Post date: Jul 06, 2020 11:2:14 PM
Hi Rozenn,
Nice job today.
A few things to follow-up.
1. Lets start with BEAST (unless you find something else you prefer).
Here is the original paper about the software:
https://bmcevolbiol.biomedcentral.com/articles/10.1186/1471-2148-7-214
There is a bunch since then if you want to dig in more (maybe look at
some recent examples and their website).
2. ANGSD is what I thought of today for estimating the effective number
of sites. You can read about it in general here,
https://scholar.google.com/scholar?q=ANGSD&btnG=Search&as_sdt=800000000001&as_sdtp=on
And here is a help page that includes effective number of sites.
http://www.popgen.dk/angsd/index.php/Thetas,Tajima,Neutrality_tests
3. I also really like the diversification rate through time/lineage
thinking.
Here is a simple example from a colleague of mine:
https://royalsocietypublishing.org/doi/full/10.1098/rspb.2010.0211
Here is another classic example:
https://royalsocietypublishing.org/doi/abs/10.1098/rspb.1997.0158
And this is a recent(ish) method. Maybe start there and see what you can
find.
https://academic.oup.com/bioinformatics/article/32/5/789/1744433
4. I am around until the middle of next week then gone for a few weeks
in the field (still e-mail contact, but less). It might be good to take
a few days to read and think and then to meet early next week?
Cheers,
Zach