Erdman Bradley, Larson Wesley, Mitro Matthew G, Griffin Joanna D T, Rowe David, Haglund Justin, Olson Kirk, Kinnison Michael T
School of Biology and Ecology, Ecology and Environmental Sciences Program University of Maine Orono Maine USA.
Department of Biological Sciences University of New Hampshire Durham New Hampshire USA.
Evol Appl. 2024 Dec 16;17(12):e70026. doi: 10.1111/eva.70026. eCollection 2024 Dec.
Fish stocking has been utilized for over a century to offset extirpations or declines in abundance of many native species. These historical declines and hatchery contributions have led to uncertainty surrounding whether many contemporary populations are native, introgressed with hatchery sources, or entirely of hatchery origin. Such uncertainty is problematic for the conservation of native biodiversity as it hampers management agencies' ability to prioritize the conservation of indigenous locally adapted populations. Fortunately, genetic and genomic tools have allowed researchers to investigate these questions, often through the use of clustering or assignment approaches that are predicated on identifiable and consistent divergence between native populations and hatchery sources. Here, we apply these methods to restriction-site associated DNA (RAD) data from 643 brook trout () originating from 13 wild populations and an exogenous hatchery strain to investigate the extent of historical extirpations, hatchery contributions, and processes affecting population structure in a small area of the previously unglaciated Driftless Area of Wisconsin, USA. The results from these analyses suggest that wild populations in this region are genetically distinct even at small spatial scales, lack strong hydrologically associated population structure, rarely exchange gene flow, and have small effective population sizes. Furthermore, wild populations are substantially diverged from known hatchery strains and show minimal evidence of introgression in clustering analyses. However, we demonstrate through empirically informed simulations that distinct wild populations may potentially be hatchery-founded and have since diverged through rapid genetic drift. Collectively, the apparent lack of hydrological population structure and potential for rapid drift in the Driftless Area suggest that many native populations may have been historically extirpated and refounded by stocking events. If this is the case, then commonly used genomic clustering methods and their associated model selection criteria may result in underestimation of hatchery introgression in the face of rapid drift.
放养鱼苗已有一个多世纪的历史，用于抵消许多本地物种的灭绝或数量下降。这些历史上的数量下降和孵化场的贡献导致了围绕许多当代种群是否为本地种群、是否与孵化场来源杂交或完全源自孵化场的不确定性。这种不确定性对于本地生物多样性的保护来说是个问题，因为它阻碍了管理机构对本地适应本地环境的种群进行保护优先级排序的能力。幸运的是，遗传和基因组工具使研究人员能够研究这些问题，通常是通过使用基于本地种群和孵化场来源之间可识别且一致的差异的聚类或分配方法。在这里，我们将这些方法应用于来自美国威斯康星州以前未冰川覆盖的无冰区小区域的13个野生种群和一个外来孵化场品系的643条溪鳟（）的限制性位点相关DNA（RAD）数据，以调查历史灭绝的程度、孵化场的贡献以及影响种群结构的过程。这些分析结果表明，该地区的野生种群即使在小空间尺度上在基因上也是不同的，缺乏与水文密切相关的种群结构，很少有基因流交换，并且有效种群规模较小。此外，野生种群与已知的孵化场品系有很大差异，并且在聚类分析中显示出极少的基因渗入证据。然而，我们通过基于经验的模拟证明，不同的野生种群可能潜在地是由孵化场建立的，并且此后通过快速的遗传漂变而分化。总体而言，无冰区明显缺乏水文种群结构以及快速漂变的可能性表明，许多本地种群在历史上可能已经灭绝，并通过放流事件重新建立。如果是这样的话，那么面对快速漂变，常用的基因组聚类方法及其相关的模型选择标准可能会导致对孵化场基因渗入的低估。
