DOI: 10.5061/dryad.26qt6
title: Data from: Conflicting phylogenies for early land plants are caused by composition biases among synonymous substitutions

description: 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).
description: Supplementary Material:
 Cox et al.Supplementary text and
 figures.Supplementary_Material_Cox_et_al.pdf