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Re: "Ratite" polyphyly and paleognathous dromornithids

David Marjanović <david.marjanovic@gmx.at> wrote:

> How did they get those guide trees? (I'll have access to the paper in a
> bit over a week.)

They considered all 15 possible rooted trees for 4 ingroup taxa
(ostrich, rheas, tinamous, emu -- rheas and tinamous were constrained
to be monophyletic and the interrelationships of outgroup taxa were
fixed) and calculated their branch lengths using maximum likelihood.
However, the guide trees were only used to assess alignment bias;
their other analyses used manual alignments.

> I ask because ModelTest used to derive its guide tree by
> neighbor-joining (and the Jukes/Cantor model), while yours truly & Laurin
> (2007, Syst. Biol.) noticed that changing it to using the most parsimonious
> guide tree yields different results... and, at least in the example we used,
> the most parsimonious guide tree is much less horribly implausible than the
> one found by neighbor-joining!

Interesting. Would be surprised if that were a general rule, though,
as neighbor-joining seems to be consistent over a wider region of
parameter space than parsimony.

> I know it's much easier said than done, but it would certainly be good to
> add more lithornithids (their monophyly hasn't been tested!) and all
> supposed Paleogene ratites (*Palaeotis*, *Eleutherornis*, *Remiornis*...).
> The number of characters, and its ratio to the number of taxa, is
> impressive.

There is some methodological weirdness in the analysis. For example,
in order to test the mtDNA-based hypothesis of moas and tinamous being
sister groups (Phillips et al. 2010), they ran a constrained analysis
where "_Pterocnemia_, _Casuarius casuarius_, _Aepyornis_ and _Apteryx
australis_ were forced to lie outside of a clade containing moa and
tinamous" (Wothy & Scofield 2012:103). However, a few pages further,
they wrote: "The analysis failed to unite tinamous and moa as a clade"
(Worthy & Scofield 2012:107). Instead, they got two trees with moas
grouping with rheas, ostriches, casuariids, elephantbirds, and kiwis
to the exclusion of tinamous. Not only did the constraint not work as
intended; it's not entirely clear what it actually did. And although
the authors weren't able to recover a moa-tinamou clade exclusive of
other paleognaths, they wrote: "This study suggests that there is
significant support for moa and tinamous as sister taxa, but does not
resolve where in the tree moa might lie, whether basal or deeply
nested" (Worthy & Scofield 2012:112).

> So... they used characters from the quadrate alone and ignored the entire
> rest of the skeleton? ...Why would anyone do that?

Not from the quadrate alone, but from the _otic part_ of the quadrate
alone. I suppose they focused mainly on comparisons of quadrate
morphology between the Tingamarra specimen and other taxa from the
anseriform and galloanserine stem groups; they called for a more
careful re-examination of dromornithid morphology in the main text.

David Černý