Data from: Paralogs are revealed by proportion of heterozygotes and deviations in read ratios in genotyping by sequencing data from natural populations

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 (mixed ploidy). Paralogs can be difficult to reliably genotype and are often excluded from genotyping-by-sequencing (GBS) analyses; however, identification of paralogs is difficult without a reference genome. We present a method for identifying paralogs in natural populations by combining two properties of duplicated loci: 1) the expected frequency of heterozygotes exceeds that for singleton loci, and 2) 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 summing allele reads over all heterozygous individuals in a population should provide sufficient power to detect deviations. 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 re-diploidized following an ancient whole genome duplication. Accuracy of our method was confirmed by comparing inferred and known copy-status for a subset of Chinook salmon loci. 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.