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

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. Although 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 a single species and up to 6 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 4 Myr. 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 9 Myr, 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.

Multiple horizontal transfers of nuclear ribosomal genes between phylogenetically distinct grass lineages

“…1B), incorporating preexisting information regarding its speciation and phylogeography (25,27,28) (Table S4). According to this analysis, the likely most ancient transfer event was Panicum 1, because this rDNA type was found in all of the Central Asian and most of the South American taxa (Fig.…”

Phylogeny, geographic distribution, and new taxonomic circumscription of the Crocus reticulatus species group (Iridaceae)

“…but also proved useful to illustrate haplotype relationships at higher taxonomic levels (Bänfer et al, 2006;Jakob and Blattner, 2006;Kiefer et al, 2009;Gurushidze et al, 2010). Here a clear split is visible in nuclear and chloroplast data, separating a clade of taxa occurring in the west and northeast of the distribution area from the clade of Turkish taxa.…”

Dated historical biogeography of the temperate Loliinae (Poaceae, Pooideae) grasses in the northern and southern hemispheres

“…Extrapolations of divergence times across plastid genes could be done as most plastid regions (e. g., ndhF, ir«TL, trnLF) show similar mutation rates in the Poaceae (Gaut, 2002) and the Loliinae . The use of plastid data to infer dated biogeographical scenarios was considered to be partly misleading in Hordeum as the past reticulation history in barleys caused strong incongruence between plastid and nuclear topologies (Jakob and Blattner, 2006). Nonetheless, we followed the procedures suggested by other authors that supported the use of more resolved combined phylogenies, which could also be a better estimate of branch lengths and thus of divergence times, to infer the biogeographical history of the plant lineages (cf.…”