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Resolving allele dosage in duplicated loci using genotyping‐by‐sequencing data: A path forward for population genetic analysis
Author(s) -
McKinney Garrett J.,
Waples Ryan K.,
Pascal Carita E.,
Seeb Lisa W.,
Seeb James E.
Publication year - 2018
Publication title -
molecular ecology resources
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 2.96
H-Index - 136
eISSN - 1755-0998
pISSN - 1755-098X
DOI - 10.1111/1755-0998.12763
Subject(s) - biology , genotyping , genetics , locus (genetics) , amplicon , population , allele , allele frequency , dna sequencing , computational biology , evolutionary biology , genotype , polymerase chain reaction , gene , demography , sociology
Whole‐genome duplications have occurred in the recent ancestors of many plants, fish and amphibians. Signals of these whole‐genome duplications still exist in the form of paralogous loci. Recent advances have allowed reliable identification of paralogs in genotyping‐by‐sequencing ( GBS ) data such as that generated from restriction‐site‐associated DNA sequencing ( RADS eq); however, excluding paralogs from analyses is still routine due to difficulties in genotyping. This exclusion of paralogs may filter a large fraction of loci, including loci that may be adaptively important or informative for population genetic analyses. We present a maximum‐likelihood method for inferring allele dosage in paralogs and assess its accuracy using simulated GBS , empirical RADS eq and amplicon sequencing data from Chinook salmon. We accurately infer allele dosage for some paralogs from a RADS eq data set and show how accuracy is dependent upon both read depth and allele frequency. The amplicon sequencing data set, using RADS eq‐derived markers, achieved sufficient depth to infer allele dosage for all paralogs. This study demonstrates that RADS eq locus discovery combined with amplicon sequencing of targeted loci is an effective method for incorporating paralogs into population genetic analyses.