Variation in genomic vulnerability to climate change across temperate populations of eelgrass (Zostera marina)

A global decline in seagrass populations has led to renewed calls for their conservation as important providers of biogenic and foraging habitat, shoreline stabilisation, and carbon storage. Eelgrass (Zostera marina) occupies the largest geographic range among seagrass species spanning a commensurately broad spectrum of environmental conditions. In Canada, eelgrass is managed as a single phylogroup despite occurring across three oceans and a range of ocean temperatures and salinity gradients. Previous research has focused on applying relatively few markers to reveal population structure of eelgrass, whereas a whole genome approach is warranted to investigate cryptic structure among populations inhabiting different ocean basins and localized environmental conditions. We used a pooled whole-genome re-sequencing approach to characterise population structure, gene flow, and environmental associations of 23 eelgrass populations ranging from the Northeast United States, to Atlantic, subarctic..., We generated allele frequencies for 23 Zostera marina populations across North America using a pooled whole-genome sequencing approach (poolseq). Individual shoots of eelgrass were collected from plants at least 2 metres apart in the field, to minimize the potential presence of clones in the data. Genomic DNA was extracted from all individuals and pooled at the population level for sequencing on an Illumina NovaSeq platform at Genome Quebec (Canada), and SNPs were called following the GATK pipeline. Analyses were conducted with Popoolation2 and R Studio. R Studio was used for all genomic-environmental association analyses, including redundancy analyses, and calculating genomic offset sensu Capblancq and Forester (2021). , , # Variation in genomic vulnerability to climate change across temperate populations of eelgrass (Zostera marina)

[https://doi.org/10.5061/dryad.xpnvx0kp2](https://doi.org/10.5061/dryad.xpnvx0kp2)

The data herein includes sample site metadata (GPS coordinates, collection dates, personnel, and site names and codes), environmental data used for genomic-environment association analyses (redundancy analyses), as well as pairwise Fst matrices for all sampling sites. All raw DNA sequences for all 23 sampling locations are contained within the National Center for Biotechnology Information ([https://www.ncbi.nlm.nih.gov/sra/PRJNA891275)](https://www.ncbi.nlm.nih.gov/sra/PRJNA891275\))

## Description of the data and file structure

The primary data in this project are the raw fastq DNA files deposited in NCBI for each of 23 populations sampled. As these fastq files represent pooled genomic DNA sequences per population, there are no individual genotypes, but rather can be processed into populat...

全球海草种群的持续衰退，使得学界再次呼吁加强海草保护——作为关键的生源性生境与觅食生境提供者、海岸稳定因子以及碳储库，海草的生态价值不容忽视。鳗草（Zostera marina）是海草属中地理分布范围最广的物种，其栖息环境涵盖了极为广泛的环境梯度。在加拿大，尽管鳗草横跨三大洋，且分布于不同海洋温度与盐度梯度区域，却仍被作为单一系统发育群进行管理。

既往研究多采用相对有限的分子标记来解析鳗草的种群结构，而全基因组手段更适合探究不同洋盆及局域环境下鳗草种群间的隐秘遗传结构。本研究采用混合样本全基因组重测序（poolseq）技术，对覆盖美国东北大西洋、亚北极区域等在内的23个鳗草种群的种群结构、基因流及环境关联展开分析。

我们通过混合样本全基因组测序技术，生成了北美地区23个鳗草种群的等位基因频率数据。实验采集时，田间选取间距至少2米的鳗草植株，以尽可能降低数据中克隆样本的占比。从所有个体中提取基因组DNA，并按种群水平进行混合，随后在加拿大魁北克基因组中心（Genome Quebec）利用Illumina NovaSeq平台完成测序；单核苷酸多态性（Single Nucleotide Polymorphism, SNP）的调用遵循GATK流程。数据分析采用Popoolation2与R Studio完成，其中所有基因组-环境关联分析（包括冗余分析）以及基于Capblancq与Forester（2021）方法的基因组偏移量计算，均通过R Studio实现。

# 温带鳗草（Zostera marina）种群对气候变化的基因组脆弱性空间差异

https://doi.org/10.5061/dryad.xpnvx0kp2

本数据集包含采样位点的元数据（GPS坐标、采集日期、采样人员、站点名称与代码）、用于基因组-环境关联分析的环境数据（含冗余分析所需数据），以及所有采样位点的两两Fst矩阵。23个采样位点的全部原始DNA序列已上传至美国国家生物技术信息中心（NCBI），具体存储链接为：https://www.ncbi.nlm.nih.gov/sra/PRJNA891275

## 数据与文件结构说明
本项目的核心原始数据为上传至NCBI的23个采样种群的fastq格式DNA原始文件。由于这些fastq文件为种群水平的混合基因组DNA序列，因此不存在单个个体的基因型数据，但可通过后续处理得到种群层面的遗传信息……