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Abstract Detail

Systematics Section / ASPT

Bell, Hester L. [1], Porter, J. Mark [1], Columbus, J. Travis [1].

Patterns of molecular evolution in ndhF: observations from Chloridoideae (Poaceae).

AS a putatively single-copy, protein-coding, chloroplast gene, ndhF is widely used for phylogenetic reconstruction and is informative in many groups including Poaceae. ndhF codes for a transmembrane polypeptide that is part of the Ndh complex implicated in photorespiration. Recent work (Lascano et al. 2003, Casano et al. 2004) has provided insights on topology of the Ndh complex within the thylakoid membrane and on function and topology of the NDH-F subunit.
We sequenced ndhF for 82 genera from all tribes and subtribes of Chloridoideae and, for an outgroup, representatives of the other subfamilies of the PACCAD clade of Poaceae. An ancestral sequence for ndhF was estimated by constraining the ndhF data set to a tree derived from noncoding trnL-F (cpDNA) sequences representing the same sampling of taxa. Codon usage was recorded for the ancestral sequence and for a subset of 18 taxa representing all major clades in the phylogeny. G-tests were performed on the five four-fold degenerate codon groups to test: (1) if third position nucleotides from extant taxa are present in equal frequencies (Ho1) and (2) if there is no significant difference between estimated ancestral and observed frequencies (Ho2). We reject Ho1; the pattern of observed codon usage strongly favors the use of A or T in the third position. We fail to reject Ho2; codon usage in extant species likely reflects the usage that existed in the common ancestor of Chloridoideae. We observe patterns of invariance, saturation, and synonymous and nonsynonymous substitutions in different functional domains of the ndhF polypeptide. These patterns are mapped onto a maximum likelihood tree derived from Bayesian analysis of ITS and trnL-F for the same sampling of taxa to illustrate the suites of molecular characters that support clades. What do Chloridoideae tell us about the evolution of ndhF?

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1 - Rancho Santa Ana Botanic Garden, 1500 North College Avenue, Claremont, California, 91711, USA

codon usage
protein topology
molecular evolution
synonymous substitution
nonsynonymous substitution.

Presentation Type: Oral Paper:Papers for Sections
Session: 73-7
Location: 106/Ayres
Date: Wednesday, August 2nd, 2006
Time: 2:30 PM
Abstract ID:350

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