Independent and combined analyses of sequences from all three genomic compartments converge on the root of flowering plant phylogeny

Todd J. Barkman, Gordon Chenery1, Joel R. McNeal, James Lyons-Weiler, Wayne J. Ellisens, G. Moore, Andi D. Wolfe, & Claude W. dePamphilis

Dept. of Biology, Institute of Molecular Evolutionary Genetics, and Life Science Consortium, Pennsylvania State University, University Park, PA 16802;

1Montgomery Bell Academy, Nashville, TN 37205.

Plant phylogenetic estimates are most reliable when congruent evidence is obtained independently from the mitochondrial, plastid, and nuclear genomes with all methods of analysis. Here, results are presented from separate and combined genomic analyses of new and previously published data, including six and nine genes (8,911 bp and 12,010 bp, respectively) for different subsets of taxa that suggest Amborella + Nymphaeales (water lilies) are the first-branching angiosperm lineage. Before and after tree-independent noise reduction, most individual genomic compartments and methods of analysis estimated the Amborella + Nymphaeales topology with high support. Previous phylogenetic estimates placing Amborella alone as the first extant angiosperm branch may have been misled due to a series of specific problems with paralogy, suboptimal outgroups, long branch taxa, and method dependence. Ancestral character state reconstructions differ between the two topologies and profoundly affect inferences about ancestral features of angiosperms.

Nymphaea sp.