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Genotyping by sequencing resolves shallow population structure to inform conservation of Chinook salmon (Oncorhynchus tshawytscha)
- Source :
- Evolutionary Applications
- Publication Year :
- 2013
-
Abstract
- Recent advances in population genomics have made it possible to detect previously unidentified structure, obtain more accurate estimates of demographic parameters, and explore adaptive divergence, potentially revolutionizing the way genetic data are used to manage wild populations. Here, we identified 10 944 single-nucleotide polymorphisms using restriction-site-associated DNA (RAD) sequencing to explore population structure, demography, and adaptive divergence in five populations of Chinook salmon (Oncorhynchus tshawytscha) from western Alaska. Patterns of population structure were similar to those of past studies, but our ability to assign individuals back to their region of origin was greatly improved (>90% accuracy for all populations). We also calculated effective size with and without removing physically linked loci identified from a linkage map, a novel method for nonmodel organisms. Estimates of effective size were generally above 1000 and were biased downward when physically linked loci were not removed. Outlier tests based on genetic differentiation identified 733 loci and three genomic regions under putative selection. These markers and genomic regions are excellent candidates for future research and can be used to create high-resolution panels for genetic monitoring and population assignment. This work demonstrates the utility of genomic data to inform conservation in highly exploited species with shallow population structure.
- Subjects :
- 0106 biological sciences
population genomics
Population
Single-nucleotide polymorphism
RAD sequencing
010603 evolutionary biology
01 natural sciences
Population genomics
03 medical and health sciences
Effective population size
Genetic linkage
Genetics
14. Life underwater
education
Ecology, Evolution, Behavior and Systematics
Selection (genetic algorithm)
Research Articles
030304 developmental biology
0303 health sciences
education.field_of_study
biology
biology.organism_classification
Evolutionary biology
Oncorhynchus
genetic stock identification
western Alaska
General Agricultural and Biological Sciences
Chinook salmon
effective population size
Genetic monitoring
SNPs
Subjects
Details
- ISSN :
- 17524571
- Volume :
- 7
- Issue :
- 3
- Database :
- OpenAIRE
- Journal :
- Evolutionary applications
- Accession number :
- edsair.doi.dedup.....2612bda19c0d484297e727edc4cef3be