From jmallet at oeb.harvard.edu Mon Sep 16 22:51:17 2024 From: jmallet at oeb.harvard.edu (James Mallet) Date: Mon, 16 Sep 2024 17:51:17 -0400 Subject: [HELICONIUS] FWD: Working group on genomics of repeated adaptation Message-ID: NB Arnaud Martin wanted this forwarded to the Heliconius mailing list From: Samuel Yeaman 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: