I don't want to exclude any species.

[maruiqi0710]

My target species is Saccharomyces cerevisiae, and I want to detect any horizontal gene transfer from other species, including other species in the Saccharomyces genus. I set groups.yaml to

Ingroup:
4932: S.cerevisiae

How should I fill in the EGP field? I don't want to exclude any species.

[GDKO]

Hi @maruiqi0710,

If you want to detect HGTs in S.cerevisiae I would recommend

---
Ingroup:
 4930: Saccharomyces
EGP:
 4932: S.cerevisiae

This will identify HGTs that are present only in S.cerevisiae and not in other Saccharomyces species.

The problem by allowing HGTs from closely related species is that we cannot distinguish between vertical and horizontal transfers.

[maruiqi0710]

I am a little confused now. Maybe my description wasn't accurate enough. My studied organism is S.cerevisiae, and I want to know HGT from other species to S.cerevisiae, including from other Saccharomyces species. If I set "Ingroup: 4930: Saccharomyces, EGP: 4932: S.cerevisiae", will I only detect HGTs from Non-Saccharomyces species to S.cerevisiae?

Thanks a lot.

[GDKO]

Let me explain with an example

Suppose your species of interest is S.cerevisiae with taxonomy

phylum:Ascomycota;class:Saccharomycetes;order:Saccharomycetales;family:Saccharomycetaceae;genus:Saccharomyces

• If you set exclude to S.cerevisiae and ingroup to Saccharomyces you are searching for HGTs present in S.cerevisiae that are not present in Saccharomyces.
• If you set exclude to Saccharomyces and ingroup to Saccharomycetaceae you are searching for HGTs present in S.cerevisiae and maybe in other species from the genus Saccharomyces but absent in the other genera of Saccharomycetaceae

It is impossible to distinguish vertical from horizontal transmission in closely related species with AvP. If you set ingroup to S. cerevisiae then apart from novel genes in this specific species everything else will be HGT according to the algorithm.

AvP is not suited for this type of analysis. If you want to find HGTs from other Saccharomyces species, I would recommend running a gene-tree vs species-tree type of analysis.