[Annelida] Eunicid phylogeny

J. Kirk Fitzhugh kfitzhug at nhm.org
Tue Mar 21 20:48:13 EST 2006


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.org
http://www.nhm.org/research/annelida/staff.html
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