ABBA-BABA D statistics to pattern introgressed loci: applicable to RNA-seq data?

Question

[TrentGenomics]

Hello,

I'm interested in detecting patterns of introgression across transcriptomes, and was advised to look into D statistics. However, I'm under the impression that these statistics can only be applied to genomes. I have RNA-seq data for closely related species and the corresponding SNPs, and a genome/transcriptome for an outgroup.

Can I use D statistics to test for an excess of shared derived variants using SNPs called from RNA-seq data?

Any info would be very appreciated. Thanks for reading.

Cheers, M.

[Gabriel R.]

can we take a step back, why do you want to test for shared derived variants? What is your initial question?

[TrentGenomics]

So, I have RNA-seq data from 4 individuals of two evolutionary-young species (two individuals per species). The two species are able to hybridize, and my RNA-seq data was obtained from individuals that were sampled from the hybrid zone which differs in degree of sympatry (ie one individual may have been sampled from a hybrid "hotspot", while another individual may have been sampled from an area where no hybridization is occurring) . I can't be certain that the individuals sampled for RNA are of "pure" parental ancestry because they were sampled from the hybrid zone, so I wanted to test for evidence of introgression because I want to compare these species in downstream analyses. Part of this research involved calling de novo SNPs between putative "pure" species so I could develop species-specific diagnostic markers to identify late-generation introgressants, which I am unable to do using a limited number of microsatellite loci.

Thank you for getting back to me, and please let me know if you need any clarification. I really appreciate the help.

[Gabriel R.]

and are you sure you have a "pure" outgroup? I mean by pure not closer to any of your 4 individuals?

[TrentGenomics]

Yes, that is correct. The "pure" outgroup is not closer to any of the 4 individuals, but is in the same family (Sciuridae).

Thanks, Gabriel.

[Gabriel R.]

I would think that you could make a statement that you have a non-negative D stat but I wonder what you can say from this. D-stat probably does not work if you have several loci under some positive or negative selection if you want to infer some admixture. My guess is that you can compute it, state what you observe but not make strong claims either way.

Answer 1

[stolarek.ir]

vast majority of such variants likely originated in the genome, so I would say, no problem, but there is nothing inherent to transcriptome here