Phylogenetic results using nucleotide data. A) Cladogram based on ML analysis (-ln = 473022.24372) of 49 gene sequences from all 43 plastomes sampled (Table 1). Mapped non-homoplastic indels are shown in yellow circles. Numbers in grey circles are indels identified with a more restrictive taxon sampling that were difficult to score across all charophycean green algae and land plants. B) Phylogram based on ML analysis (-ln = 442145.83514) of gene sequences, excluding the two Selaginella species. C) Phylogram based on ML analysis (-ln = 436696.62372) of gene sequences, excluding the three gnetophyte taxa (Ephedra equisetina, Gnetum parvifolium and Welwitschia mirabilis). ML phylogenetic results (-ln = 405904.24872) that excluded Selaginella spp. and gnetophytes were similar in topology to b (not shown). Numbers above the branches are ML bootstrap proportions and numbers below are Bayesian posterior probabilities in this order: all taxa included/Selaginella spp. excluded/gnetophytes excluded/Selaginella spp. and gnetophytes excluded. The asterisk (*) in c indicates the ML bootstrap proportion for Marchantia polymorpha sister to the remaining land plants found in bootstrap analyses that included all taxa, though the best ML tree recovered a sister relationship of M. polymorpha with the mosses Physcomitrella patens and Syntrichia ruralis. Boxes and dashed lines indicate the relative position of monilophytes (light grey) and lycophytes (dark grey).
Karol et al. BMC Evolutionary Biology 2010 10:321 doi:10.1186/1471-2148-10-321