Evolution and Diversification of Farinose Ferns in Xeric Environments: A Case Study Using Notholaena standleyi Maxon as a Model

Not all ferns grow in moist and shaded habitats. One notable example is the ecologically unusual clade of notholaenids. With approximately 40 species, the notholaenids have adapted to and diversified within the deserts of Mexico and the southwestern United States. In my dissertation, I studied the evolution and diversification of notholaenid ferns, using an approach that integrates data from multiple sources: biochemistry, biogeography, cytology, ecological niche modeling, molecular phylogeny, morphology, and physiology.

In Chapter 1, I infer a species phylogeny for notholaenid ferns using both nuclear and plastid DNA sequences, and reconstruct the evolutionary history of “farina” (powdery exudates of lipophilic flavonoid aglycones), a characteristic drought-adapted trait, that occurs on both the gametophytic and sporophytic phases of members of the the clade. Forty-nine notholaenid and twelve outgroup samples were selected for these analyses. Long (ca. 1 kb) low-copy nuclear sequences for four loci were retrieved using a recently developed amplicon sequencing protocol on the PacBio Sequel platform and a bioinformatics pipeline PURC; plastid sequences from three loci were retrieved using Sanger sequencing. Each nuclear/plastid dataset was first analyzed individually using maximum likelihood and Bayesian inference, and the species phylogeny was inferred using *BEAST. Ancestral states were reconstructed using likelihood (re-rooting method) and MCMC (stochastic mapping method) approaches. Ploidy levels were inferred using chromosome counts corroborated by spore diameter measurements. My phylogenetic analyses results are roughly congruent with previous phylogenies inferred using only plastid data; however, several incongruences were observed between them. Hybridization events among recognized species of the notholaenid clade appear to be relatively rare, compared to what is observed in other well-studied fern genera. All characters associated with farina production in the group appear to be homoplastic and have complex evolutionary histories.

In Chapter 2, I focus on the infraspecific diversification of Notholaena standleyi, a species that thrives in the deserts of the southwestern United States and Mexico and has several “chemotypes” that express differences in farina color and chemistry. Forty-eight samples were selected from across the geographic distribution of N. standleyi. Phylogenetic relationships were inferred using four plastid makers and five single/low-copy nuclear markers. Sequences were retrieved using PacBio and the PURC pipeline. Ploidy levels were inferred from relative spore size measurements calibrated with chromosome counts, and farina chemistry was compared using thin-layer chromatography (TLC). My studies of Notholaena standleyi reveal a complex history of infraspecific diversification traceable to a variety of evolutionary drivers including classic allopatry, parapatry with or without changes in geologic substrate, and sympatric divergence through polyploidization. Four divergent clades were recognized within the species. Three roughly correspond to previously recognized chemotypes: gold (G), yellow (Y), and pallid/yellow-green (P/YG). The fourth clade, cryptic (C), is newly reported here. The diploid clades G and Y are found in the Sonoran and Chihuahuan Deserts, respectively; they co-occur (and hybridize) in the Pinaleño Mts. of eastern Arizona. Clades G and Y are estimated to have diverged in the Pleistocene, congruent with the postulated timing of climatological events that divide these two deserts. Clade P/YG is tetraploid and partially overlaps the distribution of clade Y in the eastern parts of the Chihuahuan Desert. However, PY/G is apparently confined to limestone, a geologic substrate rarely occupied by members of the other clades. The newly discovered diploid clade, cryptic (C), is distributed in the southern Mexican states of Oaxaca and Puebla and is highly disjunct from the other three clades.

In Chapter 3, I study the ecological niche differentiation among the three major chemotypes––G, Y, and P/YG. Using both ordination and species distribution modelling techniques, the ecological niches for each chemotype were characterized and compared. The main environmental drivers for their distributions were identified, their suitable habitats in both geographic and environmental spaces were predicted, and their niche equivalencies and similarities were tested. My ecological niche analyses results suggest that all three chemotypes are ecologically diverged. The ecological niches of the two parapatric, sister diploid chemotypes, G and Y, are significantly different from one another. Chemotype G occupies a very extreme niche with higher solar radiation, and lower rainfall and higher temperatures in the wettest quarter. The niche space of tetraploid chemotype P/YG is similar but not equivalent to the other two chemotypes. Its distribution model is highly influenced by the high percentage of Calcids and warmer temperatures in the wet season, reflecting the fact that it is confined to limestone in areas of lower elevation/latitude.

In Chapter 4, I gather together all my other studies related to Notholaena standleyi, including: 1) morphological and anatomical observations of its desiccation-tolerant leaf, with special focus on the farina; 2) two cases of hybridization between the chemotypes, one between the diploid chemotype Y and tetraploid chemotype YG, and another between diploid chemotypes Y and G; and 3) morphological and physiological comparisons between the two diploid chemotypes Y and G. My plan is to finalize these studies and submit them for publication in the near future.

In Chapter 5, I summarize collaborative contributions that I made to other fern studies during my Ph.D.