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Systematics Section / ASPT

Simmons, Mark P. [1], Reeves, Aaron [1], Davis, Jerrold I. [2].

Character-state space versus rate of evolution in phylogenetic inference.

With o­nly four alternative character states, parallelisms and reversals are expected to occur frequently when using nucleotide characters for phylogenetic inference. Greater available character-state space has been described as o­ne of the advantages of third codon positions relative to first and second codon positions, as well as amino acids relative to nucleotides. We used simulations to quantify how character-state space and rate of evolution relate to o­ne another and how this relationship is affected by differences in: tree topology, branch lengths, rate heterogeneity among sites, probability of change among states, and frequency of character states. Specifically, we examined how inferred tree lengths, consistency and retention indices, and accuracy of phylogenetic inference are affected. Our results indicate that the relatively small increases in character-state space evident in empirical data matrices can provide enormous benefits for accuracy of phylogenetic inference. This advantage may become more pronounced with unequal probabilities of change among states. Although increased character-state space greatly improved the accuracy of topology inference, improvements in the estimation of the correct tree length were less apparent. Accuracy and inferred tree length improved most when character-state space increased initially; further increases provided more modest improvements.

1 - Colorado State University, Department of Biology, Fort Collins, Colorado, 80523-1878, U.S.A.
2 - Cornell University, L.H. Bailey Hortorium, Department of Plant Biology, Ithaca, New York, 14853, U.S.A.

character-state space
amino acid characters
nucleotide characters
character coding
phylogenetic inference
codon positions.

Presentation Type: Paper
Session: 45-3
Location: Cottonwood B (Snowbird Center)
Date: Wednesday, August 4th, 2004
Time: 8:45 AM
Abstract ID:7

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