Multigene phylogeny of land plants with special reference to bryophytes and the earliest land plants

A widely held view of land plant relationships places liverworts as the fir st branch of the land plant tree, whereas some molecular analyses and a cla distic study of morphological characters indicate that hornworts are the ea rliest land plants. To help resolve this conflict, we used parsimony and li kelihood methods to analyze a 6,095-character data set composed of four gen es (chloroplast rbcL and small-subunit rDNA from all three plant genomes) f rom all major land plant lineages. In all analyses, significant support was obtained for the monophyly of vascular plants, lycophytes,ferns (including Psilotum and Equisetum), seed plants, and angiosperms. Relationships among the three bryophyte lineages were unresolved in parsimony analyses in whic h all positions were included and weighted equally. However, in parsimony a nd likelihood analyses in which rbcL third-codon-position transitions were either excluded or downweighted (due to apparent saturation), hornworts wer e placed as sister to all other land plants, with mosses and liverworts joi ntly forming the second deepest lineage. Decay analyses and Kishino-Hasegaw a tests of the third-position-excluded data set showed significant support for the hornwort-basal topology over several alternative topologies, includ ing the commonly cited liverwort-basal topology. Among the four genes used, mitochondrial small-subunit rDNA showed the lowest homoplasy and alone rec overed essentially the same topology as the multigene tree. This molecular phylogeny presents new opportunities to assess paleontological evidence and morphological innovations that occurred during the early evolution of terr estrial plants.