Does more sequence data improve estimates of galliform phylogeny? Analyses of a rapid radiation using a complete data matrix

PeerJ
Rebecca T Kimball, Edward L Braun

Abstract

The resolution of rapid evolutionary radiations or "bushes" in the tree of life has been one of the most difficult and interesting problems in phylogenetics. The avian order Galliformes appears to have undergone several rapid radiations that have limited the resolution of prior studies and obscured the position of taxa important both agriculturally and as model systems (chicken, turkey, Japanese quail). Here we present analyses of a multi-locus data matrix comprising over 15,000 sites, primarily from nuclear introns but also including three mitochondrial regions, from 46 galliform taxa with all gene regions sampled for all taxa. The increased sampling of unlinked nuclear genes provided strong bootstrap support for all but a small number of relationships. Coalescent-based methods to combine individual gene trees and analyses of datasets that are independent of published data indicated that this well-supported topology is likely to reflect the galliform species tree. The inclusion or exclusion of mitochondrial data had a limited impact upon analyses upon analyses using either concatenated data or multispecies coalescent methods. Some of the key phylogenetic findings include support for a second major clade within the core phasian...Continue Reading

References

Dec 31, 2015·Molecular Biology and Evolution·Peter A HosnerRebecca T Kimball
Feb 18, 2016·Molecular Phylogenetics and Evolution·Nicholas W PersonsRebecca T Kimball
Jan 1, 2015·Molecular Phylogenetics and Evolution·J G BurleighEdward L Braun
Jun 15, 2014·Molecular Phylogenetics and Evolution·Kelly A MeiklejohnRebecca T Kimball
Oct 5, 2018·Frontiers in Genetics·Shubham K JaiswalVineet K Sharma
Jan 13, 2015·Systematic Biology·Paul O LewisDavid L Swofford

Citations

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Argusianus argus
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GAPDH gene
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