Synthesizing Micro- and Macro- Evolutionary Processes Shaping Prokaryotic Genomes


Deepa Agashe, Nation­al Centre for Bio­lo­gic­al Sci­ences, Ban­galore, India
Edward Feil, The Mil­ner Centre for Evol­u­tion, Uni­ver­sity of Bath, UK
Isa­bel Gordo, Insti­tuto Gul­ben­ki­an de Ciência, Por­tugal
Ruth Her­sh­berg, Tech­nion, Haifa, Israel
Olivi­er Tenail­lon, INSERM, Ecole Poly­tech­nique, France


A major goal of evol­u­tion­ary bio­logy is to elu­cid­ate the mech­an­isms that gen­er­ate observ­able pat­terns of genet­ic vari­ation. The advent of whole gen­ome sequen­cing provides new oppor­tun­it­ies to observe vari­ation in proka­ryotes on an unpre­ced­en­ted scale. Gen­ome data is now avail­able over ever increas­ing taxo­nom­ic breadth, and data for key spe­cies can run into tens of thou­sands of gen­omes. These data have revealed pat­terns of immense vari­ation across a range of gen­om­ic traits, includ­ing GC con­tent, codon bias, tRNA pools and the size of the pan-gen­ome (the total com­ple­ment of genes present in a single pop­u­la­tion). The ulti­mate source of all this genet­ic vari­ation is the pro­cess of muta­tion, whose rates and biases are affected by mul­tiple molecu­lar factors (e.g. DNA repair, recom­bin­a­tion, divi­sion times). Once they occur, the fate of these muta­tions depends on the fun­da­ment­al evol­u­tion­ary forces of nat­ur­al selec­tion and genet­ic drift, which are impacted by the effect­ive pop­u­la­tion size of a spe­cies and demo­graph­ic changes.

Thus, to under­stand the emer­gence of pat­terns of vari­ation, we need to con­nect pro­cesses across vastly dif­fer­ent times­cales, requir­ing a syn­thes­is and multi-dis­cip­lin­ary under­stand­ing of the under­ly­ing molecu­lar mech­an­isms, evol­u­tion­ary pro­cesses and eco­logy. In this ESTN we pro­pose to attempt such a syn­thes­is, using evid­ence from exper­i­ment­al evol­u­tion stud­ies with pat­terns of nuc­le­otide vari­ation observed in nat­ur­al pop­u­la­tions over a wide range of time-scales, from weeks to months (e.g. labor­at­ory evol­u­tion or single dis­ease out­break), to mil­lions of years (e.g. across spe­cies from dif­fer­ent orders). The syn­thes­is of labor­at­ory evol­u­tion data with micro- and macro-evol­u­tion­ary data from nat­ur­al pop­u­la­tions will shed light on the rel­at­ive con­tri­bu­tions of adapt­ive and stochast­ic pro­cesses as gen­omes become more diverged. The inclu­sion of exper­i­ment­al data is crit­ic­al, as this allows test­ing of spe­cif­ic hypo­theses regard­ing, for example, the main­ten­ance of GC con­tent or the drivers of codon bias/tRNA profiles.

1st Network meeting

Our main goal is to estab­lish a net­work to explore aspects of proka­ryot­ic gen­ome evol­u­tion, with the aim of integ­rat­ing across times­cales. Core themes include the pre­dict­ab­il­ity of evol­u­tion, the dis­son­ance between labor­at­ory and nat­ur­al evol­u­tion, com­pos­i­tion­al bias, selec­tion at syn­onym­ous sites, and the evol­u­tion of access­ory genes. Our first net­work meet­ing will take place in per­son at the at the Mil­ner Centre for Evol­u­tion at the Uni­ver­sity of Bath, UK, from 30 May to 1 June 2022, with about 30 par­ti­cipants. Along­side talks, we will have plenty of time for discussion.

We invite applic­a­tions from advanced PhD stu­dents and Postdoc­tor­al fel­lows who would like to join the 1st net­work meet­ing and con­trib­ute to the syn­thes­is. Accom­mod­a­tion is covered, and we are able to offer some travel sup­port for inter­na­tion­al par­ti­cipants. Apply here by 15 March 2022.

Invited speak­ers:

  • Hiroshi Akashi, Japan
  • Susan Bailey, USA
  • Jef­frey Bar­ri­ck, USA
  • San­ti­ago Castillo-Ramirez, Mexico
  • Ale­jandro Couce, Spain
  • Tal Dagan, Germany
  • Jam­ie Hall, UK
  • Fre­derique Le Roux, France
  • Hai­wei Luo, Hong Kong
  • Ivan Mat­ic, France
  • Eduardo Rocha, France
  • Tiffany Taylor, UK

Major goals

(a) Identi­fy and address aven­ues for “bite-sized” syn­theses across spe­cif­ic times­cales or address­ing a par­tic­u­lar prob­lem (e.g. HGT or GC con­tent evolution)

(b) Assemble into 3–4 work­ing groups, each focused on a one of the above aspects

© Across 2 years, work­ing groups will meet inde­pend­ently and con­duct short, intens­ive train­ing courses focused on meth­ods for work­ing across micro and macro-evol­u­tion­ary scales. Work­ing groups could focus on spe­cif­ic times­cales, a sub­set of func­tion­ally rel­ev­ant traits, a taxo­nom­ic sub­set of organ­isms, or a spe­cif­ic set of data (e.g. clin­ic­al and exper­i­ment­al evolution)

(d) Even­tu­ally, the whole net­work will recon­vene and devel­op a broad­er syn­thes­is; and we will present our find­ings at a spe­cial ESEB sym­posi­um or in a spe­cial issue of J Evol Bio or Evol­u­tion Letters.


Deepa Agashe (

Edward Feil (