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Population genomics of Salish Sea ch...

Waples, Ryan K.

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Population genomics of Salish Sea chum salmon: The legacy of the salmonid whole genome duplication.

Record Type:	Electronic resources : Monograph/item
Title/Author:	Population genomics of Salish Sea chum salmon: The legacy of the salmonid whole genome duplication./
Author:	Waples, Ryan K.
Description:	82 p.
Notes:	Source: Masters Abstracts International, Volume: 55-03.
Contained By:	Masters Abstracts International55-03(E).
Subject:	Genetics. -
Online resource:	http://pqdd.sinica.edu.tw/twdaoapp/servlet/advanced?query=10000194
ISBN:	9781339406923

Population genomics of Salish Sea chum salmon: The legacy of the salmonid whole genome duplication.
Waples, Ryan K.

Population genomics of Salish Sea chum salmon: The legacy of the salmonid whole genome duplication. - 82 p.

Source: Masters Abstracts International, Volume: 55-03.

Thesis (Master's)--University of Washington, 2015.

The common ancestor of salmonids underwent a whole genome duplication approximately 88 million years ago. This duplication event still has a lasting impact on the form and structure of salmon genomes today and is evident in many duplicated genes and ongoing residual tetrasomic inheritance. This duplication also serves to complicate genetic analyses, as paralogous genes and sequences are difficult to distinguish, and often fully excluded prior to study. The goal of this thesis is to demonstrate how to incorporate duplicated loci into genetic studies of salmonids using high-throughput sequencing of chum salmon from the Salish Sea. In the first chapter, I develop a method to resolve paralogous loci within a pedigree and include them on a high-density linkage map. I show that paralogous loci are concentrated in 16 regions near the ends of linkage groups. These regions are inferred to have ongoing residual tetrasomic inheritance and we find that they have a lower incidence of transposable elements than the rest of the genome, a possible explanation for their stability since the whole genome duplication. In the second chapter, I use the discovered paralogous loci in a population genetic study of 10 collections of chum salmon from the Salish Sea. I compare genetic diversity and population structure at paralogous and non-paralogous loci and conduct a genome scan for association with run timing. I demonstrate that it is possible to characterize paralogous loci in wild populations and that they show similar patterns of population structure as the rest of the genome. The genome scan reveals genomic regions of elevated association with run timing, highlighting the potential downside of excluding paralogous loci in studies looking for genetic signals of adaptation.

ISBN: 9781339406923Subjects--Topical Terms:

530508
Genetics.

Population genomics of Salish Sea chum salmon: The legacy of the salmonid whole genome duplication.
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020 $a 9781339406923
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100 1 $a Waples, Ryan K. $3 3190002
245 1 0 $a Population genomics of Salish Sea chum salmon: The legacy of the salmonid whole genome duplication.
300 $a 82 p.
500 $a Source: Masters Abstracts International, Volume: 55-03.
500 $a Includes supplementary digital materials.
500 $a Advisers: Lisa Seeb; James Seeb.
502 $a Thesis (Master's)--University of Washington, 2015.
520 $a The common ancestor of salmonids underwent a whole genome duplication approximately 88 million years ago. This duplication event still has a lasting impact on the form and structure of salmon genomes today and is evident in many duplicated genes and ongoing residual tetrasomic inheritance. This duplication also serves to complicate genetic analyses, as paralogous genes and sequences are difficult to distinguish, and often fully excluded prior to study. The goal of this thesis is to demonstrate how to incorporate duplicated loci into genetic studies of salmonids using high-throughput sequencing of chum salmon from the Salish Sea. In the first chapter, I develop a method to resolve paralogous loci within a pedigree and include them on a high-density linkage map. I show that paralogous loci are concentrated in 16 regions near the ends of linkage groups. These regions are inferred to have ongoing residual tetrasomic inheritance and we find that they have a lower incidence of transposable elements than the rest of the genome, a possible explanation for their stability since the whole genome duplication. In the second chapter, I use the discovered paralogous loci in a population genetic study of 10 collections of chum salmon from the Salish Sea. I compare genetic diversity and population structure at paralogous and non-paralogous loci and conduct a genome scan for association with run timing. I demonstrate that it is possible to characterize paralogous loci in wild populations and that they show similar patterns of population structure as the rest of the genome. The genome scan reveals genomic regions of elevated association with run timing, highlighting the potential downside of excluding paralogous loci in studies looking for genetic signals of adaptation.
590 $a School code: 0250.
650 4 $a Genetics. $3 530508
650 4 $a Bioinformatics. $3 553671
650 4 $a Molecular biology. $3 517296
650 4 $a Aquatic sciences. $3 3174300
690 $a 0369
690 $a 0715
690 $a 0307
690 $a 0792
710 2 $a University of Washington. $b Aquatic and Fishery Sciences. $3 2093042
773 0 $t Masters Abstracts International $g 55-03(E).
790 $a 0250
791 $a Master's
792 $a 2015
793 $a English
856 4 0 $u http://pqdd.sinica.edu.tw/twdaoapp/servlet/advanced?query=10000194