Ruhfel, Brad , Burleigh, J. Gordon , Gitzendanner, Matthew , Soltis, Douglas , Soltis, Pamela .
From algae to angiosperms–inferring the phylogeny of green plants (Viridiplantae) from 360 plastid genomes.
The rise of next-generation sequencing has produced a wealth of plastid genome data from an increasingly diverse set of taxa. Although these data have been useful for reconstructing the phylogeny of numerous clades of photosynthetic organisms (e.g., angiosperms, algae, and gymnosperms), their usefulness for inferring relationships across green plants (Viridiplantae) is unknown. Viridiplantae originated 700-1500 million years ago and contain an immense diversity of lifeforms, including some of the smallest and largest eukaryotes. Here we explore the limits and challenges of inferring a comprehensive green plant phylogeny from plastid genome data. We analyzed protein coding data from 360 taxa with complete or near complete plastid genome data available from GenBank. Our analyses recover well-supported backbone relationships across the clade and reveal relationships that were not observed in previous analyses of subclades of Viridiplantae. However, very long branches, extreme rate heterogeneity, and base composition biases can influence the results, and we obtained strongly supported, conflicting results due to the use of nucleotide or amino acid characters. We highlight the challenges of using plastid genome data in deep-level phylogenomic analyses and provide a conceptual and phylogenetic framework for future analyses that will likely incorporate plastid genome data for thousands of species.
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1 - University Of Florida, Department Of Biology, P.O. Box 118525, Carr Hall, Room 217, Gainesville, FL, 32611, USA
2 - University of Florida, Biology, P.O. Box 118525, Gainesville, FL, 32611, USA
4 - University Of Florida, Department Of Botany, 220 BARTRAM HALL, Gainesville, FL, 32611, USA
5 - University Of Florida, Florida Museum Of Natural History, PO BOX 117800, Gainesville, FL, 32611-7800, USA, 352/273-1964
Presentation Type: Oral Paper:Papers for Sections
Location: Franklin A/Hyatt
Date: Tuesday, July 10th, 2012
Time: 8:00 AM