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

Mickey Mortimer <mickey_mortimer111@msn.com> wrote:

> Has there ever been a case where a well established molecular-based 
> relationship was discarded due to morphology?  There have been 
> molecular-based relationships that were later changed by better
> molecular data which matched morphological ideas (e.g. guinea pigs aren't 
> rodents), but I don't know of any molecular-based relationship which is 
> consistantly found and which workers believe is wrong.

I can think of two, off the top of my head.

1. Whippomorpha

Molecular-based phylogenetic analyses consistently recover a
Cetacea-Hippopotamidae clade (Whippomorpha or Cetancodonta) nested
inside Artiodactyla, as a derived artiodactyl clade.  By contrast,
morphology-based phylogenetic analyses (which include fossil taxa)
fail to recover this "Whippomorpha" clade.  Instead, purely
morphology-based analyses find a more basal position for whales
(Cetacea), as the sister taxon to Artiodactyla, with hippos closer to
pigs (Suiformes).  (Uhen MD [2010; Annu. Rev. Earth Planet. Sci.
38:189–219] shows the two trees side by side, Figure 5).

By and large, paleo workers believe the molecular-based relationship
(Whippomorpha) is wrong.  I tend to agree.

2. Turtles (Testudines)

A recent morphology-based phylogenetic study of turtle origins (Lyson
et al. 2010; Biol. Lett. 2010 6: 830-833) found turtles to be
parareptilies, with Testudines as the sister taxon to the fossil
_Eunotosaurus_.  This Testudines-_Eunotosaurus_ clade directly
contradicts molecular-based analyses, which found turtles to be inside
Diapsida, as the sister group to Archosauria.

> I trust molecular data over morphological any day, since even huge analyses 
> like Livezey and Zusi's seem doomed by convergence.

Convergence can occur at the molecular level too.  As noted by Lyson
&c (and many others) molecular data is bedevilled by the same issus as
morphological data: taxon sampling, homplasy/convergence, rate
heterogeneity, missing data, etc.  It's just that these issues are not
obvious in a molecular tree because the character states are
effectively invisible.

For example, when ratites emerge as monophyletic in a morphology-based
analysis, molecular-based workers can (and do) question this topology
by saying: "This signal is due to convergence, because it's based on
shared flightlessness-related characters".  So any character states
that might be prone to convergence can be easily identified in a
morphology-based tree.  But if molecular characters are screwing up a
topology, how would we know?