Mark Siddall wrote:
>Nobody doing molecular phylogeny anymore?
>Here's a piece of food for thought:
>Consider having hit Joe's Zone due to a few highly deviant substitution
>rates on some lineages/taxa.
>How do we determine how stable these groupings are/are not.
>I would argue that bootstrapping is irellevant here because
>bootstrapping whacked out data will give you whacked out
Indeed, bootstrapping does not help when the tree-making procedure
gives a systematic bias.
>That is, in so far as bootstrapping claims to better "get-at" the
>underlying distribution, if that underlying distribution
>suffers from some systematic error so will the estimation(s) made by
Joe's Zone appears when the maximum parsimony method is applied
or when in the Neigbor-Joining (or related) method the distances between
taxa are underestimated. Do not use the parsimony when you suspect
Joe's Zone is there. I guess there is no other way except finding
an appropriate (unbiased) procedure.