Hi everyone.

I'm currently working on a project related to mito-nuclear discordance of our focal taxa, in which the phylogeny constructed by mitochondrial sequences differed from SNP data.

My question was that, when testing the impact of introgression or gene flow by scenario-testing method such as fasimcoal2 or BPP, which tree should I use for phylogeny backbone? To be more specific, could I use the tree from mtDNA and SNP data as input sequence to infer the gene flow among 'mitochondrial lineages'?

Thanks for any opinions!