Data from: Hidden diversity and phylogeographic history provide conservation insights for the edible seaweed Sargassum fusiforme in the Northwest Pacific

Understanding the evolutionary processes that have created diversity and the genetic potential of species to adapt to environmental change is an important premise for biodiversity conservation. Herein, we used mitochondrial trnW-L and cox3 and plastid rbcL-S data sets to analyze population genetic variation and phylogeographic history of the brown alga Sargassum fusiforme, whose natural resource has been largely exterminated in the Asia-Northwest Pacific in the past decades. Phylogenetic trees and network analysis consistently revealed three major haplotype-groups (A, B and C) in S. fusiforme, with A and B distributed in the Japan-Pacific coast. Group C consisted of three sub-groups (C1, C2 and C3) which were distributed in the Sea of Japan, the Yellow-Bohai Sea and East China Sea, respectively. Isolation-with-migration (IMa) analysis revealed that the three groups diverged approximately during the mid-Pleistocene (c. 756–1,224 ka). Extended Bayesian skyline plots (EBSP) showed that groups A and B underwent relatively long-term stable population size despite a subsequent rapid demographic expansion, while sub-groups C2 and C3 underwent a sudden expansion at c. 260 ka. FST and AMOVA analysis detected low population-level genetic variation and high degrees of divergence between groups. The cryptic diversity and phylogeographic patterns found in S. fusiforme not only are essential to understand how environmental shifts and evolutionary processes shaped diversity and distribution of coastal seaweeds but also provide additional insights for conserving and managing seaweed resources and facilitate predictions of their responses to future climate change and habitat loss.

阐明驱动物种多样性形成的演化进程，以及物种适应环境变化的遗传潜力，是生物多样性保护的重要前提。本研究依托线粒体（mitochondrial）trnW-L、cox3基因以及质体（plastid）rbcL-S序列数据集，分析了褐藻羊栖菜（Sargassum fusiforme）的种群遗传变异与系统地理历史——过去数十年间，该物种的天然资源在亚洲西北太平洋区域已近乎枯竭。系统发育树与网络分析均一致显示，羊栖菜可划分为A、B、C三个主要单倍型群：A群与B群分布于日本-太平洋沿岸；C群则包含C1、C2、C3三个亚群，分别分布于日本海、黄渤海及东海海域。隔离与迁移（Isolation-with-migration, IMa）分析结果显示，这三个单倍型群的分化时间大致处于更新世中期（约75.6万~122.4万年前）。扩展贝叶斯天际线图（Extended Bayesian skyline plots, EBSP）分析表明，A群与B群的种群规模虽在后续经历了快速的数量扩张，但整体长期处于相对稳定状态；而C2、C3亚群则在约26万年前发生了种群的突然扩张。FST值分析与分子方差分析（Analysis of Molecular Variance, AMOVA）结果显示，羊栖菜的种群水平遗传变异较低，而类群间的分化程度较高。本研究在羊栖菜中发现的隐蔽多样性与系统地理格局，不仅有助于阐明环境变迁与演化进程如何塑造沿海海藻的多样性与分布格局，同时也为海藻资源的保护与管理提供了新的科学认知，并可为预测其对未来气候变化及栖息地丧失的响应提供理论依据。