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

Plant phylogenetic estimates are most likely to be reliable when congruent evidence is obtained independently from the mitochondrial, plastid, and nuc lear genomes with all methods of analysis. Here, results are presented from separate and combined genomic analyses of new and previously published dat a, including six and nine genes (8,911 bp and 12,010 bp, respectively) for different subsets of taxa that suggest Amborella + Nymphaeales (water lilie s) are the first-branching angiosperm lineage. Before and after tree-indepe ndent noise reduction, most individual genomic compartments and methods of analysis estimated the Amborella + Nymphaeales basal topology with high sup port. Previous phylogenetic estimates placing Amborella alone as the first extant angiosperm branch may have been misled because of a series of specif ic problems with paralogy, suboptimal outgroups, long-branch taxa, and meth od dependence. Ancestral character state reconstructions differ between the two topologies and affect inferences about the features of early angiosper ms.