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 Evol­u­tion­ary Bio­logy and Envir­on­ment­al Stud­ies
Uni­ver­sity of Zurich
Win­ter­thur­er­strasse 190
8057 Zurich, Switzer­land
E‑mail: martin.kapun@ieu.uzh.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: https://risweb.st-andrews.ac.uk/portal/en/persons/michael-gordon-ritchie(7d2c2deb-821c-48a4-93c6-f60e3b5584cb).html

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