Data from: Phylogeny of Saxifragales (angiosperms, eudicots): analysis of a rapid, ancient radiation
Fishbein, Mark; Hibsch-Jetter, Carola; Soltis, Douglas E.; Hufford, Larry (2009), Data from: Phylogeny of Saxifragales (angiosperms, eudicots): analysis of a rapid, ancient radiation, Dryad, Dataset, https://doi.org/10.5061/dryad.684
Rapid, ancient radiations pose one of the most difficult challenges for phylogenetic estimation. We employed DNA sequence data comprising 9,006 aligned bp from five genes (chloroplast atpB, matK, rbcL, and 18S and 26S nrDNA) to elucidate relationships among major lineages of Saxifragales (angiosperms, eudicots). These relationships were poorly supported in prior studies, apparently because these lineages originated in rapid succession. Using an array of methods that explicitly incorporate assumptions about evolutionary process (weighted maximum parsimony, maximum likelihood, LogDet/paralinear transformed distances), we show that the initial diversification of Saxifragales was indeed rapid. We suggest that the poor resolution of our best phylogenetic estimate is not due to violations of assumptions or the combination of data partitions with conflicting histories or processes. We show that estimated branch lengths during the initial diversification are exceedingly short and we estimate that acquiring sufficient sequence data to resolve these relationships will require an extraordinary effort (~107 bp), assuming a linear increase in branch support with branch length. However, our simulation of much larger data sets containing a similar distribution of phylogenetic signal as the five sampled gene sequences suggests a limit to achievable branch support. We use statistical tests of differences in the likelihoods of topologies to evaluate whether the initial radiation of Saxifragales involved the simultaneous origin of major lineages. Our results are consist with predictions that resolving branching order of rapid, ancient radiations requires sampling characters that evolved rapidly at the time of the radiation, but have subsequently experienced a slower evolutionary rate.