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New Heuristic Methods for Joint Species Delimitation and Species Tree Inference
Brian C. O'Meara
Vol. 59, No. 1 (JANUARY 2010), pp. 59-73
Stable URL: http://www.jstor.org/stable/25677562
Page Count: 15
You can always find the topics here!Topics: Species, Biological taxonomies, Simulations, Topology, Gene flow, Cost structure, Parsimony, Datasets, Speciation, Phylogenetics
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Species delimitation and species tree inference are difficult problems in cases of recent divergence, especially when different loci have different histories. This paper quantifies the difficulty of jointly finding the division of samples to species and estimating a species tree without constraining the possible assignments a priori. It introduces a parametric and a nonparametric method, including new heuristic search strategies, to do this delimitation and tree inference using individual gene trees as input. The new methods were evaluated using thousands of simulations and 4 empirical data sets. These analyses suggest that the new methods, especially the nonparametric one, may provide useful insights for systematists working at the species level with molecular data. However, they still often return incorrect results.
Systematic Biology © 2010 Oxford University Press