In the paper, they show that ML outperforms MP when there is a certain amount of heterotachy. Is there a way of determining the amount of heterotachy in a data set independent of the phylogenetic method?
Yes, there has been some work in this area. Baele et al. (2006) used neighbor joining trees (not ML or Bayesian analysis) to detect heterotachy in nucleotide sequences. That being said, a lot more work needs to be done in this area.
I totally get what you are saying. Going back to my protein assay analogy, the appropriate method can also depend on the protein mixture. If you have an nearly pure sample with just one protein in it, then you can very precisely and reliably measure the concentration of the protein by using UV absorbance since specific amino acids have specific absorbances. If you have an unknown mix of proteins you can't say how many UV absorbing amino acids there are per protein molecule, so the UV method may not be as appropriate.
Now I'm curious, actually. I'm not
that familiar with protein assaying. How do you know if you have a nearly pure sample if you still don't know the concentration of the protein? Hopefully that question makes some sense.
By congruence, do you mean congruence to the accepted species tree? If so, are you assuming a lack of horizontal transfer?
Actually, by congruence I mean:
1. Congruence among the phylogenetic trees generated through ML and Bayesian analysis. Specifically, I was testing for monophyly among distantly related protein systems, so if both methods pointed to monophyly (with strong bootstrap support) -- then these trees probably accurately describe the overall relation among the sequences. The internal branches were less congruent, with weak bootstrap support.
2. Congruence to the accepted species tree (which is hard in the case of distantly related prokaryotes, since there is disagreement on the exact phylogeny for different prokaryotic phyla). I tested for horizontal gene transfer and/or gene duplication + loss using the Notung program, and indeed there were instances of horizontal gene transfer.
References
Tired and my eyes are droopy, so here's the link instead of a journal-esque citation:
Improved Statistical Method for Detecting Heterotachy in Nucleotide Sequences | Molecular Biology and Evolution | Oxford Academic
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