Browsing by Author "Shaw, A Jonathan"

Fungal endophytes are ubiquitous inhabitants of plants and can have a wide range of effects on their hosts, from pathogenic to mutualistic. These fungal associates are important drivers of plant success and therefore contribute to plant community structure. The majority of endophyte studies have focused on seed plants, but in order to understand the dynamics of endophytes at the ecosystem scale, as well as the evolution of these fungal associations, investigations are also necessary in earlier-diverging clades of plants, such as the non-vascular bryophytes (mosses, liverworts, and hornworts). This dissertation presents a survey of the diversity of fungal endophytes found in the liverwort Marchantia polymorpha L. and develops a gnotobiotic experimental system for testing the effects of these fungi on their liverwort host. The survey reveals a diverse community of fungi in M. polymorpha, with some fungi that are associated with this host across geographically distant sites. The laboratory experiments demonstrate that culturable endophytes of M. polymorpha can, in isolation, cause positive, negative, or neutral effects on host success and that these effects change in response to nutrient levels and the presence of multiple endophytes. The experimental system developed in this dissertation has great potential in the growing field of plant microbiota research to answer questions that range in scale from molecular mechanisms to ecosystem function.

*Designated as an Exemplary Master's Project for 2014-15*

Bryophytes, by their haploid dominant life cycle, possess several unique qualities ideal for study of mating patterns. In particular, the possibility of intragametophytic selfing in some species, and the vegetative propagation of gametes allow for a unique window into the haploid stage that is intractable in other groups. Despite these advantages, there have been relatively few studies on mating patterns bryophytes in natural populations. Sphagnum (peatmoss) is an excellent case study in the interactions between sexual condition, ecology, and mating patterns. In the first Chapter, we use microsatellites to characterize the genetic diversity and mating patterns in fourteen species of Sphagnum, diverse in sexual condition (separate vs combined sexes in the haploid stage) and ecology (microhabitat variance along the water table). We find that genetic diversity and mating patterns are related only in species with separate sexes, that sexual condition and ecology have interacting effects on inbreeding coefficients, and that inbreeding depression is not a common phenomenon in Sphagnum. In the second Chapter, we conduct an intensive survey of one population of Sphagnum macrophyllum, to detect whether variance in haploid fecundity and mating success is related to diploid fitness. We find a relationship between mating success and fecundity (a signal of sexual selection), and fitness of the diploid generation is connected to the parentage of the haploid generation. Finally, in Chapter 3 we use phylogenetic comparative methods to track the phylogenetic signal in microhabitat preference in Sphagnum. We find extremely fast rates of evolution along the micronutrient gradient, but high phylogenetic signal along a hydrological gradient. Given that Sphagnum species living high above the water table have reduced water availability, phylogenetic signal in the hydrological gradient has macroevolutionary implications for mating systems in Sphagnum.

Plants in the genus Sphagnum (peat moss) are the dominant biotic features of boreal peatlands that store nearly one-third of Earth’s terrestrial carbon. Peat mosses are ecosystem engineers and create the peatlands that they inhabit through the accumulation of peat, or partially decayed biomass, and the functional traits underlying this extended phenotype. Interspecific functional trait variation is hypothesized to promote niche differentiation through the creation and maintenance of ecological gradients along which species sort within communities. One prominent gradient relates to height-above-water-table wherein some species produce hummocks raised up to a meter above the water table, while others live in hollows at or near the water table. However, it is unclear how these traits evolved during Sphagnum diversification, to what extent natural selection produced functional trait variation, and which genes might contribute to such phenotypes.

In Chapter 2, a meta-analysis of data from recent studies is used to relate patterns of functional trait variation to the phylogeny of Sphagnum. The results suggest that interspecific variation in various measures of growth, decomposability, and litter biochemistry is phylogenetically conserved in Sphagnum, meaning that closely related species tend to be more similar in trait values than species selected at random from the phylogeny. Furthermore, these results suggest that patterns of trait covariation might represent adaptive syndromes related to niche. This is the first study to formally relate functional trait variation in Sphagnum to its evolutionary history.

In Chapter 3, a field experiment and phylogenetic comparative methods are used to show that natural selection is responsible for shaping interspecific variation in Sphagnum decomposability and its coevolution with niche. In the largest experiment of its kind to date, litter decomposability was measured for over 50 species of Sphagnum under natural conditions. Models of trait evolution were competed against one another to determine which best explained the evolution of this important functional trait. The best model was a multiple-peak Ornstein-Uhlenbeck process wherein the predominantly hummock and hollow clades of Sphagnum possess separate adaptive optima towards which trait values are pulled. Furthermore, the results suggest that shifts in trait optima occurred concomitantly with shifts in realized niche along the hummock-hollow gradient.

In Chapter 4, comparative genomics is used to identify genes involved in the biosynthesis of an ecologically-important class of secondary metabolites, the anthocyanins, and determine when this biosynthetic pathway first evolved in embryophyte land plants. In Sphagnum, complex phenolic molecules embedded in the cell walls influence litter decomposability and, in turn, the rate of peat accumulation. One group of such phenolics, the sphagnorubins, confer red-violet pigmentation to some species of Sphagnum. Sphagnorubins are thought to be homologous to anthocyanin pigments, known best from flowering plants, that have numerous roles including mitigation of abiotic stress. Phylogenetic analyses using full genome sequences representing nearly all major green plant lineages show that the entire anthocyanin biosynthetic pathway was not intact until the most recent common ancestor of seed plants. Furthermore, orthologs of many downstream enzymes in the pathway are absent from seedless plants including mosses, liverworts, and ferns. These results suggest that the production of red-violet flavonoid pigments in seedless plants, including sphagnorubins, requires the activity of novel enzymes and represents convergent evolution of red-violet coloration across land plants.

In Chapter 5, comparative genomics is used to test for molecular adaptation in Sphagnum genomes. Two reference-quality peat moss genomes were compared to those from other plants to identify genes bearing signatures of positive selection and gene families marked by significant rates of expansion in the Sphagnum lineage. Gene Ontology enrichment analyses were then used to identify over-represented classes of genes that might have been particularly important during the evolution of peat mosses. The results suggest adaptive evolution largely occurred in genes and gene families related to epigenetic regulation, secondary metabolism, stress response, and transmembrane transport. Together, these data suggest that selection favored changes to genes involved in response to environmental stress and provide candidate loci that might underlie adaptation to the harsh conditions of boreal peatlands.

How geographical distance and historical events affect patterns of population divergence and gene flow is an important question in evolution and biogeography. Sphagnum subgenus Acutifolia is one of the four major subgenera of Sphagnum peatmoss comprising numerous species with broad geographic ranges and diverse ecological niches within wetland habitats. One group of particular interest within the subgenus is the S. capillifolium complex which contains at least seven closely related species. Five species within the complex are circumboreal and all have overlapping geographic ranges, one species is endemic to subtropical region of eastern North America, and one species is in the tropical regions of Central and South America. The presence of both species with overlapping and disjunct distributions makes the Sphagnum capillifolium complex a natural experiment to investigate gene flow and population divergence in multiple phylogenetic scales (within and between species). Chapter 1 describes patterns of phylogenetic discordance across the genome in the Sphagnum capillifolium complex using whole genome resequencing data. The species tree phylogeny was generally well supported but phylogenetic discordance among genomic regions was prevalent, especially at nodes in the backbone. Alternative topologies for each of the backbone nodes were not random, suggesting the presence of introgression, in addition to incomplete lineage sorting (ILS). Analyses of introgression signals using ABBA/BABA tests and branch length distributions (QuIBL) showed that there were several possible introgression events within the S. capillifolium complex involving both extant and ancestral species. Most of the introgression events occurred between species that currently have overlapping geographic ranges. Further investigation of one introgression event using comparisons of terminal branch lengths showed that the biased pattern of shared derived alleles likely derives from introgression, not ancient polymorphism. These findings show that introgression played a significant role in generating phylogenetic incongruence within the S. capillifolium complex. We also show that the use of multiple phylogenomic methods and investigating localized genomic regions are essential to infer complex introgression scenarios. Chapter 2 describes phylogenetic structure of Sphagnum subgenus Acutifolia and population structure of circumboreal species within the S. capillifolium complex. Genome scale data (RAD-seq) was generated for the subgenus, with an intensive population sampling of circumboreal species within the S. capillifolium complex. Most of the species are resolved as monophyletic, although relationships among species are weakly supported in some parts of the phylogeny. Some currently recognized species are phylogenetically discernable while others are not distinguishable from the well-supported species. Within the S. capillifolium complex, five circumboreal species show similar patterns of population structure. One population system comprises plants in eastern North America and Europe, and sometimes includes plants from eastern Eurasia and the Pacific Northwest of North America. Another group comprises plants in the Pacific Northwest, or around the Beringian and Arctic regions. Our results suggest that populations of circumboreal species survived in multiple refugia during the last glacial maximum (LGM). Long-distance dispersal out of refugia, population bottlenecks, and possible adaptations to conditions unique to each refugium contribute to current geographic patterns. There are patterns of genetic admixture among distinct genotype groups within species in some restricted areas. Alaska is a hotspot for both intraspecific genetic diversity and admixture. These genetic results indicate the important role of historical events, especially Pleistocene glaciation, in shaping the complex population structure of plants with broad distribution ranges. Chapter 3 assesses the pattern of gene flow between a pair of sister Sphagnum species within the S. capillifolium complex: S. warnstorfii and S. talbotianum. The two species have different distribution ranges: S. warnstorfii is circumboreal while S. talbotianum is circumarctic, but they overlap in Alaska. Genetic data from chapter 2 were used in this chapter. Analyses of interspecific gene flow and population sizes were accomplished using coalescent simulations of site frequency spectra (SFSs), and the signature of gene flow was further corroborated by ABBA/BABA statistics. Our results indicate that S. warnstorfii and S. talbotianum were isolated after divergence. S. warnstorfii was relatively recently established in Alaska and Alaska is the only region that shows evidence of gene flow between S. talbotianum and S. warnstorfii. Gene flow occurred in only one direction from S. talbotianum into S. warnstorfii, which can possibly help S. warnstorfii survive in subarctic conditions. Molecular evidence further suggests gene flow from Alaska S. warnstorfii to other regional populations of that species. S. warnstorfii suffered a stronger population bottleneck than S. talbotianum, suggesting that Beringia could have harbored larger populations during the last glacial maximum than other, likely more southern, refugia. Although the two species are very closely related, S. talbotianum has larger pores on the convex surfaces of branch leaf apices than S. warnstorfii. Our results represent a case study of a recent gene flow between geographically sympatric peatmoss species using genomic data. Our results also support S. talbotianum as a distinct species from S. warnstorfii.

Morphological characters from the gametophyte and sporophyte generations have been used in land plants to infer relationships and construct classifications, but sporophytes provide the vast majority of data for the systematics of vascular plants. In bryophytes both generations are well developed and characters from both are commonly used to classify these organisms. However, because morphological traits of gametophytes and sporophytes can have different genetic bases and experience different selective pressures, taxonomic emphasis on one generation or the other may yield incongruent classifications. The moss order Hookeriales has a controversial taxonomic history because previous classifications have focused almost exclusively on either gametophytes or sporophytes. The Hookeriales provide a model for comparing morphological evolution in gametophytes and sporophytes, and its impact on alternative classification systems. Sometimes, placement of certain groups within Hookeriales remains challenging even at the molecular level. That is the case of the genus Calyptrochaeta. We study diversification dynamics in this genus to elucidate possible mechanisms obscuring its placement and we address biogeographic questions using the Tropical Conservatism scenario as our null hypothesis. Furthermore, to better understand biogeographic patterns in the Southern Hemisphere, infraspecific molecular patterns are compared in two species of the genus Calyptrochaeta (i.e., C. apiculata and C. asplenioides) and vicariance and recent long distance dispersal are tested to explain the disjunct distributions observed in these species.

In this study we reconstruct relationships among pleurocarpous mosses in or associated to the Hookeriales, in Calyptrochaeta, and within Calyptrochaeta. Six molecular markers are explored in total from all three genome compartments to reconstruct the evolution of morphological characters and habitat preferences in our phylogenies. Divergence times are estimated in a Bayesian framework using a relaxed molecular clock, and diversification rates are calculated on the chronograms resulting from these estimations.

As a result, we found that the Hookeriales, as currently circumscribed, are monophyletic and that both sporophyte and gametophyte characters are labile. We documented parallel changes and reversals in traits from both generations. We show that diversification rates in Calyptrochaeta have changed through its history. Also, though we lack support to clearly reject the tropical conservatism hypothesis, our data point to a more complex scenario where both temperate and tropical species can be ancient and give rise to one another, since shifts between tropical and temperate regions seem to be possible in any direction. Finally, we have show that recent long distance dispersal best explains the distribution of both C. apiculata and C. asplenioides in the Southern Hemisphere.

The delineation of closely related plant species is difficult, as finding a discrete and distinct set of characters can be problematic in taxa that exhibit extreme morphological variability. Such difficulties arise in the genus Sphagnum because of its diversity and variability, as well as its propensity to hybridize. This study asks (1) do the five Norwegian morphospecies of the Sphagnum recurvum complex, a group of closely related and taxonomically controversial boreal species, correspond to genetically distinct entities? And (2) are morphologically intermediate plants a result of phenotypic plasticity or interspecific hybridization? Using “next generation” RADseq-based phylogenetic analyses, three highly distinct clades emerged, corresponding to S. angustifolium, S. flexuosum, and a clade containing S. fallax, S. isoviitae and S. brevifolium. This result suggests the boundaries of S. fallax should be expanded. The lack of genetic differentiation among the members of the S. fallax clade and the clear separation of the three clades was supported by DAPC multivariate clustering and a novel analysis comparing the lineages revealed by individual loci. These analyses also tested for genetic admixture within plant samples. However, there were no intermediate samples between the genetic clusters discerned from any of the analyses, and the phylogenetic tree demonstrates strong clade cohesion. This lack of genetic intermediates suggests that the morphological variation observed in these populations is likely to be due to intraspecific genetic variation or phenotypic plasticity. A revised key and diagnoses for Norwegian species in the Sphagnum recurvum complex is provided to facilitate identification by collectors.