Infrageneric phylogenies: a comparison of chloroplast-expressed glutamine synthetase, cytosol-expressed glutamine synthetase and cpDNA maturase K in Passiflora

Abstract

The development of new molecular markers presenting adequate variation to clarify the relationships among closely related species remains an important issue in the field of phylogenetics. The marker most commonly used for interspecific phylogenies is the internal transcribed spacers (ITS) region of the nuclear ribosomal genes (Baldwin et al., 1995). Although this region has proved useful for the resolution of relationships among different lineages (Bell and Patterson, 2000; Compton et al., 1998; Esselman et al., 1999; Torrell et al., 1999), its use exhibits limitations in the case of closely related species, particularly when recent radiation events are involved (Ganders et al., 2000; Senchina et al., 2003; Vargas et al., 1998; Yockteng et al., 2003). In the last decade, a range of chloroplast and mitochondrial markers have been developed for phylogenetic purposes at low taxonomic levels (Demesure et al., 1995; Dumolin-Lapegue et al., 1997; Taberlet et al., 1991). Specifically, non-coding regions of the chloroplast genome have displayed an adequate level of variation. However, the phylogenies based on cytoplasmic sequences reflect an evolutionary history inherited uniparentally, which may differ from the species phylogeny (Doyle, 1992; Soltis et al., 1992). For this reason, it is considered that the organismal phylogeny is best estimated using a combination of nuclear and cytoplasmic markers (Doyle, 1992; Moritz and Hillis, 1996). In parallel, low-copy nuclear genes have demonstrated a great potential to improve the resolution and the robustness of plant phylogenetic reconstruction (Emsh-