Transcriptome sequencing reveals genome-wide variation in molecular evolutionary rate among ferns

Orthogroup data file. Zipped folder containing fasta-formatted reads identified by ProteinOrtho, used for all downstream orthogroup determination and analysis, along with readme document and relevant project-specific scripts (also available online via Dryad: http://dx.doi.org/10.5061/dryad.rg22j ). (ZIP 12021 kb

Sex and the Single Gametophyte: Revising the Homosporous Vascular Plant Life Cycle in Light of Contemporary Research

Homosporous vascular plants are typically depicted as extreme inbreeders, with bisexual gametophytes that produce strictly homozygous sporophytes. This view is promulgated in textbook life cycles despite ample evidence that natural populations of most species regularly outcross. We review research on a variety of mechanisms, including genetic load, asynchronous production of eggs and sperm, and pheromonal control of gamete production, that actively promote heterozygosity in ferns and lycophytes. Evolution of the land plants cannot be reconstructed without accurate depictions of the unique life cycle that has helped make ferns the second most diverse lineage of vascular plants on Earth. With revised illustrations and definitions, we provide scientists, educators, and students with a contemporary understanding of fern and lycophyte reproduction, revealing them as evolutionarily dynamic and exploiting a wide range of mating systems

The Evolution and Diversification of Epiphytic Ferns

Leptosporangiate ferns, with more than 9000 extant species, are truly exceptional among the non-flowering lineages of vascular plants. However, this rather remarkable diversity was not simply a consequence of being able to "hold on" as flowering plants rose to dominance. Instead, it appears to be the result of an ecological opportunistic response to the establishment of more complex, angiosperm-dominated ecosystems. The proliferation of flowering plants across the landscape undoubtedly resulted in the formation of a plethora of new niches into which leptosporangiate ferns could diversify. Many of these were evidently on shady forest floors, but many others were actually within the new angiosperm-dominated canopies. Today, almost one third of leptosporangiate species grow as epiphytes on angiosperm trees. My dissertation aims to demystify the evolution and diversification of epiphytic ferns in order to more fully understand the leptosporangiate success story. By assembling and analyzing the most inclusive molecular dataset for leptosporangiate ferns to date, I provide unprecedented insight into overall fern relationships and a solid and balanced phylogenetic framework within which the evolution of epiphytism can be examined. By employing this phylogeny and numerous constraints from the fern fossil record, I uncover the timing of epiphytic fern diversification and examine the origin of the modern tropical rain forest biome in which these ferns reside

Identifying fern gametophytes using DNA sequences

Identification of fern gametophytes is generally hampered by low morphological complexity. Here we explore an alternative: DNA-based identification. We obtained a plastid rbcL sequence from a sterile gametophyte of unknown origin (cultivated for more than 30 years) and employed BLAST to determine its affinities. Using this approach, we identified the gametophyte as Osmunda regalis. To evaluate the robustness of this determination, and the usefulness of rbcL in differentiating among species, we conducted a phylogenetic analysis of osmundaceous fern sequences. Based on our results, it is evident that DNA-based identification has considerable potential in exploring the ecology of fern gametophytes

SI_Appendix1

PAMLparser, a Python script for organizing PAML outputs (from both CODEML and BASEML) and reformated them in tab-delimited files

nucleotide_all_data

Nexus file for nucleotide-model based analyes (including a block of recoded indels)