Rank and order: evaluating the performance of SNPs for individual assignment in a non-model organism

Single nucleotide polymorphisms (SNPs) are valuable tools for ecological and evolutionary studies. In non-model species, the use of SNPs has been limited by the number of markers available. However, new technologies and decreasing technology costs have facilitated the discovery of a constantly incre...

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Published in:PloS one 2012-11, Vol.7 (11), p.e49018-e49018
Main Authors: Storer, Caroline G, Pascal, Carita E, Roberts, Steven B, Templin, William D, Seeb, Lisa W, Seeb, James E
Format: Article
Language:English
Subjects:
Alaska
Analysis
Animals
Biological evolution
Biology
Chromosomes
Computer simulation
Data processing
Ecological monitoring
Ecology
Endangered & extinct species
Evolution
Fish
Fishery sciences
Fishes
Fishing
Genetic Loci - genetics
Genetics
Genomes
Geography
Heterozygote
Innovations
Laboratories
Linux
Loci
Models, Animal
New technology
Oncorhynchus keta
Oncorhynchus nerka
Organisms
Panels
Polymorphism
Polymorphism, Single Nucleotide - genetics
Population
Principal Component Analysis
Probability
Ranking
Rankings
Reproducibility of Results
Salmon
Salmon - genetics
Sample Size
Securities analysis
Single nucleotide polymorphisms
Single-nucleotide polymorphism
Specimen Handling
Statistics, Nonparametric
Studies
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cited_by cdi_FETCH-LOGICAL-c692t-99f8bd908a5d6d16ed519de884cfcbaadc758f50281d33d99ba96b76e097bebf3
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container_issue 11
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container_title PloS one
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creator Storer, Caroline G
Pascal, Carita E
Roberts, Steven B
Templin, William D
Seeb, Lisa W
Seeb, James E
description Single nucleotide polymorphisms (SNPs) are valuable tools for ecological and evolutionary studies. In non-model species, the use of SNPs has been limited by the number of markers available. However, new technologies and decreasing technology costs have facilitated the discovery of a constantly increasing number of SNPs. With hundreds or thousands of SNPs potentially available, there is interest in comparing and developing methods for evaluating SNPs to create panels of high-throughput assays that are customized for performance, research questions, and resources. Here we use five different methods to rank 43 new SNPs and 71 previously published SNPs for sockeye salmon: F(ST), informativeness (I(n)), average contribution to principal components (LC), and the locus-ranking programs BELS and WHICHLOCI. We then tested the performance of these different ranking methods by creating 48- and 96-SNP panels of the top-ranked loci for each method and used empirical and simulated data to obtain the probability of assigning individuals to the correct population using each panel. All 96-SNP panels performed similarly and better than the 48-SNP panels except for the 96-SNP BELS panel. Among the 48-SNP panels, panels created from F(ST), I(n), and LC ranks performed better than panels formed using the top-ranked loci from the programs BELS and WHICHLOCI. The application of ranking methods to optimize panel performance will become more important as more high-throughput assays become available.
doi_str_mv 10.1371/journal.pone.0049018
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1932-6203
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subjects Alaska
Analysis
Animals
Biological evolution
Biology
Chromosomes
Computer simulation
Data processing
Ecological monitoring
Ecology
Endangered & extinct species
Evolution
Fish
Fishery sciences
Fishes
Fishing
Genetic Loci - genetics
Genetics
Genomes
Geography
Heterozygote
Innovations
Laboratories
Linux
Loci
Models, Animal
New technology
Oncorhynchus keta
Oncorhynchus nerka
Organisms
Panels
Polymorphism
Polymorphism, Single Nucleotide - genetics
Population
Principal Component Analysis
Probability
Ranking
Rankings
Reproducibility of Results
Salmon
Salmon - genetics
Sample Size
Securities analysis
Single nucleotide polymorphisms
Single-nucleotide polymorphism
Specimen Handling
Statistics, Nonparametric
Studies
title Rank and order: evaluating the performance of SNPs for individual assignment in a non-model organism
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