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...当前高通量测序仪器产出DNA序列数据的速率不断加快，这为动植物的种群遗传学与生态学研究既带来了机遇，也带来了挑战。本文阐明了当前主流的“每个测序区域仅基于单个单核苷酸多态性（Single Nucleotide Polymorphism, SNP）进行基因型分型”的常规操作，为何会忽略高通量测序仪器所产出的分相短读长序列中蕴含的大量额外信息。本研究以海带平鲉（Sebastes atrovirens）中携带多个单核苷酸多态性的测序区域为研究对象，以此鉴定“微单倍型（microhaplotype）”，随后将这些微单倍型作为各基因座上的等位基因进行分型。随后我们证实，来自96个此类基因座的多等位基因标记数据，可显著提升亲缘关系推断的统计效力。针对全同胞鉴定与单亲-子代配对鉴定这两项具有挑战性的分析流程，相较于仅基于双等位基因单核苷酸多态性进行分型的方法，微单倍型分型策略可将假阳性率降低数个数量级，用于...