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<font face="monospace">NB Arnaud Martin wanted this forwarded to the
Heliconius mailing list<br>
<br>
From: Samuel Yeaman <a class="moz-txt-link-rfc2396E" href="mailto:samuel.yeaman@ucalgary.ca"><samuel.yeaman@ucalgary.ca></a><br>
Date: Mon, Sep 16, 2024 at 9:44 AM<br>
Subject: Working group on genomics of repeated adaptation<br>
To: [clipped]<br>
<br>
Hi all,<br>
<br>
<br>
<br>
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:
<a class="moz-txt-link-freetext" href="https://yeamanlab.weebly.com/repadapt.html">https://yeamanlab.weebly.com/repadapt.html</a><br>
<br>
<br>
<br>
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:<br>
<br>
<br>
<br>
<a class="moz-txt-link-freetext" href="https://doi.org/10.1101/2024.04.02.587814">https://doi.org/10.1101/2024.04.02.587814</a><br>
<br>
<a class="moz-txt-link-freetext" href="https://doi.org/10.1038/s41559-024-02514-5">https://doi.org/10.1038/s41559-024-02514-5</a><br>
<br>
<br>
<br>
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.<br>
<br>
<br>
<br>
Suitable datasets:<br>
<br>
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.<br>
<br>
<br>
<br>
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: <a class="moz-txt-link-freetext" href="https://ucalgary.zoom.us/j/8570569393">https://ucalgary.zoom.us/j/8570569393</a>) and
will be recorded for anyone that can’t make it.<br>
<br>
<br>
<br>
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:<br>
<br>
<br>
<br>
<a class="moz-txt-link-freetext" href="https://docs.google.com/spreadsheets/d/1Jr28SWvfVt52pT1lqpfqIQyylyFrzn-NuHGBmX9D-0g/edit?usp=sharing">https://docs.google.com/spreadsheets/d/1Jr28SWvfVt52pT1lqpfqIQyylyFrzn-NuHGBmX9D-0g/edit?usp=sharing</a><br>
<br>
<br>
<br>
(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)<br>
<br>
<br>
<br>
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.<br>
<br>
<br>
<br>
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!<br>
<br>
<br>
<br>
Cheers,<br>
Sam<br>
<br>
<br>
<br>
Ps. I’m also recruiting a PhD student, if you know any interested
candidates:
<a class="moz-txt-link-freetext" href="https://yeamanlab.weebly.com/uploads/5/7/9/5/57959825/phd_position_2024.pdf">https://yeamanlab.weebly.com/uploads/5/7/9/5/57959825/phd_position_2024.pdf</a><br>
<br>
<br>
<br>
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