Contrast-FEL analyses

[JJohnSmith]

Hi ,

I am new to this field and I am currently working on my master's thesis, focusing on the evolution of a specific morphological trait., I've opted to analyze 60 genes across a smaller number of species due to time constraints. I created two separate datasets: one for mammals (15 species) and another for archosaurs (12 species). In the mammalian dataset, there are two groups exhibiting the trait, whereas in the archosaur dataset, only one group does.

For selection analyses, I used several methods in HyPhy, specifically BUSTED, aBSREL, RELAX, and Contrast-FEL. I labeled the branch of the most recent common ancestor of the groups with the trait as the foreground branches. Consequently, I have two foreground branches in the mammalian dataset and one foreground branch in the archosaur dataset.

I've noticed that Contrast-FEL detected significantly more positively selected sites in the archosaur dataset compared to the mammalian dataset. When I re-ran the analyses on the mammalian dataset, this time with just one foreground branch (I removed the other group from the alignments), the number of positively selected sites in Contrast-FEL increased.

I came across this information on the HyPhy website under Contrast-FEL specifications:

"Rules of thumb for when this method is likely to work well, and when it is not. -Generally, you need 10 or more branches in each set to be able to have any statistical power. -Too little divergence is also likely to severely throttle statistical power."

It appears that my dataset configuration is problematic, lacking the necessary number of branches in each set, leading to low statistical power and inconsistent results. Given my time constraints, I cannot make significant changes to the datasets.

I was wondering if lowering the q-value threshold from 0.2 to 0.1 (or another value within that range) would be a viable approach to mitigate these issues.

Any advice would be greatly appreciated.

Thank you so much!