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@ARTICLE{TreeBASE2Ref18949, author = {Michael James Moore and Nasr S. Hassan and Matthew A. Gitzendanner and Riva Bruenn and Matthew Croley and alexia vandeventer and James Horn and Amit Dhingra and Samuel F Brockington and Maribeth Latvis and Jeremy Ramdial and Roolse Alexandre and Ana Piedrahita and Zhenxiang Xi and Charles C. Davis and Pamela S. Soltis and Douglas E. Soltis}, title = {Analysis of a plastid inverted repeat supermatrix for 246 taxa improves confidence in deeper level angiosperm relationships.}, year = {2011}, keywords = {Angiosperm Tree of Life, plastid inverted repeat, phylogenetics, large data sets}, doi = {10.1086/658923}, url = {http://}, pmid = {}, journal = {International Journal of Plant Sciences}, volume = {172}, number = {4}, pages = {541--558}, abstract = {Recent studies employing complete plastid genome sequences have helped clarify the backbone phylogeny of angiosperms. However, the relatively limited taxon sampling in these studies has left several major clades poorly represented, precluding resolution of some regions of angiosperm phylogeny with strong support. Other recent work has suggested that the 25,000 bp plastid inverted repeat (IR) region may be a valuable source of characters for resolving these remaining problematic nodes. Consequently we constructed a data set of all available angiosperm IR sequences, resulting in a matrix of 24,702 aligned bases and 246 accessions, including 21 newly sequenced taxa. Maximum likelihood analyses of these data yielded a generally well-supported topology that was highly congruent with recent trees based on complete plastid genome sequences. Notably, IR analyses resolve Pentapetalae into three well-supported clades: (1) superasterids (including Santalales, Caryophyllales, Berberidopsidales, and Asteridae), (2) superrosids (including Vitales, Saxifragales, and Rosidae), and (3) Dilleniaceae, whose position as sister to remaining Pentapetalae had the highest maximum likelihood bootstrap support yet obtained for this recalcitrant clade using character-rich data sets. These results provide important new evidence for a stable, well-supported phylogenetic framework for angiosperms, and demonstrate the usefulness of IR data at deeper levels of angiosperm phylogeny.} }