Abstract
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.
Highlights
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
The sequence of innovations in modes of spore dispersal and body growth remains, poorly understood due to a combination of factors, including massive early extinctions[2], late radiations[10], extreme paucity in Paleozoic fossil, limited levels of morphological variation, and phylogenetic uncertainty of the order of divergences among major moss groups that make up the ordinal relationships of the moss tree of life[4]
Transcriptome-based phylogenomic analyses have contributed to resolving recalcitrant relationships in diverse groups such as molluscs[40], diatoms[41], embryophytes[42], and insects[43]
Summary
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. We designed oligonucleotide gene-baits to enrich genomic libraries for protein-coding genes from all genomic compartments (i.e., nuclear, plastid, and mitochondrial) across the Bryophyta targeting a broad taxon sampling to weaken effects of saturation on phylogenetic inferences[37,38], to address five critical areas of the moss phylogeny that have been previously contentious: (1) the earliest splits giving rise to the Takakiophytina, Sphagnophytina, Andreaeophytina, Andreaeobryophytina and Bryophytina; (2) the relationships of the nematodontous Tetraphidopsida and Polytrichopsida; (3) the early divergences among arthrodontous mosses; (4) the identity of the sister-group to the most speciose lineage, the pleurocarps or Hypnanae; and (5) the delineation of major lineages within the Hypnanae, which addresses the inconsistent placement of Hypopterygiaceae within the pleurocarpous mosses[25,39].
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