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

[Tim Williams <tijawi@gmail.com>]

Mickey Mortimer <mickey_mortimer111@msn.com> wrote:


> I don't know enough about mammals to have an informed opinion, of course.  
> But Uhen's review you mention accepts Whippomorpha as the most likely 
> hypothesis, and he is a paleontologist.  Note too
> the support of Whippomorpha from O'Leary, Spaulding, Geisler, Theodor, 
> Boisserie and other paleontologists.  The most recent and largest 
> morphological analysis I know is Spaulding et al. (2010),
> with 661 phenotypic characters (and 46587 molecular ones) and 81 taxa.


Yes, but as you say, this study relies upon total evidence (morphology
+ molecules).  As Spaulding &c themselves put it: "Trees based only on
data that fossilize continue to show the classic arrangement of
relationships within Artiodactyla with Cetacea grouping outside the
clade, a signal incongruent with the molecular data that dominate the
total evidence result."  And among the other morphology-based studies
mentioned by you are phylogenies that are at odds with both the
"classical" topology (Artiodactyla and Cetacea as sister taxa) and the
topology given by molecular-based phylogenies (Whippomorpha as the
sister taxon to ruminants).


So the Whippomorpha issue is 'messy' to say the least.  The topology
of Cetartiodactyla as given by molecular-based methods has varying
support from fossil/morphological studies.  Paleontologists who find
support for some kind of hippo-whale clade (Cetancodonta/Whippomorpha)
do not necessarily agree on the content and relative position of this
clade.



> Turtle relationships are still equivocal given the current analyses- just a 
> year earlier, two of the Lyson et al. coauthors wrote a paper suggesting 
> evidence for archosauromorph turtles.  Just because the
> latest paper supported parareptile turtles doesn't make it the morphological 
> consensus.


Yes, I'm not claiming that the "turtles-are-parareptiles" hypothesis
is the final word, or even represents the morphological consensus.  I
was just using this as an example of a morphological v molecular
conflict.  What I'm driving at here is that the molecular support for
a "turtles-are-archosauromorphs" hypothesis is not backed up by
morphological/fossil evidence.  If the problem is that inadequate
taxon sampling is generating a spurious phylogenetic signal, then this
is a problem that can be potentially redressed by future fossil
discoveries.  On the other hand, I don't think we can assume that
piling up ever-larger multigene datasets drawn from the restricted
pool of extant taxa is going to lead us to the "right" answer.



> But at least with molecular data we don't have to worry about human bias in 
> choosing characters, small numbers of characters, or miscoding (I'm sure any 
> sequencing errors are much less frequent than
> what is common in morph data matrices at least).


For molecular-based phylogenetic analyses, there are much bigger
problems than mere sequencing errors.





Cheers

Tim