HOME HELP FEEDBACK SUBSCRIPTIONS ARCHIVE SEARCH TABLE OF CONTENTS		QUICK SEARCH:   [advanced] Author: Keyword(s): Year:  Vol:  Page:

This Article Full Text Full Text (PDF) Supplementary Data Submit a response Alert me when this article is cited Alert me when eLetters are posted Alert me if a correction is posted Services Email this article to a friend Similar articles in this journal Alert me to new issues of the journal Download to citation manager Google Scholar Articles by Yuan, Y.-W. Articles by Olmstead, R. G. PubMed Articles by Yuan, Y.-W. Articles by Olmstead, R. G. Agricola Articles by Yuan, Y.-W. Articles by Olmstead, R. G.

Evolution and phylogenetic utility of the PHOT gene duplicates in the Verbena complex (Verbenaceae): dramatic intron size variation and footprint of ancestral recombination¹

Department of Biology, University of Washington, Seattle, Washington 98195 USA

ABSTRACT

A well-resolved species level phylogeny is critically important in studying organismal evolution (e.g., hybridization, polyploidization, adaptive speciation). Lack of appropriate molecular markers that give sufficient resolution to gene trees is one of the major impediments to inferring species level phylogenies. In addition, sampling multiple independent loci is essential to overcome the lineage sorting problem. The availability of nuclear loci has often been a limiting factor in plant species-level phylogenetic studies. Here the two PHOT loci were developed as new sources of nuclear gene trees. The PHOT1 and PHOT2 gene trees of the Verbena complex (Verbenaceae) are well resolved and have good clade support. These gene trees are consistent with each other and previously generated chloroplast and nuclear waxy gene trees in most of the phylogenetic backbone as well as some terminal relationships, but are incongruent in some other relationships. Locus-specific primers were optimized for amplifying and sequencing these two loci in all Lamiales. Comparing intron size in the context of the gene trees shows dramatic variation within the Verbena complex, particularly at the PHOT1 locus. These variations are largely caused by invasions of short transposable elements and frequent long deletions and insertions of unknown causes. In addition, inspection of DNA sequences and phylogenetic analyses unmask a clear footprint of ancestral recombination in one species.

Key Words: ancestral recombination • intron size variation • MITE • PHOT gene duplicates • species-level phylogenetics • Verbena complex

Received for publication 11 April 2008. Accepted for publication 13 June 2008.

FOOTNOTES

¹ The authors thank M. Simmons and two anonymous reviewers for critical comments on this manuscript. This research was supported by a Graduate Fellowship in Molecular Systematics from the University of Washington Department of Biology, an NSF Grant (DEB-0542493) to R.G.O, and an NSF Doctoral Dissertation Improvement Grant DEB-0710026 to R.G.O. for Y.W.Y.

² Author for correspondence (e-mail: colreeze{at}u.washington.edu)