Graduate Thesis Or Dissertation

 

Riverscape genetics of Oncorhynchus tshawytscha (Chinook salmon) in Siletz River, OR Public Deposited

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https://ir.library.oregonstate.edu/concern/graduate_thesis_or_dissertations/b5644x15r

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  • Traditional analysis in population genetics evaluates differences among groups of individuals and, in some cases, considers the effects of distance or potential barriers to gene flow. However, many forces may shape genetic variation of organisms in riverine systems. Similarly complex research linking habitat heterogeneity and configuration to genetic structure has integrated methods from landscape ecology, population genetics, and spatial statistics in approaches known as landscape or seascape genetics. However, challenges exist when translating these approaches into freshwater river networks due to functional differences in riverscape topography that create constrained pathways for movement. The overall goal of my dissertation was to combine the approaches applied in population genetics to identify genetic diversity within and among populations, with concepts derived from network theory to better understand how the riverscape influenced spatial genetic structure of Chinook salmon (Oncorhynchus tshawytscha) populations in Siletz River. I provide a perspective on how riverscape genetics could be used to provide a more comprehensive conceptual and applied understanding of connectivity and dispersal in freshwater systems. I describe four thematic areas of study representing current and future research opportunities and propose a basic methodology for conducting riverscape genetics analysis. I applied the proposed riverscape genetics method to attempt a novel analysis of spatial genetic structure of Chinook salmon within Siletz River, Oregon and compared results with interpretation of spatial genetic structure using traditional population genetics methods. Chinook salmon are a culturally important and economically valuable fish that express diverse life histories characterized by the season of their return migration to spawning habitat (called a “run”) and duration of freshwater or estuarine residence. Population structure among Chinook salmon of alternate run times observed in the Siletz River was investigated using 11 microsatellite markers, 96 Single Nucleotide Polymorphisms (SNPs), and three candidate gene markers that are linked to spawn time and body size. Results from all marker types identified two genetically distinct populations in the watershed (microsatellites; FST = 0.02, p < 0.05) that included a previously unrecognized spring run. This finding is an important consideration for management of the species, as spring run populations have not been recognized in smaller watersheds. Using riverscape genetics methods I characterized the spatial relationships among fall run Chinook salmon. Analysis assessed the effect of indicators of hydrology on dispersal and identified patterns of genetic variation were associated with site-specific differences in elevation of spawning habitat (MRDM; R2 = 0.11 p < 0.05). Further investigation using path-based methodology identified that the cumulative changes in gradient among stream reaches also significantly affected spatial genetic structure (MRDM; R2 = 0.14 p < 0.01). The combination of approaches that were used to investigate spatial genetic variation highlighted the utility of riverscape genetics to enhance our understanding of the relationships that contributed to observed population structure. Although fall run Chinook salmon within Siletz River exhibited high gene flow and were considered a single spawning population using traditional population genetic methods, there was evidence of differential habitat use within the group that was driven by the location of spawning habitat and the resistance to dispersal caused by habitat between these locations. Chinook salmon that traveled over steeper gradients to reach spawning habitat at higher elevations were different than individuals that traveled over shallower gradients to reach spawning habitat at lower elevations. The riverscape genetics approach applied in this chapter enhanced our understanding of habitat heterogeneity in shaping gene flow and spatial genetic structure at a fine spatial scale. Expanding quantitative genetic research, in river systems to explicitly consider riverscape scale network configurations would help develop a clear understanding of the importance of these factors in terms of population persistence.
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  • description.provenance : Submitted by Chante Davis (davischa@oregonstate.edu) on 2017-09-07T18:52:48ZNo. of bitstreams: 1DavisChanteD2017.pdf: 3588426 bytes, checksum: 6545a45a64a39f77c8f2b36cba932433 (MD5)
  • description.provenance : Rejected by Julie Kurtz(julie.kurtz@oregonstate.edu), reason: Hi Chante,Rejecting to remove the line numbers and type text message in the dissertation. For the pretext pages, remove any bold print and make the other changes I just emailed you.Everything else looks good. Once revised, log back into ScholarsArchive and go to the upload page. Replace the attached file with the revised PDF and resubmit.Thanks,Julie on 2017-09-08T16:12:49Z (GMT)
  • description.provenance : Submitted by Chante Davis (davischa@oregonstate.edu) on 2017-09-07T22:33:26ZNo. of bitstreams: 3DavisChanteD2017.pdf: 3588426 bytes, checksum: 6545a45a64a39f77c8f2b36cba932433 (MD5)DavisChanteD2017.pdf: 3587142 bytes, checksum: 86b3f224ddeea6c892852b4e35aabf47 (MD5)DavisChanteD2017.pdf: 3586480 bytes, checksum: 5c478f61b9b4fb9ee243f24b0f33887c (MD5)
  • description.provenance : Submitted by Chante Davis (davischa@oregonstate.edu) on 2017-09-11T21:09:34ZNo. of bitstreams: 1DavisChante2017.pdf: 2329429 bytes, checksum: 780c11d088933ec55841422737a962bd (MD5)
  • description.provenance : Made available in DSpace on 2017-09-20T22:19:42Z (GMT). No. of bitstreams: 1DavisChante2017.pdf: 2329429 bytes, checksum: 780c11d088933ec55841422737a962bd (MD5) Previous issue date: 2017-08-17
  • description.provenance : Approved for entry into archive by Steven Van Tuyl(steve.vantuyl@oregonstate.edu) on 2017-09-20T22:19:42Z (GMT) No. of bitstreams: 1DavisChante2017.pdf: 2329429 bytes, checksum: 780c11d088933ec55841422737a962bd (MD5)
  • description.provenance : Approved for entry into archive by Julie Kurtz(julie.kurtz@oregonstate.edu) on 2017-09-19T19:02:16Z (GMT) No. of bitstreams: 1DavisChante2017.pdf: 2329429 bytes, checksum: 780c11d088933ec55841422737a962bd (MD5)
  • description.provenance : Rejected by Julie Kurtz(julie.kurtz@oregonstate.edu), reason: Hi Chante,Rejecting because none of the revisions were made to your pretext pages and the dissertation has line numbers. I sent you an email with a copy of the revised pretext.Everything else looks good. Once revised, log back into ScholarsArchive and go to the upload page. Replace the attached file with the revised PDF and resubmit.Thanks,Julie on 2017-09-07T21:28:36Z (GMT)
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