Phylogenetic implications of trans-specific chloroplast DNA sequence polymorphism in New Zealand Gnaphalieae (Asteraceae)

The New Zealand endemic species of Gnaphalieae (Asteraceae) present a bewildering array of morphological forms recalcitrant to phylogenetic analysis using molecular or traditional characters. The chloroplast psbA-trnH intergenic spacer is highly variable in this group, with substitutions distinguishing 18 cpDNA haplotypes distributed among samples of Raoulia species and those of related genera. A subset of haplotypes was combined with sequences of the more slowly evolving trnL intron and trnL-trnF intergenic spacer region and subjected to median network and parsimony analyses. Although a number of chloroplast lineages were resolved, these do not correspond with taxonomic units, nor with groups supported by analysis of morphological characters, nor with groups indicated by nuclear rDNA ITS sequences. These data, considered in the context of morphological character state distribution in the group, suggest a complex set of interrelationships among extant species and genera as currently circumscribed. General implications for phylogeny reconstruction are discussed.