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

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Fältnamn	Indikatorer	Metadata
000		06031naa a2201213 4500
001		oai:DiVA.org:su-201382
003		SwePub
008		220124s2021 \| \|\|\|\|\|\|\|\|\|\|\|000 \|\|eng\|
024	7	a https://urn.kb.se/resolve?urn=urn:nbn:se:su:diva-2013822 URI
024	7	a https://doi.org/10.1093/molbev/msab2592 DOI
040		a (SwePub)su
041		a engb eng
042		9 SwePub
072	7	a ref2 swepub-contenttype
072	7	a art2 swepub-publicationtype
100	1	a Kapun, Martin4 aut
245	1 0	a Drosophila Evolution over Space and Time (DEST) :b A New Population Genomics Resource
264		c 2021-09-01
264	1	b Oxford University Press (OUP),c 2021
338		a print2 rdacarrier
520		a 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data repository of genomic data available for D. melanogaster to date, encompassing 271 previously published and unpublished population samples from over 100 locations in 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.
650	7	a NATURVETENSKAPx Biologi0 (SwePub)1062 hsv//swe
650	7	a NATURAL SCIENCESx Biological Sciences0 (SwePub)1062 hsv//eng
653		a Drosophila melanogaster
653		a population genomics
653		a SNPs
653		a evolution
653		a adaptation
653		a demography
700	1	a Nunez, Joaquin C. B.4 aut
700	1	a Bogaerts-Marquez, Maria4 aut
700	1	a Murga-Moreno, Jesus4 aut
700	1	a Paris, Margot4 aut
700	1	a Outten, Joseph4 aut
700	1	a Coronado-Zamora, Marta4 aut
700	1	a Tern, Courtney4 aut
700	1	a Rota-Stabelli, Omar4 aut
700	1	a Guerreiro, Maria P. Garcia4 aut
700	1	a Casillas, Sonia4 aut
700	1	a Orengo, Dorcas J.4 aut
700	1	a Puerma, Eva4 aut
700	1	a Kankare, Maaria4 aut
700	1	a Ometto, Lino4 aut
700	1	a Loeschcke, Volker4 aut
700	1	a Onder, Banu S.4 aut
700	1	a Abbott, Jessica K.4 aut
700	1	a Schaeffer, Stephen W.4 aut
700	1	a Rajpurohit, Subhash4 aut
700	1	a Behrman, Emily L.4 aut
700	1	a Schou, Mads F.4 aut
700	1	a Merritt, Thomas J. S.4 aut
700	1	a Lazzaro, Brian P.4 aut
700	1	a Glaser-Schmitt, Amanda4 aut
700	1	a Argyridou, Eliza4 aut
700	1	a Staubach, Fabian4 aut
700	1	a Wang, Yun4 aut
700	1	a Tauber, Eran4 aut
700	1	a Serga, Svitlana4 aut
700	1	a Fabian, Daniel K.4 aut
700	1	a Dyer, Kelly A.4 aut
700	1	a Wheat, Christopher W.u Stockholms universitet,Zoologiska institutionen4 aut0 (Swepub:su)cwhea
700	1	a Parsch, John4 aut
700	1	a Grath, Sonja4 aut
700	1	a Veselinovic, Marija Savic4 aut
700	1	a Stamenkovic-Radak, Marina4 aut
700	1	a Jelic, Mihailo4 aut
700	1	a Buendia-Ruiz, Antonio J.4 aut
700	1	a Gomez-Julian, Maria Josefa4 aut
700	1	a Espinosa-Jimenez, Maria Luisa4 aut
700	1	a Gallardo-Jimenez, Francisco D.4 aut
700	1	a Patenkovic, Aleksandra4 aut
700	1	a Eric, Katarina4 aut
700	1	a Tanaskovic, Marija4 aut
700	1	a Ullastres, Anna4 aut
700	1	a Guio, Lain4 aut
700	1	a Merenciano, Miriam4 aut
700	1	a Guirao-Rico, Sara4 aut
700	1	a Horvath, Vivien4 aut
700	1	a Obbard, Darren J.4 aut
700	1	a Pasyukova, Elena4 aut
700	1	a Alatortsev, Vladimir E.4 aut
700	1	a Vieira, Cristina P.4 aut
700	1	a Vieira, Jorge4 aut
700	1	a Torres, Jorge Roberto4 aut
700	1	a Kozeretska, Iryna4 aut
700	1	a Maistrenko, Oleksandr M.4 aut
700	1	a Montchamp-Moreau, Catherine4 aut
700	1	a Mukha, Dmitry4 aut
700	1	a Machado, Heather E.4 aut
700	1	a Lamb, Keric4 aut
700	1	a Paulo, Tania4 aut
700	1	a Yusuf, Leeban4 aut
700	1	a Barbadilla, Antonio4 aut
700	1	a Petrov, Dmitri4 aut
700	1	a Schmidt, Paul4 aut
700	1	a Gonzalez, Josefa4 aut
700	1	a Flatt, Thomas4 aut
700	1	a Bergland, Alan O.4 aut
710	2	a Stockholms universitetb Zoologiska institutionen4 org
773	0	t Molecular biology and evolutiond : Oxford University Press (OUP)g 38:12, s. 5782-5805q 38:12<5782-5805x 0737-4038x 1537-1719
856	4	u https://doi.org/10.1093/molbev/msab259y Fulltext
856	4	u https://academic.oup.com/mbe/article-pdf/38/12/5782/41714359/msab259.pdf
856	4 8	u https://urn.kb.se/resolve?urn=urn:nbn:se:su:diva-201382
856	4 8	u https://doi.org/10.1093/molbev/msab259

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Av författaren/redakt...: Kapun, Martin; Nunez, Joaquin C ...; Bogaerts-Marquez ...; Murga-Moreno, Je ...; Paris, Margot; Outten, Joseph; visa fler...; Coronado-Zamora, ...; Tern, Courtney; Rota-Stabelli, O ...; Guerreiro, Maria ...; Casillas, Sonia; Orengo, Dorcas J ...; Puerma, Eva; Kankare, Maaria; Ometto, Lino; Loeschcke, Volke ...; Onder, Banu S.; Abbott, Jessica ...; Schaeffer, Steph ...; Rajpurohit, Subh ...; Behrman, Emily L ...; Schou, Mads F.; Merritt, Thomas ...; Lazzaro, Brian P ...; Glaser-Schmitt, ...; Argyridou, Eliza; Staubach, Fabian; Wang, Yun; Tauber, Eran; Serga, Svitlana; Fabian, Daniel K ...; Dyer, Kelly A.; Wheat, Christoph ...; Parsch, John; Grath, Sonja; Veselinovic, Mar ...; Stamenkovic-Rada ...; Jelic, Mihailo; Buendia-Ruiz, An ...; Gomez-Julian, Ma ...; Espinosa-Jimenez ...; Gallardo-Jimenez ...; Patenkovic, Alek ...; Eric, Katarina; Tanaskovic, Mari ...; Ullastres, Anna; Guio, Lain; Merenciano, Miri ...; Guirao-Rico, Sar ...; Horvath, Vivien; Obbard, Darren J ...; Pasyukova, Elena; Alatortsev, Vlad ...; Vieira, Cristina ...; Vieira, Jorge; Torres, Jorge Ro ...; Kozeretska, Iryn ...; Maistrenko, Olek ...; Montchamp-Moreau ...; Mukha, Dmitry; Machado, Heather ...; Lamb, Keric; Paulo, Tania; Yusuf, Leeban; Barbadilla, Anto ...; Petrov, Dmitri; Schmidt, Paul; Gonzalez, Josefa; Flatt, Thomas; Bergland, Alan O ...; visa färre...

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