Over the last several years, the phylogeny of land plants and various associated questions have been investigated using analyses of single to multiple genes with different extents of taxon sampling, morphological data, and organellar genomic structural characters. At present, the following issues remain contentious: the first lineage of land plants; the sister lineage of vascular plants; relationships among Equisetum, Psilotaceae, eusporangiate and leptosporangiate ferns; monophyly of extant gymnosperms; and the exact position of Gnetales. Here we analyze a data set of six mitochondrial (atp1 and mt-LSU rDNA), plastid (rbcL and cp-LSU rDNA), and nuclear (18S and 26S rDNAs) genes from 180 species that cover all major lineages of land plants. We explore the effectiveness of this broad, moderately dense taxon and character sampling strategy in reconstructing the land plant phylogeny. The random outgroup rooting strategy was employed to evaluate the effect of sequence divergence between charophytes (as an outgroup) and land plants on identifying the oldest living land plant lineage. We also examine substitution rates of these genes across land plants and use the sequence data to estimate divergence times of land plants as well as its various component clades.

Key words: land plants, multigene analysis, phylogeny, rRNA