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

 As for the content and position of Whippomorpha within Artiodactyla,
 well that's a different matter. A whippomorph-ruminant clade is
 pretty unparsimonious in Spaulding et al.'s data- it takes 31 more
 steps. But there are lots of ways molecules conflict with morphology
 in current analyses. In Squamata, molecular phylogenies don't have

There is no morphological analysis of squamate phylogeny that is worth mention in this respect. There simply isn't. The molecules can say whatever they want without opposition.

Even Conrad's impressive attempt -- a big step in the right direction!!! -- has _way_ too few characters for its taxon sample, and _way_ too few fossils in its enormous taxon sample, which probably explains the _completely_ novel results such as snakes being just another clade of limbless skinks. Somebody should do their PhD on just the things that Conrad didn't have time to do.

Personally, I like the molecular topology. Lacertid-amphisbaenid transitional forms are turning up now, and Iguania appears in the fossil record in the Late Cretaceous (the much older fragments from India that could, I hear, just as well be sphenodontians notwithstanding), while we have gekkotans, scincomorphs and anguimorphs-or-something in the Middle Jurassic. My unqualified impression is that the traditional classification which puts Iguania as the sister-group to all other squamates is simply based on very few characters.

 In Mammalia, they don't have Ungulata.

Neither does any morphological analysis (too small as they all are at the moment). Only romerograms have Ungulata.

 Similarly, there are many molecular relationships that aren't backed
 up by morphological evidence (like you say for archosauromorph

Or crurotarsan turtles.

 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.

Since 2001, yes, with a few minor exceptions perhaps.