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• 221. [Article] THE VERTEBRATE FAUNAS OF THE PLIOCENE RINGOLD FORMATION, SOUTH-CENTRAL WASHINGTON

  72 pages

  Citation × Citation Citation Abstract Copy Title: THE VERTEBRATE FAUNAS OF THE PLIOCENE RINGOLD FORMATION, SOUTH-CENTRAL WASHINGTON Author: GUSTAFSON, ERIC PAUL Year: 2016, 1978 72 pages Title: THE VERTEBRATE FAUNAS OF THE PLIOCENE RINGOLD FORMATION, SOUTH-CENTRAL WASHINGTON Author: GUSTAFSON, ERIC PAUL Year: 2016, 1978 72 pages Close

• 222. [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

• 223. [Article] Using Natural Populations of Threespine Stickleback to Identify the Genomic Basis of Skeletal Variation

  Across vertebrates, skeletal shapes are diverse, and much of this variation appears to be adaptive. In contrast, the early developmental programs of these structures are highly conserved across vertebrates. ...

  Citation × Citation Citation Abstract Copy Title: Using Natural Populations of Threespine Stickleback to Identify the Genomic Basis of Skeletal Variation Author: Alligood, Kristin Year: 2017 Across vertebrates, skeletal shapes are diverse, and much of this variation appears to be adaptive. In contrast, the early developmental programs of these structures are highly conserved across vertebrates. The question then becomes where in the conserved genetic programs of skeletal development does variation lie to direct diversity? In threespine stickleback, rapid changes in head and body shape have been documented during repeated and independent invasions of oceanic fish into freshwater habitats in regions deglaciated approximately 13,000 years ago. However, recent research indicates that similar phenotypic and genetic divergence can occur in decades. A remaining challenge is to link stickleback population genomic variation to causal genes that underlie such rapid phenotypic evolution. Here I use genome wide association studies (GWAS) in natural populations of stickleback to uncover genomic regions that contribute to variation of two dermal bone derived traits, lateral plate number and opercle shape. The decrease of lateral plate body armor and change in opercle bone shape, important for feeding mechanics, are classically associated with freshwater divergence. GWAS has recently begun to be used in natural populations but is still under scrutiny for performance among different populations. Using a population of phenotypically variable stickleback in Oregon, GWAS proved an effective method to uncover genomic regions and genetic variants known to contribute to lateral plate number and opercle shape, as well as new genomic regions and candidate genes not previously implicated in phenotypic variation. Although successful, using similar methods on decades old stickleback populations in Alaska revealed the challenges that accompany controlling population structure created by strong natural selection. Together, I found that although lateral plate number and opercle shape rapidly evolve in a coordinated fashion during adaptation from marine to freshwater environments, phenotypic variation is largely driven by independent genetic architectures. However, in very rapidly evolving populations, despite this independence of genetic architecture, the genetic variants contributing to the traits co-localize to similar genomic regions. This finding could be either biological or methodological which highlights the promise and limitations of using GWAS to identify genetic variation that gives rise to phenotypic diversity. This dissertation includes unpublished co-authored material. Title: Using Natural Populations of Threespine Stickleback to Identify the Genomic Basis of Skeletal Variation Author: Alligood, Kristin Year: 2017 Across vertebrates, skeletal shapes are diverse, and much of this variation appears to be adaptive. In contrast, the early developmental programs of these structures are highly conserved across vertebrates. The question then becomes where in the conserved genetic programs of skeletal development does variation lie to direct diversity? In threespine stickleback, rapid changes in head and body shape have been documented during repeated and independent invasions of oceanic fish into freshwater habitats in regions deglaciated approximately 13,000 years ago. However, recent research indicates that similar phenotypic and genetic divergence can occur in decades. A remaining challenge is to link stickleback population genomic variation to causal genes that underlie such rapid phenotypic evolution. Here I use genome wide association studies (GWAS) in natural populations of stickleback to uncover genomic regions that contribute to variation of two dermal bone derived traits, lateral plate number and opercle shape. The decrease of lateral plate body armor and change in opercle bone shape, important for feeding mechanics, are classically associated with freshwater divergence. GWAS has recently begun to be used in natural populations but is still under scrutiny for performance among different populations. Using a population of phenotypically variable stickleback in Oregon, GWAS proved an effective method to uncover genomic regions and genetic variants known to contribute to lateral plate number and opercle shape, as well as new genomic regions and candidate genes not previously implicated in phenotypic variation. Although successful, using similar methods on decades old stickleback populations in Alaska revealed the challenges that accompany controlling population structure created by strong natural selection. Together, I found that although lateral plate number and opercle shape rapidly evolve in a coordinated fashion during adaptation from marine to freshwater environments, phenotypic variation is largely driven by independent genetic architectures. However, in very rapidly evolving populations, despite this independence of genetic architecture, the genetic variants contributing to the traits co-localize to similar genomic regions. This finding could be either biological or methodological which highlights the promise and limitations of using GWAS to identify genetic variation that gives rise to phenotypic diversity. This dissertation includes unpublished co-authored material. Close

• 224. [Article] Physical Oceanography, Larval Dispersal, and Settlement Across Nearshore Fronts

  The larvae of coastal species interact with nearshore currents that are complex and can alter dispersal. I investigated two sites in southern Oregon with different nearshore hydrodynamics: the first site, ...

  Citation × Citation Citation Abstract Copy Title: Physical Oceanography, Larval Dispersal, and Settlement Across Nearshore Fronts Author: Jarvis, Marley Year: 2015 The larvae of coastal species interact with nearshore currents that are complex and can alter dispersal. I investigated two sites in southern Oregon with different nearshore hydrodynamics: the first site, Sunset Bay, is a small cove with a topographic front that extends across the mouth during upwelling-favorable winds. Using holey sock drogues at 1.5 m and 5.5 m depths and surface drifters at 10 cm depth, I found that, when the front was present, water at 1.5 m was retained within the bay whereas water was exchanged across the front at a depth of 5.5 m. Surface drifters indicated a surface convergence. Surface plankton tows on either side and within the frontal convergence (a shore-parallel foam line) found significantly higher concentrations of barnacle cyprids, crab megalopae and zoea, polychaete larvae, platyhelminthes juveniles, isopods, amphipods, harpacticoid copepods, and fish eggs. Crustacean nauplii (barnacle, euphausiid, and copepod) and calanoid copepods were not concentrated in the convergence, and when the front and foam line were absent, no taxa were concentrated. Plankton tows taken within the foam line as it dissipated shoreward during a wind-reversal event found that concentrations of cyprids, megalopae, and gastropod veligers remained high as the foam line moved, suggesting that it acts as a moving convergence propagating competent larvae shoreward. I measured settlement of two taxa at Sunset Bay and Shore Acres, an open-coast site <2 km away. Barnacle settlement measured every other day from June-September 2013 was significantly cross-correlated with the maximum daily tidal height at lags of -2 days at Sunset Bay and +2 and +4 days at Shore Acres. Settlement was also significantly negatively cross-correlated with wave height at a lag of -4 days at Sunset Bay. Coralline algae settlement measured during eight 48-hr periods in July-August 2013 was significantly negatively correlated with wave height (n = 8, R2 = 0.76, P = 0.0049) at Shore Acres but not at Sunset Bay. Despite the close proximity of the Sunset Bay and Shore Acres sites, settlement patterns differed between taxa, suggesting that differences in nearshore hydrodynamics might affect the supply of water and larvae to shore. This dissertation includes unpublished co-authored material. Title: Physical Oceanography, Larval Dispersal, and Settlement Across Nearshore Fronts Author: Jarvis, Marley Year: 2015 The larvae of coastal species interact with nearshore currents that are complex and can alter dispersal. I investigated two sites in southern Oregon with different nearshore hydrodynamics: the first site, Sunset Bay, is a small cove with a topographic front that extends across the mouth during upwelling-favorable winds. Using holey sock drogues at 1.5 m and 5.5 m depths and surface drifters at 10 cm depth, I found that, when the front was present, water at 1.5 m was retained within the bay whereas water was exchanged across the front at a depth of 5.5 m. Surface drifters indicated a surface convergence. Surface plankton tows on either side and within the frontal convergence (a shore-parallel foam line) found significantly higher concentrations of barnacle cyprids, crab megalopae and zoea, polychaete larvae, platyhelminthes juveniles, isopods, amphipods, harpacticoid copepods, and fish eggs. Crustacean nauplii (barnacle, euphausiid, and copepod) and calanoid copepods were not concentrated in the convergence, and when the front and foam line were absent, no taxa were concentrated. Plankton tows taken within the foam line as it dissipated shoreward during a wind-reversal event found that concentrations of cyprids, megalopae, and gastropod veligers remained high as the foam line moved, suggesting that it acts as a moving convergence propagating competent larvae shoreward. I measured settlement of two taxa at Sunset Bay and Shore Acres, an open-coast site <2 km away. Barnacle settlement measured every other day from June-September 2013 was significantly cross-correlated with the maximum daily tidal height at lags of -2 days at Sunset Bay and +2 and +4 days at Shore Acres. Settlement was also significantly negatively cross-correlated with wave height at a lag of -4 days at Sunset Bay. Coralline algae settlement measured during eight 48-hr periods in July-August 2013 was significantly negatively correlated with wave height (n = 8, R2 = 0.76, P = 0.0049) at Shore Acres but not at Sunset Bay. Despite the close proximity of the Sunset Bay and Shore Acres sites, settlement patterns differed between taxa, suggesting that differences in nearshore hydrodynamics might affect the supply of water and larvae to shore. This dissertation includes unpublished co-authored material. Close

• 225. [Article] Cross-Linguistic Perception and Learning of Japanese Lexical Prosody by English Listeners

  xviii, 216 p. : ill. (some col.)

  Citation × Citation Citation Abstract Copy Title: Cross-Linguistic Perception and Learning of Japanese Lexical Prosody by English Listeners Author: Shport, Irina A., 1975- Year: 2012, 2011 xviii, 216 p. : ill. (some col.) Title: Cross-Linguistic Perception and Learning of Japanese Lexical Prosody by English Listeners Author: Shport, Irina A., 1975- Year: 2012, 2011 xviii, 216 p. : ill. (some col.) Close

• 226. [Article] Bacterial Stimulation of Intestinal Proliferation via the Wnt Pathway in Zebrafish

  xi, 62 p. : ill. (some col.)

  Citation × Citation Citation Abstract Copy Title: Bacterial Stimulation of Intestinal Proliferation via the Wnt Pathway in Zebrafish Author: Neal, James Thomas Year: 2012, 2013, 2011 xi, 62 p. : ill. (some col.) Title: Bacterial Stimulation of Intestinal Proliferation via the Wnt Pathway in Zebrafish Author: Neal, James Thomas Year: 2012, 2013, 2011 xi, 62 p. : ill. (some col.) Close

• 227. [Article] Patterning and Stabilizing the Zebrafish Pharyngeal Arch Intermediate Domain

  xv, 76 p. : ill. (some col.) Includes 4 video files.

  Citation × Citation Citation Abstract Copy Title: Patterning and Stabilizing the Zebrafish Pharyngeal Arch Intermediate Domain Author: Talbot, Jared Coffin, 1982- Year: 2012, 2011 xv, 76 p. : ill. (some col.) Includes 4 video files. Title: Patterning and Stabilizing the Zebrafish Pharyngeal Arch Intermediate Domain Author: Talbot, Jared Coffin, 1982- Year: 2012, 2011 xv, 76 p. : ill. (some col.) Includes 4 video files. Close

• 228. [Article] Life history trade-offs in growth and immune function: The behavioral and immunological ecology of the Shuar of Amazonian Ecuador, an indigenous population in the midst of rapid economic and ecological change

  xxi, 234 p. : ill. (some col.) A print copy of this thesis is available through the UO Libraries. Search the library catalog for the location and call number.

  Citation × Citation Citation Abstract Copy Title: Life history trade-offs in growth and immune function: The behavioral and immunological ecology of the Shuar of Amazonian Ecuador, an indigenous population in the midst of rapid economic and ecological change Author: Blackwell, Aaron D., 1978- Year: 2010, 2009 xxi, 234 p. : ill. (some col.) A print copy of this thesis is available through the UO Libraries. Search the library catalog for the location and call number. Title: Life history trade-offs in growth and immune function: The behavioral and immunological ecology of the Shuar of Amazonian Ecuador, an indigenous population in the midst of rapid economic and ecological change Author: Blackwell, Aaron D., 1978- Year: 2010, 2009 xxi, 234 p. : ill. (some col.) A print copy of this thesis is available through the UO Libraries. Search the library catalog for the location and call number. Close

• 229. [Article] Galena Watershed analysis--Supplement 2002

  818 pp. Tables, figures, maps, references, glossary, appendices, illus. "Analysis was performed on 49,4733 acres of the Davis, Placer, Vinegar, Tincup, Little Butte, Butte, Vincent, Little Boulder, Deerhorn ...

  Citation × Citation Citation Abstract Copy Title: Galena Watershed analysis--Supplement 2002 Author: Blue Mountain Ranger District (Or.) Year: 2008, 2003 818 pp. Tables, figures, maps, references, glossary, appendices, illus. "Analysis was performed on 49,4733 acres of the Davis, Placer, Vinegar, Tincup, Little Butte, Butte, Vincent, Little Boulder, Deerhorn and Granite Boulder subwatersheds and the tributaries to the Middle- Fork of the John Day River (Chapters 1-4 this document, see also Map A page 1 and Appendix E, Maps 1-31). The Middle Fork of the John Day River originates south of the North Fork of the John Day River in the Blue Mountains, and flows westerly for approximately 75 miles, then merges with the North Fork about 18 miles above Monument, Oregon. The analysis area is located about 25 air miles northeast of John Day, Oregon." Captured June 11, 2008. Title: Galena Watershed analysis--Supplement 2002 Author: Blue Mountain Ranger District (Or.) Year: 2008, 2003 818 pp. Tables, figures, maps, references, glossary, appendices, illus. "Analysis was performed on 49,4733 acres of the Davis, Placer, Vinegar, Tincup, Little Butte, Butte, Vincent, Little Boulder, Deerhorn and Granite Boulder subwatersheds and the tributaries to the Middle- Fork of the John Day River (Chapters 1-4 this document, see also Map A page 1 and Appendix E, Maps 1-31). The Middle Fork of the John Day River originates south of the North Fork of the John Day River in the Blue Mountains, and flows westerly for approximately 75 miles, then merges with the North Fork about 18 miles above Monument, Oregon. The analysis area is located about 25 air miles northeast of John Day, Oregon." Captured June 11, 2008. Close

• 230. [Article] The Columbia River's region: Politics, place and environment in the Pacific Northwest, 1933--present

  xiv, 296 p. : ill. A print copy of this title is available through the UO Libraries under the call numbers: KNIGHT F853 .V64 2007

  Citation × Citation Citation Abstract Copy Title: The Columbia River's region: Politics, place and environment in the Pacific Northwest, 1933--present Author: Vogel, Eve, 1964- Year: 2008, 2007 xiv, 296 p. : ill. A print copy of this title is available through the UO Libraries under the call numbers: KNIGHT F853 .V64 2007 Title: The Columbia River's region: Politics, place and environment in the Pacific Northwest, 1933--present Author: Vogel, Eve, 1964- Year: 2008, 2007 xiv, 296 p. : ill. A print copy of this title is available through the UO Libraries under the call numbers: KNIGHT F853 .V64 2007 Close