Data from: 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
identification. The advent of phased short-read DNA sequence data, in
conjunction with emerging analytical tools for their analysis, promises to
improve efficiency by reducing the number of loci necessary for a
particular level of statistical confidence, thereby lowering the cost of
data collection and reducing the degree of physical linkage amongst
markers used for relationship estimation. Such advances will facilitate
collaborative research and management for migratory and other widespread
species.