ADAPT – Ancient DNA studies of Adaptive Processes through Time

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

ADAPT web­site: aDNA.network

Evol­u­tion is typ­ic­ally a pro­cess rather than an event, and as such pro­gresses over time and is thus best stud­ied by sampling time series data, rather than sampling at a single time point. How­ever, the times­cales of many evol­u­tion­ary pro­cesses are great­er than the lifespans of those of us study­ing them. There­fore, evol­u­tion­ary genet­ics stud­ies would be well served by ret­ro­spect­ively sampling across evol­u­tion­ary times­cales by using ancient DNA (aDNA) tech­niques. Our pro­posed Spe­cial Top­ic Net­work would bring togeth­er lead­ers in the field of aDNA labor­at­ory work; developers of new data ana­lyses tools for hand­ling the pecu­li­ar­it­ies of gen­om­ic sequence data from ancient samples and time-series data; and empir­i­cists work­ing with time-series samples that would bene­fit from the applic­a­tion of these ancient DNA protocols.

A poten­tial short­com­ing of evol­u­tion­ary stud­ies that use con­tem­por­ary data for detect­ing nat­ur­al selec­tion act­ing on advant­age­ous alleles is that the stat­ist­ic­al meth­ods have poor sens­it­iv­ity and tem­por­al res­ol­u­tion and will be con­foun­ded by changes in eco­lo­gic­al con­di­tions, geo­graph­ic dis­tri­bu­tion, rates of intro­gress­ive gene flow and pop­u­la­tion size, all of which could have influ­enced the strength and con­sist­ency of selec­tion and the pro­gress of adapt­a­tion. Cur­rent attempts to infer both his­tor­ic­al selec­tion and demo­graphy jointly are either lim­ited to very simple mod­els of past demo­graphy or suf­fer from strong assump­tions about the strength of selec­tion and dis­tri­bu­tion of bene­fi­cial mutations.

Long-term time series data have the bene­fit of being able to estim­ate effect­ive pop­u­la­tion size through time using neut­ral mark­ers and identi­fy the tim­ing rel­at­ive to eco­lo­gic­al change, the tempo and chro­no­logy of changes in allele fre­quen­cies and sites known to be the tar­gets of nat­ur­al selec­tion dur­ing eco­lo­gic­al shifts. Giv­en the tem­por­al aspect of adapt­a­tion and spe­ci­ation, ancient DNA (aDNA) tech­niques are an obvi­ous and prom­ising tool with which to track the pro­gress of nat­ur­al selection’s effect upon the gen­ome using time-series data.

While recent ESEB and SMBE con­fer­ences have facil­it­ated indi­vidu­al talks and even sym­po­sia on paleo­ge­n­om­ic stud­ies of evol­u­tion, the ADAPT Spe­cial Top­ic Net­work will allow more focused inter­ac­tions with­in spe­cial­ist areas, integ­rat­ing across the sub-dis­cip­lines that this field encom­passes. The key dis­cip­lines we will build a dia­logue among, are those spe­cial­ising in the devel­op­ment of meth­ods and the­ory that util­ise time-series data­sets; those devel­op­ing lab meth­ods for aDNA extrac­tion, lib­rary build and sequen­cing; and those work­ing on key sys­tems for the empir­ic­al study of evol­u­tion, for which time-series data exist, but require a palaeo­ge­n­om­ics approach to unlock their poten­tial. Inter­ac­tion across these inter-related dis­cip­lines will allow the mer­ging of the indi­vidu­al spe­cial­ised fields into an innov­at­ive pipeline for study­ing evol­u­tion using ancient DNA.

By hold­ing a series of con­nec­ted events, this will allow the applic­a­tion of meth­ods developed and pro­gres­sion based upon the les­sons learned. We anti­cip­ate that this format will max­im­ise the bene­fit to the com­munity of evol­u­tion­ary bio­lo­gists with­in Europe and fur­ther afield.

Plans for the first two years of oper­a­tion of the STN include two work­shops, two train­ing courses (one on lab­work, one on bioin­form­at­ics spe­cif­ic to palaeo­ge­n­om­ics) and a sym­posi­um at either the joint Evol­u­tion meet­ing or the 2019 congress.

More inform­a­tion is avail­able at the ADAPT web­site: aDNA.network

Assoc. Prof. Andrew Foote
Depart­ment of Nat­ur­al His­tory
NTNU Uni­ver­sity Museum
Erling Skakkes gate
Trond­heim,
Nor­way

Asst. Prof. Anna-Sapfo Malaspi­nas
Uni­ver­sity of Bern,
Baltzer­strasse 6
3012 Bern
Switzer­land

Assoc. Prof. Eline Loren­zen
Nat­ur­al His­tory Museum of Den­mark
The Uni­ver­sity of Copen­ha­gen
Øster Voldgade 5–7
1350 Copen­ha­gen
Den­mark

Prof. Love Dalén
Dept. of Bioin­form­at­ics and Genet­ics
Swedish Museum Nat­ur­al His­tory
Box 50007
10405 Stock­holm
Sweden

Asst. Prof. María C. Ávila-Arcos
Inter­na­tion­al Labor­at­ory for
Human Gen­ome Research
Nation­al Autonom­ous Uni­ver­sity of Mex­ico
Mex­ico City
Mex­ico

Dr. Mar­ie Louis
Scot­tish Oceans Insti­tute
Uni­ver­sity of St Andrews
East Sands
St Andrews
KY16 8LB
United King­dom

Dr. Mat­teo Fumagalli
Depart­ment of Life Sci­ences
Sil­wood Park cam­pus
Imper­i­al Col­lege Lon­don
Buck­hurst Road
Ascot, SL5 7PY
United King­dom

Prof. Ole See­hausen
Insti­tute of Eco­logy & Evol­u­tion
Uni­ver­sity of Bern
Baltzer­strasse 6
3012 Bern
Switzer­land

Depart­ment Fish Eco­logy & Evol­u­tion
Eawag, Cen­ter for Eco­logy, Evol­u­tion and Biogeo­chem­istry
Seestrasse 79
6047 Kastan­i­en­baum
Switzer­land

Assoc. Prof. Michael D. Mar­tin
Depart­ment of Nat­ur­al His­tory
NTNU Uni­ver­sity Museum
Nor­we­gi­an Uni­ver­sity of Sci­ence and Tech­no­logy (NTNU)
7491 Trond­heim
Nor­way

Prof. M. Thomas P. Gil­bert
Sec­tion for Evol­u­tion­ary Gen­om­ics
Nat­ur­al His­tory Museum of Den­mark
The Uni­ver­sity of Copen­ha­gen
Øster Voldgade 5–7
1350 Copen­ha­gen
Den­mark

ICREA Prof. Tomas Marques-Bonet
Dir­ect­or Insti­tut Evol­u­tion­ary Bio­logy (CSIC-UPF)
Aiguader 88
08003
Bar­celona
Spain

Asst. Prof. Nina Over­gaard Therkild­sen
Depart­ment of Nat­ur­al Resources
Cor­nell Uni­ver­sity
208 Fernow Hall
NY-14853 Ithaca
USA

Dr. Jen­nifer A. Jack­son
Brit­ish Ant­arc­tic Sur­vey
High Cross
Madingley Road
Cam­bridge CB3 0ET
United King­dom

Prof. Daniel Weg­mann
Depart­ment of Bio­logy
Uni­ver­sity of Fri­bourg
Chemin du Musée 10
1700 Fri­bourg
Switzer­land