PHYLOGENOMICS AND THE PLACEMENT OF AMBORELLA Coalescent versus Concatenation Methods and the Placement of Amborella as Sister to Water Lilies

—The molecular era has fundamentally reshaped our knowledge of the evolution and diversification of angiosperms. One outstanding question is the phylogenetic placement of Amborella trichopoda Baill., commonly thought to represent the first lineage of extant angiosperms. Here, we leverage publicly available data and provide a broad coalescent-based species tree estimation of 45 seed plants. By incorporating 310 nuclear genes, our coalescent analyses strongly support a clade containing Amborella plus water lilies (i.e., Nymphaeales) that is sister to all other angiosperms across different nucleotide rate partitions. Our results also show that commonly applied concatenation methods produce strongly supported, but incongruent © The Author(s) 2014. Published by Oxford University Press, on behalf of the Society of Systematic Biologists. All rights reserved. For Permissions, please email: [email protected] Systematic Biology Advance Access published July 30, 2014 at H ealth Scences L irary on A uust 8, 2014 http://sysbfordjournals.org/ D ow nladed from