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Re: New paper on Neoaves
David Marjanovic wrote:
That was a late-night oversight on my part. If some of the taxa in a data
matrix have a base-
composition bias, an evolution model estimated from the data can clearly
lead to a wrong result.
Yes. But even worse, adding data can actually make the situation worse by
making the erroneous topology well-supported, and deluding you into thinking
that the 'fake' clade is 'real'. The tree looks 'better' (nicer bootstrap
or posterior probabities) but the topology is 'worse', because homoplasy is
no longer the 'noise' but the signal.
Adding taxa seems to be a good idea in general, however.
I general, yes. Nevertheless, I think we need a method to determine whether
more taxa are helping the analysis, rather than just assuming that more taxa
There's also the matter that improved taxon sampling. Some lineages make
life difficult by leaving us only a few lingering species. Try resolving
the relationships of hyracoids, elephants, and sea cows, for example.
Between them they muster about a dozen extant species, and even less genera.
(OK, you might get lucky and get your hands on some Steller's sea-cow or
mammoth DNA; but even then the taxon sampling dries up at 13 species.) Then
there's the tubulidentates, perissodactyls, etc., which are also stingy in
this regard. I'm not blaming them, of course. They tried their hardest to
survive into the Present. And it's not as though humans made it easy for
Since this was 1998 (you know, when some people honestly believed Rodentia
was paraphyletic to the rest of Placentalia, and Passeriformes the
sister-group to all other extant birds), I'll simply blame the model, and
perhaps the fact that Bayesian analysis was not yet available.
No, the "wrong model" isn't the problem here; they tried many different
models (four substitution, four among-site rate-heterogeneity), which are
used today. Bayesian analysis didn't solve the problem either (I know one
of the authors personally).
The reason is obvious: molecular characters all look the same and are thus
To a morphologist, yet. But people who study molecules beg to differ. We
need to get these people on board so we can delve deeper into the sequence
data and get a handle on what exactly is driving the signal, if not