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RE: Shaking up the bird family tree
Mike Keesey wrote:
>> Kind of like how flying bats evolved from flightless bears, right?
> (Not quite the best analogy, but I'm having trouble thinking of a good one.)
>> Right? Doesn't that just make so much sense?!
> Yeah, given the many independent occurrences of flightlessness among
> avialans, it seems more likely to me that, if their topology is
> correct, flight was lost three times among palaeognathes: once in
> stem-ostriches, once in stem-rheas, and once in the Apteryx-casuariid
> stem group. Maybe more, depending on where the extinct flightless
> clades go. (Who knows, though?)
I think the operative clause here is "if their topology is correct." It's
worth remembering that molecular phylogenies are not inherently superior to
morphological phylogenies. They are both susceptible to the same weaknesses,
despite the datasets being superficially very different (bases/amino acids
versus morphological traits). In any dataset there may be many signals that
are vying for attention, and the algorithm has no magical ability to pick out
the 'correct' one (= the historical/phylogenetic signal). Simply piling on the
taxa and/or sequences does not necessarily help either. Very few people are
actually interested in *why* a molecular phylogeny pulls certain taxa together;
they just assume a given clade reflects a unique shared descent, especially if
the bootstrap/posterior probability value is high enough. For example, we know
almost nothing about which changes in beta-fibrinogen positions support a given
node, and how the sequence is influenced by the secondary or
tertiary structure of the protein. By contrast, a morphological phylogeny
lets you know *explicitly* which characters are supporting a given clade, and
it can be evaluated in light of what we know (or what we think we know) about
the ecomorphology of these taxa.
When it comes to Aves, the advantage of a molecular over a morphological
phylogeny is there is no shortage of extant taxa for expanded sampling. Also,
Neornithes have a cruddy fossil record (at least when it comes to the early
history of most extant 'orders'), and morphological analyses tend to lead to
many poorly-supported clades. So molecular analyses are intuitively
attractive. But frankly, I'm highly skletical of some of the conclusions from
the aforementioned phylogeny (e.g., nesting tinamous inside flightless ratites;
diphyletic Falconiformes). The only thing that will convince me is independent
corroboration from morphological/fossil data - not another (and even bigger)
molecular analysis. I'm not saying the entire tree is wrong. I'm only saying
that just because some expected, time-honored clades turn up (and with good
support), doesn't mean that the entire tree is 'correct'.
In short: molecular phylogenies are not a panacea. The fact that different
molecular phylogenies produce conflicting topologies is not simply due to the
size of the respective datasets, or the identity of the sequences used. It can
be a consequence of the limits of the phylogenetic analysis. There is no
guarantee that ever-expanding datasets will improve the odds of the algorithm
recovering the 'correct' signal for every lineage.
I'll get down off my soapbox now.
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