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© 2008 Society of Systematic Biologists
Resolving an Ancient, Rapid Radiation in Saxifragales
1 South China Botanical Garden, the Chinese Academy of Sciences Guangzhou 510650, China
2 Department of Botany, University of Florida Gainesville, FL 32611, USA; E-mail: dsoltis{at}botany.ufl.edu
3 Florida Museum of Natural History, University of Florida Gainesville, Florida 32611, USA
4 Department of Ecology and Evolutionary Biology, University of Michigan Ann Arbor, Michigan 48109, USA
5 Department of Horticulture and Landscape Architecture, Washington State University Pullman, Washington 99164, USA
6 Department of Biological Sciences, University of New Orleans New Orleans, Louisiana 70148, USA
7 Current Address: Biology Department, Oberlin College Oberlin, Ohio 44074-1097, USA
Edited by Vincent Savolainen
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Abstract |
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Despite the prior use of 
9000 bp, deep-level relationships within the angiosperm clade, Saxifragales remain enigmatic, due to an ancient, rapid radiation (89.5 to 110 Ma based on the fossil record). To resolve these deep relationships, we constructed several new data sets: (1) 16 genes representing the three genomic compartments within plant cells (2 nuclear, 10 plastid, 4 mitochondrial; aligned, analyzed length = 21,460 bp) for 28 taxa; (2) the entire plastid inverted repeat (IR; 26,625 bp) for 17 taxa; (3) "total evidence" (50,845 bp) for both 17 and 28 taxa (the latter missing the IR). Bayesian and ML methods yielded identical topologies across partitions with most clades receiving high posterior probability (pp = 1.0) and bootstrap (95% to 100%) values, suggesting that with sufficient data, rapid radiations can be resolved. In contrast, parsimony analyses of different partitions yielded conflicting topologies, particularly with respect to the placement of Paeoniaceae, a clade characterized by a long branch. In agreement with published simulations, the addition of characters increased bootstrap support for the putatively erroneous placement of Paeoniaceae. Although having far fewer parsimony-informative sites, slowly evolving plastid genes provided higher resolution and support for deep-level relationships than rapidly evolving plastid genes, yielding a topology close to the Bayesian and ML total evidence tree. The plastid IR region may be an ideal source of slowly evolving genes for resolution of deep-level angiosperm divergences that date to 90 My or more. Rapidly evolving genes provided support for tip relationships not recovered with slowly evolving genes, indicating some complementarity. Age estimates using penalized likelihood with and without age constraints for the 28-taxon, total evidence data set are comparable to fossil dates, whereas estimates based on the 17-taxon data are much older than implied by the fossil record. Hence, sufficient taxon density, and not simply numerous base pairs, is important in reliably estimating ages. Age estimates indicate that the early diversification of Saxifragales occurred rapidly, over a time span as short as 6 million years. Between 25,000 and 50,000 bp were needed to resolve this radiation with high support values. Extrapolating from Saxifragales, a similar number of base pairs may be needed to resolve the many other deep-level radiations of comparable age in angiosperms.
Keywords: Large data sets; long branch attraction; mtDNA; nuclear ribosomal DNA; plastid inverted repeat; rapid radiation; Saxifragales; slowly evolving genes
Received June 9, 2007; Revised August 14, 2007; Accepted September 26, 2007
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