Veale Andrew J, Russello Michael A
Department of Biology, The University of British Columbia, Kelowna, British Columbia, Canada.
Department of Environmental and Animal Sciences, Unitec, 139 Carrington Rd, Auckland, New Zealand.
Genome Biol Evol. 2017 Oct 1;9(10):2921-2939. doi: 10.1093/gbe/evx215.
Mechanisms underlying adaptive evolution can best be explored using paired populations displaying similar phenotypic divergence, illuminating the genomic changes associated with specific life history traits. Here, we used paired migratory [anadromous vs. resident (kokanee)] and reproductive [shore- vs. stream-spawning] ecotypes of sockeye salmon (Oncorhynchus nerka) sampled from seven lakes and two rivers spanning three catchments (Columbia, Fraser, and Skeena) in British Columbia, Canada to investigate the patterns and processes underlying their divergence. Restriction-site associated DNA sequencing was used to genotype this sampling at 7,347 single nucleotide polymorphisms, 334 of which were identified as outlier loci and candidates for divergent selection within at least one ecotype comparison. Sixty-eight of these outliers were present in two or more comparisons, with 33 detected across multiple catchments. Of particular note, one locus was detected as the most significant outlier between shore and stream-spawning ecotypes in multiple comparisons and across catchments (Columbia, Fraser, and Snake). We also detected several genomic islands of divergence, some shared among comparisons, potentially showing linked signals of differential selection. The single nucleotide polymorphisms and genomic regions identified in our study offer a range of mechanistic hypotheses associated with the genetic basis of O. nerka life history variation and provide novel tools for informing fisheries management.
利用表现出相似表型差异的配对种群，能够最好地探究适应性进化的潜在机制，从而阐明与特定生活史特征相关的基因组变化。在此，我们使用了从加拿大不列颠哥伦比亚省跨越三个集水区（哥伦比亚、弗雷泽和斯基纳）的七个湖泊和两条河流中采集的红大马哈鱼（Oncorhynchus nerka）的配对洄游型（溯河洄游型与定居型（红大麻哈鱼））和繁殖型（海岸产卵型与溪流产卵型）生态型，来研究它们分化的模式和过程。利用限制性位点相关DNA测序技术，对该样本在7347个单核苷酸多态性位点进行基因分型，其中334个被确定为异常位点，并在至少一种生态型比较中作为趋异选择的候选位点。这些异常位点中有68个出现在两个或更多的比较中，33个在多个集水区中被检测到。特别值得注意的是，在多个比较和多个集水区（哥伦比亚、弗雷泽和斯内克）中，有一个位点被检测为海岸产卵型和溪流产卵型生态型之间最显著的异常位点。我们还检测到了几个分化的基因组岛，其中一些在比较中是共享的，可能显示出差异选择的连锁信号。我们研究中确定的单核苷酸多态性和基因组区域提供了一系列与红大马哈鱼生活史变异的遗传基础相关的机制假说，并为渔业管理提供了新的工具。
