| Summary: | Substantial ambiguities still remain concerning the broad backbone of moss phylogeny. I surveyed 17 slowly evolving plastid genes from representative taxa to reconstruct phylogenetic relationships among the major lineages of mosses in the overall context of land-plant phylogeny. I first designed 78 bryophyte-specific primers and demonstrated that they permit straightforward amplification and sequencing of 14 core genes across a broad range of bryophytes (three of the 17 genes required more effort). In combination, these genes can generate sturdy and well-resolved phylogenetic inferences of higher-order moss phylogeny, with little evidence of conflict among different data partitions or analyses. Liverworts are strongly supported as the sister group of the remaining land plants, and hornworts as sister to vascular plants. Within mosses, besides confirming some previously published findings based on other markers, my results substantially
improve support for major branching patterns that were ambiguous before. The monogeneric classes Takakiopsida and Sphagnopsida likely represent the first and second split within moss phylogeny, respectively. However, this result is shown to be sensitive to the strategy used to estimate DNA substitution model parameter values and to different data partitioning methods. Regarding the placement of remaining nonperistomate lineages, the [[[Andreaeobryopsida, Andreaeopsida], Oedipodiopsida], peristomate mosses] arrangement receives moderate to strong support. Among peristomate mosses, relationships among Polytrichopsida, Tetraphidopsida and
Bryopsida remain unclear, as do the earliest splits within sublcass Bryidae. A Funariidae, [Timmiidae, [Dicranidae, Bryidae]]] arrangement is strongly supported, as are major relationships within subclasses Funariidae and Dicranidae. I also reconstructed the phylogeny of the nonperistomate moss family Andreaeaceae, with a focus on costate taxa, using two complementary sets of plastid markers and taxa. The major subgenera (Andreaea and Chasmocalyx) and sections of Andreaea (Andreaea and Nerviae) are rejected as monophyletic. Well-supported lineages include clades comprising: (1) Andreaea nivalis and A. rigida (northern hemisphere members of subgenus Chasmocalyx) and A. blyttii (section Nerviae); (2) most of the remainder of Nerviae; (3) a mixture of costate and ecostate species from Chasmocalyx, Nerviae,
all sampled members of section Andreaea, and subgenus Acroschisma. Relationships among the major lineages, including the root of the family, are all well supported.
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