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MBE Advance Access originally published online on November 3, 2008
Molecular Biology and Evolution 2009 26(2):313-326; doi:10.1093/molbev/msn248
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© The Author 2008. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oxfordjournals.org

Research Articles

Toward Resolving Deep Neoaves Phylogeny: Data, Signal Enhancement, and Priors

Renae C. Pratt*, Gillian C. Gibb*, Mary Morgan-Richards*, Matthew J. Phillips{dagger}, Michael D. Hendy* and David Penny*

* Allan Wilson Centre for Molecular Ecology and Evolution, Massey University, Palmerston North, New Zealand
{dagger} Centre for Macroevolution and Macroecology, School of Botany and Zoology, Australian National University, Canberra ACT, Australia

E-mail: r.c.pratt{at}massey.ac.nz.

Accepted for publication October 27, 2008.

We report three developments toward resolving the challenge of the apparent basal polytomy of neoavian birds. First, we describe improved conditional down-weighting techniques to reduce noise relative to signal for deeper divergences and find increased agreement between data sets. Second, we present formulae for calculating the probabilities of finding predefined groupings in the optimal tree. Finally, we report a significant increase in data: nine new mitochondrial (mt) genomes (the dollarbird, New Zealand kingfisher, great potoo, Australian owlet-nightjar, white-tailed trogon, barn owl, a roadrunner [a ground cuckoo], New Zealand long-tailed cuckoo, and the peach-faced lovebird) and together they provide data for each of the six main groups of Neoaves proposed by Cracraft J (2001). We use his six main groups of modern birds as priors for evaluation of results. These include passerines, cuckoos, parrots, and three other groups termed "WoodKing" (woodpeckers/rollers/kingfishers), "SCA" (owls/potoos/owlet-nightjars/hummingbirds/swifts), and "Conglomerati." In general, the support is highly significant with just two exceptions, the owls move from the "SCA" group to the raptors, particularly accipitrids (buzzards/eagles) and the osprey, and the shorebirds may be an independent group from the rest of the "Conglomerati". Molecular dating mt genomes support a major diversification of at least 12 neoavian lineages in the Late Cretaceous. Our results form a basis for further testing with both nuclear-coding sequences and rare genomic changes.

Key Words: Neoaves • mitochondrial genomes • site-stripping • down-weighting • hypothesis testing • avian evolution

Manolo Gouy, Associate Editor


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