Browsing by Subject "Biogeography"
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Item Open Access Evolution and Diversification of Farinose Ferns in Xeric Environments: A Case Study Using Notholaena standleyi Maxon as a Model(2020) Kao, Tzu-TongNot 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.
Item Open Access Mistakes and Small Steps Can Take You Far: Exploring Fern Variation and Biogeography in Cheilanthes (Pteridaceae), with a Focus on Spore Diversity and Range Expansion in Cheilanthes distans(2022) Sosa, KarlaWhy do species exist where they do? Understanding the forces and processes that shape species’ ranges—and that affect their dispersal and range expansion—have long fascinated biologists. In this work, I focus on understanding diversity and dispersal in Cheilanthes ferns. I first describe a species new to science, Cheilanthes ecuadorensis, from among the understudied South American members of this genus. I then turn to studying the widely distributed, asexual, Australasian species C. distans. Careful review of samples from this species allowed me to find sexual specimens previously unknown to science that exist in a narrow range, as well as to catalogue extensive spore diversity that has gone unrecorded. I find strong evidence for trade-offs related to spore size, with larger spores having higher germination while smaller spores have greater dispersal. Excitingly, I find that spores previously catalogued as abortive are in fact viable, and contribute to the spore size diversity I observe. I then place these findings into phylogenetic context by building a phylogeny for all Australasian Cheilanthes, and use it to explore the relationships of sexual and asexual lineages, of different ploidy levels, and of geographic distributions. These analyses reveal that most dispersal in C. distans occurs over shorter rather than longer distances, in contrast to previous hypotheses posited by fern biologists. I observe that lineages are not limited to particular geographic regions, as well finding that dispersal is asymmetrical and seems to be tracking trade winds. For all my work I rely heavily on herbarium specimens and use them to catalogue morphological variation as well as to obtain DNA sequences that are used for phylogenetic analysis. I implement a variety of statistical and systematic analyses to explore correlations between spore size, reproductive mode, ploidy, germination, and dispersal. While this work expands our knowledge of fern diversity and biogeography, much still remains to be understood, including cataloguing possible novel species, understanding the biology behind spore size determination, and exploring the role of niche in the dispersal and range expansion of C. distans.
Item Open Access Systematics and Ecology of Truffles (Tuber)(2009) Bonito, Gregory MichaelThe truffle genus Tuber (Ascomycota, Pezizales, Tuberaceae) produces underground mushrooms widely sought as edible fungi. Tuber species are distributed throughout Northern hemisphere forests and form obligate ectomycorrhizal symbiosis with trees within the Pinaceae, Fagaceae, Betulaceae, and Juglandaceae.
The transition to a truffle form (from an epigeous form) has occurred independently, multiple times in both the Ascomycetes and Basidiomycetes. One instance has given rise to the Tuberaceae, which is composed entirely of obligate ectomycorrhizal species. Attempts to cultivate European truffle species T. melanosporum, T. aestivum, and T. borchii are underway in North America and other parts of the world and have been met with mixed success.
The overarching goal of my dissertation is to address the systematics, ecology, and biogeography of Tuber within a phylogenetic framework. Multiple loci were sequenced from Tuber ascoma collected worldwide including ectomycorrhizae, though an emphasis was placed on sampling taxon within North American. Maximum likelihood, maximum parsimony, and Bayesian inference were used for phylogenetic reconstructions.
A taxonomic and phylogenetic overview of the family Tuberaceae is presented in Chapter 1. Tuber is resolved as monophyletic. In Chapter 2, through greater taxon sampling including epigeous and hypogeous Helvellaceae outgroups and related South American taxa, a resolved multi-gene phylogeny of the Tuberaceae and putative epigeous ancestor of Tuber is presented. A previously unknown South American lineage that contains both epigeous and hypogeous taxa is resolved as sister to the Tuberaceae. Chapter 3 is focused on issues of cryptic speciation and taxonomy within the Tuber gibbosum clade. The four species resolved in the Gibbosum clade appear to be endemic to the Pacific Northwest and associated primarily with Gymnosperms. Chapter 4 is a meta-analysis of all known Tuber ITS rDNA sequences (e.g. from Genbank and generated from herbarium collections) available at the time. These were placed within the Tuber phylogeny to assess species diversity, long-distance dispersal, and host associations. In total, 120 phylotypes were detected (based on a 96% similarity criterion). Tuber shows high levels of continental endemism. I hypothesize that species shared between continents and having low ITS variability (<1%) are the result of recent human-mediated introduction events. Chapters 5 and 6 are focused on the ectomycorrhizal ecology of the economic truffle T. lyonii, which is native to Eastern and Southern North America. There is a phenomenon of Tuber lyonii fruiting in pecan orchards. Pecans (Carya illinoinensis) are in the Juglandaceae, an understudied ectomycorrhizal plant family. I sampled the ectomycorrhizal communities of pecan orchards (associated with the production of the North American truffle species Tuber lyonii). In Chapter 5 I discuss four Tuber taxa discovered in these pecan orchards, their abundance and haplotype diversity. Chapter 6 examines the ectomycorrhizal communities across the five pecan orchards sampled. I show that multiple Tuber species, including Tuber lyonii, are dominant in the ectomycorrhizal community. Chapters 7 and 8 focus on black truffles in the Melanosporum clade. In Chapter 7 I document that Tuber indicum has been introduced into North America multiple times, and through ectomycorrhizal synthesis I demonstrate that this Asian species can associate readily with angiosperm and gymnosperm hosts endemic to North American. In Chapter 8 I describe a quick and reliable method for the determination of Tuber melanosporum. The method is based on direct PCR and species-specific primers and is very useful for rapid diagnostics. I have adapted this approach for other truffle and mushroom species.
Three major findings emerge from my dissertation research: 1) Tuber is more diverse than previously realized; 2) Tuber exhibits high levels of regional and continental endemism; 3) Taxonomic issues remain in many species complexes worldwide (including the Tuber candidum complex in North America, the Tuber excavatum complex in Europe, the Tuber indicum complex in Asia). Taxonomic challenges also remain regarding species known only from ectomycorrhizal or anamorphic states. The discovery of additional Tuber species is expected as the truffle flora of undersampled regions become better studied and incorporated into the Tuberaceae phylogeny.