1. Garrett McKinney Jim Seeb Lisa Seeb
Something for nothing: Free SNPs increase power for genetic stock identification
Garrett McKinney
Jim Seeb
Lisa Seeb

2. GSI Traditionally examine a single SNP per marker
Assume that SNPs that are physically close are tightly linked and provide redundant information
SNPs that are physically close are not necessarily redundant
More information can be gained by combining adjacent SNPs into haplotypes T G C A

3. Origin of SNPs
SNPs arise when a substitution occurs within a DNA sequence
SNP
Alleles
Ancestral
DNA sequence A A T T

4. Spread of SNPs
Distribution and frequency of a SNP reflects geneflow, drift, and selection following its genesis
SNP origin
Current SNP distribution
Time
Pop. 1
Pop. 1 A T A
Pop. 2
Pop. 3
Pop. 2
Pop. 3 T A A T A A

5. Origin of Haplotypes
Haplotypes arise when multiple substitutions occur within a single DNA sequence
SNP1
SNP2
Alleles A C AC T C TC T G TG
Not observed: AG

6. Spread of Haplotypes
Distribution and frequency of a haplotype reflects geneflow, drift, and selection following its genesis
Haplotype origin
Current Haplotype distribution
Time AC AC TC TC TG TG AC AC AC AC TC TC

7. Haplotypes Improve Fine-scale Resolution
SNP1 Distribution
SNP2 Distribution
Haplotype distribution AC TC T A G C TG T A A C C AC AC TC
Differentiates Pop. 1 and 2
from Pop. 3
Differentiates Pop. 2 and 3
from Pop. 1
All populations differentiated

8. Western Alaska Chinook
Recent population declines
Culturally and economically important
Accurate GSI is critical to effective management
Low population differentiation
24% of loci have multiple SNPs
Good candidate for haplotype analysis
Templin et al. 2011

9. Haplotypes Improve GSI
Accuracy of GSI mixture simulation increases up to 10% when using haplotypes.
Genotypes
Haplotypes

10. Conclusion
Large amounts of time and money are often spent on incremental improvements for GSI
New sequencing technologies used for GSI produce haplotypes
Haplotypes increase accuracy of GSI with no extra cost or effort for analysis
We can improve GSI using data that already exists by changing analysis methods

11. Acknowledgements
Funding from AKSSF projects and 44913