Congruent population structure across paralogous and nonparalogous loci in Salish Sea chum salmon (Oncorhynchus keta)

Whole‐genome duplications are major evolutionary events with a lasting impact on genome structure. Duplication events complicate genetic analyses as paralogous sequences are difficult to distinguish; consequently, paralogs are often excluded from studies. The effects of an ancient whole‐genome dupli...

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Bibliographic Details
Published in:Molecular ecology 2017-08, Vol.26 (16), p.4131-4144
Main Authors: Waples, R. K., Seeb, J. E., Seeb, L. W.
Format: Article
Language:English
Subjects:
Animals
Canada
Chromosome Mapping
chum salmon
Deoxyribonucleic acid
DNA
DNA sequencing
Evolution
Gene Duplication
Gene loci
Gene sequencing
Genetic diversity
Genetic Linkage
Genetic Variation
Genetics, Population
Genome
Genomes
Heredity
linkage mapping
Nucleotide sequence
Oncorhynchus keta
Oncorhynchus keta - genetics
Pedigree
Ploidies
Polyploidy
Population genetics
Population structure
Population studies
Salmon
Salmonids
Statistical methods
tetrasomic inheritance
United States
whole‐genome duplication
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Summary:Whole‐genome duplications are major evolutionary events with a lasting impact on genome structure. Duplication events complicate genetic analyses as paralogous sequences are difficult to distinguish; consequently, paralogs are often excluded from studies. The effects of an ancient whole‐genome duplication (approximately 88 MYA) are still evident in salmonids through the persistence of numerous paralogous gene sequences and partial tetrasomic inheritance. We use restriction site‐associated DNA sequencing on 10 collections of chum salmon from the Salish Sea in the USA and Canada to investigate genetic diversity and population structure in both tetrasomic and rediploidized regions of the genome. We use a pedigree and high‐density linkage map to identify paralogous loci and to investigate genetic variation across the genome. By applying multivariate statistical methods, we show that it is possible to characterize paralogous loci and that they display similar patterns of population structure as the diploidized portion of the genome. We find genetic associations with the adaptively important trait of run‐timing in both sets of loci. By including paralogous loci in genome scans, we can observe evolutionary signals in genomic regions that have routinely been excluded from population genetic studies in other polyploid‐derived species.
ISSN:0962-1083
1365-294X
DOI:10.1111/mec.14163