title: Paralogs are revealed by proportion of heterozygotes and deviations in read ratios in genotyping-by-sequencing data from natural populations.
abstract: Whole-genome duplications have occurred in the recent ancestors of many plants, fish, and amphibians, resulting in a pervasiveness of paralogous loci and the potential for both disomic and tetrasomic inheritance in the same genome. Paralogs can be difficult to reliably genotype and are often excluded from genotyping-by-sequencing (GBS) analyses; however, removal requires paralogs to be identified which is difficult without a reference genome. We present a method for identifying paralogs in natural populations by combining two properties of duplicated loci: (i) the expected frequency of heterozygotes exceeds that for singleton loci, and (ii) within heterozygotes, observed read ratios for each allele in GBS data will deviate from the 1:1 expected for singleton (diploid) loci. These deviations are often not apparent within individuals, particularly when sequence coverage is low; but, we postulated that summing allele reads for each locus over all heterozygous individuals in a population would provide sufficient power to detect deviations at those loci. We identified paralogous loci in three species: Chinook salmon (Oncorhynchus tshawytscha) which retains regions with ongoing residual tetrasomy on eight chromosome arms following a recent whole-genome duplication, mountain barberry (Berberis alpina) which has a large proportion of paralogs that arose through an unknown mechanism, and dusky parrotfish (Scarus niger) which has largely rediploidized following an ancient whole-genome duplication. Importantly, this approach only requires the genotype and allele-specific read counts for each individual, information which is readily obtained from most GBS analysis pipelines.
authors.affiliation: School of Aquatic and Fishery Sciences, University of Washington, 1122 NE Boat Street, Box 355020, Seattle, WA, 98195-5020, USA.
authors.forename: Garrett J
authors.initials: GJ
authors.lastname: McKinney
authors.affiliation: School of Aquatic and Fishery Sciences, University of Washington, 1122 NE Boat Street, Box 355020, Seattle, WA, 98195-5020, USA.
authors.forename: Ryan K
authors.initials: RK
authors.lastname: Waples
authors.affiliation: School of Aquatic and Fishery Sciences, University of Washington, 1122 NE Boat Street, Box 355020, Seattle, WA, 98195-5020, USA.
authors.forename: Lisa W
authors.initials: LW
authors.lastname: Seeb
authors.affiliation: School of Aquatic and Fishery Sciences, University of Washington, 1122 NE Boat Street, Box 355020, Seattle, WA, 98195-5020, USA.
authors.forename: James E
authors.initials: JE
authors.lastname: Seeb
mesh_terms: D000818:Animals; D028142:Berberis / Q000235:genetics*; D002874:Chromosome Mapping; D030541:Databases, Genetic; D056426:Genetic Loci; D005828:Genetics, Population; D005838:Genotype; D060005:Genotyping Techniques; D006579:Heterozygote; D012474:Salmon / Q000235:genetics*
keywords: Chinook salmon; RADseq; genome duplication; genotyping-by-sequencing; natural populations; paralog