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

Abstract

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.

Is the sword moss (Bryoxiphium) a preglacial Tertiary relict?

“…The split of continental ancestral populations is too recent to match with a continental drift scenario but is spatially and temporally remarkably congruent with that observed in Tertiary angiosperm relict species (Xiang et al, 2000), corresponding to the fragmentation of a once continuous mixed mesophytic forest that occurred throughout the Northern Hemisphere due to climatic cooling (Milne, 2006). Together with fossil (Schuster, 1983, but see Heinrichs et al, 2015, about the uncertainty of the assignment of fossils to extant species) and phylogeographic (Aigoin et al, 2009;Bell and Hyvönen, 2010;Patiño et al, 2013) evidence of cases of palaeoendemism in bryophytes, our results thus support the notion that, even in highly mobile organisms as spore-producing plants, high dispersal capacities do not necessarily erase historical signal in extant distribution patterns.…”

Characterization and Phylogenetic Analysis of Chloroplast and Mitochondria Genomes from the Antarctic Polytrichaceae Species Polytrichum juniperinum and Polytrichum strictum

“…Polytrichaceae representatives appear to form a clade, but Atrichum angustatum appears inside this clade, close to P. strictum. Although A. angustatum is a more basal species in Polytrichaceae phylogeny [4], here, the species seems to be placed incorrectly in the mitochondrial tree. However, this result can generate two interpretations, the first involving a possible misunderstanding due to the reference genome used in assembling the plastids sequenced for the Polytrichum species used since the reference was based on the genome of P. patens; this may induce the resulting genomes to be more similar to the genomes of P. patens than A. angustatum.…”

“…Polytrichum strictum has morphological characteristics similar to those of P. juniperinum [74][75][76][77] and it differs from P. juniperinum in that it occurs in habitats in the north, such as wetlands (North America), and has, among other morphological characteristics, a remarkable coverage of white rhizoids [78]. Bell and Hyvönen conducted a study on the phylogeny of mosses of the class Polytrichopsida and proposed that the origin of P. strictum (samples used were from Chile and Finland) could be from a cross-linking event [4]. For these authors, P. strictum could be the product of hybridization between the P. juniperinum lineage (sample used from Finland) and a basal lineage of another Polytrichaceae representative.…”

“…They play an important role in the terrestrial vegetation of this biome as essential constituents in various communities of moss turf subformations as well as fruticose lichens [1]. The phylogenetic relationships of Polytrichales are particularly relevant when considering the evolutionary history of mosses, since the group is probably one of the first lineages to diverge from the common ancestor of all mosses [3,4]. A recent development in plastome sequencing is the use of total genomic DNA as the template for next-generation sequencing [5,6].…”

To network or not to network, that is the question

“…Exceptionally, when sequence information originating from different genes is analysed and found to be incongruent, it may be preferable to construct a single phylogeny representing this incongruence based on separate analyses of individual genes rather than conduct simultaneous analysis of the data (e.g. Bell and Hyvönen 2010). Network methods such as splits graph have the ability to highlight the predominant signal in the data and the extent to which that signal may or may not be treelike.…”