Possibility of applying PhyloNetworks to mitochondrial data

[Matheus Salles]

Hello there,

I hope you're doing well!

I'm wondering if using PhyloNetworks for mitochondrial data is a good idea, and would be glad to hear your thoughts on this matter.

I've been thinking about it mostly because it's recommended to use independent genes in the analysis. However, splitting up mitochondrial genes into different partitions might not be the best option, for biological reasons. On the other hand, using the entire mitochondrial genome as one single partition might not be feasible for calculating concordance factors since this requires multiple genes, right?

So, is the only practical option here to combine nuclear and mitochondrial data (let's say, using 100 nuclear genes along with the whole mitogenome, totaling "101 genes" as input), or am I overlooking any other possibilities? Or should we not even consider using PhyloNetworks to analyze mitochondrial data?

Thanks in advance!

Best regards,

Matheus