[HELICONIUS] FWD: Working group on genomics of repeated adaptation

[James Mallet]

NB Arnaud Martin wanted this forwarded to the Heliconius mailing list

From: Samuel Yeaman <samuel.yeaman at ucalgary.ca>
Date: Mon, Sep 16, 2024 at 9:44 AM
Subject: Working group on genomics of repeated adaptation
To: [clipped]

Hi all,



I’m interested in organizing a working group to study the genomic basis 
of adaptation using studies of repeated patterns across species – I 
think at some point I’ve chatted with you about this (or if I didn’t, I 
intended to), so I hope you’re still interested. The big goal is to see 
if we can find broad patterns that allow us to test predictions of 
population genetic theory, described in more detail here: 
https://yeamanlab.weebly.com/repadapt.html



The approach would be to bring together groups of researchers that each 
have genomic data on one or a few species in various parts of the big 
tree of life that are comparatively well studied (e.g., brassicas, 
compositae, mammals, fish, insects, etc), ideally with >5 species per 
group, and hopefully many more (as well as additional data in 
repositories). Each group will identify a few leaders to conduct the 
analysis, which would include calling variants using a common method for 
each species in the group, reconstructing orthology relationships, 
applying tests to detect signatures of selection within each species 
(e.g. selective sweeps, GEA scans), and then making comparisons across 
species using PicMin – basically, repeating the methods we used in these 
two papers:



https://doi.org/10.1101/2024.04.02.587814

https://doi.org/10.1038/s41559-024-02514-5



A first step is just to see how many genes each group can find that 
repeatedly drive adaptation and explore any patterns of enrichment 
within these genes, and then start to compare notes among groups and see 
if we can say anything more generally about overall patterns that 
do/don’t conform to predictions. From there, there are many possible 
extensions.



Suitable datasets:

At this point, as the methods rely upon calling orthology using genic 
regions, we need to use sequencing datasets that have reads directly in 
genic regions (WGS, seqcap, poolseq), with a reasonable quality 
annotated reference genome (or one in a closely related species. 
Unfortunately RADseq/GBS won’t work well for this, but an eventual goal 
could be to update methods to use signatures at the closest-sequenced 
site to a gene. At a minimum, there should be enough individuals within 
a species to allow detection of selective sweeps, but ideally it would 
be nice to also have lots of populations sampled to enable GEA scans.



The aim of this initial meeting is to make connections among 
researchers, form groups, and decide on methods and timelines. To give 
time to plan ahead, I’m aiming for the first meeting on Tuesday October 
22nd at 9am Mountain time/3pm UCT. The meeting will be on zoom (link: 
https://ucalgary.zoom.us/j/8570569393) and will be recorded for anyone 
that can’t make it.



In preparation for the meeting (and especially if you can’t make the 
meeting but would like to participate) please add details of suitable 
datasets to this spreadsheet:



https://docs.google.com/spreadsheets/d/1Jr28SWvfVt52pT1lqpfqIQyylyFrzn-NuHGBmX9D-0g/edit?usp=sharing



(not all details need to be filled in now – just getting an estimate of 
the number of species in each group and the contributors would be very 
helpful)



Eventually, I hope to organize a workshop in Banff where we can get 
together and compare results and synthesize/write papers, and perhaps 
draft grant applications for deepening/broadening the study.



Importantly: I’ve almost certainly overlooked lots of people that would 
have appropriate data and would be interested in contributing to 
this…please forward this email to them!



Cheers,
Sam



Ps. I’m also recruiting a PhD student, if you know any interested 
candidates: 
https://yeamanlab.weebly.com/uploads/5/7/9/5/57959825/phd_position_2024.pdf



--
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <https://www.mailinglists.ucl.ac.uk/pipermail/heliconius/attachments/20240916/f43a45f4/attachment.htm>