Microhaplotypes provide increased power from short-read DNA sequences for relationship inference

The accelerating rate at which DNA sequence data is now generated by high-throughput sequencing instruments provides both opportunities and challenges for population genetic and ecological investigations of animals and plants. We show here how the common practice of calling genotypes from a single SNP per sequenced region ignores substantial additional information in the phased short-read sequences that are provided by high-throughput sequencing instruments. We target sequenced regions with multiple SNPs in kelp rockfish (Sebastes atrovirens) to determine “microhaplotypes” and then call these microhaplotypes as alleles at each locus. We then demonstrate how these multi-allelic marker data from 96 such loci dramatically increase power for relationship inference. The microhaplotype approach decreases false positive rates by several orders of magnitude, relative to calling bi-allelic SNPs, for two challenging analytical procedures, full sibling and single parent-offspring pair identificati...