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RE: New paper on Neoaves
Thank you to Tim for sending me a copy of this. Unfortunately, the
supplementary material doesn't yet appear to be available on the
interweb, so I'll just have to comment on the paper itself...
The genes used for the tree are c-myc, RAG-1, myoglobin,
beta-fibrinogen and ornithine decarboxylase - 5007bp in total - under
Bayesian analysis. The published tree only gives those ranches that
had posterior probabilities higher than 0.95 (but doesn't give any
further support values...), and it is:
0--Palaeognathae
`--+--Galloanserae
`--Neoaves
|--Metaves
| |--+--Phaethontidae
| | |--Opisthocomidae
| | |--+--Eurypygidae
| | | `--Rhynochetidae
| | |--+--Pteroclidae
| | | `--Columbidae
| | `--+--Mesitornithidae
| | `--+--Phoenicopteridae
| | `--Podicipedidae
| `--[Caprimulgiformes]
| |--Caprimulgidae
| |--Steatornithidae
| |--Nyctibiidae
| |--Podargidae
| `--+--Aegothelidae
| `--+--Trochilidae
| `--+--Hemiprocnidae
| `--Apodidae
`--Coronaves
|--Charadriiformes
| |--Charadriidae
| `--+--Jacanidae
| |--Rhynchopidae
| `--Turnicidae
|--[waterbird assemblage]
| |--Otididae
| |--Cuculidae
| |--Musophagidae
| |--[Grues]
| | |--+--Heliornithidae
| | | `--Rallidae
| | `--+--Psophiidae
| | `--+--Aramidae
| | `--Gruidae
| `--+--Gaviidae
| |--Spheniscidae
| |--Ciconiidae
| |--+--Fregatidae
| | `--+--Sulidae
| | `--+--Anhingidae
| | `--Phalacrocoracidae
| |--Procellariiformes
| `--+--Ardeidae
| |--Threskiornithidae
| `--+--Balaenicipitidae
| |--Scopidae
| `--Pelecanidae
`--[Anomalogonatae]
|--+--Cariamidae
| |--Falconidae
| |--Passeriformes
| `--Psittaciformes
`--+--Leptosomidae
|--Cathartidae
|--Strigiformes
|--[Accipitres]
| |--Sagittariidae
| `--+--Pandionidae
| `--Accipitridae
`--+--Coliidae
|--Trogonidae
|--+--Bucerotidae
| `--+--Upupidae
| `--Phoeniculidae
`--+--Coraciiformes
| |--Meropidae
| |--+--Brachypteraciidae
| | `--Coraciidae
| `--+--Todidae
| `--+--Momotidae
| `--Alcedinidae
`--Piciformes
|--+--Galbulidae
| `--Bucconidae
`--+--+--Ramphastidae
| `--Capitonidae
`--+--Indicatoridae
`--Picidae
The names in square brackets are ones that weren't used in the
paper but which I've included so I can use them in this e-mail. In
particular, the clade I've labelled 'Anomalogonatae' is a little
different from previous usage of this name, but still corresponds to
the bulk of the Anomalogonatae minus the members that have been
shifted to the Metaves plus Cuculidae + Musophagidae, so I feel it's
still a pretty usable name for this clade.
The coverage of Charadriiformes isn't as good as Fain & Houde
(2004), but Leptosomidae and Upupiformes get a look in (Leptosomidae
being especially welcome). Otherwise it's pretty comparable. The tree
looks fairly plausible in that it is generally consistent with other
studies for taxa whose phylogeny is reasonably well known
(Accipitres, Coraciiformes, Piciformes, Suloidea, Procellariiformes,
Caprimulgiformes).
Most noticeable is that the Metaves-Coronaves distinction still
stands! According to the text, the two clades were only resolved as
separate when the beta-fibrinogen sequences were included - not too
surprising, as this was the gene used in Fain and Houde (2004) where
the clades were first recognised. Strangely enough, analysis of the
beta-fibrinogen data alone apparently _didn't_ separate the two
clades, only the combined analysis. _Opisthocomus_ was not sister to
the other Metaves as in Fain & Houde. However, while relationships
within Metaves were essentially unresolved in Fain & Houde, this
analysis did recover monophyly of Caprimulgiformes (incl.
Apodiformes), Columbiformes and Podicipedidae + Phoenicopteridae.
Within Caprimulgiformes, Aegothelidae sister to Apodiformes is in
line with morphological data as suggested by Mayr et al. Note that
the metavian taxa previously included in Gruiformes weren't close to
each other, but as they weren't ever regarded as closely associated
within Gruiformes that's not that surprising.
The tripartite division of Coronaves into Charadriiformes (incl.
Turnicidae), a [mostly] water-bird assemblage and Anomalogonatae is
consistent with Fain & Houde, though Anomalogonatae was not resolved
in the latter (nor was it contradicted). This consistence includes
the inclusion of Cuculidae and Musophagidae in the water-bird
assemblage. Whether or not these two families form a monophyletic
Cuculiformes is not resolved, but it's worth noting that they weren't
close in Fain & Houde (though, again, nor were there any
well-supported nodes separating them IIRC). Also consistent with Fain
& Houde is the exclusion of Otididae and Grues from the main
water-bird assemblage proper. The Cariamidae, which was the basalmost
branch of the water-bird assemblage in Fain & Houde, is here within
the Anomalogonatae - again, this doesn't violate any well-supported
nodes in the former.
Within what might be called the 'core water-birds', the most
interesting result is that Steganopodes is far from monophyletic,
with Pelecanidae forming a clade with Balaenicipitidae and Scopidae
which is in turn associated with Threskiornithidae and Ardeidae,
while _Fregata_ + Suloidea are outside this clade. My question - is
this inconsistent with morphological data or not? In the Scopidae +
(Balaenicipitidae + Steganopodes) topology suggested by Mayr (2003),
how much of the supporting characters are shared between the first
two families and any member of Steganopodes _other_ than _Pelecanus_?
In other words, was _Pelecanus_ pulling the other two in towards an
assumed Steganopodes?
The Anomalogonatae divides basally into two clades whose
composition is a bit of a surprise - the one containing
Passeriformes, Psittaciformes, Falconidae and Cariamidae, while the
other contains Accipitres, Coraciiformes, Piciformes, Bucerotidae,
Upupiformes, Trogonidae, Coliidae, Strigiformes, Cathartidae and
_Leptosomus_. I can't comment too much on these, though I would say
that this division is pretty radical (I've never heard of anything
foreshadowing it). The inclusion of _Leptosomus_ tidies up the major
loose end that was left by Fain and Houde, and it's noteworthy that
while _Leptosomus_ is within Anomalogonatae (not Metaves as was
halfway expected - http://dml.cmnh.org/2004Dec/msg00148.html), it's
nowhere near Coraciiformes proper. Its position is not inconsistent
with an association with Strigiformes, which was another possibility
suggested by Houde in his e-mail to the DML.
I won't comment on the molecular dating - I'm deeply distrustful
of such things, and I doubt that I could say much that would really
add to a discussion (beyond wild mutterings and howls).
Cheers,
Christopher Taylor
>---- Original Message ----
>From: gerarus@westnet.com.au
>To: dinosaur@usc.edu
>Subject: RE: New paper on Neoaves
>Date: Fri, 11 Aug 2006 08:58:15 +0800
>
>>I've just received notification of a new article in _Biology
>Letters_:
>>
>>Per G.P. Ericson, Cajsa L. Anderson, Tom Britton, Andrzej
>Elzanowski,
>>Ulf S. Johansson, Mari Källersjö, Jan I. Ohlson, Thomas J. Parsons,
>>Dario Zuccon & Gerald Mayr. 2006. Diversification of Neoaves:
>>integration of molecular sequence data and fossils. Biology Letters:
>>FirstCite Early Online Publishing (DOI: 10.1098/rsbl.2006.0523).
>>
>>"Patterns of diversification and timing of evolution within Neoaves,
>>which includes almost 95% of all bird species, are virtually
>unknown.
>>On the other hand, molecular data consistently indicate a Cretaceous
>>origin of many neoavian lineages and the fossil record seems to
>>support an Early Tertiary diversification. Here, we present the
>first
>>well-resolved molecular phylogeny for Neoaves, together with
>>divergence time estimates calibrated with a large number of
>>stratigraphically and phylogenetically well-documented fossils. Our
>>study defines several well-supported clades within Neoaves. The
>>calibration results suggest that Neoaves, after an initial split
>from
>>Galloanseres in Mid-Cretaceous, diversified around or soon after the
>>K/T boundary. Our results thus do not contradict palaeontological
>>data and show that there is no solid molecular evidence for an
>>extensive pre-Tertiary radiation of Neoaves."
>>
>> Unfortunately, I don't have access to Biology Letters. If anyone
>>could send me this article, I would be incredibly grateful.
>>Please.....
>>
>> Cheers,
>>
>> Christopher Taylor