Data from: Conflicting phylogenies for early land plants are caused by composition biases among synonymous substitutions
Foster, Peter G. et al. (2014), Data from: Conflicting phylogenies for early land plants are caused by composition biases among synonymous substitutions, Dryad, Dataset, https://doi.org/10.5061/dryad.26qt6
Plants are the primary producers of the terrestrial ecosystems that dominate much of the natural environment. Occurring approximately 480 MYA (Sanderson 2003; Kenrick et. al. 2012), the evolutionary transition of plants from an aquatic to a terrestrial environment was accompanied by several major developmental innovations. The freshwater charophyte ancestors of land plants have a haplobiontic life cycle with a single haploid multicellular stage, whereas land plants, which include the bryophytes (liverworts, hornworts, and mosses) and tracheophytes (also called vascular plants, namely, lycopods, ferns, and seed plants), exhibit a marked alternation of generations with a diplobiontic life-cycle with both haploid and diploid multicellular stages and where the embryo remains attached to, and is nourished by, the gametophyte (Haig 2008). The interjection of a multicellular diploid phase into the land plant life cycle was an important adaptation that enabled long-distance dispersal via mitotic spores where water-borne male gametes have restricted motility in dry terrestrial environments. Despite the similarity among land-plant life-cycles, they differ in one significant aspect: in the three bryophyte groups, the haploid gametophytic stage is the dominant vegetative stage, whereas in vascular plants the diploid sporophyte dominates. A common assumption, and one implied by the tradition of referring to bryophytes as “lower plants” - in contrast to the “higher plants”, the tracheophytes - is that the bryophytes and their life-cycle are primitive (Kato and Akiyama 2005). However, without a strong phylogenetic hypothesis of land-plant relationships, it is not clear which (if either) of the gametophyte or sporophyte was the dominant ancestral vegetative state present in the earliest land plants (Renzaglia et al. 2007; Qiu et al. 2012). Early land plants have a relatively poor fossil record with few intermediate forms (Kenrick and Crane 1997; Wellman et al. 2003; Clarke et al. 2011), so most of the evidence for early land plant evolution has been based upon the patterns of morphological change that are implied by phylogenetic trees of relationships among extant land plant and algal groups. In this context, several recent studies based on large molecular data sets have converged upon a phylogenetic solution to land plant origins wherein tracheophytes are derived from bryophyte ancestors (Karol et al. 2001; Qiu et al. 2006; Gao et al. 2010; Karol et al. 2010; Chang and Graham 2011). In this hypothesis, the three bryophyte groups, namely liverworts, mosses, and hornworts, diverged sequentially and form a paraphyletic group with the hornworts sister to the tracheophytes. This phylogeny supports an intuitively elegant evolutionary trajectory whereby plants increased in morphological complexity from single-celled algae to seed plants via bryophyte intermediates (Karol et al. 2001; McCourt et al. 2004). Specifically, it implies that the gametophyte-dominant bryophyte life-cycle was ancestral among land plants and that the complex modular growth form of the vascular plant sporophyte evolved from the simplistic bryophyte sporophyte that consists only of a single growth module (Kato and Akiyama 2005; Barthélémy and Caraglio 2007).