Species–level phylogeny of Allium subgenus Melanocrommyum: Incomplete lineage sorting, hybridization and trnF gene duplication

Abstract

AbstractNoncoding chloroplast DNA sequences are widely employed markers in plant species–level phylogenetics and phylogeography. However, chloroplast capture (hybridization) and incomplete sorting of ancestral lineages could confound phylogenetic inference using chloroplast DNA. Recently, we studied the phylogeny of Allium subg. Melanocrommyum based on nuclear rDNA internal transcribed spacer (ITS) sequences and showed that, although the subgenus is monophyletic, most sections are either para– or polyphyletic. To get insights from the chloroplast genome we sequenced the plastid trnL–trnF region in 434 individuals representing 100 species of A. subg. Melanocrommyum and found 74 chloroplast haplotypes. The sequences were analyzed using tree–based (Bayesian and maximum parsimony) and network–based (statistical parsimony network) approaches. The analyses revealed high level of chloroplast haplotype sharing among up to 15 species, as well as presence of several closely related haplotypes within single species. Several characteristics of the data violate the main assumptions of standard tree building methods that is the persistence of ancestral haplotypes and their co–existence with descendant alleles as well as multifurcating relationships among these alleles. The taxon groups inferred from chloroplast trnL–trnF sequence analyses were congruent with the nuclear phylogeny. Thus, bi– and uniparentally inherited datasets strongly contradict the morphology–based taxonomic classification of A. subg. Melanocrommyum. Also, the present study (1) reports a trnF gene duplication in A. subg. Melanocrommyum, (2) infers few putative homoploid hybrid taxa, and (3) shows that natural interspecies hybrids occur rarely in the subgenus. Generally, our data strongly advocate including multiple accessions per species in species–level phylogenetic studies, and show the advantages of networks over tree building methods for analyzing sequences from noncoding chloroplast loci in closely related species.