Amplified fragment length polymorphisms and sequence data in the phylogenetic analysis of polyploids: multiple origins of Veronica cymbalaria (Plantaginaceae)

doi:10.1111/j.1469-8137.2007.02172.x

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Wiley InterScience

New Phytologist

Volume 176 Issue 2, Pages 481 - 498

Published Online: 26 Jul 2007

Published on behalf of the New Phytologist Trust

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Amplified fragment length polymorphisms and sequence data in the phylogenetic analysis of polyploids: multiple origins of Veronica cymbalaria (Plantaginaceae)

Dirk C. Albach

Institut für Spezielle Botanik, Johannes Gutenberg-Universität Mainz, Bentzelweg 9b, 55099 Mainz, Germany

Author for correspondence: Dirk C. Albach
Tel: +49 61313923169
Fax: +49 61313923524
Email: albach@uni-mainz.de

KEYWORDS

amplified fragment length polymorphism (AFLP) • Bayesian inference • distance analysis • parsimony • phylogenetic analysis • polyploidy • Veronica cymbalaria

New Phytologist (2007) 176: 481–498

ABSTRACT

•
The origin of polyploid Veronica cymbalaria (Plantaginaceae) was investigated using DNA sequence data and amplified fragment length polymorphism (AFLP) fingerprints to reveal the parentage of this taxon. The use of AFLP fingerprints in phylogenetic analysis is problematic and various methods have therefore been compared.
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DNA sequence data (for the internal transcribed spacer (ITS) region and the plastid trnL-F region (trnL intron, 3'exon, and trnL-F spacer)) and polymerase chain reaction–restriction fragment length polymorphism (PCR-RFLP) analysis of the ITS region suggested a reliable hypothesis for the evolution of the V. cymbalaria complex. This hypothesis allowed evaluation of the effect of different distance measures (Jaccard and Nei–Li) in phenetic, character-state weighted parsimony, and Bayesian analyses of AFLP markers.
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The study establishes that tetraploid V. cymbalaria originated at least twice in the eastern Mediterranean, with one parent differing in the two separate origins. Hexaploid V. cymbalaria originated even more often. The results illustrate that even subtle differences in the analyses of AFLP markers can lead to drastically different conclusions.
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The study reveals multiple origins of a Mediterranean polyploid species. Furthermore, it demonstrates that the analysis of a complex marker system such as AFLP fingerprints using only one type of analysis can easily be misleading.