The genomic and adaptive consequences of extreme, human-mediated population decline

人们对野生生物数量严重下降的后果知之甚少。经历这种衰退的物种的生存可能受到适应不断变化的环境的能力有限、生育力下降和对疾病的更大易感性的阻碍——所有这些都源于遗传多样性低。当应用于由于人类活动而经历人口瓶颈的系统时，基因组工具使我们能够从近亲繁殖、遗传负荷、抗病能力和适应性方面检查基因组的后果。我们的目的是通过一个极端的人为干预的例子来了解人口急剧下降的后果，在这个例子中，整个湖泊的鱼类资源被消灭并重新繁殖。鲑鱼类外寄生虫旋毛虫（Gyrodactylus salaris）被引入挪威，导致野生大西洋鲑鱼数量锐减。因此，当局将鱼藤酮——一种广谱杀菌剂——应用于整个河流集水区，以杀死所有的宿主鱼。一旦经过处理，水道就会重新放归当地鱼类中未受感染的人工繁殖幼鱼。2012年，福斯塔集水区（四个线性相连的亚北极湖泊）进行了鱼藤酮项目。在处理之前，鱼类群落包括湖间洄游的褐鳟。遗传评估显示种群结构显著，在海上捕获的溯河鳟鱼可分配给富斯塔种群的比例很高。此外，这些分析还发现了选择下的位点，表明整个系统存在局部适应。特别是褐鳟和溯河型，近年来数量大幅下降，这种处理可能会威胁到褐鳟的遗传健康。该系统提供了一个独特的机会，可以了解(i)极端瓶颈对物种基因组的影响，（ii）遗传多样性的丧失如何影响对寄生虫的免疫力，以及（iii）在遗传不足的种群中快速适应的过程。

The consequences of severe population decline in wild organisms are poorly understood. Survival of species experiencing such declines may be hampered by a limited ability to adapt to changing environments, reduced fertility and greater susceptibility to disease - all stemming from low genetic diversity. When applied to systems that have experienced population bottlenecks as a result of human activities, genomic tools allow us to examine the genomic consequences in terms of inbreeding, genetic load, disease resistance and adaptability. Our aim is to understand the consequences of extreme, rapid population decline using an example of drastic human intervention in which the fish stocks of entire lakes were eradicated and repopulated.The introduction of the salmonid ectoparasite Gyrodactylus salaris to Norway resulted in the collapse of wild Atlantic salmon populations. Consequently, authorities applied Rotenone - a broad-spectrum biocide - to entire river catchments to kill all fish hosts. Once treated, waterways are restocked with uninfected captive-bred juveniles from local fish stocks. In 2012 the Fusta catchment (four linearly-connected sub-arctic lakes) underwent a rotenone program. Prior to treatment, fish communities included inter-lake migratory brown trout. Genetic assessment revealed significant population structure and a high proportion of anadromous trout caught at sea could be assigned to Fusta populations. Furthermore, these analyses detected loci under selection suggesting local adaptation across the system. Brown trout and the anadromous form, in particular, have experienced substantial declines in recent years and such treatments may threaten the genetic health of brown trout. This system represents a unique opportunity to understand (i) the impact of extreme bottlenecks on the genome of a species, (ii) how loss of genetic diversity influences immunity to parasites and (iii) the processes by which rapid adaptation occurs in genetically depauperate populations.