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 (Sander vitreus) 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.

中文翻译：

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过去传播的幽灵：单倍型信息阐明了放养史和系统地理学过程对当代角膜白斑（Sander vitreus）种群结构的相对影响

鱼类放养是维持渔业的重要工具，但也可以显着改变种群遗传结构并侵蚀物种内部多样性，这对促进复原力和适应性至关重要。角膜白斑（Sander玻璃体）是美国中西部地区价值很高的河豚，该地区的特征是冰川后的殖民化，来自多个血统，并且拥有广泛的放养史。我们利用基因组数据和最近开发的分析方法来探索中西部两个州明尼苏达州和威斯康星州的角膜白斑的种群结构。我们通过基因分型通过测序对来自23个种群的954角膜白斑进行了基因分型，在〜20,000个基因座处进行了基因型分型，并使用单SNP和微单倍型数据测试了种群结构的模式。明尼苏达州和威斯康星州的人口彼此高度分化，在每个州都有其他亚结构。人口结构并没有始终如一地遵循流域边界，因为观察到了高流域内部和低流域间差异的情况。在威斯康星州上游和奇珀瓦河上游流域的种群之间观察到较低的遗传结构，它们之间的间隔仅为50 km，并且可能通过历史种群进行了均质化。尽管如此，我们仍能够使用基于微单倍型的共同祖先分析来区分这些人群，与以前的微卫星研究和其他基于单核苷酸多态性的单一分析相比，提供了更高的分辨率。尽管我们的结果表明，过去的放养习惯已经影响了角膜白斑的种群结构，但大多数种群中仍存在本地血统，并且在没有种群的情况下，角膜白斑种群可能能够清除非本地等位基因和单倍型。