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Re: New Phylogeny of Birds in PLoS ONE



> Tis is probably because I don't
> really understand the nitty-gritty of these sorts of
> analyses, but why only 32 species?  

It's simply negligent if tree resilience to selective taxon pruning is not 
tested:
Wang et al (2012) "Testing Hypotheses about the Sister Group of the 
Passeriformes Using an Independent 30-Locus Data Set" MolBiolEvol 29(2): 
737-750 
http://people.biology.ufl.edu/rkimball/publications_files/Wangetal.2012.MolBiolEvol.pdf

They cite it but give no indication that they took this effect into account, 
treating it as something that can be fixed with "more characters". But Wang et 
al show the effect is more dependent on taxon sampling, not on characters 
sampling if anything.

It makes a lot of difference whether you include tropicbirds or not, mousebirds 
or not (this was specifically tested by Wang et al; my results concur with 
theirs), whether you include Tyto, Tyto and Phodilus, or no tytonids at all, 
etc. 
Barn owls are especially insidious, given 2 tytonids are often necessary to 
recover monophyletic Strigiformes at all (the tytonid-strigid split is very 
deep, earliest Paleogene I'd guess). Using 1 vs 0 tytonids has an annoying 
tendency to completely alter the "landbirds" part of the tree (I tested this 
with the Hackett et al dataset). But in the latter respect, Leptosomus, Cariama 
and trogons are even worse, and interestingly Eurypyga/Rhynochetos have a 
similar effect though they are *not* in the "landbirds" clade AFAICT.

Essentially, what I found is "landbirds" and to a lesser extent Aeqornithes 
internal phylogeny switches between 3 more-or-less discrete states depending 
not on character sample but on taxon sample and differing most significantly in 
the position of Passeriformes.
IONO whether this is publishable since it is basically just a controlled 
reanalysis of Hackett et al (2008) bearing in mind Wang et al (2012) so I'll 
just put it in my thesis (ATM I estimate to be done with that mid-2014 or so).


FWIW a similar effect has been noted for osteological data. Coliiformes are 
also 
e here, compare:
Zelenkov & Dyke (2008) "The fossil record and evolution of mousebirds (Aves: 
Coliiformes)" Palaeontology 51(6): 1403-1418.
Ksepka et al (2009): "Affinities of Palaeospiza bella and the phylogeny and 
biogeography of mousebirds (Coliiformes)" Auk 126(2): 245-259.
Ksepka & Clarke (2010): "New fossil mousebird (Aves: Coliiformes) with feather 
preservation provides insight into the ecological diversity of an Eocene North 
American avifauna" ZoolJLinnSoc 160(4): 685–706.

It can also be seen in (pan)Psittaciformes:
Mayr et al (2010) "Quercypsitta-Like Birds from the Early Eocene of India 
(Aves, Psittaciformes)" JVertebrPaleontol 30(2):467-478.
Ksepka et al (2011) "Stem Parrots (Aves, Halcyornithidae) from the Green River 
Formation and a Combined Phylogeny of Pan-Psittaciformes" JPaleontol 85(5): 
835-854.

And in Strisores:
Mayr (2005) "A new cypselomorph bird from the Middle Eocene of Germany and the 
early diversification of avian aerial insectivores" Condor 107(2): 342–352. 
http://www.senckenberg.de/files/content/forschung/abteilung/terrzool/ornithologie/cypselomorph.pdf
Mayr (2005) "A Fluvioviridavis-like bird from the Middle Eocene" CanJEarthSci 
42(11): 2021-2037. 
http://www.senckenberg.de/files/content/forschung/abteilung/terrzool/ornithologie/eurofluvioviridavis.pdf
Nesbitt et al (2011) "Podargiform Affinities of the Enigmatic Fluvioviridavis 
platyrhamphus and the Early Diversification of Strisores ("Caprimulgiformes" + 
Apodiformes)" PLoS ONE 6(11): e26350. 
http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0026350

I am presently building matrices to test this effect for osteology data - 
whether it is genuine as in sequence data or whether it results from 
fragmentary hypodigm, and if the later can be overcome by partitioning the 
data. But I'm still in the early stages; this summer I might be able to tell 
you more.



Regards,


Eike