DOI: 10.5061/dryad.0nn45
title: Data from: Another look at the root of the angiosperms reveals a familiar tale

description: Since the advent of molecular phylogenetics more than 25 years ago, a
 major goal of plant systematists has been to discern the root of the
 angiosperms. While most studies indicate that Amborella trichopoda is
 sister to all remaining extant flowering plants, support for this position
 has varied with respect to both the sequence data sets and analyses
 employed. Recently, Goremykin et al. (2013) questioned the
 “Amborella-sister hypothesis” using a “noise-reduction” approach and
 reported a topology with Amborella + Nymphaeales (water lilies) sister to
 all remaining angiosperms. Through a series of analyses of both plastid
 genomes and mitochondrial genes, we continue to find mostly strong support
 for the Amborella-sister hypothesis and offer a rebuttal of Goremykin et
 al. (2013). The major tenet of Goremykin et al. is that the
 Amborella-sister position is determined by noisy data – i.e. characters
 with high rates of change and lacking true phylogenetic signal. To
 investigate the signal in these noisy data further, we analyzed the
 discarded characters from their noise-reduced alignments. We recovered a
 tree identical to that of the currently accepted angiosperm framework,
 including the position of Amborella as sister to all other angiosperms, as
 well as all other major clades. Thus, the signal in the “noisy” data is
 consistent with that of our complete data sets – arguing against the use
 of their noise-reduction approach. We also determined that one of the
 alignments presented by Goremykin et al. yields results at odds with their
 central claim – their data set actually supports Amborella as sister to
 all other angiosperms, as do larger plastid data sets we present here that
 possess more complete taxon sampling both within the monocots and for
 angiosperms in general. Previous unpartitioned, multi-locus analyses of
 mtDNA data have provided the strongest support for Amborella + Nymphaeales
 as sister to other angiosperms. However, our analysis of third codon
 positions from mtDNA sequence data also supports the Amborella-sister
 hypothesis. Finally, we challenge the conclusion of Goremykin et al. that
 the first flowering plants were aquatic and herbaceous, reasserting that
 even if Amborella + water lilies, or water lilies alone, are sister to the
 rest of the angiosperms, the earliest angiosperms were not necessarily
 aquatic and/or herbaceous.
description: Supplemental data;
 alignments & treesArchive
 2.zipS15236-taxon,
 58,944-character alignment sorted according to pairwise
 distances.S16S16. ML tree resulting
 from 236-taxon sorted alignment with the most variable 22% of characters
 removed.S17S17. 222-taxon,
 58,860-character alignment sorted according to pairwise
 distances.S18S18. ML tree resulting
 from 222-taxon sorted alignment with the most variable 35% of characters
 removed.Figure
 S1Per-site likelihoods
 calculated from ML trees based on a 17-gene region alignment from Soltis
 et al. (2011). Values above 0 are sites that support Amborella sister to
 all other extant angiosperms, and values below 0 support Amborella sister
 to Nymphaeales.Fig.
 S1.pdfFigure
 S2Per-site likelihoods
 calculated from ML trees based on the 13-gene region alignment (4 mtDNA
 genes excluded) of Soltis et al. (2011). Values above 0 are sites that
 support Amborella sister to angiosperms, and values below 0 support
 Amborella sister to Nymphaeales.Fig.
 S2.pdf