Population genomic analyses of the sea urchin Echinometra sp. EZ across an extreme environmental gradient

Extreme environmental gradients represent excellent study systems to better understand the variables that mediate patterns of genomic variation between populations. They also allow for more accurate predictions of how future environmental change might affect marine species. The Persian/Arabian Gulf is extreme in both temperature and salinity, whereas the adjacent Gulf of Oman has conditions more typical of tropical oceans. The sea urchin Echinometra sp. EZ inhabits both of these seas and plays a critical role in coral reef health as a grazer and bioeroder, but, to date, there have been no population genomic studies on this or any urchin species in this unique region. E. sp. EZ’s life history traits (e.g., large population sizes, large reproductive clutches, and long life spans), in theory, should homogenize populations unless nonneutral processes are occurring. Here, we generated a draft genome and a restriction site-associated DNA sequencing data set from seven populations along an env..., FILES (please see manuscript for more details):
ESPEZ_final_v2.fa : Final assembled draft genome for Echinometra sp. EZ.
barcodes.txt: RAD barcode file
raw.vcf : The raw vcf file generated by aligning RADtags to the draft genome (for this alignment, we removed the reads which were <200bp from the draft genome), and running Freebayes to call SNPs. 
SNP_FINAL_HARDFILT_918.vcf : Final filtered VCF file used for all downstream analyses, contains 918 high quality SNPs.,

极端环境梯度是解析调控种群间基因组变异模式的变量的极佳研究系统，同时可更精准地预测未来环境变化对海洋物种的影响。波斯湾/阿拉伯海湾（Persian/Arabian Gulf）的温度与盐度均处于极端水平，而邻近的阿曼湾（Gulf of Oman）则具备更典型的热带海洋环境条件。海胆Echinometra sp. EZ栖息于这两片海域，作为植食者与生物侵蚀者，在珊瑚礁健康维持中发挥关键作用，但截至目前，该独特区域尚未开展针对该种海胆或任何海胆物种的群体基因组学研究。理论上，E. sp. EZ的生活史特征（如种群规模庞大、繁殖产卵量大、寿命较长）本应使种群间产生遗传均质化，除非存在非中性进化过程。本研究从沿环境梯度分布的7个种群中构建了草图基因组（draft genome），并生成了限制性酶切位点关联DNA测序（restriction site-associated DNA sequencing）数据集，相关文件详见手稿以获取更多细节：
1. ESPEZ_final_v2.fa：Echinometra sp. EZ的最终组装草图基因组序列文件。
2. barcodes.txt：RAD测序条形码文件。
3. raw.vcf：将RAD标签比对至草图基因组（比对过程中移除了距离草图基因组小于200bp的测序reads）后，通过Freebayes调用单核苷酸多态性（Single Nucleotide Polymorphism，SNP）得到的原始VCF文件。
4. SNP_FINAL_HARDFILT_918.vcf：用于所有后续分析的最终过滤后VCF文件，共包含918个高质量单核苷酸多态性位点。