migration when mtDNA are reciprocally monophyletic

[MikePittsburgh]

Hello. My apologies if this question is naive. I don't use migrate, but I am looking for help in interpreting a published manuscript using migrate.

There are two subspecies. Mitochondrial haplogroups of each subspecies are monophyletic (>99% support of each clade). Does it make sense to even try to estimate magnitude and direction of migration between these subspecies, using mtDNA sequences? I am trying to envision, conceptually, how any nonzero estimate of m is consistent with a tree with reciprocal monophyly of each subspecies. I am only considering mtDNA for both the tree and the migrate analyses.

thanks, Mike

[Peter Beerli]

Mike, 

in situations like this, migrate will add a single migration event near the root of the tree, and depending on the composition of the two clades the direction may be clear or not (e.g the mutation model may be important here) thus there could be support for a particular direction. Although I would expect considerable uncertainty about that direction when enough trees were samples, in any case the migration rate should be low. 

Whether such an analysis makes sense or not may depend on the original hypothesis, but given that it the ‘best’ tree is monophyletic, migrate may not be that useful to talk about migration; but perhaps the estimation of population sizes (or their differences) may be still of value.

Peter

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