SNP data for Northern Alligator Lizards

Understanding the processes that shape genetic diversity by either promoting or preventing population divergence can help identify geographic areas that either facilitate or limit gene flow. Furthermore, broadly distributed species allow us to understand how biogeographic and ecogeographic transitions affect gene flow. We investigated these processes using genomic data in the Northern Alligator Lizard (Elgaria coerulea), which is widely distributed in Western North America across diverse ecoregions (California Floristic Province and Pacific Northwest) and mountain ranges (Sierra Nevada, Coastal Ranges, and Cascades). We collected single nucleotide polymorphism (SNP) data from 120 samples of E. coerulea. Biogeographic analyses of squamate reptiles with similar distributions have identified several shared diversification patterns that provide testable predictions for E. coerulea, including deep genetic divisions in the Sierra Nevada, demographic stability of southern populations, and recent post-Pleistocene expansion into the Pacific Northwest. We use genomic data to test these predictions by estimating the structure, connectivity, and phylogenetic history of populations. At least ten distinct populations are supported, with mixed-ancestry individuals situated at most population boundaries. A species tree analysis provides strong support for the early divergence of populations in the Sierra Nevada Mountains and recent diversification into the Pacific Northwest. Admixture and migration analyses detect gene flow among populations in the Lower Cascades and Northern California, and a spatial analysis of gene flow identified significant barriers to gene flow across both the Sierra Nevada and Coast Ranges. The distribution of genetic diversity in E. coerulea is uneven, patchy, and interconnected at population boundaries. The biogeographic patterns seen in E. coerulea are consistent with predictions from co-distributed species.

解析通过促进或抑制种群分化来塑造遗传多样性的过程，有助于识别那些促进或限制基因流的地理区域。此外，广布物种可帮助我们探究生物地理与生态地理过渡带如何影响基因流。我们以广泛分布于北美西部多样生态区（加州植物区省、太平洋西北地区）及山脉（内华达山脉、海岸山脉、喀斯喀特山脉）的北鳄蜥（Elgaria coerulea）为研究对象，利用基因组数据解析上述过程。我们共采集了120份北鳄蜥样本的单核苷酸多态性（SNP）数据。针对分布模式相似的有鳞目爬行动物开展的生物地理学分析，已识别出多种共有的分化模式，可为北鳄蜥提供可验证的预测假说，包括内华达山脉存在深度遗传分化、南部种群的人口统计学稳定性，以及更新世后近期向太平洋西北地区的扩张。我们通过估算种群结构、连通性及系统发育历史，利用基因组数据对上述预测假说进行验证。分析结果支持至少10个独立种群的存在，多数种群交界区域均存在遗传混合的个体。物种树分析为内华达山脉种群的早期分化以及近期向太平洋西北地区的分化提供了强有力的支持。遗传混合与基因流分析检测到下喀斯喀特山脉与加利福尼亚北部的种群间存在基因交流，而空间基因流分析则识别出内华达山脉与海岸山脉均存在显著的基因流阻隔。北鳄蜥的遗传多样性分布不均、呈斑块状，且在种群交界区域存在遗传连通性。北鳄蜥所呈现的生物地理学模式，与同分布物种的预测结果相符。