Pl. Syst. Evol. 215:85-99 (1999) --Plant. Systematics and Evolution © Springer-Verlag 1999 Printed in Austria The use of a non-coding region of chloroplast DNA in phylogenetic studies of the subtribe Sonchinae (Asteraceae: Lactuceae) SEUNG-CHUL KIM, DANIELJ. CRAWFORD,ROBERT K. JANSEN, and ARNOLDO SANros-GUERRA Received July 10, 1997; in revised version November 18, 1997 Key words: Sonchinae, Asteraceae. - cpDNA, non-coding region (psbA-trnHöU6), phylogeny. Abstract: The systematic utility of sequences from a non-coding region of chloroplast DNA (cpDNA) between psbA and trnH (6v6) was examined by assessing phylogenetic relationships in subtribe Sonchinae (Asteraceae: Lactuceae). Primers constructed against highly conserved regions of tRNA genes were used for PCR amplification and sequencing. The psbA-trnH intergenic spacer contains several insertions and deletions (indels) in Sonchinae with the length varying from 385 to 450bp. Sequence divergence ranges from 0.00% to 7.54% within Sonchinae, with an average of 2.4%. Average sequence divergence in Sonchus subg. Sonchus is 2.0%, while the mean for subg. Dendrosonchus and its close relatives in Macaronesia (the woody Sonchus alliance) is 1.0%. Our results suggest that this region does not evolve rapidly enough to resolve relationships among closely related genera or insular endemics in the Asteraceae. The phylogenetic utility of psbA-trnH sequences of the non-coding cpDNA was compared to sequences from the ITS region of nuclear ribosomal DNA. The results suggest that ITS sequences evolve nearly four times faster than psbA-trnH intergenic spacer sequences. Furthermore, the ITS sequences provide more variable and phylogenetically informative sites and generate more highly resolved trees with more strongly supported clades, and thus are more suitable for phylogenetic comparisons at lower taxonomic levels than the psbA-trnH intergenic chloroplast sequences. Chloroplast DNA (cpDNA) has been used extensively to investigate phylogenetic relationships at a wide range of taxonomic levels in plants. Chloroplast genes are now used routinely to infer phylogenies because direct sequencing of polymerase chain reaction (PCR) products makes it relatively easy to obtain sequence data. DNA sequences from several chloroplast genes, such as rbcL, matK, ndhF, atpB, and rps2, have been used to estimate phylogenetic relationships at higher taxonomic levels. For example, rbcL has been widely used at the family level or above (PrUCE & PAL~R 1993, SMrrn & al. 1993, SCOTLAND & al. 1995, SOLrIS & al. 1995, PLtmKErT & al. 1995). Several studies have also shown that rbcL can be used