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京都大学 / 新制・課程博士 / 博士(理学) / 甲第24453号 / 理博第4952号 / 新制||理||1707(附属図書館) / 京都大学大学院理学研究科生物科学専攻 / (主査)教授 森 哲, 教授 中務 真人, 教授 中川 尚史 / 学位規則第4条第1項該当 / Doctor of Science / Kyoto University / DGAM

Evolutionary relationships are key to modern understanding of biological systems. Phylogenetic search is the means by which these relationships are inferred. Phylogenetic search is NP-Hard. As such it is necessary to employ heuristic methods. This work proposes new methods based on viewing the relationships between species as sets of partitions. These methods produce more parsimonious phylogenies than current methods.

Marstonia lustrica is a poorly understood aquatic snail, relatively rare throughout its range and listed in the State of Massachusetts as Endangered (MNHESP 2010, Hershler et. al 1987). It is the northern-most cold temperate species of its genus, with other members of the genus occurring along the southern edge of its range and in the southeastern United States (Thompson 1977). The current range of M. lustrica appears to follow the maximum extent of the Laurentide Glacier (20–25 kya), extending from Minnesota to western Massachusetts. Research regarding the distribution, ecology, and phylogeny of M. lustrica in the State of Massachusetts and eastern New York raised the possible role of glaciers and pro-glacial lakes in the establishment and distribution of the snail, leading to the hypothesis that its distribution and evolution may be dependent upon glacial processes. A full range survey was completed in 2007 and 2008, with populations identified in 20 water bodies from Minnesota to Massachusetts, and Ohio to Ontario, Canada. Fifty-seven specimens from the 20 populations were sequenced for two mtDNA markers (COI and NDI), developing both phylogenetic trees and haplotype networks. Here I present those trees and networks, and correlate the distribution of these populations and their representative haplotypes with both glacial events and contemporary watersheds, using AMOVAs and Mantel tests to examine several v phylogeographic models. In addition to the results for M. lustrica, the unexpected occurrence of several other species of Marstonia spp. found across the range of M. lustrica are presented, including M. pachyta, M. comalensis, and M. hershleri.

A fundamental goal of evolutionary biology is to understand what processes have led to the great diversity of organisms we see today. An important factor of diversification is an organism’s environment. Abiotic factors can shape the evolutionary trajectory of species by affecting fundamental mechanisms of evolution, including mutation, gene flow, genetic drift, and natural selection. In my thesis, I investigated how abiotic factors, such as habitat and landscape, have influenced the genetic diversification of catfishes (Siluriformes). More specifically, I compared genetic data within and between species to understand how natural barriers have shaped the origins and evolutionary trajectory of species. In Chapter 1, I investigated whether habitat preferences and segregation of breeding populations in lacustrine-like and fluvial habitats affected the genetic structure of a sympatric population of channel catfish (Ictalurus punctatus). In Chapter 2, I elucidated the origins of cave species within North American catfishes (Ictaluridae), determining whether they shared a common ancestor or evolved in parallel from surface-dwelling ancestors. In Chapter 3, I tested whether impermeable and semi-permeable boundaries between South American river basins have restricted gene flow and resulted in potentially new species within the widespread ornate pim catfish (Pimelodus ornatus). In Chapter 4, I determined whether orogenesis and river capture corresponded with speciation events and cladogenesis within Neotropical long-whiskered catfishes (Pimelodidae). Throughout my thesis, I observed evolutionary patterns related to gene flow, vicariance, and dispersal. Physical barriers imposed on populations often coincided with genetic diversification and allopatric speciation. These barriers reduced gene flow, allowing populations to genetically diverge in response to unique selective pressures. As these barriers changed over time, dispersal opportunities may have further promoted diversification as species radiated into new areas. I also observed that ecological gradients, such as water chemistry, may have facilitated parapatric speciation; however, differences between habitats do not always restrict gene flow. Given that patterns of genetic diversification and speciation are not uniform across the tree of life, it is important for evolutionary biologists to document trends among different taxa to elucidate macroevolutionary patterns.

Arbuscular mycorrhizal (AM) fungi are ubiquitous symbionts of terrestrial plant species with associations predominantly characterized as mutualistic. In addition to well-documented enhancement of host growth response, more recent analyses have demonstrated the conferral of host benefits under numerous biotic and abiotic stressors. However, much of the established evidence originates from studies involving limited AM fungal diversity. Accordingly, this study sought to evaluate the potential effects of inoculation on plant host physiological traits within a growth chamber environment, investigate potential correlations between host trait responses, & assess the degree of phylogenetic signal observed in trait responses due to the presence of AM fungi. Overall, inoculation did not result in meaningfully different effects in host trait responses relative to controls. The effects of unique inoculum identity were also not meaningfully different from one another, although some instances of deviation from this trend were observed. Trait correlations were also largely absent after accounting for species relatedness. Further, model selection criteria tended to endorse an effect of unique inoculum identity but was not suggestive of effects due to evolutionary history. The presently described experimental implementation of AM phylogenetic diversity, comprising 36 taxa across 8 families, contributes to a greater contextual understanding of the AM symbiosis and offers an approach suitable for future studies.

Phylogenomics, the study of genome-scale data containing many genes and species, has advanced our understanding of patterns of evolutionary relationships and processes throughout the Tree of Life. Recent research studies frequently use such large-scale datasets with the expectation of recovering historical species relationships with high statistical confidence. At the same time, the computational complexity and resource requirements for analyzing such large-scale data increase with the number of genomic loci and sites. Therefore, different crucial steps of phylogenomic studies, like model selection and estimating bootstrap confidence limits on inferred phylogenetic trees, are often not feasible on regular desktop computers and generally time-consuming on high-performance computing systems. Moreover, increasing the number of genes in the data increases the chance of including genomic loci that may cause biased and cause fragile species relationships that spuriously receive high statistical support. Such data errors in phylogenomic datasets are major impediments to building a robust tree of life. Contemporary approaches to detect such data error require alternative tree hypotheses for the fragile clades, which may be unavailable a priori or too numerous to evaluate. In addition, finding causal genomic loci under these contemporary statistical frameworks is also computationally expensive and increases with the number of alternatives to be compared. In my Ph.D. dissertation, I have pursued three major research projects: (1) Introduction and advancement of the bag of little bootstraps approach for placing the confidence limits on species relationships from genome-scale phylogenetic trees. (2) Development of a novel site-subsampling approach to select the best-fit substitution model for genome-scale phylogenomic datasets. Both of these approaches analyze data subsamples containing a small fraction of sites from the full phylogenomic alignment. Before analysis, sites in a subsample are repeatedly chosen randomly to build a new alignment that contains as many sites as the original dataset, which is shown to retain the statistical properties of the full dataset. Analyses of simulated and empirical datasets exhibited that these approaches are fast and require a minuscule amount of computer memory while retaining similar accuracy as that achieved by full dataset analysis. (3) Development of a supervised machine learning approach based on the Evolutionary Sparse Learning framework for detecting fragile clades and associated gene-species combinations. This approach first builds a genetic model for a monophyletic clade of interest, clade probability for the clade, and gene-species concordance scores. The clade model and these novel matrices expose fragile clades and highly influential as well as disruptive gene-species candidates underlying the fragile clades. The efficiency and usefulness of this approach are demonstrated by analyzing a set of simulated and empirical datasets and comparing their performance with the state-of-the-art approaches. Furthermore, I have actively contributed to research projects exploring applications of these newly developed approaches to a variety of research projects. / Biology

The deep ocean holds a diversity of life that remains to be discovered and described. Marine ecosystems fueled by chemosynthesis, such as hydrothermal vents and hydrocarbon seeps, represent biodiversity hotspots along the ocean floor. Yet, investigations into the diversity, genetic connectivity, and biogeography of life at such ecosystems are still ongoing. The present dissertation explores the diversity and biogeography of deep-sea gastropod mollusks from hydrocarbon seeps at the Pacific Costa Rica Margin to understand what factors lead to the generation and maintenance of novel biodiversity at chemosynthesis-based ecosystems in the ocean. The Pacific Costa Rica Margin was extensively sampled and explored between 2017 and 2019 and yielded an abundance and diversity of marine life. Gastropod mollusks were chosen as the model organisms for this research as they are taxonomically diverse, are found in high abundance, and occur at chemosynthesis-based ecosystems worldwide. Integrating taxonomic, phylogenetic, population genetic, and biogeographic methods, this dissertation contributes new species, occurrence records, genetic data, taxonomic tools, and biogeographic knowledge for deep-sea gastropods. As global biodiversity continues to be threatened by anthropogenic impacts such as overexploitation and climate change, documenting and understanding deep-sea biodiversity and the factors that influence it is of critical importance. / Biology

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