In many human-altered ecosystems, organisms are increasingly faced with more diverse and complex environmental stressors and pollutant mixtures, to which the adaptations necessary to survive exposure are likely to be numerous and varied. Improving our understanding of the molecular mechanisms that underlie complex polygenic adaptations in natural settings requires significant toxicological, biochemical, physiological, and genomic data rarely available for non-model organisms. Here, we build upon two decades of study of adaptation to anthropogenic pollutants in a population of Atlantic killifish (Fundulus heteroclitus) that inhabits the creosote-contaminated Atlantic Wood Industries Superfund (AW) site on the Elizabeth River, Virginia in the United States. To better understand the genotypes that underlie previously characterized resistance to PCBs and PAHs, we performed Restriction site-Associated DNA sequencing (RADseq) on killifish from AW and two relatively clean reference sites (King's Creek-KC, and Mains Creek-MC). Across the genome, we analyzed over 83,000 loci and 12,000 single nucleotide polymorphisms (SNPs). Shared across both comparisons of killifish from polluted (AW) and relatively unpolluted (KC and MC) sites, we found eight genomic regions with smoothed FST values significantly (p < 0.001) elevated above background. Using the recently published F. heteroclitus reference genome, we identified candidate genes in these significant regions involved in the AHR pathway (e.g. AIP, ARNT1c), as well as genes relating to cardiac structure and function. These genes represent both previously characterized and potentially novel molecular adaptations involved with various aspects of resistance to these environmental toxins.

中文翻译：

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全基因组扫描揭示了非模式河口大西洋鳉鱼（Fundulusheteroclitus）与污染适应相关的选择特征。

在许多人类改变的生态系统中，生物体日益面临更加多样化和复杂的环境压力源和污染物混合物，为了在这些环境压力下生存而必须进行的适应可能是多种多样的。为了提高我们对自然环境中复杂多基因适应的分子机制的理解，需要大量的毒理学、生化、生理和基因组数据，而这些数据对于非模式生物来说很少可用。在这里，我们以二十年来对大西洋鳉鱼（Fundulusheteroclitus）种群对人为污染物的适应的研究为基础，这些大西洋鳉鱼栖息在美国弗吉尼亚州伊丽莎白河受杂酚油污染的大西洋木材工业超级基金（AW）地点。为了更好地了解先前表征的 PCB 和 PAH 抗性背后的基因型，我们对来自 AW 的鳉鱼和两个相对干净的参考位点（King's Creek-KC 和 Mains Creek-MC）进行了限制性位点相关 DNA 测序 (RADseq)。在整个基因组中，我们分析了超过 83,000 个基因座和 12,000 个单核苷酸多态性 (SNP)。通过对来自污染（AW）和相对未污染（KC 和 MC）地点的鳉鱼的比较，我们发现平滑 FST 值显着（p < 0.001）高于背景的 8 个基因组区域。利用最近发表的异斜镰刀菌参考基因组，我们鉴定了参与AHR通路的这些重要区域的候选基因（例如AIP、ARNT1c），以及与心脏结构和功能相关的基因。这些基因代表了先前表征的和潜在的新颖的分子适应，涉及对这些环境毒素的抵抗的各个方面。