Population genomic and morphological datasets from: An evolutionary mosaic challenges traditional monitoring of a foundation species in a coastal environment - the Baltic Fucus vesiculosus

Genetic diversity in foundation species is critical for ecosystem functions and resilience under environmental change but remains largely overlooked in environmental monitoring. In the Baltic Sea, a key species for monitoring is the brown seaweed Fucus vesiculosus, which forms sublittoral 3D habitats providing shelter and food for fish and invertebrates.  Ecological distribution models predict a significant loss of Baltic F. vesiculosus due to ocean warming unless populations can adapt. Genetic variation and recombination during sexual reproduction are essential for adaptation, but studies have revealed large-scale clonal reproduction within the Baltic Sea. We analyzed genome-wide SNP data from the east Atlantic, the "Transition zone", and the Baltic Sea, and found a mosaic of divergent lineages in the Baltic Sea contrasting an outside dominance of a few genetic groups. We determined that the previously described endemic species Fucus radicans is predominantly a large female clone of F. vesiculosus in its northern Baltic distribution. In two Estonian sites, however, individuals are sexual but reproductively isolated from Baltic F. vesiculosus, revealing a separate diverged lineage that predates the formation of the Baltic Sea. Monitoring Baltic Fucus without considering this genetic complexity will fail to prioritise populations with adaptive potential to new climate conditions. From our genomic data, we can extract informative and diagnostic genetic markers that differentiate major genetic entities. Such an SNP panel will provide a straightforward tool for spatial and temporal monitoring and informing management decisions and actions.

Methods
Population genomic data was obtained through individually barcoded 2b-RAD libraries that were constructed following the procedures in Pereyra et al. (2023). The libraries were sequenced using a Novaseq6000 Illumina platform at SciLifeLab, Uppsala. A total of 962 individuals from 55 different sites were sequenced. Removal of PCR duplicates, quality filtering, and variant calling was performed in the computer cluster Albiorix (M. Töpel, IVL, Sweden), following a reference-based pipeline modified from Mikhail Matz available at https://github.com/z0on/2bRAD_GATK. Reads were mapped to an F. vesiculosus draft genome assembly previously used for population genomic studies (Kinnby et al., 2020; Pereyra et al., 2023; NCBI Bioproject No. PRJNA629489). Variant calling calibration was carried out with technical replicates labeled with the Individual name followed by the suffix "Rep". These replicates are included in the dataset. 

Morphological data comprises three morphometric characters: Frond width (FW), the distance between dichotomies (DBD), and the undulation index (UX). The first two characters have been used as a diagnostic to differentiate F. radicans from F. vesiculosus (Bergström et al., 2005; Pereyra et al., 2013). Each individual was characterized using the average of three measurements taken from different branches with the image analysis software ImageJ64 (Schneider et al., 2012).

The data includes a list of Sample ID codes and corresponding localities and geographic coordinates.

建群种的遗传多样性对于环境变化下的生态系统功能与恢复力至关重要，但在环境监测中却长期被大幅忽视。波罗的海的关键监测物种为褐藻囊岩藻（Fucus vesiculosus），其形成的潮下带三维生境可为鱼类与无脊椎动物提供庇护场所与食物来源。生态分布模型预测，若种群无法适应环境变化，波罗的海的囊岩藻将因海洋暖化出现大规模消亡。有性生殖过程中的遗传变异与重组是物种适应环境的关键，但已有研究显示波罗的海海域内存在大规模的克隆繁殖现象。我们对东大西洋、‘过渡带’以及波罗的海的全基因组单核苷酸多态性（Single Nucleotide Polymorphism, SNP）数据进行分析后发现，波罗的海海域内存在多种分化谱系的镶嵌分布格局，而海域外则以少数遗传类群占据主导。研究证实，此前被描述为特有种的辐射囊岩藻（Fucus radicans）在其波罗的海北部分布区内，本质上多为囊岩藻的大型雌性克隆株。但在爱沙尼亚的两个采样点中，个体以有性生殖方式繁殖，且与波罗的海的囊岩藻存在生殖隔离，这揭示出一个独立的分化谱系，其起源早于波罗的海的形成。若在监测波罗的海囊岩藻时未考虑这种遗传复杂性，将无法精准识别具备适应新气候条件潜力的种群并进行优先保护。基于本研究的基因组数据，我们可筛选出可区分主要遗传类群的信息性诊断遗传标记。此类单核苷酸多态性检测面板将为时空监测以及管理决策与行动提供便捷可靠的技术工具。

研究方法
种群基因组数据通过带有个体条码的2b-RAD文库获取，文库构建流程参照Pereyra等人（2023年）的方法。本研究使用Illumina NovaSeq6000测序平台于瑞典乌普萨拉的生命科学实验室（SciLifeLab）完成测序，共对来自55个采样点的962个个体进行了测序。测序数据的PCR重复序列去除、质量过滤以及变异位点识别均在瑞典IVL研究所M. Töpel维护的Albiorix计算机集群上完成，分析流程基于Mikhail Matz开发的参考基因组比对流程修改而来，相关代码可在https://github.com/z0on/2bRAD_GATK获取。测序读段被比对至此前用于种群基因组研究的囊岩藻草图基因组组装版本（Kinnby等，2020；Pereyra等，2023；NCBI生物项目编号：PRJNA629489）。变异位点识别的校准通过技术重复样本完成，此类样本以个体名称加后缀"Rep"进行标注，且已包含在本数据集内。

形态学数据
形态学数据包含3个形态测量特征：叶状体宽度（Frond width, FW）、二叉分枝间距（distance between dichotomies, DBD）以及褶皱指数（undulation index, UX）。前两个特征曾被用于区分辐射囊岩藻与囊岩藻（Bergström等，2005；Pereyra等，2013）。每个个体的特征值通过使用图像分析软件ImageJ64（Schneider等，2012）对不同分枝的三次测量结果取平均值得到。

本数据集包含样本ID编码列表以及对应的采样地点与地理坐标信息。