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• 1. [Article] Evaluating the Influence of Policy and Technology in Driving Aquaculture Land Use Patterns in Thailand, 1990-2013

  Since the 1980's shrimp aquaculture has been one of Thailand's largest industries and has created cultivation ponds as a dominant feature on the landscape. While shrimp farming has been economically successful, ...

  Citation × Citation Citation Abstract Copy Title: Evaluating the Influence of Policy and Technology in Driving Aquaculture Land Use Patterns in Thailand, 1990-2013 Author: Mosurinjohn, Nathan Year: 2014 Since the 1980's shrimp aquaculture has been one of Thailand's largest industries and has created cultivation ponds as a dominant feature on the landscape. While shrimp farming has been economically successful, it has received criticism for being environmentally harmful, most notably because of farms replacing mangrove forests. Legislation regulating aquaculture development and technological responses to disease outbreak have had a large influence on the land use of the Thai coast. The objective of this research is to provide a systematic examination of how regulation and technology development have influenced land use in this region. To accomplish this, Landsat derived data were analyzed at the national and provincial scale to determine how Thai coastal land use systems change over time. I found that interrelated changes in technology and legislation have had complex influences on the landscape, which encourage both the restriction and expansion of aquaculture growth depending on time and location. Title: Evaluating the Influence of Policy and Technology in Driving Aquaculture Land Use Patterns in Thailand, 1990-2013 Author: Mosurinjohn, Nathan Year: 2014 Since the 1980's shrimp aquaculture has been one of Thailand's largest industries and has created cultivation ponds as a dominant feature on the landscape. While shrimp farming has been economically successful, it has received criticism for being environmentally harmful, most notably because of farms replacing mangrove forests. Legislation regulating aquaculture development and technological responses to disease outbreak have had a large influence on the land use of the Thai coast. The objective of this research is to provide a systematic examination of how regulation and technology development have influenced land use in this region. To accomplish this, Landsat derived data were analyzed at the national and provincial scale to determine how Thai coastal land use systems change over time. I found that interrelated changes in technology and legislation have had complex influences on the landscape, which encourage both the restriction and expansion of aquaculture growth depending on time and location. Close

• 2. [Article] Woven Into the Community: Resilience and Tsunami Evacuation Route Configuration in Neskowin, Oregon

  89 pages. Examining committee chair: Chris Enright

  Citation × Citation Citation Abstract Copy Title: Woven Into the Community: Resilience and Tsunami Evacuation Route Configuration in Neskowin, Oregon Author: Davis, Bryn Year: 2017 89 pages. Examining committee chair: Chris Enright Title: Woven Into the Community: Resilience and Tsunami Evacuation Route Configuration in Neskowin, Oregon Author: Davis, Bryn Year: 2017 89 pages. Examining committee chair: Chris Enright Close

• 3. [Article] Recombination Rate Heterogeneity Compartmentalizes Genomic Variation and Facilitates Adaptive Evolution in the Threespine Stickleback

  72 pages. A thesis presented to the Department of Biology and the Clark Honors College of the University of Oregon in partial fulfillment of the requirements for degree of Bachelor of Science, Spring 2...

  Citation × Citation Citation Abstract Copy Title: Recombination Rate Heterogeneity Compartmentalizes Genomic Variation and Facilitates Adaptive Evolution in the Threespine Stickleback Author: Crandall, Johnathan Gage Williams Year: 2017 72 pages. A thesis presented to the Department of Biology and the Clark Honors College of the University of Oregon in partial fulfillment of the requirements for degree of Bachelor of Science, Spring 2017 Title: Recombination Rate Heterogeneity Compartmentalizes Genomic Variation and Facilitates Adaptive Evolution in the Threespine Stickleback Author: Crandall, Johnathan Gage Williams Year: 2017 72 pages. A thesis presented to the Department of Biology and the Clark Honors College of the University of Oregon in partial fulfillment of the requirements for degree of Bachelor of Science, Spring 2017 Close

• 4. [Article] THE ORIGINS AND MAINTENANCE OF GENOMIC VARIATION IN THE THREESPINE STICKLEBACK (Gasterosteus aculeatus)

  Genetic variation is the raw material of evolution. The sources of this variation within a population, and its maintenance within a species, have been mysterious since the birth of the field of evolutionary ...

  Citation × Citation Citation Abstract Copy Title: THE ORIGINS AND MAINTENANCE OF GENOMIC VARIATION IN THE THREESPINE STICKLEBACK (Gasterosteus aculeatus) Author: Nelson, Thomas Year: 2017 Genetic variation is the raw material of evolution. The sources of this variation within a population, and its maintenance within a species, have been mysterious since the birth of the field of evolutionary genetics. In this work, I study divergently adapted freshwater and marine populations of the threespine stickleback (Gasterosteus aculeatus) as an evolutionary model to track the origin of adaptive genetic variation and to describe the evolutionary processes maintaining variation across the genome. The stickleback is a small fish with a large geographic range encompassing the northern half of the Northern Hemisphere and composed of coastal marine habitats, freshwater lakes, and river systems. Populations of stickleback adapt rapidly to changes in habitat, and fossil evidence suggests that similar adaptive transitions have been ongoing in this lineage for at least ten million years. In this work, I develop a significant extension of restriction site-associated DNA sequencing (RAD-seq) to generate phased haplotype information to estimate gene tree topologies and divergence times at thousands of loci simultaneously. I find anciently derived clades of variation associated with marine and freshwater habitats in genomic regions involved in recent adaptive divergence; some divergence times extend to over ten million years ago. This history of adaptive divergence has had profound effects on genetic variation elsewhere in the genome: chromosomes harboring freshwater-adaptive variants retain anciently derived variation in linked genomic regions, while marine chromosomes have much more recent ancestry. I present a conceptual model of asymmetric selective and demographic processes to explain this result, which will form a nucleus for future research in this species. Lastly, by incorporating genome-wide recombination rates estimated from multiple genetic maps, I describe a recombination landscape that is favorable to the maintenance of marine-freshwater genomic divergence. Low recombination rates in key chromosomal regions condense widespread divergence of the physical genome, encompassing many megabases, into a small number of Mendelian loci. Combined, my results demonstrate the interconnectedness of evolutionary processes taking place on ecological and geological timescales. The genetic variation available for adaptive evolution today is a product of the long-term evolutionary history of a species. Title: THE ORIGINS AND MAINTENANCE OF GENOMIC VARIATION IN THE THREESPINE STICKLEBACK (Gasterosteus aculeatus) Author: Nelson, Thomas Year: 2017 Genetic variation is the raw material of evolution. The sources of this variation within a population, and its maintenance within a species, have been mysterious since the birth of the field of evolutionary genetics. In this work, I study divergently adapted freshwater and marine populations of the threespine stickleback (Gasterosteus aculeatus) as an evolutionary model to track the origin of adaptive genetic variation and to describe the evolutionary processes maintaining variation across the genome. The stickleback is a small fish with a large geographic range encompassing the northern half of the Northern Hemisphere and composed of coastal marine habitats, freshwater lakes, and river systems. Populations of stickleback adapt rapidly to changes in habitat, and fossil evidence suggests that similar adaptive transitions have been ongoing in this lineage for at least ten million years. In this work, I develop a significant extension of restriction site-associated DNA sequencing (RAD-seq) to generate phased haplotype information to estimate gene tree topologies and divergence times at thousands of loci simultaneously. I find anciently derived clades of variation associated with marine and freshwater habitats in genomic regions involved in recent adaptive divergence; some divergence times extend to over ten million years ago. This history of adaptive divergence has had profound effects on genetic variation elsewhere in the genome: chromosomes harboring freshwater-adaptive variants retain anciently derived variation in linked genomic regions, while marine chromosomes have much more recent ancestry. I present a conceptual model of asymmetric selective and demographic processes to explain this result, which will form a nucleus for future research in this species. Lastly, by incorporating genome-wide recombination rates estimated from multiple genetic maps, I describe a recombination landscape that is favorable to the maintenance of marine-freshwater genomic divergence. Low recombination rates in key chromosomal regions condense widespread divergence of the physical genome, encompassing many megabases, into a small number of Mendelian loci. Combined, my results demonstrate the interconnectedness of evolutionary processes taking place on ecological and geological timescales. The genetic variation available for adaptive evolution today is a product of the long-term evolutionary history of a species. Close