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Re: Morpho v molecular (was Re: Tinamous: living dinosaurs)
----- Original Message -----
> From: Mickey Mortimer <firstname.lastname@example.org>
But remember my original statement was "I don't
> know of any molecular-based relationship which is consistantly found and
> workers believe is wrong." In none of these cases do most people think the
> DNA is wrong. They generally recognize the morphological analyses suck, and
> molecular analyses suck less, so they go with the latter. When the two
> consistantly give different topologies, it's always the addition of new taxa
> and characters to morph analyses that move things closer to molecular results
> (e.g. the recently discovered amphibeanean fossil with lacertid charaxcters,
> which molecules predicted). You never see more genes and sequenced taxa
> to molecular results that resemble the traditional morphological results
> all. The changes always seem to go one way.
> Mickey Mortimer
You want a case where molecular results keep finding phylogenies that are not
well agreed upon, simply look at the _Gavialis_ - _Tomistoma_ back and forths.
Molecular phylogenies routinely found a sister group relationship of
_Tomistoma_ and _Gavialis_ in a sister group to Crocodylidae, while
morphological results split them off with _Tomistoma_ being a crocodylid and
_Gavialis_ being a basal crocodylian. See also the archosaur turtle nonsense.
I am in full support of Tim Williams' views on morpho vs. molecular. The only
folks that I have come across that accept molecules over morphology have been
organismal biologists. Every systematist I've talked to that deals with
molecular phylogenies is quick to point out the biases and problems associated
with molecular datasets, and all are strong supporters of incorporating
morphology. Hillis (1994) gives a nice rundown of all the many ways in which
convergences happen in sequence data. It is one of those things that, in
hindsight, appears pretty obvious. With only 4 base pairs to choose f
pure random shuffling is actually quite good.
Also, I'm curious as to what papers you and David Marjanovic have been reading
in regards to squamate phylogeny. The (or one of the) most recent phylogenies
to come out using a "total evidence" approach found monophyly among
amphisbaenians (Wiens et al. 2010). This supports the morphological data, but
goes against what the molecular data has said (Townsend 2002, Townsend et al.
According to the authors:
"...although our main focus is the impact of molecular data on fossil taxa, we
also show that addition of morphological data can change the placement of
living taxa relative to analyses of molecular data alone. In our study, the
molecular data alone (15,794 characters) show strong support for nonmonophyly
of amphisbaenians (i.e., Rhineura outside amphisbaenians)
in both parsimony and Bayesian analyses (bs = 98%; Pp = 1.00), possibly due to
long-branch attraction. Yet, monophyly of amphisbaenians is strongly supported
when the 363 morphological characters are added in both analyses (bs = 83%; Pp
The authors found here, and previously (Wiens 2005) that despite the small
number of morphological characters relative to molecular data, these phenotypic
data carry much greater "weight' in analyses than the molecules. Despite
David's complaints about small character samplings, when it comes to "total
evidence" even a little bit of morph data can drastically change a phylogeny.
The authors point out the importance of considering this in future phylogenetic
"An obvious alternative approach to integrating molecular and fossil
data sets is to analyze the morphological data alone (with both living
and fossil taxa), but to use the tree from molecular data to constrain
relationships among living taxa. A potential disadvantage of this
approach is that the molecular tree is assumed to be true and
unchangeable, and there is no opportunity for the morphological data to
contribute to estimating relationships among living taxa."
Another good example
ates back to the _Gavialis_ - _Tomistoma_ debacle. Gatesy et al. (2003) took a
total evidence approach and came up with a novel result that agreed with BOTH
the molecular and morphological data; making these two taxa sister groups, but
sinking them both deeply within Crocodylidae.
Morphology may be misleading, but molecules are no better. They're just easier
to score. Hopefully the combinations of both techniques makes up for the
weaknesses of each.
Gatesy, J., Amato, G., Norell, M., DeSalle, R.,
Hayashi, C. 2003. Combined Support for Wholesale Taxic Atavism in Gavialine
Crocodylians. Syst.Biol. Vol.52(3):403-422.
D.M. 1994. Homology in Molecular Biology. in Hall, B.K.(ed) Homology: the
Hierarchical Basis of Comparative Biology. Academic Press. San Diego CA.
Townsend, T. M. 2002. Squamate Molecular Phylogenetics: Mitochondrial and
Nuclear Perspectives. Ph.D. thesis. Washington University, St. Louis, Missouri
Townsend T.M., Larson A., Louis E.J., Macey J.R. 2004. Molecular Phylogenetics
of Squamata: The Position of Snakes, Amphisbaenians, and Dibamids, and the Root
of the Squamate Tree. Syst. Biol. 53:735–757
Wiens J.J. 2005. Can Incomplete Taxa Rescue Phylogenetic Analyses from
Long-Branch Attraction? Syst.Biol. Vol.54:731–742.
Wiens, J.J., Kuczynski, C.A., Townsend, T., Reeder, T.W., Mulcahy, D.G., Sites
Jr, J.W. 2010. Combining Phylogenomics and Fossils in Higher-Level Squamate
Reptile Phylogeny: Molecular Data Change the Placement of Fossil Taxa.