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. 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: 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, 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 re-diploidized 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.