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Effectiveness of Managed Gene Flow t...

Waters, Charles D.

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Effectiveness of Managed Gene Flow to Reduce Genetic and Phenotypic Change Associated with Captive Breeding of Chinook Salmon.

紀錄類型:	書目-電子資源 : Monograph/item
正題名/作者:	Effectiveness of Managed Gene Flow to Reduce Genetic and Phenotypic Change Associated with Captive Breeding of Chinook Salmon./
作者:	Waters, Charles D.
出版者:	Ann Arbor : ProQuest Dissertations & Theses, : 2018,
面頁冊數:	207 p.
附註:	Source: Dissertation Abstracts International, Volume: 79-12(E), Section: B.
Contained By:	Dissertation Abstracts International79-12B(E).
標題:	Aquatic sciences. -
電子資源:	http://pqdd.sinica.edu.tw/twdaoapp/servlet/advanced?query=10827307
ISBN:	9780438175488

Effectiveness of Managed Gene Flow to Reduce Genetic and Phenotypic Change Associated with Captive Breeding of Chinook Salmon.
Waters, Charles D.

Effectiveness of Managed Gene Flow to Reduce Genetic and Phenotypic Change Associated with Captive Breeding of Chinook Salmon. - Ann Arbor : ProQuest Dissertations & Theses, 2018 - 207 p.

Source: Dissertation Abstracts International, Volume: 79-12(E), Section: B.

Thesis (Ph.D.)--University of Washington, 2018.

This dissertation characterizes genetic and phenotypic changes associated with captive breeding using novel genome-wide approaches and explicitly tests the effectiveness of managed gene flow to minimize these changes using two hatchery populations of Chinook salmon, Oncorhynchus tshawytscha. The hatchery populations were derived from the same wild population but are now managed as separate lines, one integrated with and one segregated from the source stock, and thus provide an ideal system for comparing the two alternative management strategies. I used genomic and phenotypic data spanning five generations to examine the two hatchery populations across a range of measures.

ISBN: 9780438175488Subjects--Topical Terms:

3174300
Aquatic sciences.

Effectiveness of Managed Gene Flow to Reduce Genetic and Phenotypic Change Associated with Captive Breeding of Chinook Salmon.
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245 1 0 $a Effectiveness of Managed Gene Flow to Reduce Genetic and Phenotypic Change Associated with Captive Breeding of Chinook Salmon.
260 1 $a Ann Arbor : $b ProQuest Dissertations & Theses, $c 2018
300 $a 207 p.
500 $a Source: Dissertation Abstracts International, Volume: 79-12(E), Section: B.
500 $a Includes supplementary digital materials.
500 $a Adviser: Kerry A. Naish.
502 $a Thesis (Ph.D.)--University of Washington, 2018.
520 $a This dissertation characterizes genetic and phenotypic changes associated with captive breeding using novel genome-wide approaches and explicitly tests the effectiveness of managed gene flow to minimize these changes using two hatchery populations of Chinook salmon, Oncorhynchus tshawytscha. The hatchery populations were derived from the same wild population but are now managed as separate lines, one integrated with and one segregated from the source stock, and thus provide an ideal system for comparing the two alternative management strategies. I used genomic and phenotypic data spanning five generations to examine the two hatchery populations across a range of measures.
520 $a First, I used over 9000 loci to test whether managed gene flow between natural and captive environments, when compared to broodstock segregation, reduced genome-wide divergence from the wild founding population over four generations of captive rearing. Genetic divergence from the source population was minimal in the integrated hatchery line, which implemented managed gene flow by using only naturally-born adults as captive broodstock, but significant in the segregated line, which bred only captive-origin individuals. Estimates of effective number of breeders revealed that the rapid divergence observed in the segregated line was largely attributable to genetic drift. However, we also identified temporally-consistent signatures of adaptive divergence within the segregated line, indicative of domestication selection. The results empirically demonstrated that using managed gene flow for propagating a captive-reared population reduces genetic divergence over the short term compared to one that relies solely on captive-origin parents. The findings also provided insight into the rate at which divergence may occur in integrated and segregated hatchery programs.
520 $a Second, I computed genomic-based estimates of pairwise relatedness and individual inbreeding within the integrated and segregated hatchery lines across four generations and determined if managed gene flow successfully reduced the risks of inbreeding over time. I also quantified the effect of inbreeding coefficient on eight fitness-related traits that had been measured in returning adults. The segregated line had slight but significantly lower levels of relatedness than the integrated line in the first generation but significantly higher levels in the third and fourth generations. Levels of inbreeding were similar between the two hatchery lines in the first, third, and fourth generations, despite 3- to 27-fold differences in estimates of effective numbers of breeders. However, inbreeding in the segregated line was significantly higher in the second generation. Inbreeding coefficient did not affect fecundity, reproductive effort, return timing, and fork length. In contrast, inbreeding significantly affected spawn timing, weight, condition factor, and daily growth coefficient, although the effects varied by sex, hatchery line, and generation. While the results indicated that managed gene flow may reduce the genetic risks of inbreeding, they also suggested that short-term risks may not be severe in small, segregated hatchery populations. The effects of inbreeding on fitness, however, require further examination, particularly at earlier life stages.
520 $a Third, I identified loci associated with six fitness-related traits in adult Chinook salmon using an approach suitable for polygenic traits, Random Forest, and then explored the use of trait-associated loci within a management context; namely, whether they could serve as tools for monitoring the effects of alternative management approaches on genetic change underlying phenotypic traits. I identified 226 unique loci associated with the six traits. Mapping of these trait-associated loci, gene annotations, and integration of results across multiple studies revealed candidate regions involved in fitness. Genotypes at trait-associated loci were then compared between the integrated and segregated hatchery lines. While no broad scale change was detected between the lines across four generations, there were numerous regions where trait-associated loci overlapped with signatures of adaptive divergence identified in Chapters 1 and 2. Many regions of overlap, primarily with loci linked to return and spawn timing, were either unique to, or more divergent in, the segregated line, suggesting that these traits may be responding to domestication selection.
520 $a Last, I combined lessons learned from my analyses in Chapter 4 with information from colleagues and other studies to provide a simple, introductory guide to facilitate the use of Random Forest to identify genotype-phenotype associations in non-model organisms. The guide first provides an overview of the Random Forest algorithm. Next, steps are described to prepare data for Random Forest, including initial data exploration and the identification of important covariates and possible confounding factors. Advice is then provided on the initiation and optimization of the Random Forest algorithm, along with a summary of methods for interpreting the results and identifying trait-associated, or predictor, loci. (Abstract shortened by ProQuest.).
590 $a School code: 0250.
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