[Date Prev][Date Next][Thread Prev][Thread Next][Date Index][Thread Index][Subject Index][Author Index]
Re: Shaking up the bird family tree
> Interestingly, Metaves and Coronaves are found, but not
> supported, perhaps
> because of the pesky hoatzin. The interesting part is that
> only two of the
> 19 loci find it, but, in spite of this, the other 17 do not
> manage to
> overcome this signal.
Found, but the branches leading to them and to each of its principal groups are
even shorter than in the rest of the "backbone". So the signal is not
overruled, but worn down to almost nothing. It would be good to know where the
signal comes from. If you include beta-fibrinogen, you will find this apparent
dichotomy; that much is known. If you for example compare mt-genomes, the
dichotomy disappear without a trace. And to quote the original paper:
"Metaves and Coronaves are broadly distinguished by four indels: a five-base
deletion in Coronaves, a 15-base deletion in Coronaves plus Syrrhaptes (one of
two genera of sandgrouse, both studied), a 21-base deletion in Coronaves plus
ostrich or insertion in Metaves plus Galloanserae, and a four-base deletion in
Metaves plus bustards."
So "a 21-base deletion [...] or insertion" is something that *did* happen
convergently, and the last deletion/(if the dichotomy is bogus) insertion shows
that frame-shift indels *did* happen convergently too.
Another way to put the original rationale for the Metaves would be "presently
supported by at most one unambiguous apomorphy in a character type where
extreme convergent evolution is known". And it is probably not a good idea to
make much of such "clades" either (Would anyone here confidently write a
16-pages paper proposing clades based on a *morph* analysis yielding such a
The beta-fibrinogen signal is known to be VERY strong; it can override 5 times
the amount of data contradicting it. But as you can see, it is not very robust.
It is strong simply because it's whole blocks of identical bases missing or
inserted in a single instant, overruling single-base changes across the entire
sequence. OTOH, there is sufficient evidence that certain loci "attract"
transposons: the "21bp deletion" may just as well be a widespread 21bp
insertion (you cannot tell in the scope of a cladistic analysis).
So a single evolutionary indel event changes, for the purpose of this analysis,
several characters. Whereas a single point mutation event changes a single
Changing the alignment algorithm (in BLAST terms: using PAM and not BLOSUM)
would probably prevent you from ever finding this supposed dichotomy.
Alternatively, one might treat indels as a single character each - which they
technically *are*. In that case too, the signal would be easily overwhelmed.
The problem with molecular phylogenetics in deep time, at its present state, is
that the belief (founded upon its power in not-so-deep-time analyses) in its
capabilities is vast, but the knowledge about what precisely the limitations
are is marginal. doi:10.1080/10635150590947843 gives a good indication of the
direction research has to take before there can be any chance to resolve such
And if I am correct, the neoavian "backbone" is characterized by drift and
random lineage sorting as heavy as can be expected in lineages that barely
manage to make it through a catastrohic mass extinction... all evidence
suggests that it is simply wrong to assume "normal" molecular evolution in that
region of the neornithine tree.
In conclusion: we need bones (or analyses thereof), because the bases simply
Gesendet von Yahoo! Mail.
Dem pfiffigeren Posteingang.