Kurland Sara, Saha Atal, Keehnen Naomi, de la Paz Celorio-Mancera Maria, Díez-Del-Molino David, Ryman Nils, Laikre Linda
Division of Population Genetics, Department of Zoology, Stockholm University, Stockholm, Sweden.
Department of Earth Sciences, Natural Resources and Sustainable Development, Uppsala University, Uppsala, Sweden.
Mol Ecol. 2024 Jan;33(2):e17213. doi: 10.1111/mec.17213. Epub 2023 Nov 28.
International policy recently adopted commitments to maintain genetic diversity in wild populations to secure their adaptive potential, including metrics to monitor temporal trends in genetic diversity - so-called indicators. A national programme for assessing trends in genetic diversity was recently initiated in Sweden. Relating to this effort, we systematically assess contemporary genome-wide temporal trends (40 years) in wild populations using the newly adopted indicators and whole genome sequencing (WGS). We use pooled and individual WGS data from brown trout (Salmo trutta) in eight alpine lakes in protected areas. Observed temporal trends in diversity metrics (nucleotide diversity, Watterson's ϴ and heterozygosity) lie within proposed acceptable threshold values for six of the lakes, but with consistently low values in lakes above the tree line and declines observed in these northern-most lakes. Local effective population size is low in all lakes, highlighting the importance of continued protection of interconnected systems to allow genetic connectivity for long-term viability of these populations. Inbreeding (F ) spans 10%-30% and is mostly represented by ancient (<1 Mb) runs of homozygosity, with observations of little change in mutational load. We also investigate adaptive dynamics over evolutionarily short time frames (a few generations); identifying putative parallel selection across all lakes within a gene pertaining to skin pigmentation as well as candidates of selection unique to specific lakes and lake systems involved in reproduction and immunity. We demonstrate the utility of WGS for systematic monitoring of natural populations, a priority concern if genetic diversity is to be protected.
国际政策最近承诺要维持野生种群的遗传多样性，以确保其适应潜力，包括监测遗传多样性时间趋势的指标，即所谓的指示指标。瑞典最近启动了一项评估遗传多样性趋势的国家计划。与此项工作相关，我们使用新采用的指标和全基因组测序（WGS）系统地评估了野生种群当代全基因组的时间趋势（40年）。我们使用了来自保护区内八个高山湖泊的褐鳟（Salmo trutta）的混合和个体WGS数据。在六个湖泊中，观察到的多样性指标（核苷酸多样性、Watterson's ϴ和杂合性）的时间趋势处于提议的可接受阈值范围内，但林线以上湖泊的值一直较低，且在最北部的这些湖泊中观察到了下降。所有湖泊的本地有效种群规模都很低，这凸显了持续保护相互连接的系统以实现这些种群长期生存能力的遗传连通性的重要性。近亲繁殖系数（F）在10% - 30%之间，主要由古老的（<1 Mb）纯合子片段体现，且观察到突变负荷变化不大。我们还研究了在进化时间尺度较短（几代）内的适应性动态；确定了与皮肤色素沉着相关的一个基因在所有湖泊中可能存在的平行选择，以及在涉及繁殖和免疫的特定湖泊和湖泊系统中独特的选择候选基因。我们展示了WGS在系统监测自然种群方面的效用，如果要保护遗传多样性，这是一个优先关注的问题。
