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人口统计历史的认知，并可识别自然种群中受选择的基因组区域。为此，借助下一代测序技术探究海洋无脊椎动物生态与演化的群体基因组学方法，为检验海洋生物学与保护生物学领域的长期未解难题提供了重要助力。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，对星状海葵（Nematostella vectensis）自然种群中的SNPs进行鉴定。星状海葵是一种新兴的刺胞动物模式生物，其在北美、南美及英国部分地区的河口生境中拥有广泛的分布范围。本研究从30个带有条形码标记的个体中，在覆盖从新斯科舍省至南卡罗来纳州4个采样点位的数千个RAD位点里，鉴定出了数百个携带SNPs的标签序列。基于高置信度SNPs的群体基因组学分析，得到了分辨率极高的系统地理学结果——这是以往采用传统分子标记的研究未能实现的突破。以位点特异性F统计量（FST）对杂合度绘制的散点图显示，绝大多数多态位点为中性位点，仅小部分位点呈现平衡选择的信号。被推断为受平衡选择的位点被定位至参考基因组，其中90%位于基因编码区内，表明这些位点可能是选择作用的靶标。有无参考基因组的分析结果均得到了一致结论，进一步凸显了RAD-seq技术可被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技术在新兴星状海葵研究，以及其他刺胞动物类群（尤其是珊瑚与水母）中的应用价值，可用于解析种群的系统地理关系并鉴定基因组中受选择的区域。