[Taxacom] Molecular data and synapomorphies

[Richard Zander]

Been away and apparently missed a good discussion. My comments:

 

John Grehan:

just went through the molecular data for 44 taxa and 1134 sequences
which generated a parsimony analysis supporting a human-chimpanzee clade
(Prasad et al 2008 Mol Biol Evol 25: 1795-1808) for sequences
orthologous to a 1.0 Mb region of human chromosome 7.  In the coding
sequences found no apomorphies at all for the large bodied hominoids so
the result is cladistically impossible. 

Comment: What happens in that if you have a terminal group of six
exemplars, the ones with shared traits of any sort will pop out first in
the cladogram and the ones without any additional shared apomorphies are
tacked on terminally, even if they share nothing more than traits that
put them in the groups. I've done what John did and found exemplars of
different genera paired as sister groups on the basis of no shared data
beyond being crowded together.

 

Alan DAvid Forrest:

In this case molecular data are just another form of data. Incongruence 
between data types requires analysis of what causes the incongruence, 
not rejection of one data in favour of another based on a priori 
preferences.

Comment: Absolutely wrong. Molecular data have the failings of
morphological data and few of the benefits. About a quarter of
non-coding traits are suspected to be promoters and silencers and other
regulatory features of the genome and therefore subject to selection,
and therefore any analysis based on molecular analysis will have some
convergence and parallelism. "Morphological" traits is a simplification
for 250 years of analyzing the evolution (stabilizing selection that
keeps species intact over millions of years), particularly finding
conservative traits that organize other traits, using thousands of
specimens and a multiplicity of techniques: morphometry, cultivation,
cytology, mating behavior, biogeography, sequences, allozymes, cluster
analysis including parsimony, coming up with basic taxonomic units and
higher clusterings that minimize the chance of convergence and
parallelism. Molecular data are based on a few exemplars and, if
reliable, do give you an idea of genetic continuity and isolation
events, but genetic continuity of a lineage and isolation events do not
require speciation, particularly in the case of punctuated equilibrium.
Combining analyses of evolutionary taxonomy (recognizing paraphyly and
giving apposite rank to evolutionary novelties) and molecular analyses
(genetic continuity) gives a good result that maximizes evolutionary
information in a classification. 

 

*****************************
Richard H. Zander 
Voice: 314-577-0276
Missouri Botanical Garden
PO Box 299
St. Louis, MO 63166-0299 USA
richard.zander at mobot.org
Web sites: http://www.mobot.org/plantscience/resbot/
and http://www.mobot.org/plantscience/bfna/bfnamenu.htm
*****************************