Wormers,
I was just reading the very interesting paper by Torsten Struck, Gunter
Purschke, and Ken Halanych in Systematic Biology, 'Phylogeny of Eunicida
(Annelida) and Exploring Data Congruence Using a Partition Addition
Bootstrap Alteration (PABA) Approach.' In this paper the authors make the
follow statement (pp. 54-55):
Three general approaches to analyzing multiple data sets (i.e., partitions)
have been proposed: analyze each partition separately and build a consensus
tree..., combine partitions prior to analysis..., and combine partitions
only after certain conditions are met.... For the purposes of our study, we
were not interested in whether or not to combine data, but were more
interested in the agreement or disagreement for particular clades across
data partitions.
I have a paper in a recent issue of Zootaxa (1145), as well as a paper
coming out this June in Biology & Philosophy that show that the approach
taken by Struck et al. of conducting partitioned analyses is scientifically
unacceptable, and the results obtained from such analyses cannot be
rationally investigated. Any comparisons of phylogenetic hypotheses
derived from different data sets are entirely meaningless.
Struck et al. also rely on so-called 'maximum likelihood' and Bayesian
approaches to infer hypotheses. As I point out in my Zootaxa paper, the
notion of likelihood is not correctly applied in 'maximum likelihood'
methods in phylogenetics, and Bayesian inference is only useful in the
process of changing beliefs in hypotheses subsequent to confirmation, not
as a procedure for inferring hypotheses in the first place. I also point
out that bootstrap methods are applicable to statistical hypotheses, but
not to explanatory hypotheses.
Kirk
-----------------------------------------------------
J. Kirk Fitzhugh, Ph.D.
Curator of Polychaetes
Invertebrate Zoology Section
Research & Collections Branch
Los Angeles County Museum of Natural History
900 Exposition Blvd
Los Angeles CA 90007
Phone: 213-763-3233
FAX: 213-746-2999
e-mail: kfitzhug at nhm.orghttp://www.nhm.org/research/annelida/staff.htmlhttp://www.nhm.org/research/annelida/index.html
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