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Re: Metaves and Coronaves



    Wow, this is pretty impressive stuff. The analysis in the paper looks
pretty solid - the authors tested a number of alignment adjustments,
parameter changes, etc., and still recovered the two major clades. The
clades are both supported by indels (with some homoplasy), and bootstrap
support for Metaves in particular is fairly high.
    As shown in Mickey's tree (thanks to Mickey for that - the tree in the
paper shows a higher resolution, but many of the branches are not
well-supported, and it's easier to see the decent results in Mickey's tree)
relationships within the clades are mostly unresolved. It's good to see that
those few that are supported are mostly pretty uncontroversial. The only
exceptions I can spot are the inclusion of Turnicidae among the
Charadriiformes, the failure to resolve Glareolidae as monophyletic
(coursers appear in the tree twice), and the association of Bucerotidae and
Trogonidae (not controversial except in the sense that trogons have never
really been accepted as sitting _anywhere_). Does anyone know if a list is
available anywhere of the exact species used?
    The association of the 'Metaves' taxa (which include also include
Phaethontidae - Mickey seems to have accidentally left them out) is
definitely weird, but perhaps not so unacceptable as it might appear. As the
authors point out, the problem isn't really that relationships between these
taxa have been rejected in the past, they've mostly just never been
considered. Apodiformes and Caprimulgiformes have generally been considered
as related, and they're both Metaves, as have Columbidae and Pteroclidae.
Those relationships which _have_ been broken up - _Opisthocomus_ and
Cuculidae, Phoenicopteridae and "Ciconiiformes", the "Gruiformes", and
Caprimulgiformes and Strigiformes, were arguably not that well-established
in the first place.
    Among the weakly supported branches on the paper's tree which Mickey
didn't show, probably the only ones worth mentioning are that Passeriformes
were monophyletic, and formed a clade with Piciformes and Coraciiformes.
Charadriiformes (incl. Turnicidae) were monophyletic, and pelicans, the
shoebill and the hammerkop formed a clade. Most other associations were
fairly unusual.
    Most families of non-passerine birds were covered, and those that were
omitted are fairly surely related to included taxa (assuming, for instance,
that hoopoes would have been related to Bucerotidae). The only significant
omission I can see is _Leptosomus_, the cuckoo roller, which has
traditionally been included in Coraciiformes (Coronaves). This position has
been treated with suspicion in recent years, and Mayr, Manegold & Johansson
(2003) even found weak evidence to associate it with Caprimulgiformes
(Metaves). If we accept the classification of Fain & Houde, this is probably
the only family that should currently be treated as Neoaves incertae sedis,
and not assigned to either Metaves or Coronaves.

    Cheers,

        Christopher Taylor

On 5/12/04 10:56 am, "Mickey Mortimer" <Mickey_Mortimer111@msn.com> wrote:

> Houde recently sent me a pdf of an interesting paper-
> 
> Fain and Houde, 2004. Parallel radiations in the primary clades of birds.
> Evolution. 58(11), p. 2558-2573.
> 
> It contains a phylogenetic analysis of intron 7 of the beta-fibrinogen gene,
> which is said to have low rates of mutation which are less variant across
> sites, and more homogeneous substitutions among character states.  There are
> also numerous insertions and deletions, which the authors find useful.  The
> 50% bootstrap maximum parsimony consensus tree (from 262 mpt's) is-
> 
> |--ostrich
> `--Neognathae
>  |--Galloanserae
>  |  |--Anseriformes
>  |  |  |--screamers
>  |  |  `--+--magpie goose
>  |  |     `--+--whistling ducks
>  |  |        `--ducks
>  |  `--Galliformes
>  |     |--currasows
>  |     `--+--pheasants
>  |        `--megapodes
>  `--Neoaves
>     |--Metaves
>     |  |--hoatzin
>     |  `--+--sandgrouse
>     |     |--doves
>     |     |--frogmouths
>     |     |--nighthawks
>     |     |--owlet nightjars
>     |     |--+--swifts
>     |     |  `--hummingbirds
>     |     |--mesites
>     |     |--+--kagu
>     |     |  `--sunbittern
>     |     |--grebes
>     |     `--flamingos
>     `--Coronaves
>        |--+--+--rails
>        |  |  `--finfoots
>        |  `--+--trumpeters
>        |     `--+--limpkin
>        |        `--cranes
>        |--bustards
>        |--seriamas
>        |--turacos
>        |--herons
>        |--ibises
>        |--new world vultures
>        |--storks
>        |--hammerkop
>        |--shoebill
>        |--pelecans
>        |--+--frigatebirds
>        |  `--+--cormorants
>        |     |--anhingas
>        |     `--boobies
>        |--+--shearwaters
>        |  `--storm petrels
>        |--loons
>        |--penguins
>        |--thick knees
>        |--coursers
>        |--+--plovers
>        |  `--+--plovers
>        |     `--+--stilts
>        |        `--oystercatchers
>        |--+--+--sandpipers
>        |  |  `--+--+--plains wanderer
>        |  |     |  `--seedsnipe
>        |  |     `--+--painted snipe
>        |  |        `--jacanas
>        |  `--+--buttonquail
>        |     `--+--coursers
>        |        `--+--jaegers
>        |           `--+--auks
>        |              |--gulls
>        |              `--skimmers
>        |--falcons
>        |--+--secretary bird
>        |  `--+--osprey
>        |     `--hawks
>        |--+--owls
>        |  `--barn owls
>        |--+--hornbills
>        |  `--trogons
>        |--parrots
>        |--mousebirds
>        |--+--bee-eaters
>        |  |--jacamars
>        |  |--rollers
>        |  |--+--kingfishers
>        |  |  `--motmots
>        |  `--+--+--toucans
>        |     |  `--barbets
>        |     `--+--honeyguides
>        |        `--+--wryneck
>        |           `--woodpeckers
>        |--cuckoos
>        |--+--new world flycatchers
>        |  `--cotingas
>        `--+--crows
>           `--+--old world flycatchers
>              `--+--creepers
>                 `--seedeaters
> 
> No, neither Metaves nor Coronaves are defined.
> 
> "MP and ML bootstrap values support the monophyly of Metaves at 73% and 58%
> and Coronaves at 58% and 62% when analyzed using only nucleotide characters.
> MP and NJ bootstrap values are 85% and 82% for Metaves and 60% and 52% for
> Coronaves when indel characters are included in the analysis. Bayesian
> posterior probabilities are 95% for Metaves (99% excluding hoatzin) and 83%
> for Coronaves using only nucleotide characters. A likelihood-ratio test
> shows that the branches to Metaves and Coronaves are significantly different
> from zero at the P , 0.001 level."
> "... Metaves and Coronaves are recovered as strictly monophyletic by
> analysis of alternative alignments
> produced using ClustalX at a variety of gap and extension penalties, and by
> Dialign2."
> "Metaves and Coronaves are recovered as monophyletic even under alignment
> parameters that give obviously unreasonable alignments."
> 
> "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 fourbase
> deletion in Metaves plus bustards (for list of all vernacular and Latin
> family names see Fig. 2). Less than perfect
> consistency of these indels demonstrate that they are not evolving in a
> perfectly correlated fashion."
> 
> "ML analysis excluding these regions of the alignment (nucleotide data
> subset 3, see Methods) still recover
> Metaves and Coronaves as monophyletic, although with reduced bootstrap
> support, 71% and 39%, respectively. In other words, the neoavian dichotomy
> is obtained even when these regions of homology to the metavian- and
> coronavian- specific indels are completely removed from the dataset."
> 
> One point the authors make is that metavians and coronavians have converged
> to a remarkable degree.  This is illustrated convincingly by their
> comparative photos in figures 4 and 5.  I never realized how similar monias
> and thrashers were, or sandgrouse and seedsnipe.
> 
> Pdf's are available by asking me offlist.
> 
> Mickey Mortimer
> Undergraduate, Earth and Space Sciences
> University of Washington
> The Theropod Database - http://students.washington.edu/eoraptor/Home.html
>