Chloroplast Phylogeny Indicates that Bryophytes Are Monophyletic

Abstract

Opinions on the basal relationship of land plants vary considerably and no phylogenetic tree with significant statistical support has been obtained. Here, we report phylogenetic analyses using 51 genes from the entire chloroplast genome sequences of 20 representative green plant species. The analyses, using translated amino acid sequences, indicated that extant bryophytes (mosses, liverworts, and hornworts) form a monophyletic group with high statistical confidence and that extant bryophytes are likely sisters to extant vascular plants, although the support for monophyletic vascular plants was not strong. Analyses at the nucleotide level could not resolve the basal relationship with statistical confidence. Bryophyte monophyly inferred using amino acid sequences has a good statistical foundation and is not rejected statistically by other data sets. We propose bryophyte monophyly as the currently best hypothesis.

The deepest divergences in land plants inferred from phylogenomic evidence

“…3). Previously, strongly supported bryophyte monophyly was recovered in analyses of cp-genome sequences with virtually the same data set except for the lack of lycophytes (16,17). The analyses performed here and most recently (12,13) indicate that, after lycophytes were included, a critical taxon sampling density has been reached to resolve relationships among the four major land plant lineages using this type of data.…”

“…In alternative topology test analyses of the multigene supermatrix, we were initially unable to reject the three competing hypotheses: mosses sister to vascular plants (5,6), hornworts basal (14,15), and bryophytes monophyletic (13,16,17), although the first two were close to the rejection threshold under ML (Tables 1 and 2, which are published as supporting information on the PNAS web site). We implemented a second constraint search in which relationships within the four major land plant clades were constrained based on the 50% majority BS trees obtained from ML and MP analyses.…”

“…The eight cp-genome matrices, seven of nucleotides and one of amino acids, are character-rich but taxon-sparse. With the multigene and the intron matrices, such data enable us to examine issues that have surfaced repeatedly in analyzing character-dense but taxon-sparse DNA sequence data: relative merits of character vs. taxon sampling, use of nucleotide vs. amino acid sequences, and inclusion͞exclusion of different codon positions (12,13,16,17,(22)(23)(24)26).…”

The first complete chloroplast genome sequence of a lycophyte, Huperzia lucidula (Lycopodiaceae)

“…Currently, relationships among the three bryophyte clades and vascular plants are unresolved; at least three alternative topologies have been proposed recently (Nishiyama et al, 2004). We predict that this uncertainty will continue until taxon sampling improves.…”

Newly resolved relationships in an early land plant lineage: Bryophyta class Sphagnopsida (peat mosses)

“…Recent data sets appear to favor the hypothesis that liverworts (phylum Marchantiophyta) comprise the earliest-diverging lineage, followed by the mosses (Bryophyta) and hornworts (Anthocerophyta) ( Qiu et al, 1998 ;Nickrent et al, 2000 ;Shaw and Renzaglia, 2004 ). However, the most data-rich studies to date, based on chloroplast or mitochondrial organellar proteins, like analyses based on sperm cell morphology ( Garbary et al, 1993 ), identify a clade uniting liverworts and mosses, and additional data are still needed before we can consider the branching order of early land plant lineages to be fi nally resolved ( Nishiyama et al, 2004 ;Rodr í guez-Ezpeleta et al, 2007 ;Terasawa et al, 2007 ; but see also Qiu, et al, 2006 ).Notwithstanding that much remains to do, great progress has been made toward resolving phylogenetic relationships within the mosses (phylum Bryophyta s.s.) (e.g., Cox and Hedderson, 1999 ;Cox et al, 2000 ;Newton et al, 2000 ; Goffi net et al, 2001 ;Stech and Frey, 2008 ; Goffi net et al, 2009 ;Wahrmund et al, 2010 ). Major clades resolved by molecular data to a large extent mirror previous classifi cations based on morphology (e.g., Fleischer, 1923 ; Brotherus, 1924 Brotherus, -1925Vitt, 1984 • Premise of the study : The Sphagnopsida, an early-diverging lineage of mosses (phylum Bryophyta), are morphologically and ecologically unique and have profound impacts on global climate.…”