How to choose background branches? about hyphy

[stevenweaver]

Dear @Buckaroo1,

Considering the context of your research question, aBSREL may not be the most suitable as it tests for selection on each branch individually. Please see this thread for recommendations.

Alternative Methods:

1. BUSTED-PH : This method is suitable if you have a clear hypothesis about selection differences between foreground (desert species) and background (non-desert species) branches.
   • Benefit: It explicitly tests for differences in selection pressures between specified groups of branches.
2. RELAX: This method tests whether selection is relaxed or intensified along branches of interest compared to background branches.
   • Benefit: Useful for identifying changes in selective pressure intensity, rather than just positive selection.
3. Contrast-FEL (Fixed Effects Likelihood): This method allows for site-by-site comparison of selection pressures between foreground and background branches.
   • Benefit: Identifies individual sites with different selective regimes between groups.

Practical Recommendations:

• Diverse Background: Include various non-desert species to enhance contrast. For example, not only include species from the same genus that live in other environments, but also a broader phylogenetic tree that includes a representative species from the same family. Please see this detailed comment for more recommendations for dataset construction.
• Exploratory Testing: Use aBSREL for an exploratory approach where each branch is tested independently.

Best,
Steven

[Buckaroo1]

Dear @stevenweaver ,

Thank you for your prompt and detailed response. Your explanation has given me a clearer understanding of how to choose background branches.

I am intrigued by your suggestion to "include various non-desert species to enhance contrast." Could you elaborate on why using non-desert species, as opposed to desert species, would enhance contrast? If possible, could you provide some references or examples to illustrate this point?

Thank you once again for your assistance.

Best regards,
Buckaroo1