<p>Maintaining high genetic diversity within and among wildlife populations is an important component to the management of threatened species. Population genomics utilizes recent advancements in high-throughput next-generation sequencing to obtain genome-wide data that can yield deeper perspectives on intraspecific genetic variation and elucidate evolutionary significant units that may require conservation management or augmentation. The semi-aquatic Blanding’s Turtle (<i>Emydoidea blandingii</i>) has experienced drastic population declines in North America due in large part to anthropogenic activities. This species is listed as threatened or endangered across most of its range. A population genomic study can help to understand the status of this species and guide future management practices. Hence, a population genomic analysis was conducted using 3RAD to discover and analyze SNPs across the range using samples from Nebraska, Indiana, Michigan, Ohio, and Nova Scotia,. Range-wide analysis used 8,602 SNPs while analysis within the Great Lakes region used 7,893 SNPs. High amounts of missing data were found across all individuals and loci. Low levels of genetic variation relative to other turtle species were detected both across the range and within the Great Lakes region. Minimal population structure was detected range-wide via clustering and admixture analyses; however, a signal of population differentiation was detected among Nebraska, Nova Scotia, and the Great Lakes. Clustering and differentiation analyses focused on the Great Lakes region found a signal of population structure and differences between the Lake Michigan and Lake Erie watershed. These results may prove useful for conservation management of Blanding’s Turtle populations, particularly related to efforts using translocation or head-starting practices.</p>

Horizontal gene transfer (HGT) and gene loss are important processes in the evolution of prokaryotic lineages. HGT involves the movement of genetic material between distantly related species, and can facilitate adaptation when gained genes confer advantageous phenotypes to recipient lineages. However, high levels of gene gain and loss are predicted to obfuscate patterns of vertical descent and homogenise nucleotide diversity across ecological and phylogenetic boundaries. Thus, a holistic understanding of the role of genome fluctuation in the emergence and maintenance of genetically and ecologically cohesive bacterial groups remains to be fully elucidated. In this thesis, I use the plant-associated bacterium Pseudomonas syringae as a model system to investigate the impact of HGT and gene loss on evolutionary processes such as adaptation, diversification and speciation. The Gram-negative Gammaproteobacterium P. syringae is an opportunistic plant pathogen, and has been used for decades as a model system with which to study the interaction between plants and their microbial pathogens. Recently, the diversification of lineages within this species has involved a number of host jumps onto a range of woody host plant species, resulting in the emergence of diseases such as bacterial canker of kiwi and bleeding canker of the European horse chestnut. Using whole-genome sequence data and a range of comparative genomics and phylogenetics methods, I quantitatively reconstruct the history of gene gain and loss in P. syringae and show HGT to be the predominant evolutionary force in this species. Genomes of this species are under constant permutation, are subject to a highly diverse HGT genepool and show marked differences in patterns of codon usage between imported and core genes. I then generate additional genome data for 26 strains of P. syringae that are pathogenic on a range of different woody plants, and investigate the contribution from HGT to the adaptation of these strains into the woody niche. Using a method that accounts for the underlying phylogenetic relationships among P. syringae strains, I look for the correlated evolution between gained genes and the woody niche, and find that a substantial proportion of the genome is associated with this ecological niche. I then investigate the recent adapitation of P. syringae pv. aesculi onto the European horse chestnut, and show that a number of genomic events that include both homologous and non-homologous recombination are likely to have led to the evolution of this bacterium onto its host, where it has become the causal agent of the bleeding canker disease that is currently epidemic across much of northern and central Europe. Overall, this thesis is an investigation into how HGT contributes to niche adaptation in P. syringae, and aims to further our understanding of the mechanisms that underlie bacterial evolution.

Marine organisms occupy environments spanning wide distributions of conditions across large (e.g., latitudinal gradients) and small (e.g., different depths) scales. Populations that exist across these environments might be adapted to local conditions and exhibit genetic divergence between habitats, sometimes to the point of becoming different species or lineages within a species complex. Corals are excellent organisms in which to study dynamics across large geographic ranges spanning divergent environments. They not only contain many species rich genera and exhibit local adaptation and long-range dispersal potential, but they are also the structural engineers of coral reef ecosystems that are facing serious threat from warming oceans, acidification, and other anthropogenic disturbances. Thus, investigating mechanisms of adaptation to environmental conditions in corals is critical because these processes also secondarily impact many reef-dependent marine organisms. My dissertation investigates population genomic variation across different ecological (latitudinal, local and within colony gradients) and evolutionary (populations and species) scales. First, I obtained samples of the ubiquitous pacific reef-building coral Acropora hyacinthus from its subtropical habitat in the Ryukyus Islands and temperate habitat in mainland Japan and uncovered the presence of three cryptic lineages in the region. Of these three, only one exists in temperate environments and this lineage has also recently expanded its range even further north along the coast of mainland Japan with warming oceans. I found genetic structure separating the recently expanded site and the other northernmost edge sites from core temperate sites. This divergence existed despite a model of larval dispersal suggesting higher connectivity of marginal and core sites relative to pairs of marginal sites. These findings suggest that cryptic lineages evolved to occupy different niches along a latitudinal gradient and that range expansion has been facilitated by adaptions to higher latitudes. Second, I investigated the role of the coral’s algal symbiont and bacterial communities in adaptation across smaller spatial scales by characterizing these communities in the massive scleractinian coral Porites lobata across a sedimentation gradient and across individual colonies in Guam. I found that both algal and bacterial communities varied within a single colony, but only bacteria showed clear structuring by colony position and only rare bacterial taxa were structured by the sedimentation gradient. Lastly, I investigated the contributions of host and symbiont to thermal adaptation in the facultatively symbiotic corals Astrangia and Oculina. I uncovered the existence of four genetic lineages of coral, two within each genus, with inter-lineage differences in distributions, thermal performance, and symbiotic partnerships. I also found evidence for shared genetic variation between Oculina and Astrangia when they exist sympatrically, suggesting the potential for adaptive introgression between these lineages. The findings of this dissertation shed light on the complex and dynamic nature of coral populations, highlighting the importance of considering multiple spatial scales and levels of evolutionary divergence when studying adaptation in marine organisms. Overall, this dissertation advances our understanding of the population genomics of corals and the ecological and evolutionary processes that shape their adaptation to diverse environments.

Studying the microbiome in natural populations could improve our understanding of the biological factors that influence microbiome variation. If host genetic variation is important in microbiota assembly, then understanding genetic divergence among natural populations could be informative. Despite advances in sequencing technology, we have not yet taken full advantage of this technology in natural populations. Here we integrate genome-wide population genomic and microbiome analyses in wild threespine stickleback (Gasterosteus aculeatus) fish distributed throughout western Oregon, USA. We found that gut microbiome varied in diversity and composition more among than within wild host populations. Furthermore, this among population variation was better explained by host population genetic divergence than by environment and geography. We also identified a subset of gut microbial taxa that were most strongly sorted both across environments and across genetically divergent populations. We believe this study contributes generalizable methods and findings in host systems. This thesis includes supplemental materials. / 2021-04-30

The ancient continent of Sahul, encompassing Australia, New Guinea and Tasmania, contains some of the earliest archaeological evidence for humans outside of Africa, dating back to at least 50 thousand years ago (kya). New Guinea was also one of the sites were humans developed agriculture in the last 10 thousand years. Despite the importance of this part of the world to the history of humanity outside Africa, little is known about the population history of the people living here. In this thesis I present population-genetic studies using whole-genome sequencing and genotype array datasets from more than 500 indigenous individuals from Australia and New Guinea, as well as initial work on large-scale sequencing of other, worldwide, human populations in the Human Genome Diversity Project panel. Other than recent admixture after European colonization of Australia, and Southeast Asian ad- mixture in the lowlands of New Guinea in the last few millennia, the populations of Sahul appear to have been genetically independent from the rest of the world since their divergence ∼50 kya. There is no evidence for South Asian gene flow to Australia, as previously suggested, and the highlands of Papua New Guinea (PNG) have remained unaffected by non-New Guinean gene flow until the present day. Despite Sahul being a single connected landmass until ∼8 kya, different groups across Australia are nearly equally related to Papuans, and vice versa, and the two appear to have separated genetically already ∼30 kya. In PNG, all highlanders strikingly appear to form a clade relative to lowlanders, and population structure seems to have been reshaped, with major population size increases, on the same timescale as the spread of agriculture. However, present- day genetic differentiation between groups is much stronger in PNG than in other parts of the world that have also transitioned to agriculture, demonstrating that such a lifestyle change does not necessarily lead to genetic homogenization. The results presented here provide detailed insights into the population history of Sahul, and sug- gests that its history can serve as an independent source of evidence for understanding human evolutionary trajectories, including the relationships between genetics, lifestyle, languages and culture.

Southern African populations harbour great genetic diversity enhanced by  population migration to the area in the last two millennia. Africa is perhaps the least studied continent in regards to population genetics and is often underrepresented in global studies. Studying sex-biased admixture in admixed populations is a great tool to understand population demographic history as well as sex-biased admixture from past events. Various studies on sex-biased admixture in Southern Africa have shown male sex-biased admixture from the incoming Bantu-speaking populations. One study by Hollfelder (2018) shows female Bantu-speaking sex-biased admixture. Here I will try to determine if ascertainment bias is the cause of the unexpected results in Hollfelder (2018). I will do this by comparing the original results, genotyped using the Illumina Omni 2.5M Array, to overlapping SNPs in two different arrays, the Affymetrix Human Origin Array and the Infinium H3Africa Consortium Array. Additionally, I will use whole genome data containing same individuals and individuals from similar populations to form a hypothesis on how the sex-biased admixture should look like without ascertainment. Then extracting variants from the whole genome data to two array SNP panels, the Illumina 2.5M Array and the Infinium H3Africa Consortium Array. For both parts in my project a method by Goldberg and Rosenberg (2015) will be used to calculate female and male contribution from admixture proportions of the X-chromosome and the autosomes estimated using the software ADMIXTURE. The results obtained could not determine if ascertainment bias was the sole factor skewing the results. The overlap with the Affymetrix Human Origin Array showed results closest to expected results based on previous studies, suggesting that ascertainment bias likely affects the results. The results attained using the whole genome indicated that the genotype calls of individuals present in both parts of the study did not fully match and that was confirmed using a principal component analysis. Unfortunatly the data used and analytical limitations in this project did not yield answers to how ascertainment bias affects calculations on sex-biased admixture. The X-chromosome is difficult to work with, especially when using data from multiple publications, as there is no standard common best-practice pipeline available on how to process the data leading to different data sets having been treated differently, which possibly affects downstream analysis when combining data sets.

Northern Pike (Esox lucius) is an economically and ecologically valuable species with a circumpolar distribution across the Northern Hemisphere. Northern Pike have been shown to have low levels of genetic variation despite their great capacity to colonize new environments. Here, high-resolution resequencing data from 47 Northern Pike from across North America was used for SNP discovery and population analysis. Our analysis reveals an extraordinary lack of genetic variation among Northern Pike with observed heterozygosity (Ho) of just 0.0835. Our analyses suggest that two major groups of Northern Pike exist in North America that are separated by the North American Continental Divide. Genetic variation associated with the stratification of these two groups resides across the genome particularly in gene regions with multiple copy number variants and functions related to immunity, tissue permeability, and development. Northern Pike from Alaska and the Yukon River harbour about two times more heterozygosity than Northern Pike east of the Continental Divide with an average of one heterozygous SNP every 6,250 bases. Populations east of the Continental Divide possess a remarkable level of genetic homogenization with an average of just one heterozygous SNP every 16,500 bases. For comparison, an average of one heterozygous SNP per 309 bases was reported in herring (Martinez Barrio et al., 2016), one per 500 in Atlantic cod (Star et al., 2011), and one per 750 bases in Coho and chinook salmon (Koop, 2018). This is at least 5 – 10 fold less variation than is seen in humans (the 1000 Genomes Project Consortium, 2015). We observed a recently described master sex-determining gene, amhby, in three western North American populations but not in populations east of the Continental Divide. We could not resolve any signals indicating a genetic sex determination system was present in populations from southern Manitoba or the St. Lawrence River. This may indicate that environmental sex determination is at play in these populations. We found evidence of a possible female-heterozygous, male homozygous ZW-ZZ genetic sex-determination system in New Jersey Northern Pike. With the highest average of 181,268 heterozygous SNPs genome wide and the greatest Ho (0.3228) of all populations, as well as the presence of the sex-determining gene amhby indicate that Northern Pike from our Alaskan population are the oldest in North America. Fewer numbers of heterozygous SNPs (61,073), low Ho (0.0922), and the absence of amhby in Northern Pike east of the Continental Divide suggests that these are relatively young populations and are descended from a small founding population. These results imply that Northern Pike first came to North America through Beringia and colonized its North American range from there, possibly via pro-glacial lake formation and drainage. However, from the data herein it was not possible to trace how re-colonization occurred after the final retreat of glaciers at the end of the last ice age. This thesis provides a genetically high-resolution snapshot of Northern Pike population structure in North America. It demonstrates that organisms with largely homogenous genomes can be incredibly successful and resilient. Finally, it adds to the complex subject of sex determination in fish and provides insight into a sex determination system in transition. / Graduate / 2020-10-15

京都大学 / 新制・課程博士 / 博士(農学) / 甲第24676号 / 農博第2559号 / 新制||農||1100(附属図書館) / 学位論文||R5||N5457(農学部図書室) / 京都大学大学院農学研究科応用生物科学専攻 / (主査)教授 寺内 良平, 教授 髙野 義孝, 教授 吉田 健太郎 / 学位規則第4条第1項該当 / Doctor of Agricultural Science / Kyoto University / DFAM

京都大学 / 0048 / 新制・課程博士 / 博士(農学) / 甲第22898号 / 農博第2441号 / 新制||農||1083(附属図書館) / 学位論文||R3||N5318(農学部図書室) / 京都大学大学院農学研究科応用生物科学専攻 / (主査)教授 松浦 健二, 教授 大門 高明, 教授 寺内 良平 / 学位規則第4条第1項該当 / Doctor of Agricultural Science / Kyoto University / DFAM

Temperate tree species exhibit seasonal growth cycling, and the timing of such transition varies with local climate. Under anthropogenic climate change, the local pattern of growth and dormancy in tree populations is expected to become uncoupled with shifting seasonal environmental signals, particularly temperature. Thus, an understanding of the genetic underpinnings of local adaptation is key to predicting the fate of tree populations in the future. In this thesis, we coupled sampling of range-wide natural accessions of P. trichocarpa with adaptive trait phenotyping and genome-wide genotyping to uncover relationships between genotype, phenotype, and environment. We detected strong correlations between adaptive phenotypes, climate, and geography, which suggested climatic selection driving adaptation of these populations to local environments. We subsequently combined genotype-phenotype association tests with sliding window analysis and identified regions strongly associated with these adaptive traits. We also compared adaptive markers identified in two independent GWAS on samples across latitude and altitude transects and found a set of associated variants shared across both transects. We further scanned the genome with three selection tests to identify regions showing evidence of recent positive and divergent selection. By comparing candidate selection regions across altitude and latitude, we detected a set of overlapping regions showing differentiation across gradients of the same climate variables. We validated the functional imortance of these selection regions by combining GWAS and showed that selection regions contain a strong signature of phenotypic associations. We also studied the distribution of deleterious allels across genome and natural populations, and found that deleterious alleles preferentially accumulate in regions of low recombination and hithihking regions. Finally, marginal populations contained more deleterious alleles compared with central populations, which is likely due to ineffective selection in small populations and recent bottlenecks associated with postglacial recolonization. These findings provide new insights into the genomic architecture underlying climatic adaptation and how selection drives adaptive evolution of tree species. / Ph. D.