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Systematics Section / ASPT

Zhang, Li-Bing [1], Simmons, Mark P. [1], Reeves, Aaron [1].

How can 3rd codon positions outperform 1st and 2nd codon positions in phylogenetic inference?.

Greater phylogenetic signal is often found in third codon positions of protein-coding genes relative to their corresponding first and second codon positions, even for early derived (“basal”) clades. This greater phylogenetic signal is surprising given third codon positions’ faster rate of evolution, which results in multiple hits that can obscure synapomorphy and result in long-branch attraction. We used the Soltis et al. (2000) data matrix of atpB and rbcL from 567 seed plants to quantify how each of six factors (observed character-state space, frequencies of character states, substitution probabilities among states, rate heterogeneity among sites, overall rate of evolution, and number of parsimony-informative characters) contributed to this phenomenon. Each of these six factors was estimated from the original data matrix for parsimony-informative first and second codon positions separately from parsimony-informative third codon positions. One of the most parsimonious trees found was used as the constraint topology, and branch lengths were estimated using likelihood-based distances. Each of these six factors was simulated independently of one another, as well as in all possible combinations. Performance of phylogenetic inference was measured by subtracting the number of clades incorrectly resolved from the number of clades correctly resolved in jackknife trees. Our results indicated that differential frequencies of character states was the most limiting of the factor simulated – for all three codon positions. Differential frequencies of character states and differential substitution probabilities among states were advantages for first and second codon positions. In contrast, differential numbers of observed character states, differential rate heterogeneity among sites, the greater number of parsimony-informative characters, and the higher overall rate of evolution were advantages of third codon positions.

1 - Colorado State University, Department of Biology, Fort Collins, Colorado, 80523-1878, U.S.A.

codon positions
phylogenetic inference
character-state space
rate heterogeneity
seed plants.

Presentation Type: Paper
Session: 45-5
Location: Cottonwood B (Snowbird Center)
Date: Wednesday, August 4th, 2004
Time: 9:15 AM
Abstract ID:91

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