MBE Advance Access published online on November 3, 2008
Molecular Biology and Evolution, doi:10.1093/molbev/msn248
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Research Article |
Towards resolving deep Neoaves phylogeny: data, signal enhancement and priors
1 Allan Wilson Centre for Molecular Ecology and Evolution, Massey University, Private Bay 11-222, Palmerston North, New Zealand
2 Centre for Macroevolution and Macroecology, School of Botany and Zoology, Australian National University, Canberra ACT, Australia
Author for correspondence: r.c.pratt{at}massey.ac.nz, Phone:+64 6 350 9099 extn 7626, Fax:+64 6 350 5626
Received for publication August 17, 2008. Revision received October 25, 2008. Accepted for publication October 27, 2008.
We report three developments towards 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 datasets. 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 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 in 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 mitochondrial 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
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