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Toward resolving deep neoaves phylogeny : data, signal enhancement, and priors

Pratt, R.C., Gibb, G.C., Morgan-Richards, M., Phillips, M.J., Hendy, M.D., & Penny, D. (2008) Toward resolving deep neoaves phylogeny : data, signal enhancement, and priors. Molecular Biology and Evolution, 26(2), pp. 313-326.

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Abstract

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.

Impact and interest:

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39 citations in Web of Science®

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ID Code: 50540
Item Type: Journal Article
Keywords: Neoaves, Mitochondrial genomes, Site-stripping, Downweighting, Hypothesis testing, Avian evolution
DOI: 10.1093/molbev/msn248
ISSN: 1537-1719
Subjects: Australian and New Zealand Standard Research Classification > BIOLOGICAL SCIENCES (060000) > GENETICS (060400)
Divisions: Current > QUT Faculties and Divisions > Science & Engineering Faculty
Deposited On: 24 May 2012 07:50
Last Modified: 26 Jun 2014 13:03

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