UBC Theses and Dissertations
Systematics of deep and recent lineages of bryophytes using phylogenomic approaches Bell, David
I use organellar phylogenomic approaches to infer overall land-plant phylogeny and higher-order relationships in mosses, liverworts and hornworts, and perform more focused studies of relationships in two bryophyte clades, the granite mosses (Andreaeaceae), and the liverwort genus Herbertus. Using plastid and mitochondrial phylogenomic data sets, I infer conflicts in overall embryophyte relationships across different analyses. These conflicts mask an underlying unrooted tree that is also consistent with most published studies: [(liverworts, mosses), (hornworts, vascular plants)]. Inferred relationships within the major bryophyte clades (mosses, liverworts, hornworts) largely agree across analyses, and between trees inferred from the two organellar genomes. I show that combining genomic and transcriptomic data sources can mislead phylogeny locally for heavily RNA-edited taxa, but that excluding putative edit sites restores cases of unexpected non-monophyly to monophyly. I find that relaxed purifying selection affects multiple plastid genes in a mycoheterotrophic liverwort (Aneura mirabilis) but not a putatively mycoheterotrophic moss, Buxbaumia. Plastid genome structure is nearly invariant across autotrophic bryophytes, but the tufA locus, presumed lost in embryophytes, is unexpectedly retained in several mosses. I reconstruct the broad phylogeny of Andreaeaceae, one of a handful of non-peristomate moss lineages, using a variety of phylogenetic and nuclear phylogenomic data sets and approaches. I infer largely congruent relationships across disparate molecular data sources. These inferences conflict with traditional infrageneric classification, likely reflecting an overreliance on homoplasious morphological characters. I confirm that Andreaea wilsonii is deeply nested in Andreaea, refuting its circumscription as a distinct genus by several authors. I propose an updated infrageneric classification for Andreaea, including three new sections, providing a framework for future systematic studies of the genus. I also use various phylogenetic and nuclear phylogenomic approaches to address species diversity and relationships in Herbertus, a leafy liverwort genus with a complex taxonomic history. My analyses demonstrate an incomplete understanding of species diversity in Herbertus, and reveal widespread misapplication of names due to imperfect morphological species concepts. A reassessment of morphological, ecological, and distributional data in Herbertus, made in light of the new molecular inferences, helps delineate taxa and highlights overlooked species diversity and cryptic species.
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