Marine metapopulations often exhibit subtle population structure that can be difficult to detect. Given recent advances in high‐throughput sequencing, an emerging question is whether various genotyping approaches, in concert with improved sampling designs, will substantially improve our understanding of genetic structure in the sea. To address this question, we explored hierarchical patterns of structure in the coral reef fish Elacatinus lori using a high‐resolution approach with respect to both genetic and geographic sampling. Previously, we identified three putative E. lori populations within Belize using traditional genetic markers and sparse geographic sampling: barrier reef and Turneffe Atoll; Glover's Atoll; and Lighthouse Atoll. Here, we systematically sampled individuals at ~10 km intervals throughout these reefs (1,129 individuals from 35 sites) and sequenced all individuals at three sets of markers: 2,418 SNPs; 89 microsatellites; and 57 nonrepetitive nuclear loci. At broad spatial scales, the markers were consistent with each other and with previous findings. At finer spatial scales, there was new evidence of genetic substructure, but our three marker sets differed slightly in their ability to detect these patterns. Specifically, we found subtle structure between the barrier reef and Turneffe Atoll, with SNPs resolving this pattern most effectively. We also documented isolation by distance within the barrier reef. Sensitivity analyses revealed that the number of loci (and alleles) had a strong effect on the detection of structure for all three marker sets, particularly at small spatial scales. Taken together, these results illustrate empirically that high‐throughput genotyping data can elucidate subtle genetic structure at previously‐undetected scales in a dispersive marine fish.

中文翻译：

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揭示海洋种群中的层次遗传结构：三种高通量基因分型方法的比较。

海洋种群通常表现出难以察觉的微妙的种群结构。鉴于高通量测序的最新进展，一个新出现的问题是，各种基因分型方法与改进的采样设计相结合，是否会大大改善我们对海洋遗传结构的了解。为了解决这个问题，我们使用高分辨率方法针对遗传和地理采样探索了珊瑚礁鱼Elacatinus lori中的结构分层模式。之前，我们确定了三个推定的大肠杆菌伯利兹境内的人口使用传统遗传标记和稀疏地理采样：堡礁和特内菲环礁；格洛弗环礁；和灯塔环礁。在这里，我们以大约10 km的间隔对这些珊瑚礁中的个体进行了系统采样（来自35个站点的1,129个体），并按三组标记对所有个体进行了测序：2,418个SNP；89个微卫星；57个非重复性核基因座。在广泛的空间尺度上，标记物彼此一致并且与先前的发现一致。在更精细的空间尺度上，有新的遗传亚结构证据，但我们的三个标记集检测这些模式的能力略有不同。具体来说，我们在屏障礁和特内菲环礁之间发现了微妙的结构，其中SNP最有效地解决了这种情况。我们还记录了隔离礁内的距离隔离情况。敏感性分析表明，基因座（和等位基因）的数量对所有三个标记集的结构检测都有很强的影响，尤其是在小空间尺度下。综上所述，这些结果从经验上说明，高通量基因分型数据可以阐明以前未发现的散布海鱼的细微遗传结构。