Resolution of the ordinal phylogeny of mosses using targeted exons from organellar and nuclear genomes.

Mosses are a highly diverse lineage of land plants, whose diversification, spanning at least 400 million years, remains phylogenetically ambiguous due to the lack of fossils, massive early extinctions, late radiations, limited morphological variation, and conflicting signal among previously used markers. Here, we present phylogenetic reconstructions based on complete organellar exomes and a comparable set of nuclear genes for this major lineage of land plants. Our analysis of 142 species representing 29 of the 30 moss orders reveals that relative average rates of non-synonymous substitutions in nuclear versus plastid genes are much higher in mosses than in seed plants, consistent with the emerging concept of evolutionary dynamism in mosses. Our results highlight the evolutionary significance of taxa with reduced morphologies, shed light on the relative tempo and mechanisms underlying major cladogenic events, and suggest hypotheses for the relationships and delineation of moss orders.

Placing the regionally threatened moss Orthodontium gracile in the big picture - Phylogeny, genome incongruence and anthropogenic dispersal in the order Orthodontiales.

The Orthodontiaceae is a small family of predominantly Southern Hemisphere temperate and South East Asian mosses that has a key phylogenetic position for research into the evolution of pleurocarpy. In the United Kingdom it is represented by the rare conservation priority species Orthodontium gracile and the abundant exotic O. lineare, introduced from the Southern Hemisphere around a century ago. Although the two species are superficially very similar and difficult to tell apart in the field, very little is known about how closely they are related or about the phylogeny, biogeography and evolutionary history of the genus Orthodontium as a whole. Phylogenetic inference and divergence time estimation were used to explore relationships within the genus globally, date major lineage splits, detect reticulate evolutionary processes and test monophyly of taxa. It was shown that Orthodontium gracile belongs to a Holarctic and Asian clade that diverged from the exclusively southern temperate lineage of O. lineare approximately 53 Ma and that it is sister to the Himalayan and South Siberian bispecific genus Orthodontopsis, which we now recognise as a single species within Orthodontium, O. lignicola. Orthodontium lignicola is quite distinct from O. gracile morphologically but may have a closely overlapping centre of extant diversity in the Himalaya, in contrast to O. lineare which is morphologically similar but biogeographically dissimilar. The introduced European populations of Orthodontium lineare were shown to share plastid and nuclear haplotypes with four collections from Tasmania and Southern Chile, but to be distinct from other Chilean and South African haplotypes. Finally, well-supported incongruence between nuclear and plastid sequences in some Western North American populations of Orthodontium gracile strongly implies one or more chloroplast capture or horizontal genome transfer events involving this species and the regionally sympatric O. pellucens. An appeal is made for targeting phylogenetic research at the intersection points of practical conservation, taxonomic uncertainty and wider biological questions and for the factoring of historical evolutionary and phylogenetic diversity into conservation assessments.

Multiple innovations underpinned branching form diversification in mosses.

Broad-scale evolutionary comparisons have shown that branching forms arose by convergence in vascular plants and bryophytes, but the trajectory of branching form diversification in bryophytes is unclear. Mosses are the most species-rich bryophyte lineage and two sub-groups are circumscribed by alternative reproductive organ placements. In one, reproductive organs form apically, terminating growth of the primary shoot (gametophore) axis. In the other, reproductive organs develop on very short lateral branches. A switch from apical to lateral reproductive organ development is proposed to have primed branching form diversification. Moss gametophores have modular development and each module develops from a single apical cell. Here we define the architectures of 175 mosses by the number of module classes, branching patterns and the pattern in which similar modules repeat. Using ancestral character state reconstruction we identify two stages of architectural diversification. During a first stage there were sequential changes in the module repetition pattern, reproductive organ position, branching pattern and the number of module classes. During a second stage, vegetative changes occurred independently of reproductive fate. The results pinpoint the nature of developmental change priming branching form diversification in mosses and provide a framework for mechanistic studies of architectural diversification.

Organellar genomes of the four-toothed moss, Tetraphis pellucida.

BACKGROUND: Mosses are the largest of the three extant clades of gametophyte-dominant land plants and remain poorly studied using comparative genomic methods. Major monophyletic moss lineages are characterised by different types of a spore dehiscence apparatus called the peristome, and the most important unsolved problem in higher-level moss systematics is the branching order of these peristomate clades. Organellar genome sequencing offers the potential to resolve this issue through the provision of both genomic structural characters and a greatly increased quantity of nucleotide substitution characters, as well as to elucidate organellar evolution in mosses. We publish and describe the chloroplast and mitochondrial genomes of Tetraphis pellucida, representative of the most phylogenetically intractable and morphologically isolated peristomate lineage. RESULTS: Assembly of reads from Illumina SBS and Pacific Biosciences RS sequencing reveals that the Tetraphis chloroplast genome comprises 127,489 bp and the mitochondrial genome 107,730 bp. Although genomic structures are similar to those of the small number of other known moss organellar genomes, the chloroplast lacks the petN gene (in common with Tortula ruralis) and the mitochondrion has only a non-functional pseudogenised remnant of nad7 (uniquely amongst known moss chondromes). CONCLUSIONS: Structural genomic features exist with the potential to be informative for phylogenetic relationships amongst the peristomate moss lineages, and thus organellar genome sequences are urgently required for exemplars from other clades. The unique genomic and morphological features of Tetraphis confirm its importance for resolving one of the major questions in land plant phylogeny and for understanding the evolution of the peristome, a likely key innovation underlying the diversity of mosses. The functional loss of nad7 from the chondrome is now shown to have occurred independently in all three bryophyte clades as well as in the early-diverging tracheophyte Huperzia squarrosa.

Phylogeny of the moss class Polytrichopsida (BRYOPHYTA): Generic-level structure and incongruent gene trees.

Analysis of an extensive new molecular dataset for the moss class Polytrichopsida provides convincing support for many traditionally recognised genera and identifies higher level phylogenetic structure with a strong geographic component. A large apical clade that is most diverse in the northern hemisphere is subtended by a grade of southern temperate and tropical genera, while the earliest diverging lineages have widely separated relictual distributions. However, there is strongly supported topological incongruence between the nuclear 18S rRNA gene tree and the chloroplast and mitochondrial data for the positions of some taxa and notably for the status of Pogonatum. While Pogonatum is unambiguously paraphyletic in the 18S tree, it is well supported as monophyletic by the combined chloroplast and mitochondrial data, this being corroborated by several distinctive morphological synapomorphies and a 51-53 bp deletion in the rps4-trnS spacer. We explore various reticulate historical processes and methodological issues as possible explanations for incongruence, and suggest that either (1) the 18S topology is an artefact created by convergence of substitutions at specific sites due to functional and/or molecular-structural constraints not accounted for by the model, or (2) the incongruence is a product of ancient hybridization events. Under the latter scenario, incongruent topologies for Pogonatum are parsimoniously explained if Polytrichum (including Polytrichastrum sect. Aporotheca) is ultimately descended from a hybridization event involving an extinct maternal taxon derived from the branch ancestral to the combined Pogonatum/Polytrichum s.l. clade, and a paternal taxon belonging to (or ancestral to) the apical Pogonatum group to which the majority of extant species belong. Numerous novel relationships of taxonomic and evolutionary significance are supported. Notably, both Polytrichastrum and Oligotrichum are polyphyletic. While Polytrichastrum sect. Aporotheca is closely related to Polytrichum, other species, including the type, are not. The large majority of Oligotrichum species sampled occur in one of two distantly related clades with predominantly northern and southern hemisphere distributions, respectively, implying convergent evolution of this morphology in each of the two temperate zones.

A phylogenetic circumscription of Polytrichastrum (Polytrichaceae): Reassessment of sporophyte morphology supports molecular phylogeny.

Mosses arguably possess the most structurally complex sporangia of any extant land plants, a consequence of being the monosporangiophyte lineage most strongly adapted to terrestrial environments. Morphological and functional variation in the mechanisms that regulate spore release in one of the major classes of mosses, the Polytrichopsida, is largely unexplored, while recent research indicates that the most distinctive structure, the peristome, has evolved independently in the Polytrichopsida and in other mosses. The genus Polytrichastrum was separated from Polytrichum on the basis of such sporangial characters, although the critical features had until recently only been examined using light microscopy, and strong evidence from molecular data indicated that Polytrichastrum as currently circumscribed is polyphyletic. Here we use Bayesian ancestral character state reconstruction in conjunction with extensive scanning electron micrographic studies to elucidate probable morphology at ancestral nodes and define natural taxa. As well as clarifying the structure, evolution, and aspects of development of the peristome-epiphragm complex in this highly prominent group of mosses, the results provide a basis for a revised phylogenetic taxonomy in which the species of Polytrichastrum sect. Aporotheca are recognized once more within Polytrichum.