With only a few absolute geographic barriers in marine environments, the factors maintaining reproductive isolation among marine organisms remain elusive. However, spatial structuring in breeding habitat can contribute to reproductive isolation. This is particularly important for marine organisms that migrate to use fresh‐ or brackish water environments to breed. The Japanese Gasterosteus stickleback species, the Pacific Ocean three‐spined stickleback (G. aculeatus) and the Japan Sea stickleback (G. nipponicus) overwinter in the sea, but migrate to rivers for spawning. Although they co‐occur at several locations across the Japanese islands, they are reproductively isolated. Our previous studies in Bekanbeushi River showed that the Japan Sea stickleback spawns in the estuary, while the Pacific Ocean stickleback mainly spawns further upstream in freshwater. Overall genomic divergence was very high with many interspersed regions of introgression. Here, we investigated genomic divergence and introgression between the sympatric species in the much shorter Tokotan River, where they share spawning sites. The levels of genome‐wide divergence were reduced and introgression was increased, suggesting that habitat isolation substantially contributes to a reduction in gene flow. We also found that genomic regions of introgression were largely shared between the two systems. Furthermore, some regions of introgression were located near loci with a heterozygote advantage for juvenile survival. Taken together, introgression may be partially driven by adaptation in this system. Although, the two species remain clearly genetically differentiated. Regions with low recombination rates showed especially low introgression. Speciation reversal is therefore likely prevented by barriers other than habitat isolation.

中文翻译：

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具有重叠繁殖栖息地的日本刺鱼物种之间的基因组差异和基因渗入模式

由于海洋环境中只有少数绝对地理障碍，维持海洋生物之间生殖隔离的因素仍然难以捉摸。然而，繁殖栖息地的空间结构可能会导致生殖隔离。这对于迁移到淡水或微咸水环境中繁殖的海洋生物尤为重要。日本刺鱼、太平洋三刺刺鱼（G. aculeatus）和日本海刺鱼（G. nipponicus）在海中越冬，但迁移到河流产卵。尽管它们同时出现在日本各岛的多个地点，但它们在生殖上是孤立的。我们之前在别干贝志河的研究表明，日本海刺鱼在河口产卵，而太平洋刺鱼主要在淡水上游产卵。整体基因组差异非常高，具有许多散布的基因渗入区域。在这里，我们调查了更短的 Tokotan 河中同域物种之间的基因组差异和基因渗入，它们在那里共享产卵地点。全基因组差异水平降低，基因渗入增加，表明栖息地隔离大大有助于减少基因流。我们还发现基因渗入的基因组区域在两个系统之间主要共享。此外，一些基因渗入区域位于具有杂合子优势的基因座附近，以促进幼鱼存活。总之，基因渗入可能部分是由该系统的适应驱动的。虽然，这两个物种在基因上仍然存在明显差异。具有低重组率的区域表现出特别低的基因渗入。因此，除了栖息地隔离之外，其他障碍可能会阻止物种形成逆转。