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

On Thu, Jun 30, 2011 at 5:49 PM, David Marjanovic
<david.marjanovic@gmx.at> wrote:

> The former. Work on placental phylogeny didn't end in 2001, that's when it 
> started in earnest.
> Come on. "They" are not more intellectually dishonest than "we".

Oh no - I wasn't implying intellectual dishonesty.  Not a bit.  What I
was implying by the passeriform and rodent examples is that highly
speciose clades are not fully sampled in terms of taxa.  A
representative sample of these groups is taken, rather than sampling
over 5000 species of songbirds and ~2300 species of rodent.  This
makes sense, for obvious practical reasons.  But what if (from a
molecular perspective) problematic taxa are lurking somewhere among
these thousands of species?  We sample the small groups (like extant
hippopotamids and ratites) to exhaustion, because we need to, and
because we can.  But when we recover the phylogenetic position of the
Muridae based on a handful of murid species, there is no point testing
all 600 murid species.  This isn't intellectual dishonesty, it's
commonsense: let's focus our resources on the problematic taxa that
are hard-to-place.  Nevertheless, what if there are card-carrying
murid species that, based on molecular data, were to fall outside the
Muridae?  We'll never know unless we test them all.  I'm not saying we
*should* do this.  I'm just pondering the consequences of *if* we did.

What I'm driving at here is that when looking at the molecular
phylogeny of Placentalia or crown Aves, the taxon sampling is not
random.  We make sure we include the 'problematic' taxa (= those that
are hard-to-place on morphological grounds), and we make sure all
'orders' are sampled.  Again, this makes intuitive sense.  But in
doing so we may be missing problematic molecular taxa, and their
absence might be giving us a false sense of security regarding the
efficacy of molecular-based analyses.

> The tragulids, the extant sister-group to all other extant ruminants, have
> incomplete rumination in that the third chamber of the stomach is poorly
> developped. At least part of the system does seem to have evolved twice.

Nevertheless, tragulids have four-chambered stomachs, as in 'higher
ruminants' (Pecora).  I'm fine with the hypothesis that rumination
evolved twice in the Artiodactyla, BTW (in Tylopoda and Ruminantia).
My take-home message was that these molecular-based phylogenies
sometimes require us to re-write morphological evolution, and that's
something I'm not always comfortable with - unless it's also supported
by morphological evidence.