European Drosophila Population Genomics Network (DrosEU)

Organizers: Andrea Betancourt (University of Liverpool, UK), Thomas Flatt (University of Fribourg, CH), Josefa González (Institute of Evolutionary Biology (CSIC-UPF), Barcelona, ES), Mike Ritchie (University of St. Andrews, UK), Bas Zwaan (Wageningen University, NL)

Please find below the factsheet on DrosEU  – or download it here: DrosEU Fact Sheet

Logo_DrosEu

The European Drosophila Population Genomics Consortium (DrosEU)

generously funded by a European Society for Evolutionary Biology (ESEB) Special Topics Network (STN)

DrosEU consortium website: http://droseu.net

Follow us on twitter: @Dros_EU

Rationale

  • This is an extremely exciting time for population genomic studies. The recent advent of powerful next-generation sequencing (NGS) techniques allows us researchers to examine genetic variation at unprecedented scale, at the whole-genome level and with single nucleotide resolution. The continuing technological improvements and the dropping costs of these methods means that even single labs can now generate terabytes of sequence data very rapidly a relatively low cost. However, the resulting data are typically used to address only a very limited number of specific questions, so that the overall value of these data sets for the community as a whole is somewhat limited. The best-suited organisms to track genetic changes and adaptation are those that are easy to collect, which are broadly distributed, possess a short generation time, have a well-annotated genome and for which hypotheses about climate adaptation can be tested in the laboratory. The fruit fly Drosophila melanogaster and its sibling species are ideally suited for this purpose and have already been shown to respond to global and local climatic changes over short periods of time. Indeed, the genus Drosophila is one of the most powerful model systems for studying adaptation. However, in contrast to other continents, population samples of Drosophila from Europe are so far available only from a few environments and from single time points of collection.

Objectives of DrosEU

  • To foster the integration and exchange of population genomic information and data, we have founded in 2013 the European Drosophila Population Genomics Consortium (DrosEU), a collaborative consortium of scientists and laboratories interested in evolutionary genetics and genomics of Drosophila melanogaster. Our main objective is to cooperate closely in collecting, generating and analyzing genomic and environmental data for numerous Drosophila populations across Europe (and beyond). While our initial focus is on sampling and analysis of the most tractable species, D. melanogaster, we also plan in the future to include related species such as D. simulans, D. subobscura (a model for climate change adaptation) and D. suzukii (a recent invasive pest species). Our long-term goal is to regularly sample and sequence Drosophila populations through both space and time in order to track their eco-evolutionary dynamics. We plan this to be a continuing multi-year effort. Importantly, many of the sampled populations are being kept as isofemale lines by the members of the consortium as a resource for phenotypic, functional (genotype-phenotype mapping) work.
  • A similar consortium already exists in the US: the Drosophila Real Time Evolution Consortium (Dros-RTEC), coordinated by Alan Bergland (Virginia), Dmitri Petrov (Stanford) and Paul Schmidt (Philadelphia). The goal of DrosEU is to extend and complement the North American efforts by implementing a similar initiative focused on Europe. We are closely collaborating with Dros-RTEC.

What we have achieved so far & future plans

  • To date, we are approximately 62 different laboratories from 24 European countries, and also including several North American colleagues from Dros-RTEC and researchers from Morocco, Israel, Australia, and Colombia. Overall, more than 140 scientists are part of DrosEU.
  • Between 2014 and 2016 we have collected and pool-sequenced 170 population samples across all of Europe, from approximately 20-30 different locations, most of which have been sampled once in summer and once in fall; additional annual collections will be sequenced in the near future. The funds to generate the already existing sequencing data have all been raised internally within our consortium. The resulting population genomic data are being analyzed by our different internal working groups; our US colleagues from Dros-RTEC are actively contributing to some of our working groups.
  • We have submitted our first joint consortium paper based on the first 2014 set of sequencing data, with everyone who has actively contributed being involved as co-authors (under revision).This manuscript is also available on the preprint server bioRxiv (https://doi.org/10.1101/313759).
  • We are extending sampling to D. simulans, D. suzukii, and species of the Obscura group and we are improving our geographic coverage for D. melanogaster thanks to the effort of the growing number of consortium members. For many of the sampled populations, we are maintaining live isofemale lines.
  • Currently we are starting a comprehensive phenotyping effort for European D. melanogaster, to take place in 2018/2019.

Joining DrosEU

  • We encourage scientists – especially members of ESEB (!) – interested in joining us to contact Josefa González (josefa.gonzalez@ibe.upf-csic.es), cc to Thomas Flatt (thomas.flatt@unifr.ch); we accept applications for active consortium membership.
  • Active consortium membership requires a commitment and contribution to a minimum of 2 out of the 3 requirements:

(1) to perform sampling for a minimum of 1 geographic location and for a minimum of 2 timepoints (once in summer and once in fall/autumn), following our sampling protocol for pool-seq.

(2) to make a financial contribution to covering consortium costs.

(3) to make another valuable contribution to the consortium. This could, for example, include: data analysis; maintenance of live isofemale lines; coordinating a working group; organizing and hosting a consortium workshop; data storage; coordination tasks within the network; developing, hosting and maintaining databases; developing, hosting and maintaining web-based communication tools for the consortium, e.g. websites, twitter, etc.; generating funding for the consortium, e.g. via grant writing; and so forth.

  • Active membership entails being involved in all democratic decisions of the consortium, having access and being privy to all consortium-internal information, communications, data, analyses outputs, and so forth.
  • Statements of interest should be sent to Josefa González and/or Thomas Flatt; the commitment agreement form is available from us upon request.

Main consortium organizers

Josefa González
Institute of Evolutionary Biology
CSIC-Universitat Pompeu Fabra
Passeig Maritim de la Barceloneta, 37-49
08003, Barcelona
Spain
E-mail: josefa.gonzalez@ibe.upf-csic.es
Website: http://gonzalezlab.eu

Martin Kapun
Department of Biology
University of Fribourg
Chemin du Musée 10
CH-1700 Fribourg, Switzerland
E-mail: martin.kapun@unifr.ch

Thomas Flatt
Department of Biology
University of Fribourg
Chemin du Musée 10
CH-1700 Fribourg, Switzerland
E-mail: thomas.flatt@unifr.ch
Phone: +41 26 300 8833
http://www.unifr.ch/biology/research/flatt/

DrosEU ESEB STN Steering Committee

Dr. Andrea Betancourt
Institute of Integrative Biology
Biosciences Building
University of Liverpool
Crown Street
Liverpool
L69 7ZB
UK
E-mail: A.Betancourt@liverpool.ac.uk
Phone: +44 (0)151 795 4516
https://www.flyevolution.net/

Prof. Thomas Flatt
Department of Biology
University of Fribourg
Chemin du Musée 10
CH-1700 Fribourg, Switzerland
E-mail: thomas.flatt@unifr.ch
Phone: +41 26 300 8833
http://www.unifr.ch/biology/research/flatt/

Dr. Josefa González
Institute of Evolutionary Biology (CSIC-UPF)
Passeig Marítim de la Barceloneta 37-49
08003 Barcelona, Spain
E-mail: josefa.gonzalez@ibe.upf-csic.es
Phone: +34 932309637
http://gonzalezlab.eu

Prof. Michael G. Ritchie
Centre for Biological Diversity, School of Biology
University of St. Andrews
St. Andrews, Fife, Scotland KY16 9TH, United Kingdom
E-mail: mgr@st-andrews.ac.uk
Phone: +44 1334 463495
Web: http://biology.st-andrews.ac.uk/ritchielab/

Prof. Bas J. Zwaan
Laboratory of Genetics – Plant Sciences Group
Wageningen University
PO Box 16
6700AA Wageningen, Netherlands
E-mail: bas.zwaan@wur.nl
Phone: +31 317 484619