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MBE Advance Access published online on June 5, 2006
Molecular Biology and Evolution, doi:10.1093/molbev/msl018
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© The Author 2006. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oxfordjournals.org
Accepted May 19, 2006

Research Article

A Chloroplast Genealogy of Hordeum (Poaceae): Long-term Persisting Haplotypes, Incomplete Lineage Sorting, Regional Extinction, and the Consequences for Phylogenetic Inference

Sabine S. Jakob 1 and Frank R. Blattner 1 *

1 Leibniz Institute of Plant Genetics and Crop Science (IPK), D-06466 Gatersleben, Germany

* To whom correspondence should be addressed.
Frank R. Blattner, E-mail: blattner{at}ipk-gatersleben.de


  Abstract

To analyze reasons for inconclusive results of earlier chloroplast phylogenies in the grass genus Hordeum we established a genealogy of chloroplast haplotypes by sequencing the trnL-trnF region in 875 individuals, covering all 31 species of the genus. While the outcomes of phenetic and parsimony analyses of 88 haplotypes were ambiguous, a network approach showed that in Hordeum ancient chloroplast types co-occur with their descendants. Moreover, we found up to 18 different chloroplast haplotypes within single species and up to six species sharing single haplotypes. Persisting polymorphisms together with incomplete lineage sorting occurred preferentially in the rapidly speciating New World taxa of the genus, where ancient chloroplast types have survived for at least four million years. Lineages-through-time plots and a high number of missing chloroplast haplotypes indicated far reaching extinction of chloroplast lineages in Europe and particularly the Mediterranean. Survival of these lineages in East Asia and North America resulted in chloroplast relationships that markedly differed from nuclear estimations of species relationships. Thus, even for the deepest splits in the genus, reaching back more than nine million years, no safe phylogenetic inference from chloroplast data is possible in Hordeum. The chloroplast genealogy, however, revealed biogeographic patterns and indicated processes involved in speciation in Hordeum. We conclude that the described phenomena are not restricted to Hordeum, and that the knowledge of the chloroplast relationships within a genus is indispensable to prevent misinterpretation of phylogeographic data within single species.

Keywords: chloroplast genealogy; extinction; Hordeum; incomplete lineage sorting; phylogeography; trnL-F; speciation rates.
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