Ancestral Genotype Reconstruction to use as Outgroup

[joaomsouto]

Hi,

I'm working on a system where we want to perform phylogenetic analyses using whole-genome population data. Typically, these analyses require an outgroup, but in our case, there isn’t a feasible outgroup available—the closest lineage is ~250 million years diverged, making it too distant for reliable mapping and variant calling.

Given this limitation, we are considering reconstructing ancestral genotypes along the genome using population data as a substitute for an outgroup. Our dataset consists of: 10 species, with 6 to 10 short-read, unphased whole-genomes per species; and Scaffold-level assemblies from long-read sequencing for each species

From what I understand, tskit can be used to reconstruct ancestral genotypes, and I was wondering if anyone has experience doing this, especially in a comparative/population genomics context across multiple species?

Do you have any advice on how to approach this with tskit or tsinfer? Are there recommended tools or workflows for genome wide ancestral state reconstruction that integrate well with tskit? And has anyone attempted to use reconstructed ancestral genotypes as a functional "outgroup" for phylogenetic or evolutionary analyses?

Any insights or suggestions would be greatly appreciated!