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Re: Reduced Consensus (Was: Afrotheria revisited)



Allen Hazen wrote-

I'm still not 100% convinced it isn't cheating: I'm genuinely not sure. I think there can be legitimate and principled reasons for excluding taxa, but throwing away data always makes me nervous. Yes the data matrix gives a well-resolved tree for 22 taxa, but is that because of "gerrymandering"? Would it be possible to get a DIFFERENT well-resolved tree by excluding one of the other taxa (this is something that time and computer power could check!)? I saw no comment in the paper or supplementary information indicating how Arsinoitherium was excluded (from tree or from matrix, to raise the issue David Marjanovic raises) or what the rationale was: some discussion would have been reassuring.

Micky Mortimer crowed on the DML forum recently about a published criticism of a paper that had achieved a well-resolved tree by excluding taxa from consideration: crowed because he had made a similar criticism some months ago on the forum. I'm hoping he will comment: does he think Tabuce et al. are doing something good, or bad like the people he crowed over.

I haven't seen the relevent paper (maybe someone could send me a copy...), but if Mike represented it correctly, it did the right thing. The key is that they excluded Arsinoitherium AFTER they ran the analysis. So they didn't throw away its data. Think of it this way...


Say you run an analysis with five taxa, and get two equally long trees-

|--possum
`--+--tenrec
  `--+--hyrax
     `--+--Arsinoitherium
        `--elephant

|--possum
`--+--Arsinoitherium
  `--+--tenrec
     `--+--hyrax
        `--elephant

A strict consensus tree would look like-

|--possum
`--+--tenrec
  |--hyrax
  |--Arsinoitherium
  `--elephant

But they both have the same topology EXCEPT FOR Arsinoitherium. So it's perfectly fair to say your analysis found-

|--possum
`--+--tenrec
  `--+--hyrax
     `--elephant

It figured out where everything went besides Arsinoitherium. That seems to be the case in Tabuce et al.. Why did Arsinoitherium have multiple equally parsimonious positions? I'd bet you're correct that it's too specialized in one or more ways.

As an aside, deleting a taxon from an analysis BEFORE running the analysis will often cause different results. It all depends on the size and quality of the matrix of course. Makes you wonder about the stability of phylogenies when you consider how few taxa are ever analyzed at once.

Mickey Mortimer