Randle, Christopher , Freudenstein, John .
The effect of within-replicate search strategies on jackknife support of clades of different size.
Empirical phylogenetic studies demonstrate a correlation between clade size and Bayesian clade support, with large and small clades often receiving greater support than clades of intermediate size. This is not surprising in that a non-uniform prior on topologies induces just such a relationship on the prior probabilities of component clades. What is surprising is that the same relationship exists for parsimony jackknife, though no such prior on topologies is explicitly included in their estimation. This surprising correlation may be due in large part to homoplasy; theoretically, jackknife values should be uniform on clades of any size supported by the same number of uncontraverted synapomorphies. Within-replicate search strategy may have substantial effects on the inference of jackknife support. In general, less thorough within-replicate search strategies yield lower jackknife support values because suboptimal trees sampled from these replicates will be randomized in respect to each other. This randomization of inferred topologies across replicates should mirror the effect on clade support induced by the uniform topology in Bayesian inference. In this study we investigate the effect of within-replicate search strategy on jackknife support across clades of different size, using two well-characterized empirical data sets. Search strategies differed in 1) the number of random addition searches per replicate, 2) the number of trees held during searching, 3) the number of trees retained from each replicate, 4) the branch-swapping algorithm used, and 5) how trees were summarized across replicates.
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1 - Sam Houston State University, Department of Biological Sciences, 1900 Avenue I, Huntsville, TX, 77340, USA
2 - Ohio State University, MUSEUM OF BIOLOGICAL DIVERSITY, 1315 KINNEAR RD, COLUMBUS, OH, 43212-1157, USA
Presentation Type: Oral Paper:Papers for Sections
Location: Lindell B/Chase Park Plaza
Date: Wednesday, July 13th, 2011
Time: 9:30 AM