Data from: Going where traditional markers have not gone before: utility of and promise for RAD-sequencing in marine invertebrate phylogeography and population genomics

Characterization of large numbers of single-nucleotide polymorphisms (SNPs) throughout a genome has the power to refine the understanding of population demographic history and to identify genomic regions under selection in natural populations. To this end, population genomic approaches that harness the power of next-generation sequencing to understand the ecology and evolution of marine invertebrates represent a boon to test long-standing questions in marine biology and conservation. We employed restriction-site-associated DNA sequencing (RAD-seq) to identify SNPs in natural populations of the sea anemone Nematostella vectensis, an emerging cnidarian model with a broad geographic range in estuarine habitats in North and South America, and portions of England. We identified hundreds of SNP-containing tags in thousands of RAD loci from 30 barcoded individuals inhabiting four locations from Nova Scotia to South Carolina. Population genomic analyses using high-confidence SNPs resulted in a highly-resolved phylogeography, a result not achieved in previous studies using traditional markers. Plots of locus-specific FST against heterozygosity suggest that a majority of polymorphic sites are neutral, with a smaller proportion suggesting evidence for balancing selection. Loci inferred to be under balancing selection were mapped to the genome, where 90% were located in gene bodies, indicating potential targets of selection. The results from analyses with and without a reference genome supported similar conclusions, further highlighting RAD-seq as a method that can be efficiently applied to species lacking existing genomic resources. We discuss the utility of RAD-seq approaches in burgeoning Nematostella research as well as in other cnidarian species, particularly corals and jellyfishes, to determine phylogeographic relationships of populations and identify regions of the genome undergoing selection.

对全基因组范围内大量单核苷酸多态性（single-nucleotide polymorphisms, SNPs）进行分型，能够深化我们对种群历史动态的认知，并鉴定自然种群中受选择作用的基因组区域。为此，利用下一代测序技术（next-generation sequencing）解析海洋无脊椎动物生态与演化的种群基因组学方法，为检验海洋生物学与保护生物学领域的长期科学问题提供了宝贵契机。本研究采用限制性酶切位点相关DNA测序（restriction-site-associated DNA sequencing, RAD-seq）技术，在海葵（Nematostella vectensis）的自然种群中鉴定SNPs；该物种是一种新兴的刺胞动物模型，在北美、南美以及英国部分地区的河口生境中拥有广泛的地理分布范围。我们从30个带有条形码标记的个体（采样自新斯科舍至南卡罗来纳的4个采样点）的数千个RAD位点中，鉴定出数百个携带SNPs的标签序列。基于高置信度SNPs的种群基因组学分析得到了分辨率极高的系统地理格局，这一结果是此前使用传统分子标记的研究未能达成的。基于位点特异性遗传分化系数（FST）与杂合度的散点图分析显示，多数多态位点为中性位点，仅少量位点呈现平衡选择的信号。被推断受平衡选择作用的位点被定位至参考基因组，其中90%位于基因区，表明这些位点可能为选择作用的靶标。有无参考基因组的分析结果均得到了一致的结论，进一步凸显了RAD-seq技术可高效应用于缺乏现有基因组资源的物种。本研究还探讨了RAD-seq技术在快速发展的海葵研究以及其他刺胞动物类群（特别是珊瑚与水母）中的应用潜力，用于解析种群的系统地理关系并鉴定基因组中受选择作用的区域。