Re: Morpho v molecular (was Re: Tinamous: living dinosaurs)

[Jura <pristichampsus@yahoo.com>]

----- Original Message -----

> From: Mickey Mortimer <mickey_mortimer111@msn.com>

But remember my original statement was "I don't 
> know of any molecular-based relationship which is consistantly found and 
> which 
> 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 
> the 
> molecular analyses suck less, so they go with the latter.  When the two 
> methods 
> 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 
> leading 
> to molecular results that resemble the traditional morphological results 
> after 
> 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. 
2004).

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 
= 1.00)."

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 
studies:

"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.


Jason

References


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.
Hillis,
D.M. 1994. Homology in Molecular Biology. in Hall, B.K.(ed) Homology: the
Hierarchical Basis of Comparative Biology. Academic Press. San Diego CA.
pps:339-368

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. 
Syst.Biol. Vol.59(6):674-688