Who is the postivist?

[Ted Schultz]

>Richard Zander responded to my recent posting with:
>
>Wonderful! I would like to see statistical phylogeneticists deal more
>knowledgeable with priors in such a way that we get better results. I do
>think, however, that they already are being lenient in assuming a
>neutralist selection position for all genes, as well as a number of
>other (somewhat outrageous) assumptions.

There are a number of problematic assumptions that go into the phylogenetic
analysis of DNA sequences but, the last time I looked, neutral selection
was not one of them.  Perhaps you are suggesting that parallel selection on
genes in distantly related species will cause their sequences to converge.
If so, this could cause problems; however, I am not at all sure that
presuming that this has NOT happened is more "outrageous" than presuming
that it HAS happened.  And it seems fairly reasonable to me that we would
not expect the same directional selection in multiple genes, or in multiple
genes + multiple morphological characters, so to the extent that
phylogenies are constructed from diverse data sources we are compensating
for this problem.

>>I said:
>> Two other reasons that blunt Zander's critique are:
>>
>> 1. An entire tree is not really a single hypothesis.  Instead, it is the
>> conjunction of multiple hypotheses of monophyletic groups.  Some of these
>> monophyletic groups may appear in many of the suboptimal trees surrounding
>> the optimal (most likely/most parsimonious) tree, i.e., they may be very
>> well supported and thus highly "probable."  Judging the probability of
>> subtrees rather than trees is certainly more fair to phylogenetic
>> methodology.

>Zander responded:
>Okay. Bremer support is fine. How much Bremer support is needed to make
>a subclade a probabilistic reconstruction of phylogeny? Now, I am not
>talking about obvious relationships like ((man chimp) dog). That's a
>nicely parsimonious subclade. It is the fine structure of big trees,
>dealing with very similar taxa differing by simple characters that I
>question.

I am not just talking about Bremer support and, indeed, Bremer support
cannot be applied to likelihood trees.  Any number of ways have been
proposed for calculating "confidence limits" around subtopologies have been
suggested (e.g., the Kishino-Hasegawa parametric test, Page's median trees,
parametric and non-parametric bootstraps).  I am curious about your
criterion that makes ((man chimp) dog) "obvious."  Whatever that criterion
is, you should be able to apply it to those "very similar taxa" as well.
If they don't pass the test, then more character data are needed.
>

>>I also said:
>> . . . When trees or subtrees are framed as a
>> priori null hypotheses, and when they are subsequently corroborated because
>> they appear in the optimal tree or in the "confidence-set" of
>> optimal+suboptimal trees in some specified confidence interval, then we
>> have failed to reject these null groupings and, again, a probability is
>> conferred upon them that is greater than what is implied by Zander above.

>Zander:
>They are not corroborated. Coincidence may be due to convergence among
>daughter lines. There is no independent test. Failing to reject a null
>hypothesis confers ... what? A probability higher than something else?
>Failing to reject a null hypothesis just means it could be true.

In modern statistics, we attempt to reject a null (with reference to one or
more alternatives) and report the results of that attempt as a "P" value.
If the P value is high, and if all possibilities are covered by the
alternative hypotheses, then the data have indeed conferred a high
probability to the null (or, conversely, a low probability to the
alternative(s)).  In Bayesian terms, the framing of a null corresponds to
conferring higher a priori probability to one set of (sub)trees over
another.  If I predict, based on a morphological phylogeny, that a
particular group of species is monophyletic and if I then find that a DNA
sequence phylogeny corroborates that prediction, I have indeed increased my
confidence in that null.  You seem to be saying there is an additional
alternative hypothesis that needs to be accounted for, that of
convergence/parallelism.  I would not disagree with that, but I would
suggest that the obvious test is to construct phylogenies from multiple
character systems.  If, however, you are saying that your NULL hypothesis
is that all character states shared in common between members of a
"pseudoclade" are due to universal, unrelenting convergence in every
observed and unobserved character system, then I am not sure how we would
proceed to test such a null: can you suggest a way?
>
>>Then I said:
>> In non-statistical terms, impugning phylogenetics because complex trees
>> consisting of many taxa are rarely entirely "true" or "false" ignores the
>> fact that phylogeneticists have discovered and continue to discover real,
>> highly corroborated monophyletic groups.

>Zander:
>No, no. Complex trees usually include disparate taxa that you don't need
>a computer to arrange in a reasonable tree vis-a-vis a shared ancestor
>with some outgroup. Phylogeneticists have not "discovered" these trees.
>They are guesses based on like produces like (mostly). It is when there
>are lots of alternative trees (optimal+suboptimal as above) that
>parsimony methods fail and should be impugned most vigorously.
>

I don't think it's fair NOT to give phylogeneticisits credit for anything
you consider obvious, but then to impugn them for the cases where the
character data are problematic.  As a first step in extending our knowledge
of evolutionary history, we need to tackle the difficult cases with those
methods that seemed to work in tackling the more "obvious" ones.  If you
are saying that phylogeneticists should not attempt to make the difficult
cases seem more trustworthy than they really are, then you should be
heartened by the increasing use of tests, Bremer supports, bootstraps,
multiple character systems, etc.  The researchers I know care a great deal
about discovering the phylogenies of the groups they work on.  They don't
want shaky answers: they want to be sure.  Personally, I require lots of
character support from lots of different character systems.  When
completely unrelated systems keep telling me the same answer over and over,
I start to think that maybe there's phylogenetic signal coming through.  It
certainly can't be due to chance, and it strains my credulity to think that
such congruence (nuclear genes, mitochondrial genes, adult characters,
larval characters, etc.) could be due to convergence/parallelism as well.

___________________________________
Ted Schultz, Research Entomologist
Department of Entomology, MRC 165
National Museum of Natural History
Smithsonian Institution
Washington, DC 20560
U.S.A.

schultz at onyx.si.edu
Phone (voice and fax): 202-357-1311