A nonflowering land plant phylogeny inferred from nucleotide sequences of seven chloroplast, mitochondrial, and nuclear genes

Nucleotide sequences of seven chloroplast (atpB and rbcL, SSU and LSU rDNAs), mitochondrial (atp1, LSU rDNA), and nuclear (18S rDNA) genes from 192 land plants and their algal relatives were analyzed using maximum likelihood and maximum parsimony methods. Liverworts, mosses, hornworts, lycophytes, monilophytes (ferns), seed plants, and angiosperms all represent strongly supported monophyletic groups. Three bryophyte lineages form a paraphyletic group to vascular plants, with liverworts representing the sister to all other land plants and hornworts being sister to vascular plants. Lycophytes are sister to all other vascular plants, which are divided into two clades, one being monilophytes, which include Equisetum, Psilotaceae-Ophioglossaceae, Marattiaceae, and leptosporangiate ferns, and the other being seed plants. Relationships among the monilophyte lineages remain unresolved. Within seed plants, extant gymnosperms form a moderately supported clade in which Gnetales are related to conifers. This clade is sister to angiosperms. Most of the relationships among all major lineages of nonflowering land plants are supported by bootstrap values of 75% or higher, except those among basal monilophyte lineages and among some gymnosperm lineages, probably because of extinctions. The closest algal relative of land plants is Characeae, and this relationship is well supported. Several methodological issues on reconstructing large, deep phylogenies are also discussed.