DEB-1240045: Collaborative Research: AToL: Assembling the Pleurocarp Tree of Life: Resolving the rapid radiation using genomics and transcriptomics.

Phylogeny of mosses. A. Most likely tree inferred from 10 loci from all three genomes. All nodes are highly or maximally supported. Red dots mark ambiguous nodes (Cox et al. 2004). The taxon sampling includes two members of the pleurocarps. Orange names: lineage for which we already have complete organellar genomes + nrDNA; green names =lineages currently in the genomic pipeline. B. Phylogram inferred from 3 loci for 527 generic exemplars of mosses (Cox et al. 2010) highlighting the short branches within the pleurocarps.

This project fills a significant knowledge gap about the green plant (Embryophyte) tree of life. Mosses (phylum Bryophyta) compose a speciose early lineage of land plants that diversified in the Paleozoic long before the angiosperms arose, at a time when plant gametophytes were the dominant and perennial life history stage. The crown group of mosses, the so-called pleurocarps (subclass Hypnanae), comprises nearly half of all moss species, and dominates various terrestrial ecosystems throughout the world. Previous research indicates that the pleurocarps represent a rapid Mesozoic radiation and, not surprisingly, attempts to reconstruct their phylogenetic relationships based on limited genomic sampling (i.e., < 10 loci), even with extensive taxon sampling, have been largely unsuccessful. Divergence at individual loci is weak, and alternative systematic hypotheses remain tentative at best. Slightly over 5,000 species distributed among 500 genera compose the Hypnanae. Transitions between terricolous, epiphytic and even aquatic habitats occurred repeatedly and in all directions, often erasing the morphological signatures of evolutionary history. Consequently, the circumscription of and the relationships among genera as proposed based on morphological traits are widely contradicted by phylogenetic inferences from DNA data. This project utilizes the latest innovations in genome technology to reconstruct relationships among the mosses, with an emphasis on the recalcitrant pleurocarps. Specifically, the project includes three major activities. (1) A gene enrichment strategy will be used to target approximately 100 plastid and mitochondrial exons, and 1000 nuclear loci to reconstruct the Moss Tree of Life with a focus on the phylogenetic relationships within the Hypnanae, for which 400 examplars spanning the phylogenetic spectrum will be targeted. Baits for organellar gene capture will be developed based on recently acquired genomes and baits for nuclear gene enrichment will be developed from transcriptome data derived from four phylogenetically divergent taxa.(2) Transcriptome data will be generated from 36 additional exemplars to investigate gene family evolution and detect any signature of past whole genome duplication(s) that might have been associated with the rapid radiation of pleurocarps. (3) Conduct an aggressive outreach program targeting school kids, undergraduates, and developing bryologists. Post-doctoral training will benefit from tight collaboration among the three participating labs such that each trainee gains expertise in all aspects of the research, laboratory and analytical. The outreach program includes workshops especially tailored to bryophyte systematists who need to learn how to deal with the vast amounts of data available in today’s genomic era. Workshops will be complemented by student-produced webinar presentations.