Low-copy nuclear sequence data confirm complex patterns of farina evolution in notholaenid ferns (Pteridaceae).

Notholaenids are an unusual group of ferns that have adapted to, and diversified within, the deserts of Mexico and the southwestern United States. With approximately 40 species, this group is noted for being desiccation-tolerant and having "farina"-powdery exudates of lipophilic flavonoid aglycones-that occur on both the gametophytic and sporophytic phases of their life cycle. The most recent circumscription of notholaenids based on plastid markers surprisingly suggests that several morphological characters, including the expression of farina, are homoplasious. In a striking case of convergence, Notholaena standleyi appears to be distantly related to core Notholaena, with several taxa not before associated with Notholaena nested between them. Such conflicts can be due to morphological homoplasy resulting from adaptive convergence or, alternatively, the plastid phylogeny itself might be misleading, diverging from the true species tree due to incomplete lineage sorting, hybridization, or other factors. In this study, we present a species phylogeny for notholaenid ferns, using four low-copy nuclear loci and concatenated data from three plastid loci. A total of 61 individuals (49 notholaenids and 12 outgroup taxa) were sampled, including 31 out of 37 recognized notholaenid species. The homeologous/allelic nuclear sequences were retrieved using PacBio sequencing and the PURC bioinformatics pipeline. Each dataset was first analyzed individually using maximum likelihood and Bayesian inference, and the species phylogeny was inferred using *BEAST. Although we observed several incongruences between the nuclear and plastid phylogenies, our principal results are broadly congruent with previous inferences based on plastid data. By mapping the presence of farina and their biochemical constitutions on our consensus phylogenetic tree, we confirmed that the characters are indeed homoplastic and have complex evolutionary histories. Hybridization among recognized species of the notholaenid clade appears to be relatively rare compared to that observed in other well-studied fern genera.

Inferring the evolutionary reduction of corm lobation in Isoëtes using Bayesian model-averaged ancestral state reconstruction.

PREMISE OF THE STUDY: Inferring the evolution of characters in Isoëtes has been problematic, as these plants are morphologically conservative and yet highly variable and homoplasious within that conserved base morphology. However, molecular phylogenies have given us a valuable tool for testing hypotheses of character evolution within the genus, such as the hypothesis of ongoing morphological reductions. METHODS: We examined the reduction in lobe number on the underground trunk, or corm, by combining the most recent molecular phylogeny with morphological descriptions gathered from the literature and observations of living specimens. Ancestral character states were inferred using nonstationary evolutionary models, reversible-jump MCMC, and Bayesian model averaging. KEY RESULTS: Our results support the hypothesis of a directional reduction in lobe number in Isoëtes, with the best-supported model of character evolution being one of irreversible reduction. Furthermore, the most probable ancestral corm lobe number of extant Isoëtes is three, and a reduction to two lobes has occurred at least six times. CONCLUSIONS: From our results, we can infer that corm lobation, like many other traits in Isoëtes, shows a degree of homoplasy, and yet also shows ongoing evolutionary reduction.