evogytis
commented
6 years ago Not sure how I feel about this one. Isn't the whole point of structured coalescent to infer coalescence rates from available data and use that information to parts of the tree where sequences aren't available? Part of our inference should also come from asymmetry in migration - a backbone lineage in humans is unlikely because migration rate out of humans is low. Should we argue this and add text or shall I make an ML tree with labels reconstructed via parsimony that prefers longest branch state? Thoughts?
trvrb
A comparison to ML tree reconstruction could potentially be illuminating. We think you could be clearer about what drives the results in your paper. It is unusual for a phylogenetic ancestral reconstruction, that the results seem to be determined as much by the coalescent assumptions as by the tree topology. The two-patch model had a much higher coalescent rate in the human deme than in the camel deme - so long branches are only really possible in the camel deme. This may be why for example, staring at the top clade of figure 1, one can see camel ancestry to a whole bunch of human sequences that are not topologically separated by camel sequences. If this is correct, these results may not necessarily be wrong, but it made us slightly uncomfortable that the results are driven by the coalescent model, not the tree topology. Please elaborate, either correcting us, or explaining better. A simple test of this hypothesis would be that an ML ancestral reconstruction on the ML tree would not give the same clusters. I don't think that would make the ML result correct, but it might be an enlightening comparison. Or you may prefer another way to address this.