Data from: Discovery and characterization of a large number of diagnostic markers to discriminate Oncorhynchus mykiss and O. clarkii

Hybridization of cutthroat trout and steelhead/rainbow trout is ubiquitous where they are sympatric, either naturally or due to introductions. The ability to detect hybridization between them has been hampered by a paucity of genetic markers that have been validated across the many phylogenetic lineages in the two species. Here, we describe 81 novel genetic markers and associated assays for discriminating the genomes of these sister species. These diagnostic nucleotide polymorphisms were discovered by sequencing of rainbow trout expressed sequence tags (ESTs) in a diverse panel of both cutthroat trout and steelhead/rainbow trout. The resulting markers were validated in a large number of lineages of both species, including all extant subspecies of cutthroat trout and most of the lineages of rainbow trout that are found in natural sympatry with cutthroat trout or used in stocking practices. Most of these markers (79%) distinguish genomic regions for all lineages of the two species, but a small number do not reliably diagnose coastal, westslope, and/or other subspecies of cutthroat trout. Surveys of natural populations and hatchery strains of trout and steelhead found rare occurrences of the alternative allele, which may be due to either previous introgression or shared polymorphism. The availability of a large number of genetic markers for distinguishing genomic regions originating in these sister species will allow the detection of both recent and more distant hybridization events, facilitate the study of the evolutionary dynamics of hybridization and provide a powerful set of tools for the conservation and management of both species.

割喉鳟（cutthroat trout）与钢头鳟/虹鳟（steelhead/rainbow trout）在自然同域分布区域或人为引种后的同域区域内，二者间的杂交现象极为普遍。此前，由于缺乏可在这两个物种的众多系统发育谱系中验证的遗传标记，二者间的杂交检测能力受到极大限制。本研究开发了81个全新的遗传标记及配套检测方法，用于区分这对姊妹物种的基因组。这些诊断性核苷酸多态性位点，是通过对涵盖割喉鳟与钢头鳟/虹鳟的多样化研究群体的样本进行虹鳟表达序列标签（expressed sequence tags, ESTs）测序发掘得到的。所得标记已在两个物种的大量谱系中完成验证，涵盖割喉鳟的所有现存亚种，以及自然与割喉鳟同域分布或用于养殖放流的多数虹鳟谱系。其中79%的标记可区分两个物种所有谱系的基因组区域，但少数标记无法稳定鉴定沿海亚种、西坡亚种及其他割喉鳟亚种。对鳟鱼与钢头鳟的自然种群及养殖品系开展的调查显示，罕见的替代等位基因变异时有发生，其成因可能为既往基因渐渗或共享多态性。本研究开发的大量可区分姊妹物种来源基因组区域的遗传标记，将能够检测近期及远期的杂交事件，助力杂交演化动力学研究，并为这两个物种的保护与管理提供一套强有力的工具。