozeretska, Iryna, Maistrenko, Oleksandr M., Montchamp-Moreau, Catherine, Mukha, Dmitry, Machado, Heather E., Lamb, Keric, Paulo, Tania, Yusuf, Leeban, Barbadilla, Antonio, Petrov, Dmitri, Schmidt, Paul, Gonzalez, Josefa, Flatt, Thomas, and Bergland, Alan O.

Abstract

Drosophila melanogaster is a leading model in population genetics and genomics, and a growing number of whole-genome data sets from natural populations of this species have been published over the last years. A major challenge is the integration of disparate data sets, often generated using different sequencing technologies and bioinformatic pipelines, which hampers our ability to address questions about the evolution of this species. Here we address these issues by developing a bioinformatics pipeline that maps pooled sequencing (Pool-Seq) reads from D. melanogaster to a hologenome consisting of fly and symbiont genomes and estimates allele frequencies using either a heuristic (PoolSNP) or a probabilistic variant caller (SNAPE-pooled). We use this pipeline to generate the largest data repository of genomic data available for D. melanogaster to date, encompassing 271 previously published and unpublished population samples from over 100 locations in >20 countries on four continents. Several of these locations have been sampled at different seasons across multiple years. This data set, which we call Drosophila Evolution over Space and Time (DEST), is coupled with sampling and environmental metadata. A web-based genome browser and web portal provide easy access to the SNP data set. We further provide guidelines on how to use Pool-Seq data for model-based demographic inference. Our aim is to provide this scalable platform as a community resource which can be easily extended via future efforts for an even more extensive cosmopolitan data set. Our resource will enable population geneticists to analyze spatiotemporal genetic patterns and evolutionary dynamics of D. melanogaster populations in unprecedented detail.

Published
2021
Full Text
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32. The discovery, distribution, and diversity of DNA viruses associated with Drosophila melanogaster in Europe

Author

Natural Environment Research Council (UK), Wellcome Trust, Biotechnology and Biological Sciences Research Council (UK), Swiss National Science Foundation, Agence Nationale de la Recherche (France), European Commission, European Research Council, Fundación Española para la Ciencia y la Tecnología, Ministerio de Economía y Competitividad (España), German Research Foundation, Academy of Finland, Austrian Science Fund, Danish Research Council, The Scientific and Technological Research Council of Turkey, Ministry of Education, Science and Technological Development (Serbia), European Society for Evolutionary Biology, Wallace, Megan A., Coffman, Kelsey A., Gilbert, Clément, Ravindran, Sanjana, Albery, Gregory F., Abbott, Jessica, Argyridou, Eliza, Bellosta, Paola, Betancourt, Andrea J., Colinet, Hervé, 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, Stamenkovic-Radak, Marina, Tanaskovic, Marija, Savic Veselinovic, Marija, Vieira, Jorge, Vieira, Cristina P., Kapun, Martin, Flatt, Thomas, González Pérez, Josefa, Staubach, Fabian, Obbard, Darren, J., Natural Environment Research Council (UK), Wellcome Trust, Biotechnology and Biological Sciences Research Council (UK), Swiss National Science Foundation, Agence Nationale de la Recherche (France), European Commission, European Research Council, Fundación Española para la Ciencia y la Tecnología, Ministerio de Economía y Competitividad (España), German Research Foundation, Academy of Finland, Austrian Science Fund, Danish Research Council, The Scientific and Technological Research Council of Turkey, Ministry of Education, Science and Technological Development (Serbia), European Society for Evolutionary Biology, Wallace, Megan A., Coffman, Kelsey A., Gilbert, Clément, Ravindran, Sanjana, Albery, Gregory F., Abbott, Jessica, Argyridou, Eliza, Bellosta, Paola, Betancourt, Andrea J., Colinet, Hervé, 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, Stamenkovic-Radak, Marina, Tanaskovic, Marija, Savic Veselinovic, Marija, Vieira, Jorge, Vieira, Cristina P., Kapun, Martin, Flatt, Thomas, González Pérez, Josefa, Staubach, Fabian, and Obbard, Darren, J.

Abstract

Drosophila melanogaster is an important model for antiviral immunity in arthropods, but very few DNA viruses have been described from the family Drosophilidae. This deficiency limits our opportunity to use natural host-pathogen combinations in experimental studies, and may bias our understanding of the Drosophila virome. Here, we report fourteen DNA viruses detected in a metagenomic analysis of 6668 pool-sequenced Drosophila, sampled from forty-seven European locations between 2014 and 2016. These include three new nudiviruses, a new and divergent entomopoxvirus, a virus related to Leptopilina boulardi filamentous virus, and a virus related to Musca domestica salivary gland hypertrophy virus. We also find an endogenous genomic copy of galbut virus, a double-stranded RNA partitivirus, segregating at very low frequency. Remarkably, we find that Drosophila Vesanto virus, a small DNA virus previously described as a bidnavirus, may be composed of up to twelve segments and thus represent a new lineage of segmented DNA viruses. Two of the DNA viruses, Drosophila Kallithea nudivirus and Drosophila Vesanto virus are relatively common, found in 2 per cent or more of wild flies. The others are rare, with many likely to be represented by a single infected fly. We find that virus prevalence in Europe reflects the prevalence seen in publicly available datasets, with Drosophila Kallithea nudivirus and Drosophila Vesanto virus the only ones commonly detectable in public data from wild-caught flies and large population cages, and the other viruses being rare or absent. These analyses suggest that DNA viruses are at lower prevalence than RNA viruses in D.melanogaster, and may be less likely to persist in laboratory cultures. Our findings go some way to redressing an earlier bias toward RNA virus studies in Drosophila, and lay the foundation needed to harness the power of Drosophila as a model system for the study of DNA viruses.

Published
2021

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

Author

European Society for Evolutionary Biology, Austrian Science Fund, European Research Council, Ministerio de Ciencia e Innovación (España), Swiss National Science Foundation, German Research Foundation, National Institutes of Health (US), Academy of Finland, Danish Natural Science Research Council, Israel Science Foundation, Ministry of Education, Science and Technological Development (Serbia), Natural Sciences and Engineering Research Council of Canada, Kapun, Martin, Nunez, Joaquin C. B., Bogaerts-Márquez, María, Murga-Moreno, Jesús, Paris, Margot, Outten, Joseph, Coronado, Marta, Tern, Courtney, Rota-Stabelli, Omar, Garcia Guerreiro, Maria Pilar, Casillas, Sònia, Orengo, Dorcas J., Puerma, Eva, Kankare, Maaria, Ometto, Lino, Loeschcke, Volker, Onder, Banu Sebnem, Abbott, Jessica, Schaeffer, Stephen W., Rajpurohit, Subhash, Behrman, Emily L., Schou, Mads Fristrup, Merritt, Thomas J. S., Lazzaro, Brian P., Glaser-Schmitt, Amanda, Argyridou, Eliza, Staubach, Fabian, Wang, Yun, Tauber, Eran, Serga, Svitlana, Fabian, Daniel K., Dyer, Kelly A., Wheat, Christopher, Parsch, John, Grath, Sonja, Savic Veselinovic, Marija, Stamenkovic-Radak, Marina, Jelic, Mihailo, Buendía-Ruíz, Antonio J., Gómez-Julián, M. Josefa, Espinosa-Jimenez, M. Luisa, Gallardo-Jiménez, Francisco D., Patenkovic, Aleksandra, Eric, Katarina, Tanaskovic, Marija, Ullastres, Ana, Guio, Lain, Merenciano, Miriam, Guirao-Rico, Sara, Horváth, Vivien, Obbard, Darren, J., Pasyukova, Elena G., 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, Tânia, Yusuf, Leeban, Barbadilla, Antonio, Petrov, Dmitri A., Schmidt, Paul S., González Pérez, Josefa, Flatt, Thomas, Bergland, Alan O., European Society for Evolutionary Biology, Austrian Science Fund, European Research Council, Ministerio de Ciencia e Innovación (España), Swiss National Science Foundation, German Research Foundation, National Institutes of Health (US), Academy of Finland, Danish Natural Science Research Council, Israel Science Foundation, Ministry of Education, Science and Technological Development (Serbia), Natural Sciences and Engineering Research Council of Canada, Kapun, Martin, Nunez, Joaquin C. B., Bogaerts-Márquez, María, Murga-Moreno, Jesús, Paris, Margot, Outten, Joseph, Coronado, Marta, Tern, Courtney, Rota-Stabelli, Omar, Garcia Guerreiro, Maria Pilar, Casillas, Sònia, Orengo, Dorcas J., Puerma, Eva, Kankare, Maaria, Ometto, Lino, Loeschcke, Volker, Onder, Banu Sebnem, Abbott, Jessica, Schaeffer, Stephen W., Rajpurohit, Subhash, Behrman, Emily L., Schou, Mads Fristrup, Merritt, Thomas J. S., Lazzaro, Brian P., Glaser-Schmitt, Amanda, Argyridou, Eliza, Staubach, Fabian, Wang, Yun, Tauber, Eran, Serga, Svitlana, Fabian, Daniel K., Dyer, Kelly A., Wheat, Christopher, Parsch, John, Grath, Sonja, Savic Veselinovic, Marija, Stamenkovic-Radak, Marina, Jelic, Mihailo, Buendía-Ruíz, Antonio J., Gómez-Julián, M. Josefa, Espinosa-Jimenez, M. Luisa, Gallardo-Jiménez, Francisco D., Patenkovic, Aleksandra, Eric, Katarina, Tanaskovic, Marija, Ullastres, Ana, Guio, Lain, Merenciano, Miriam, Guirao-Rico, Sara, Horváth, Vivien, Obbard, Darren, J., Pasyukova, Elena G., 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, Tânia, Yusuf, Leeban, Barbadilla, Antonio, Petrov, Dmitri A., Schmidt, Paul S., González Pérez, Josefa, Flatt, Thomas, and Bergland, Alan O.

Abstract

Drosophila melanogaster is a leading model in population genetics and genomics, and a growing number of whole-genome datasets from natural populations of this species have been published over the last years. A major challenge is the integration of disparate datasets, often generated using different sequencing technologies and bioinformatic pipelines, which hampers our ability to address questions about the evolution of this species. Here we address these issues by developing a bioinformatics pipeline that maps pooled sequencing (Pool-Seq) reads from D. melanogaster to a hologenome consisting of fly and symbiont genomes and estimates allele frequencies using either a heuristic (PoolSNP) or a probabilistic variant caller (SNAPE-pooled). We use this pipeline to generate the largest data repository of genomic data available for D. melanogaster to date, encompassing 271 previously published and unpublished population samples from over 100 locations in > 20 countries on four continents. Several of these locations have been sampled at different seasons across multiple years. This dataset, which we call Drosophila Evolution over Space and Time (DEST), is coupled with sampling and environmental meta-data. A web-based genome browser and web portal provide easy access to the SNP dataset. We further provide guidelines on how to use Pool-Seq data for model-based demographic inference. Our aim is to provide this scalable platform as a community resource which can be easily extended via future efforts for an even more extensive cosmopolitan dataset. Our resource will enable population geneticists to analyze spatio-temporal genetic patterns and evolutionary dynamics of D. melanogaster populations in unprecedented detail.

Published
2021

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

Author

Kapun, Martin, Barrón, Maite G., Staubach, Fabian, Vieira, Jorge, Obbard, Darren, J., Rota-Stabelli, Omar, Kankare, Maaria, Haudry, Annabelle, Wiberg, R. Axel W., Waidele, Lena, Kozeretska, Iryna, Pasyukova, Elena G., Loeschcke, Volker, Pascual, Marta, Vieira, Cristina P., Serga, Svitlana, Montchamp-Moreau, Catherine, Abbott, Jessica, Gibert, Patricia, Porcelli, Damiano, Posnien, Nico, Grath, Sonja, Sucena, Élio, Bergland, Alan O., Garcia Guerreiro, Maria Pilar, Onder, Banu Sebnem, Argyridou, Eliza, Guio, Lain, Schou, Mads Fristrup, Deplancke, Bart, Vieira, Cristina, Ritchie, Michael G., Zwaan, Blas J., Tauber, Eran, Orengo, Dorcas J., Puerma, Eva, Aguadé i Porres, Montserrat, Schmidt, Paul S., Parsch, John, Betancourt, Andrea J., Flatt, Thomas, González Pérez, Josefa, Agencia Estatal de Investigación (España), University of Freiburg, Academy of Finland, Russian Foundation for Basic Research, Danish Natural Science Research Council, Ministerio de Economía y Competitividad (España), European Commission, Centre National de la Recherche Scientifique (France), Swedish Research Council, German Research Foundation, National Institutes of Health (US), Ministerio de Ciencia, Innovación y Universidades (España), Agence Nationale de la Recherche (France), Israel Science Foundation, Austrian Science Fund, Biotechnology and Biological Sciences Research Council (UK), Swiss National Science Foundation, Kapun, Martin [0000-0002-3810-0504], Barrón, Maite G. [0000-0001-6146-6259], Staubach, Fabian [0000-0002-8097-2349], Vieira, Jorge [0000-0001-7032-5220], Obbard, Darren, J. [0000-0001-5392-8142], Rota-Stabelli, Omar [0000-0002-0030-7788], Kankare, Maaria [0000-0003-1541-9050], Haudry, Annabelle [0000-0001-6088-0909], Wiberg, R. Axel W. [0000-0002-8074-8670], Waidele, Lena [0000-0002-6323-6438], Kozeretska, Iryna [0000-0002-6485-1408], Pasyukova, Elena G. [0000-0002-6491-8561], Loeschcke, Volker [0000-0003-1450-0754], Pascual, Marta [0000-0002-6189-0612], Vieira, Cristina P. [0000-0002-7139-2107], Serga, Svitlana [0000-0003-1875-3185], Montchamp-Moreau, Catherine [0000-0002-5044-9709], Abbott, Jessica [0000-0002-8743-2089], Gibert, Patricia [0000-0002-9461-6820], Porcelli, Damiano [0000-0002-9019-5758], Posnien, Nico [0000-0003-0700-5595], Grath, Sonja [0000-0003-3621-736X], Sucena, Élio [0000-0001-8810-870X], Bergland, Alan O. [0000-0001-7145-7575], Onder, Banu Sebnem [0000-0002-3003-248X], Argyridou, Eliza [0000-0002-6890-4642], Guio, Lain [0000-0002-5481-5200], Schou, Mads Fristrup [0000-0001-5521-5269], Deplancke, Bart [0000-0001-9935-843X], Vieira, Cristina [0000-0003-3414-3993], Ritchie, Michael G. [0000-0001-7913-8675], Zwaan, Blas J. [0000-0002-8221-4998], Tauber, Eran [0000-0003-4018-6535], Orengo, Dorcas J. [0000-0001-7911-3224], Puerma, Eva [0000-0001-7261-187X], Aguadé i Porres, Montserrat [0000-0002-3884-7800], Schmidt, Paul S. [0000-0002-8076-6705], Parsch, John [0000-0001-9068-5549], Betancourt, Andrea J. [0000-0001-9351-1413], Flatt, Thomas [0000-0002-5990-1503], González Pérez, Josefa [0000-0001-9824-027X], Kapun, Martin, Barrón, Maite G., Staubach, Fabian, Vieira, Jorge, Obbard, Darren, J., Rota-Stabelli, Omar, Kankare, Maaria, Haudry, Annabelle, Wiberg, R. Axel W., Waidele, Lena, Kozeretska, Iryna, Pasyukova, Elena G., Loeschcke, Volker, Pascual, Marta, Vieira, Cristina P., Serga, Svitlana, Montchamp-Moreau, Catherine, Abbott, Jessica, Gibert, Patricia, Porcelli, Damiano, Posnien, Nico, Grath, Sonja, Sucena, Élio, Bergland, Alan O., Onder, Banu Sebnem, Argyridou, Eliza, Guio, Lain, Schou, Mads Fristrup, Deplancke, Bart, Vieira, Cristina, Ritchie, Michael G., Zwaan, Blas J., Tauber, Eran, Orengo, Dorcas J., Puerma, Eva, Aguadé i Porres, Montserrat, Schmidt, Paul S., Parsch, John, Betancourt, Andrea J., Flatt, Thomas, and González Pérez, Josefa

Abstract

Genetic variation is the fuel of evolution. However, analyzing evolutionary dynamics in natural populations is challenging, sequencing of entire populations remains costly and comprehensive sampling logistically difficult. To tackle this issue and to define relevant spatial and temporal scales of variation, we have founded the European Drosophila Population Genomics Consortium (DrosEU). Here we present the first analysis of 48 D. melanogaster population samples collected across Europe in 2014. Our analysis uncovers novel patterns of variation at multiple levels: genome-wide neutral SNPs, mtDNA haplotypes, inversions, and TEs showing previously cryptic longitudinal population structure; signatures of selective sweeps shared among populations; presumably adaptive clines in inversions; and geographic variation in TEs. Additionally, we document highly variable microbiota and identify several new Drosophila viruses. Our study reveals novel aspects of the population biology of D. melanogaster and illustrates the power of extensive sampling and pooled sequencing of populations on a continent-wide scale.

Published
2018

36. Variation in mutation, recombination, and transposition rates in Drosophila melanogasterand Drosophila simulans

Author

Wang, Yiguan, McNeil, Paul, Abdulazeez, Rashidatu, Pascual, Marta, Johnston, Susan E., Keightley, Peter D., and Obbard, Darren J.

Abstract

The rates of mutation, recombination, and transposition are core parameters in models of evolution. They impact genetic diversity, responses to ongoing selection, and levels of genetic load. However, even for key evolutionary model species such as Drosophila melanogasterand Drosophila simulans, few estimates of these parameters are available, and we have little idea of how rates vary between individuals, sexes, or populations. Knowledge of this variation is fundamental for parameterizing models of genome evolution. Here, we provide direct estimates of mutation, recombination, and transposition rates and their variation in a West African and a European population of D. melanogasterand a European population of D. simulans. Across 89 flies, we observe 58 single-nucleotide mutations, 286 crossovers, and 89 transposable element (TE) insertions. Compared to the European D. melanogaster, we find the West African population has a lower mutation rate (1.67 × 10−9site−1gen−1vs. 4.86 × 10−9site−1gen−1) and a lower transposition rate (8.99 × 10−5copy−1gen−1vs. 23.36 × 10−5copy−1gen−1), but a higher recombination rate (3.44 cM/Mb vs. 2.06 cM/Mb). The European D. simulanspopulation has a similar mutation rate to European D. melanogaster, but a significantly higher recombination rate and a lower, but not significantly different, transposition rate. Overall, we find paternal-derived mutations are more frequent than maternal ones in both species. Our study quantifies the variation in rates of mutation, recombination, and transposition among different populations and sexes, and our direct estimates of these parameters in D. melanogasterand D. simulanswill benefit future studies in population and evolutionary genetics.

Published
2023
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37. Male morphology and dishonest signalling in a fig wasp

Author

Moore, Jamie C., Obbard, Darren J., Reuter, Caroline, West, Stuart A., and Cook, James M.

Subjects
Evolutionary biology, Zoology and wildlife conservation
Abstract

To link to full-text access for this article, visit this link: http://dx.doi.org/10.1016/j.anbehav.2009.04.006 Byline: Jamie C. Moore (a), Darren J. Obbard (a), Caroline Reuter (b)(c), Stuart A. West (a), James M. Cook (b)(c) Abstract: Despite theoretical predictions, dishonest signalling has rarely been observed in aggressive interactions. We present evidence of such signalling in the nonpollinating fig wasp Philotrypesis sp. A ex Ficus rubiginosa. First, morphometric data indicated that an alternative 'atypical' male morph (17.8% of individuals) exists that tends to be larger in body size and has longer mandibles for a given body size than other 'typical' males. Second, behavioural observations suggested that males use mandible gape width (which depends on mandible length) as a cue to assess opponents before fights and retreat without escalating if they are unlikely to win, and, probably because their greater mandible gape width causes more opponents to retreat without escalating, that atypical males engaged in fewer fights than typical males for a given body size but had higher mating success. Third, atypical males were less likely to win fights than typical males of similar mandible length relative to opponents. In addition, we found that atypical males incur more injuries (greater receiver-dependent signal costs) than typical males of similar body size relative to rivals. We discuss the implications of our findings for future work on dishonest signalling. Author Affiliation: (a) Institute of Evolutionary Biology, University of Edinburgh, U.K. (b) Division of Biology, Imperial College, U.K. (c) School of Biological Sciences, University of Reading, U.K. Article History: Received 23 August 2008; Revised 4 November 2008; Accepted 9 April 2009 Article Note: (miscellaneous) MS. number: 08-00552R

Published
2009

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

Author

Agencia Estatal de Investigación (España), University of Freiburg, Academy of Finland, Russian Foundation for Basic Research, Danish Natural Science Research Council, Ministerio de Economía y Competitividad (España), European Commission, Centre National de la Recherche Scientifique (France), Swedish Research Council, German Research Foundation, National Institutes of Health (US), Ministerio de Ciencia, Innovación y Universidades (España), Agence Nationale de la Recherche (France), Israel Science Foundation, Austrian Science Fund, Biotechnology and Biological Sciences Research Council (UK), Swiss National Science Foundation, Kapun, Martin [0000-0002-3810-0504], Barrón, Maite G. [0000-0001-6146-6259], Staubach, Fabian [0000-0002-8097-2349], Vieira, Jorge [0000-0001-7032-5220], Obbard, Darren, J. [0000-0001-5392-8142], Rota-Stabelli, Omar [0000-0002-0030-7788], Kankare, Maaria [0000-0003-1541-9050], Haudry, Annabelle [0000-0001-6088-0909], Wiberg, R. Axel W. [0000-0002-8074-8670], Waidele, Lena [0000-0002-6323-6438], Kozeretska, Iryna [0000-0002-6485-1408], Pasyukova, Elena G. [0000-0002-6491-8561], Loeschcke, Volker [0000-0003-1450-0754], Pascual, Marta [0000-0002-6189-0612], Vieira, Cristina P. [0000-0002-7139-2107], Serga, Svitlana [0000-0003-1875-3185], Montchamp-Moreau, Catherine [0000-0002-5044-9709], Abbott, Jessica [0000-0002-8743-2089], Gibert, Patricia [0000-0002-9461-6820], Porcelli, Damiano [0000-0002-9019-5758], Posnien, Nico [0000-0003-0700-5595], Grath, Sonja [0000-0003-3621-736X], Sucena, Élio [0000-0001-8810-870X], Bergland, Alan O. [0000-0001-7145-7575], Onder, Banu Sebnem [0000-0002-3003-248X], Argyridou, Eliza [0000-0002-6890-4642], Guio, Lain [0000-0002-5481-5200], Schou, Mads Fristrup [0000-0001-5521-5269], Deplancke, Bart [0000-0001-9935-843X], Vieira, Cristina [0000-0003-3414-3993], Ritchie, Michael G. [0000-0001-7913-8675], Zwaan, Blas J. [0000-0002-8221-4998], Tauber, Eran [0000-0003-4018-6535], Orengo, Dorcas J. [0000-0001-7911-3224], Puerma, Eva [0000-0001-7261-187X], Aguadé i Porres, Montserrat [0000-0002-3884-7800], Schmidt, Paul S. [0000-0002-8076-6705], Parsch, John [0000-0001-9068-5549], Betancourt, Andrea J. [0000-0001-9351-1413], Flatt, Thomas [0000-0002-5990-1503], González Pérez, Josefa [0000-0001-9824-027X], Kapun, Martin, Barrón, Maite G., Staubach, Fabian, Vieira, Jorge, Obbard, Darren, J., Rota-Stabelli, Omar, Kankare, Maaria, Haudry, Annabelle, Wiberg, R. Axel W., Waidele, Lena, Kozeretska, Iryna, Pasyukova, Elena G., Loeschcke, Volker, Pascual, Marta, Vieira, Cristina P., Serga, Svitlana, Montchamp-Moreau, Catherine, Abbott, Jessica, Gibert, Patricia, Porcelli, Damiano, Posnien, Nico, Grath, Sonja, Sucena, Élio, Bergland, Alan O., Garcia Guerreiro, Maria Pilar, Onder, Banu Sebnem, Argyridou, Eliza, Guio, Lain, Schou, Mads Fristrup, Deplancke, Bart, Vieira, Cristina, Ritchie, Michael G., Zwaan, Blas J., Tauber, Eran, Orengo, Dorcas J., Puerma, Eva, Aguadé i Porres, Montserrat, Schmidt, Paul S., Parsch, John, Betancourt, Andrea J., Flatt, Thomas, González Pérez, Josefa, Agencia Estatal de Investigación (España), University of Freiburg, Academy of Finland, Russian Foundation for Basic Research, Danish Natural Science Research Council, Ministerio de Economía y Competitividad (España), European Commission, Centre National de la Recherche Scientifique (France), Swedish Research Council, German Research Foundation, National Institutes of Health (US), Ministerio de Ciencia, Innovación y Universidades (España), Agence Nationale de la Recherche (France), Israel Science Foundation, Austrian Science Fund, Biotechnology and Biological Sciences Research Council (UK), Swiss National Science Foundation, Kapun, Martin [0000-0002-3810-0504], Barrón, Maite G. [0000-0001-6146-6259], Staubach, Fabian [0000-0002-8097-2349], Vieira, Jorge [0000-0001-7032-5220], Obbard, Darren, J. [0000-0001-5392-8142], Rota-Stabelli, Omar [0000-0002-0030-7788], Kankare, Maaria [0000-0003-1541-9050], Haudry, Annabelle [0000-0001-6088-0909], Wiberg, R. Axel W. [0000-0002-8074-8670], Waidele, Lena [0000-0002-6323-6438], Kozeretska, Iryna [0000-0002-6485-1408], Pasyukova, Elena G. [0000-0002-6491-8561], Loeschcke, Volker [0000-0003-1450-0754], Pascual, Marta [0000-0002-6189-0612], Vieira, Cristina P. [0000-0002-7139-2107], Serga, Svitlana [0000-0003-1875-3185], Montchamp-Moreau, Catherine [0000-0002-5044-9709], Abbott, Jessica [0000-0002-8743-2089], Gibert, Patricia [0000-0002-9461-6820], Porcelli, Damiano [0000-0002-9019-5758], Posnien, Nico [0000-0003-0700-5595], Grath, Sonja [0000-0003-3621-736X], Sucena, Élio [0000-0001-8810-870X], Bergland, Alan O. [0000-0001-7145-7575], Onder, Banu Sebnem [0000-0002-3003-248X], Argyridou, Eliza [0000-0002-6890-4642], Guio, Lain [0000-0002-5481-5200], Schou, Mads Fristrup [0000-0001-5521-5269], Deplancke, Bart [0000-0001-9935-843X], Vieira, Cristina [0000-0003-3414-3993], Ritchie, Michael G. [0000-0001-7913-8675], Zwaan, Blas J. [0000-0002-8221-4998], Tauber, Eran [0000-0003-4018-6535], Orengo, Dorcas J. [0000-0001-7911-3224], Puerma, Eva [0000-0001-7261-187X], Aguadé i Porres, Montserrat [0000-0002-3884-7800], Schmidt, Paul S. [0000-0002-8076-6705], Parsch, John [0000-0001-9068-5549], Betancourt, Andrea J. [0000-0001-9351-1413], Flatt, Thomas [0000-0002-5990-1503], González Pérez, Josefa [0000-0001-9824-027X], Kapun, Martin, Barrón, Maite G., Staubach, Fabian, Vieira, Jorge, Obbard, Darren, J., Rota-Stabelli, Omar, Kankare, Maaria, Haudry, Annabelle, Wiberg, R. Axel W., Waidele, Lena, Kozeretska, Iryna, Pasyukova, Elena G., Loeschcke, Volker, Pascual, Marta, Vieira, Cristina P., Serga, Svitlana, Montchamp-Moreau, Catherine, Abbott, Jessica, Gibert, Patricia, Porcelli, Damiano, Posnien, Nico, Grath, Sonja, Sucena, Élio, Bergland, Alan O., Garcia Guerreiro, Maria Pilar, Onder, Banu Sebnem, Argyridou, Eliza, Guio, Lain, Schou, Mads Fristrup, Deplancke, Bart, Vieira, Cristina, Ritchie, Michael G., Zwaan, Blas J., Tauber, Eran, Orengo, Dorcas J., Puerma, Eva, Aguadé i Porres, Montserrat, Schmidt, Paul S., Parsch, John, Betancourt, Andrea J., Flatt, Thomas, and González Pérez, Josefa

Abstract

Genetic variation is the fuel of evolution. However, analyzing evolutionary dynamics in natural populations is challenging, sequencing of entire populations remains costly and comprehensive sampling logistically difficult. To tackle this issue and to define relevant spatial and temporal scales of variation, we have founded the European Drosophila Population Genomics Consortium (DrosEU). Here we present the first analysis of 48 D. melanogaster population samples collected across Europe in 2014. Our analysis uncovers novel patterns of variation at multiple levels: genome-wide neutral SNPs, mtDNA haplotypes, inversions, and TEs showing previously cryptic longitudinal population structure; signatures of selective sweeps shared among populations; presumably adaptive clines in inversions; and geographic variation in TEs. Additionally, we document highly variable microbiota and identify several new Drosophila viruses. Our study reveals novel aspects of the population biology of D. melanogaster and illustrates the power of extensive sampling and pooled sequencing of populations on a continent-wide scale.

Published
2018

40. Fighting strategies in two species of fig wasp

Author

Moore, Jamie C., Obbard, Darren J., Reuter, Caroline, West, Stuart A., and Cook, James M.

Subjects
Zoology and wildlife conservation
Abstract

To link to full-text access for this article, visit this link: http://dx.doi.org/10.1016/j.anbehav.2008.01.018 Byline: Jamie C. Moore, Darren J. Obbard, Caroline Reuter, Stuart A. West, James M. Cook Abstract: Although theory exists concerning the types of strategies that should be used in contests over resources, empirical work explicitly testing its predictions is relatively rare. We investigated male fighting strategies in two nonpollinating fig wasp species associated with Ficus rubiginosa figs. In Sycoscapter sp. A, males did not assess each other before or during fights over mating opportunities. Instead, fights continued until the loser reached an energetic cost threshold that was positively correlated with its body size (fighting ability) and retreated. In Philotrypesis sp. B, prefight assessment was indicated, with males attacking competitively inferior rivals to remove them from the competitor pool (they then continued to do so until they reached a cost threshold that was again positively correlated with body size). Using data on species ecology, we discuss our findings with respect to theory on when different fighting strategies should evolve. We argue that the type of strategy used by a fig wasp species is determined by its relative benefits in terms of inclusive fitness. Author Affiliation: (a) Institute of Evolutionary Biology, University of Edinburgh, U.K. (a ) Division of Biology, Imperial College London, U.K. (a ) School of Biological Sciences, University of Reading, U.K. Article History: Received 5 August 2007; Revised 28 September 2007; Accepted 9 January 2008 Article Note: (miscellaneous) MS. number: 9484

Published
2008

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

Author

Kapun, Martin, Barrón, Maite G, Staubach, Fabian, Obbard, Darren J, Wiberg, R Axel W, Vieira, Jorge, Goubert, Clément, Rota-Stabelli, Omar, Kankare, Maaria, Bogaerts-Márquez, María, Haudry, Annabelle, Waidele, Lena, Kozeretska, Iryna, Pasyukova, Elena G, Loeschcke, Volker, Pascual, Marta, Vieira, Cristina P, Serga, Svitlana, Montchamp-Moreau, Catherine, Abbott, Jessica, Gibert, Patricia, Porcelli, Damiano, Posnien, Nico, Sánchez-Gracia, Alejandro, Grath, Sonja, Sucena, Élio, Bergland, Alan O, Guerreiro, Maria Pilar Garcia, Onder, Banu Sebnem, Argyridou, Eliza, University of Zurich, Falush, Daniel, and Kapun, Martin

Subjects
10127 Institute of Evolutionary Biology and Environmental Studies, 1105 Ecology, Evolution, Behavior and Systematics, 1311 Genetics, Ecology, Behavior and Systematics, Evolution, 1312 Molecular Biology, Genetics, 570 Life sciences, biology, 590 Animals (Zoology), Molecular Biology
Published
2020

42. A new lineage of segmented RNA viruses infecting animals

Author

Obbard, Darren J., Shi, Mang, Roberts, Katherine E., Longdon, Ben, and Dennis, Alice B.

Subjects
RNA virus, viruses, Microbiology, metagenome, Homology (biology), Virus, Conserved sequence, 03 medical and health sciences, RNA interference, Drosophilidae, Virology, arthropod, Polymerase, 030304 developmental biology, 0303 health sciences, biology, 030306 microbiology, RNA, biology.organism_classification, Metagenomics, Evolutionary biology, biology.protein, dark virus, Research Article
Abstract

Metagenomic sequencing has revolutionised our knowledge of virus diversity, with new virus sequences being reported faster than ever before. However, virus discovery from metagenomic sequencing usually depends on detectable homology: without a sufficiently close relative, so-called ‘dark’ virus sequences remain unrecognisable. An alternative approach is to use virus-identification methods that do not depend on detecting homology, such as virus recognition by host antiviral immunity. For example, virus-derived small RNAs have previously been used to propose ‘dark’ virus sequences associated with the Drosophilidae (Diptera). Here we combine published Drosophila data with a comprehensive search of transcriptomic sequences and selected meta-transcriptomic datasets to identify a completely new lineage of segmented positive-sense single-stranded RNA viruses that we provisionally refer to as the Quenyaviruses. Each of the five segments contains a single open reading frame, with most encoding proteins showing no detectable similarity to characterised viruses, and one sharing a small number of residues with the RNA-dependent RNA polymerases of single- and double-stranded RNA viruses. Using these sequences, we identify close relatives in approximately 20 arthropods, including insects, crustaceans, spiders and a myriapod. Using a more conserved sequence from the putative polymerase, we further identify relatives in meta-transcriptomic datasets from gut, gill, and lung tissues of vertebrates, reflecting infections of vertebrates or of their associated parasites. Our data illustrate the utility of small RNAs to detect viruses with limited sequence conservation, and provide robust evidence for a new deeply divergent and phylogenetically distinct RNA virus lineage.

Published
2020

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

Author

CSIC - Unidad de Recursos de Información Científica para la Investigación (URICI), Stanford University, European Society for Evolutionary Biology, Wellcome Trust, University of Freiburg, German Research Foundation, Academy of Finland, Russian Foundation for Basic Research, Danish Natural Science Research Council, Ministerio de Economía y Competitividad (España), Ministerio de Ciencia, Innovación y Universidades (España), Agencia Estatal de Investigación (España), Centre National de la Recherche Scientifique (France), Swedish Research Council, National Institutes of Health (US), The Scientific and Technological Research Council of Turkey, Agence Nationale de la Recherche (France), European Commission, Israel Science Foundation, Austrian Science Fund, Biotechnology and Biological Sciences Research Council (UK), Swiss National Science Foundation, European Research Council, Generalitat de Catalunya, Kapun, Martin, Barrón, Maite G., Staubach, Fabian, Obbard, Darren, J., Wiberg, R. Axel W., Vieira, Jorge, Goubert, Clément, Rota-Stabelli, Omar, Kankare, Maaria, Bogaerts-Márquez, María, Haudry, Annabelle, Waidele, Lena, Kozeretska, Iryna, Pasyukova, Elena G., Loeschcke, Volker, Pascual, Marta, Vieira, Cristina P., Serga, Svitlana, Montchamp-Moreau, Catherine, Abbott, Jessica, Gibert, Patricia, Porcelli, Damiano, Posnien, Nico, Sánchez-Gracia, Alejandro, Grath, Sonja, Sucena, Élio, Bergland, Alan O., Garcia Guerreiro, Maria Pilar, Onder, Banu Sebnem, Argyridou, Eliza, Guio, Lain, Schou, Mads Fristrup, Deplancke, Bart, Vieira, Cristina, Ritchie, Michael G., Zwaan, Blas J., Tauber, Eran, Orengo, Dorcas J., Puerma, Eva, Aguadé i Porres, Montserrat, Schmidt, Paul S., Parsch, John, Betancourt, Andrea J., Flatt, Thomas, González Pérez, Josefa, CSIC - Unidad de Recursos de Información Científica para la Investigación (URICI), Stanford University, European Society for Evolutionary Biology, Wellcome Trust, University of Freiburg, German Research Foundation, Academy of Finland, Russian Foundation for Basic Research, Danish Natural Science Research Council, Ministerio de Economía y Competitividad (España), Ministerio de Ciencia, Innovación y Universidades (España), Agencia Estatal de Investigación (España), Centre National de la Recherche Scientifique (France), Swedish Research Council, National Institutes of Health (US), The Scientific and Technological Research Council of Turkey, Agence Nationale de la Recherche (France), European Commission, Israel Science Foundation, Austrian Science Fund, Biotechnology and Biological Sciences Research Council (UK), Swiss National Science Foundation, European Research Council, Generalitat de Catalunya, Kapun, Martin, Barrón, Maite G., Staubach, Fabian, Obbard, Darren, J., Wiberg, R. Axel W., Vieira, Jorge, Goubert, Clément, Rota-Stabelli, Omar, Kankare, Maaria, Bogaerts-Márquez, María, Haudry, Annabelle, Waidele, Lena, Kozeretska, Iryna, Pasyukova, Elena G., Loeschcke, Volker, Pascual, Marta, Vieira, Cristina P., Serga, Svitlana, Montchamp-Moreau, Catherine, Abbott, Jessica, Gibert, Patricia, Porcelli, Damiano, Posnien, Nico, Sánchez-Gracia, Alejandro, Grath, Sonja, Sucena, Élio, Bergland, Alan O., Garcia Guerreiro, Maria Pilar, Onder, Banu Sebnem, Argyridou, Eliza, Guio, Lain, Schou, Mads Fristrup, Deplancke, Bart, Vieira, Cristina, Ritchie, Michael G., Zwaan, Blas J., Tauber, Eran, Orengo, Dorcas J., Puerma, Eva, Aguadé i Porres, Montserrat, Schmidt, Paul S., Parsch, John, Betancourt, Andrea J., Flatt, Thomas, and González Pérez, Josefa

Abstract

Genetic variation is the fuel of evolution, with standing genetic variation especially important for short-term evolution and local adaptation. To date, studies of spatiotemporal patterns of genetic variation in natural populations have been challenging, as comprehensive sampling is logistically difficult, and sequencing of entire populations costly. Here, we address these issues using a collaborative approach, sequencing 48 pooled population samples from 32 locations, and perform the first continent-wide genomic analysis of genetic variation in European Drosophila melanogaster. Our analyses uncover longitudinal population structure, provide evidence for continent-wide selective sweeps, identify candidate genes for local climate adaptation, and document clines in chromosomal inversion and transposable element frequencies. We also characterize variation among populations in the composition of the fly microbiome, and identify five new DNA viruses in our samples.

Published
2020

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

Author

Falush, Daniel, Falush, D ( Daniel ), Kapun, Martin; https://orcid.org/0000-0002-3810-0504, Barrón, Maite G, Staubach, Fabian, Obbard, Darren J, Wiberg, R Axel W; https://orcid.org/0000-0001-5392-8142, Vieira, Jorge, Goubert, Clément, Rota-Stabelli, Omar, Kankare, Maaria; https://orcid.org/0000-0003-1541-9050, Bogaerts-Márquez, María, Haudry, Annabelle, Waidele, Lena, Kozeretska, Iryna, Pasyukova, Elena G, Loeschcke, Volker, Pascual, Marta, Vieira, Cristina P, Serga, Svitlana, Montchamp-Moreau, Catherine, Abbott, Jessica, Gibert, Patricia, Porcelli, Damiano, Posnien, Nico; https://orcid.org/0000-0003-0700-5595, Sánchez-Gracia, Alejandro, Grath, Sonja, Sucena, Élio, Bergland, Alan O, Guerreiro, Maria Pilar Garcia, Onder, Banu Sebnem, Argyridou, Eliza, Falush, Daniel, Falush, D ( Daniel ), Kapun, Martin; https://orcid.org/0000-0002-3810-0504, Barrón, Maite G, Staubach, Fabian, Obbard, Darren J, Wiberg, R Axel W; https://orcid.org/0000-0001-5392-8142, Vieira, Jorge, Goubert, Clément, Rota-Stabelli, Omar, Kankare, Maaria; https://orcid.org/0000-0003-1541-9050, Bogaerts-Márquez, María, Haudry, Annabelle, Waidele, Lena, Kozeretska, Iryna, Pasyukova, Elena G, Loeschcke, Volker, Pascual, Marta, Vieira, Cristina P, Serga, Svitlana, Montchamp-Moreau, Catherine, Abbott, Jessica, Gibert, Patricia, Porcelli, Damiano, Posnien, Nico; https://orcid.org/0000-0003-0700-5595, Sánchez-Gracia, Alejandro, Grath, Sonja, Sucena, Élio, Bergland, Alan O, Guerreiro, Maria Pilar Garcia, Onder, Banu Sebnem, and Argyridou, Eliza

Abstract

Genetic variation is the fuel of evolution, with standing genetic variation especially important for short-term evolution and local adaptation. To date, studies of spatiotemporal patterns of genetic variation in natural populations have been challenging, as comprehensive sampling is logistically difficult, and sequencing of entire populations costly. Here, we address these issues using a collaborative approach, sequencing 48 pooled population samples from 32 locations, and perform the first continent-wide genomic analysis of genetic variation in European Drosophila melanogaster. Our analyses uncover longitudinal population structure, provide evidence for continent-wide selective sweeps, identify candidate genes for local climate adaptation, and document clines in chromosomal inversion and transposable element frequencies. We also characterize variation among populations in the composition of the fly microbiome, and identify five new DNA viruses in our samples.

Published
2020

46. The discovery, distribution, and diversity of DNA viruses associated withDrosophila melanogasterin Europe

Author

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

Published
2021
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48. The discovery, distribution and diversity of DNA viruses associated withDrosophila melanogasterin Europe

Author

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

Published
2020
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49. Genomic Analysis of European Drosophila melanogaster Populations Reveals Longitudinal Structure, Continent-Wide Selection, and Previously Unknown DNA Viruses

Author

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

Published
2020
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