Bootsma Matthew L, Miller Loren, Sass Greg G, Euclide Peter T, Larson Wesley A
Wisconsin Cooperative Fishery Research Unit College of Natural Resources University of Wisconsin-Stevens Point Stevens Point WI USA.
Minnesota Department of Natural Resources University of Minnesota St. Paul MN USA.
Evol Appl. 2021 Jan 29;14(4):1124-1144. doi: 10.1111/eva.13186. eCollection 2021 Apr.
Stocking of fish is an important tool for maintaining fisheries but can also significantly alter population genetic structure and erode the portfolio of within-species diversity that is important for promoting resilience and adaptability. Walleye () are a highly valued sportfish in the midwestern United States, a region characterized by postglacial recolonization from multiple lineages and an extensive history of stocking. We leveraged genomic data and recently developed analytical approaches to explore the population structure of walleye from two midwestern states, Minnesota and Wisconsin. We genotyped 954 walleye from 23 populations at ~20,000 loci using genotyping by sequencing and tested for patterns of population structure with single-SNP and microhaplotype data. Populations from Minnesota and Wisconsin were highly differentiated from each other, with additional substructure found in each state. Population structure did not consistently adhere to drainage boundaries, as cases of high intra-drainage and low inter-drainage differentiation were observed. Low genetic structure was observed between populations from the upper Wisconsin and upper Chippewa river watersheds, which are found as few as 50 km apart and were likely homogenized through historical stocking. Nevertheless, we were able to differentiate these populations using microhaplotype-based co-ancestry analysis, providing increased resolution over previous microsatellite studies and our other single SNP-based analyses. Although our results illustrate that walleye population structure has been influenced by past stocking practices, native ancestry still exists in most populations and walleye populations may be able to purge non-native alleles and haplotypes in the absence of stocking. Our study is one of the first to use genomic tools to investigate the influence of stocking on population structure in a nonsalmonid fish and outlines a workflow leveraging recently developed analytical methods to improve resolution of complex population structure that will be highly applicable in many species and systems.
鱼类放养是维持渔业的一项重要手段，但也可能显著改变种群遗传结构，并侵蚀物种内部多样性组合，而这种多样性对于提升恢复力和适应性至关重要。大眼狮鲈（）是美国中西部一种备受珍视的游钓鱼类，该地区的特点是多个谱系的冰川后重新定殖以及悠久的放养历史。我们利用基因组数据和最近开发的分析方法，探究了来自明尼苏达州和威斯康星州这两个中西部州的大眼狮鲈种群结构。我们通过测序基因分型对来自23个种群的954条大眼狮鲈在约20,000个位点进行了基因分型，并使用单核苷酸多态性（SNP）和微单倍型数据测试了种群结构模式。明尼苏达州和威斯康星州的种群彼此高度分化，且每个州内都发现了额外的亚结构。种群结构并不总是遵循排水边界，因为观察到了流域内分化高而流域间分化低的情况。在威斯康星河上游和奇珀瓦河上游流域的种群之间观察到低遗传结构差异，这两个流域相距仅50公里，可能通过历史放养实现了同质化。尽管如此，我们能够使用基于微单倍型的共同祖先分析来区分这些种群，比之前的微卫星研究和我们其他基于单SNP的分析提供了更高的分辨率。虽然我们的结果表明大眼狮鲈种群结构受到过去放养实践的影响，但大多数种群中仍存在本地血统，并且在没有放养的情况下，大眼狮鲈种群可能能够清除非本地等位基因和单倍型。我们的研究是最早使用基因组工具来研究放养对非鲑科鱼类种群结构影响的研究之一，并概述了一种利用最近开发的分析方法来提高复杂种群结构分辨率的工作流程，这将在许多物种和系统中高度适用。
