BARKMAN, TODD J., JOEL R. MCNEAL, GORDON CHENERY, AND CLAUDE W. DEPAMPHILIS.* Department of Biology and Institute of Molecular Evolutionary Genetics, Pennsylvania State University, University Park, PA 16802 and Montomery Bell Academy, Nashville, TN 37205. - Evolutionary genomic analyses converge on basal angiosperm phylogeny.
Plant evolutionary genomic analyses have the greatest potential to
reveal phylogeny when congruent evidence is obtained independently
from the plastid, mitochondrial, and nuclear genomes with all methods
of analysis. Incongruent genomic compartment estimates were obtained
in analyses of previously assembled multigene data sets for basal
angiosperms due in part to a combination of suboptimal outgroup
choice, phylogenetic noise, and incorrect homology assignment. In
spite of these potential sources of systematic error, method of
analysis had the strongest effect on the results obtained. In this
study, results are presented from combined analyses of 3 mitochondrial
(cox1, atpA, matR), 2 plastid (rbcL, atpB) and 1 nuclear gene (18S)
that suggest Amborella+ Nymphaeales as the first-branching angiosperm
lineage. Individual genomic compartments and most methods of analysis
estimated the Amborella+Nymphaeales topology with high support.
Surprisingly, unweighted parsimony alone estimated Amborella-only as
the first branching angiosperm, but support for this result was low
after noise reduction. Ancestral character state reconstructions
differ between the two topologies and profoundly affect inferences
about angiosperm evolution. Relative Apparent Synapomorphy Analysis
(RASA)-based data exploration was a critical step involved in these
analyses and illustrated the advantage of evaluating data prior to
formal phylogenetic study.
Key words: Amborella, atpA, cox1, evolutionary genomics, Nymphaeales, RASA