PHYLOGENETIC INFERENCE Leigh A. Johnson andIN SAXIFRAGACEAE Douglas E. Soltis2SENSU STRICTO AND GILIA(POLEMONIACEAE) USINGmatK SEQUENCES'A BSTRACT Comparative sequencing of the maturase-encoding chloroplast gene matK has great potential for reconstructingphylogenetic relationships not only within families, but also within genera of land plants. This gene of 1550 bp iseasily amplified due to highly conserved, flanking coding regions that include the trnK exons, rpsl6, and psbA.Several available sequencing primers also have wide applicability. Parsimony analysis of 45 matK sequences repre-senting Saxifragaceae sensu stricto provides a level of resolution comparable to that obtained via chloroplast DNArestriction site analysis. Furthermore, this analysis suggests relationships among genera and species that are highlyconcordant with the results of separate analyses of rbcL sequences and chloroplast DNA restriction sites, and withthose of combined analyses of these three chloroplast DNA data sets. Parsimony analysis of 31 matK sequencesrepresenting ail six sections of Gilia (Polemoniaceae) and 10 allied genera provides strong evidence for the polyphylyof Gilia and suggests relationships among sections of Gilia that are highly concordant with a recent ITS sequenceanalysis of the Polemoniaceae. Our analyses suggest that matK sequences are not strongly biased toward transitions,and the frequency of mutations at the first and second codon positions approach the frequency of mutations in thethird codon position. Investigation of the chloroplast genome, eitherthrough analysis of restriction site mutations, struc-tural rearrangements, or DNA sequences, has dom-inated plant molecular systematic research duringthe past decade. These approaches have provenextremely useful in addressing a broad range ofsystematic and evolutionary questions at ail levelsof taxonomic hierarchy. Of these approaches, com-parative sequencing of chloroplast, as well as nu-clear, genes has become particularly popular inrecent years, due in large part to the relative easeof generating sequences and the unambiguity ofthe data. The large number of recent systematicstudies employing sequencing of the chloroplastgene rbcL attests to the enormous phylogeneticpotential of comparative sequencing (e.g., Bruns-feld et al., 1994; Chase et al., 1993; Conti et al.,1993; Donoghue et al., 1992; Gadek & Quinn,1993; Giannasi et al., 1992; Kim et al., 1992;Kron & Chase, 1993; Olmstead et al., 1993; Mor-gan & Soltis, 1993; Price & Palmer, 1993; Qiuet al., 1993; Rodman et al., 1993; Smith et al.,1993; Soltis et al., 1990). Although rbcL sequenceanalysis has overshadowed the use of other genesequences in plant systematics, the phylogeneticutility of several other DNA regions, both nuclearand organellar, has been investigated in plants.Among chloroplast genes, atpf (Ritland & Clegg,1987; Hoot et al., 1995 this issue), matK (Johnson& Soltis, 1994; Steele & Vilgalys, 1994), andndhF (Olmstead & Sweere, 1994; Olmstead &Reeves, 1995, this issue) provide regions with dem-onstrated utility for inferring phylogenies at tax-onomic levels unresolvable with rbcL sequencesalone. The use of these, and other regions of chlo-roplast DNA (cpDNA), such as noncoding inter-genic spacers (Gielly & Taberlet, 1994; Golenberget al., 1993), for phylogenetic inference suggeststhat analysis of the chloroplast genome will con-tinue to provide important information for system-atics. Among protein coding regions in the chloroplastgenome, matK (ORFK) is one of the most rapidlyevolving (Wolfe, 1991 ). The chloroplast gene matK ' We thank Paul Gadek, Christopher Quinn, Clifford Morden, and Jeff Palmer for sharing unpublished results oftheir studies involving matK; John Wiens and Tod Reeder for providing their unpublished manuscript on "pseudo-fossils"; Mark Porter for providing information and discussion concerning his ITS sequence analysis of the Polemon-iaceae; Robert Jansen for providing ndhF sequences for comparative purposes; Mark Chase, Paul Gadek, and PamSoltis for providing helpful comments on an earlier draft of this manuscript; and the many individuals who providedplant material used for sequencing. This research was supported by NSF grants BSR 9007614 and DEB 9307000to DES, DEB 9321788 to LAJ and DES, and grants from Sigma Xi, the American Society of Plant Taxonomists,and the California Native Plant Society to LAJ. 2 Department of Botany, Washington State University, Pullman, Washington 99164-4238, U.S.A. ANN. MISSOURI BOT. GARD. 82: 149-175. 1995.