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Fw: Livezey and Zusi's big bird morph analysis

Forwarded with permission, my comments interspersed.

----- Original Message ----- From: <gerarus@westnet.com.au>
To: <david.marjanovic@gmx.at>
Sent: Monday, January 29, 2007 7:36 AM
Subject: Livezey and Zusi's big bird morph analysis


Hi David,

    While I've dropped out of the DML, I feel the need to add my two
cents to the discussion on the Livezey & Zusi paper. Forward my
comments to the DML if you think they add anything.

Apparently, the data matrix and such are available in another
publication:

Livezey BC, Zusi RL. 2006. Higher-order phylogeny of modern birds
(Theropoda, Aves: Neornithes) based on comparative anatomy: I. -
Methods and characters. Bulletin of the Carnegie Museum of Natural
History 37: 1-556.

It would be interesting to see how many characters were actually
factors in resolving the higher-level clades in the tree, as opposed
to smaller, less contentious taxa (Note on page 42 - brach length of
186 for Spheniscus alone, as opposed to just 41 for Neornithes as a
whole).

Livezey & Zusi mention that some characters are autapomorphies, so not all 2954 characters are really parsimony-informative. More importantly, when *Spheniscus* is the only penguin, and when *Waimanu* is absent, *Spheniscus* must be expected to have a very long branch.

I agree with you that the shortage of fossil taxa is a
potential issue, and it would be interesting to see how they would
affect the final result.

I would have also liked to see how the tree compared statistically
with any constrained to match alternative hypotheses. It's notable
how many of the higher-level branches fail to receive strong
bootstrapping support (take a look at figure 10). If we collapse any
nodes that receive less than 75% support, we lose Livezey & Zusi's
Natatores, Terrestrornithes, Charadriimorphae (plus the relationships
between the orders therein, and most of the relationships within
Charadriiformes), Dendrornithes, Raptores, Anomalogonates (and most
of the relationships between superorders therein) and Coraciiformes.

Livezey and Zusi pretty much dismiss the concept of Metaves out of
hand ("an eclectic assemblage defying plausible explanation"). When
Fain and Houde (2004) gets a mention, it's in fairly abrupt, caustic
terms (they don't even warrant a place among the multiple examples
shown of trees for past molecular analyses). I actually think Fain
and Houde did themselves a disservice by showing a highly resolved
tree in their paper rather than one only showing the properly
supported branches, as it seems to have made it easier for other
authors to attack them on sometimes fairly spurious grounds.
Unfortunately, Ericson et al. (2006) obviously came out too late for
Livezey and Zusi's consideration.

I also wish morphological phylogeneticists would refrain from
attacking molecular studies on the grounds of a supposed requirement
of a steady evolutionary rate. Modern molecular analystical methods
such as likelihood do not require a constant rate of evolution, and
are no more vulnerable to rate variation than are morphological
methods (which can also be affected by differences in evolutionary
rate if synapomorphies become obscured by autapomorphies).

Did they make such a claim? I must have overlooked it... But anyways, Livezey & Zusi are concerned about long-branch attraction in their morphological data and mention that several times.

But what distressed me most of all about the paper, I have to say,
was the final classification. Even if one is willing to forgive
paraphyletic taxa, the vast number of redundant taxa made me shudder.
Even traditional Linnean-based taxonomy only requests redundancy in
the major ranks of order and family.

Note that, contrary to tradition, the ICZN does _not_ require these. Only genus and species are mandatory.

But "Subdivision Dendrornithes
comprises a single Section Raptores, which in turn comprises a single
Superorder Raptoromorphae"? Yuck.

BTW, that's not true. Dendrornithes contains Raptores and Anomalogonates (both of them sections).

The worst point by far comes in the
Charadriiformes, where we are presented with:

Superfamily Haematopoidea (Bonaparte, 1838)
   Family Haematop[od]idae Bonaparte, 1838
        Subfamily Haematopodinae (Bonaparte, 1838)
        Subfamily Ibidorhynchinae Bonaparte, 1856
    Family Recurvirostridae (Bonaparte, 1831)
        Subfamily Recurvirostrinae Bonaparte, 1831
        Subfamily Himantopodinae Reichenbach, 1849
            Tribe Himantopodini Sibley et al., 1988
            Tribe Cladorhynchini new taxon

   But these two families together only contain five genera -
Haematopus, Ibidorhyncha, Recurvirostra, Himantopus and
Cladorhynchus. So we have a higher taxon for each individual genus!

    Oh yes, and will the concept of a Columbiformes + Psittaciformes
clade never die? This was, after all, originally based on study of
Didunculus, which has since turned out to be a highly derived taxon
within Columbiformes, with the characters shared with Psittaciformes
definite homoplasies.

    Cheers,

Christopher Taylor

To be fair, *Didunculus* is in their tree, and there it is highly derived within Columbiformes.