RE: New paper on Neoaves

[Tim Williams <twilliams_alpha@hotmail.com>]

Christopher Taylor wrote:

>     The genes used for the tree are c-myc, RAG-1, myoglobin, 
> beta-fibrinogen and ornithine decarboxylase - 5007bp in total - under 
> Bayesian analysis.

> From the article:

"In concordance with other recent analyses (Sibley & Ahlquist 1990; Cracraft 
et al. 2004; Fain & Houde 2004), our data recover a clade (figure 1, node 4) 
that includes the secretarybird and accipitrid diurnal birds of prey 
(osprey, hawks and allies) to the exclusion of falcons. This grouping is 
recovered in separate analyses of four of the five investigated genes. The 
New World vultures clearly have their affinity with other raptors and not 
with storks (contra, e.g. Sibley & Ahlquist 1990)."

One question to keep in mind is: Do the analyses that incorporate single 
gene regions yield the same or similar topology as the combined dataset, but 
with less support; or do they yield a very different topology to the 
combined dataset tree, with strong support?  In other words, does the tree 
based on a combined dataset (=5007 bp drawn from five different gene 
regions) improve the resolution of each of the single-gene trees, or does it 
contradict these single-gene trees?  I'd hate to think that there is a 
belief that you can 'improve' the phylogenetic signal simply by expanding 
the dataset (=stringing together more and more DNA sequences).

Also, are each of the single-gene trees consistent?  Individual gene regions 
may be better at capturing divergence at a certain level, which means that 
you're going to get a very muddled phylogenetic signal if you simply string 
these genes together.

>     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'm not ready to give up on a monophyletic Falconiformes quite yet.  I'm 
also a little suspicious of the fact that the analysis failed to recover a 
monophyletic Palaeognathae, based on _Apteryx_ and _Rhea_.  Perhaps greater 
sampling of the palaeognaths could have solved this; but this begs the 
question, how many other clades were not recovered because of inadequate 
taxon sampling?  As a general principle, does increased taxon sampling even 
help?  I'm not certain it does.  If a gene is unable to capture the 
phylogenetic signal, or the analysis is unable to tease out this signal, no 
amount of taxa will improve the situation.

Cheers

Tim