Data from: Targeted approach to identify genetic loci associated with evolved dioxin tolerance in Atlantic Killifish (Fundulus heteroclitus)

Background: The most toxic aromatic hydrocarbon pollutants are categorized as dioxin-like compounds (DLCs) to which extreme tolerance has evolved independently and contemporaneously in (at least) four populations of Atlantic killifish (Fundulus heteroclitus). Surprisingly, the magnitude and phenotype of DLC tolerance is similar among these killifish populations that have adapted to varied, but highly aromatic hydrocarbon-contaminated urban/industrialized estuaries of the US Atlantic coast. Multiple tolerant and neighboring sensitive killifish populations were compared with the expectation that genetic loci associated with DLC tolerance would be revealed. Results: Since the aryl hydrocarbon receptor (AHR) pathway partly or fully mediates DLC toxicity in vertebrates, single nucleotide polymorphisms (SNPs) from 42 genes associated with the AHR pathway were identified to serve as targeted markers. Wild fish (N = 36/37) from four highly tolerant killifish populations and four nearby sensitive populations were genotyped using 59 SNP markers. Similar to other killifish population genetic analyses, strong genetic differentiation among populations was detected, consistent with isolation by distance models. When DLC-sensitive populations were pooled and compared to pooled DLC-tolerant populations, multi-locus analyses did not distinguish the two groups. However, pairwise comparisons of nearby tolerant and sensitive populations revealed high differentiation among sensitive and tolerant populations at these specific loci: AHR 1 and 2, cathepsin Z, the cytochrome P450s (CYP1A and 3A30), and the NADH dehydrogenase subunits. In addition, significant shifts in minor allele frequency were observed at AHR2 and CYP1A loci across most sensitive/tolerant pairs, but only AHR2 exhibited shifts in the same direction across all pairs. Conclusions: The observed differences in allelic composition at the AHR2 and CYP1A SNP loci were identified as significant among paired sensitive/tolerant populations of Atlantic killifish with multiple statistical tests. The genetic patterns reported here lend support to the argument that AHR2 and CYP1A play a role in the adaptive response to extreme DLC contamination. Additional functional assays are required to isolate the exact mechanism of DLC tolerance.

研究背景：毒性最强的芳香烃污染物被归类为类二噁英化合物（dioxin-like compounds, DLCs）。至少已有4个大西洋鳉（Fundulus heteroclitus）种群独立且同步演化出了对这类污染物的极端耐受性。令人意外的是，这些适应了美国大西洋沿岸不同但均被高浓度芳香烃污染的城市/工业化河口的鳉鱼种群，其对DLC的耐受程度与耐受表型却高度相似。本研究选取多个耐受种群及其邻近的敏感种群进行比对，以期揭示与DLC耐受相关的遗传位点。

研究结果：鉴于脊椎动物中芳香烃受体（aryl hydrocarbon receptor, AHR）通路部分或完全介导DLC的毒性，本研究从与AHR通路相关的42个基因中筛选出单核苷酸多态性（single nucleotide polymorphisms, SNPs）作为靶向标记。使用59个SNP标记，对来自4个高耐受鳉鱼种群以及4个邻近敏感种群的野生个体（每组样本量N=36/37）进行基因分型。与其他鳉鱼种群遗传分析结果一致，本研究检测到种群间存在显著遗传分化，符合距离隔离模型的特征。当将所有DLC敏感种群合并、所有DLC耐受种群合并后进行多位点分析时，无法区分这两类种群。但对邻近的耐受与敏感种群进行两两比对时，发现二者在以下特定位点存在显著分化：AHR1、AHR2、组织蛋白酶Z（cathepsin Z）、细胞色素P450家族（cytochrome P450s, CYP1A与3A30）以及NADH脱氢酶亚基（NADH dehydrogenase subunits）。此外，在绝大多数敏感-耐受种群配对中，AHR2与CYP1A位点的次要等位基因频率均发生了显著变化，但仅AHR2在所有配对中均表现出方向一致的频率偏移。

研究结论：本研究通过多种统计学检验证实，在成对的大西洋鳉敏感与耐受种群中，AHR2与CYP1A的SNP位点的等位基因组成存在显著差异。本研究报道的遗传模式进一步支持了"AHR2与CYP1A参与极端DLC污染的适应性响应"这一论点。后续仍需开展功能实验，以明确DLC耐受的具体分子机制。