How environmental and anthropogenic factors influence genetic variation and local adaptation is a central issue in evolutionary biology. The Mexican golden trout (Oncorhynchus chrysogaster), one of the southernmost native salmonid species in the world, is susceptible to climate change, habitat perturbations and the competition and hybridization with exotic rainbow trout (O. mykiss). The present study aimed for the first time to use genotyping-by-sequencing to explore the effect of genetic hybridization with O. mykiss and of riverscape and climatic variables on the genetic variation among O. chrysogaster populations. Genotyping-by-sequencing (GBS) was applied to generate 9767 single nucleotide polymorphisms (SNPs), genotyping 272 O. chrysogaster and O. mykiss. Population genomics analyses were combined with landscape ecology approaches into a riverine context (riverscape genetics). The clustering analyses detected seven different genetic groups (six for O. chrysogater and one for aquaculture O. mykiss) and a small amount of admixture between aquaculture and native trout with only two native genetic clusters showing exotic introgression. Latitude and precipitation of the driest month had a significant negative effect on genetic diversity and evidence of isolation by river resistance was detected, suggesting that the landscape heterogeneity was preventing trout dispersal, both for native and exotic individuals. Moreover, several outlier SNPs were identified as potentially implicated in local adaptation to local hydroclimatic variables. Overall, this study suggests that O. chrysogater may require conservation planning given (i) exotic introgression from O. mykiss locally threatening O. chrysogater genetic integrity, and (ii) putative local adaptation but low genetic diversity and hence probably reduced evolutionary potential especially in a climate change context.

环境和人为因素如何影响遗传变异和局部适应性是进化生物学的中心问题。墨西哥金鳟鱼（Oncorhynchus chrysogaster）是世界上最南端的鲑科鱼类之一，易受气候变化，栖息地扰动以及与异国虹鳟（O. mykiss）竞争和杂交的影响。本研究的目的是首次利用测序进行基因分型，以探索与O. mykiss和河景和气候变量的基因杂交对O. chrysogaster种群遗传变异的影响。应用测序基因分型（GBS）生成9776个单核苷酸多态性（SNP），进行基因分型272O. chrysogaster和O. mykiss。人口基因组学分析与景观生态学方法结合到河流环境中（河流景观遗传学）。聚类分析检测到七个不同的基因组（金黄色O. chrysogater六个，水产养殖O. mykiss的一个）和水产养殖与鳟鱼之间的少量掺混物，只有两个原生遗传簇显示出外来的渗入。最干旱月份的纬度和降水对遗传多样性产生了显着的负面影响，并发现了通过河道阻力进行隔离的证据，这表明景观异质性在本地和外来个体中均阻止了鳟鱼的扩散。此外，一些异常单核苷酸多态性被确定可能与对当地水文气候变量的局部适应有关。总体而言，这项研究表明，澳chrysogater可能需要提供：（i）从异国情调的渗入保护规划O.虹鳟本地威胁O. chrysogater 遗传完整性，以及（ii）假定的局部适应性但遗传多样性低，因此可能降低了进化潜力，尤其是在气候变化的情况下。