Data from: Seascape genetics along environmental gradients in the Arabian Peninsula: insights from ddRAD sequencing of anemonefishes

Understanding the processes that shape patterns of genetic structure across space is a central aim of landscape genetics. However, it remains unclear how geographic features and environmental variables shape gene flow, particularly for marine species in large complex seascapes. Here, we evaluated the genomic composition of the two-band anemonefish Amphiprion bicinctus across its entire geographic range in the Red Sea and Gulf of Aden, as well as its close relative, Amphiprion omanensis endemic to the southern coast of Oman. Both the Red Sea and the Arabian Sea are complex and environmentally heterogeneous marine systems that provide an ideal scenario to address these questions. Our findings confirm the presence of two genetic clusters previously reported for A. bicinctus in the Red Sea. Genetic structure analyses suggest a complex seascape configuration, with evidence of both Isolation by Distance (IBD) and Isolation by Environment (IBE). In addition to IBD and IBE, genetic structure among sites was best explained when two barriers to gene flow were also accounted for. One of these coincides with a strong oligotrophic-eutrophic gradient at around 16-20˚N in the Red Sea. The other agrees with an historical bathymetric barrier at the straight of Bab al Mandab. Finally, these data support the presence of inter-specific hybrids at an intermediate suture zone at Socotra and indicate complex patterns of genomic admixture in the Gulf of Aden with evidence of introgression between species. Our findings highlight the power of recent genomic approaches to resolve subtle patterns of gene flow in marine seascapes.

解析塑造空间遗传结构格局的过程，是景观遗传学（landscape genetics）的核心目标之一。然而，目前仍不清楚地理特征与环境变量如何塑造基因流，对于大型复杂海洋景观中的海洋物种而言尤其如此。本研究评估了双带小丑鱼（Amphiprion bicinctus）在红海与亚丁湾全境的基因组组成，同时也对其近缘物种——仅分布于阿曼南部海岸的阿曼双锯鱼（Amphiprion omanensis）进行了分析。红海与阿拉伯海均为结构复杂、环境异质性强的海洋系统，为解答上述问题提供了理想的研究场景。本研究结果证实了此前报道的红海双带小丑鱼存在两个遗传集群。遗传结构分析显示海洋景观格局较为复杂，同时存在距离隔离（Isolation by Distance, IBD）与环境隔离（Isolation by Environment, IBE）现象。除距离隔离与环境隔离外，当同时纳入两个基因流障碍因素时，对各采样点间遗传结构的解释效果最佳。其中一处障碍与红海约16°N至20°N区间的强寡营养-富营养梯度相契合；另一处则与曼德海峡的历史水深屏障一致。此外，本研究数据支持在索科特拉岛的中间过渡杂交带存在种间杂交个体，并证实亚丁湾存在复杂的基因组混合模式，且存在物种间的渐渗现象。本研究结果凸显了新兴基因组学方法在解析海洋景观中细微基因流格局方面的应用价值。