Data from: Antarctic krill population genomics: apparent panmixia, but genome complexity and large population size muddies the water

Antarctic krill (Euphausia superba; hereafter krill) are an incredibly abundant pelagic crustacean which has a wide, but patchy, distribution in the Southern Ocean. Several studies have examined the potential for population genetic structuring in krill, but DNA-based analyses have focused on a limited number of markers and have covered only part of their circum-Antarctic range. We used mitochondrial DNA and restriction site associated DNA sequencing (RAD-seq) to investigate genetic differences between krill from five sites, including two from East Antarctica. Our mtDNA results show no discernible genetic structuring between sites separated by thousands of kilometres, which is consistent with previous studies. Using standard RAD-seq methodology we obtained over a billion sequences from >140 krill, and thousands of variable nucleotides were identified at hundreds of loci. However, down-stream analysis found that markers with sufficient coverage were primarily from multi-copy genomic regions. Careful examination of these data highlights the complexity of the RAD-seq approach in organisms with very large genomes. To characterise the multi-copy markers we recorded sequence counts from variable nucleotide sites rather than the derived genotype; we also examined a small number of manually curated genotypes. Although these analyses effectively fingerprinted individuals, and uncovered a minor laboratory batch effect, no population structuring was observed. Overall, our results are consistent with panmixia of krill throughout their distribution. This result may indicate ongoing gene flow. However, krill's enormous population size creates substantial panmictic inertia, so genetic differentiation may not occur on an ecologically relevant timescale even if demographically separate populations exist.

南极磷虾（Euphausia superba，下文简称磷虾）是一类数量极为庞大的浮游甲壳动物，在南大洋分布广泛但呈斑块状聚集。已有多项研究探讨了磷虾种群遗传结构的可能性，但基于DNA的分析仅聚焦于有限的分子标记，且仅覆盖了其环南极分布范围的一部分。本研究利用线粒体DNA（mitochondrial DNA）与限制性酶切位点相关DNA测序（restriction site associated DNA sequencing，RAD-seq）技术，对来自5个采样点（其中2个位于东南极洲）的磷虾开展遗传差异分析。我们的线粒体DNA分析结果显示，相隔数千公里的采样点之间未出现可识别的遗传结构，这与既往研究结论一致。采用标准RAD-seq实验流程，我们从140余只磷虾样本中获得了超过10亿条测序序列，并在数百个基因座上鉴定出数千个可变核苷酸位点。但后续分析发现，覆盖度足够的分子标记主要来自多拷贝基因组区域。对这些数据的细致分析凸显了RAD-seq技术在拥有超大基因组的生物中的应用复杂性。为了表征这些多拷贝标记，我们对可变核苷酸位点的序列计数（而非推导得到的基因型）进行了记录，同时还对少量经过人工整理的基因型开展了分析。尽管此类分析可有效实现个体识别，并发现了轻微的实验批次效应，但未观察到种群遗传结构。综上，我们的结果支持磷虾在整个分布范围内均为泛交（panmixia）种群，这一结果可能暗示当前仍存在基因交流。但磷虾庞大的种群规模造就了极强的泛交惯性，因此即便存在种群统计上相互独立的种群，在生态学相关的时间尺度上也可能不会出现遗传分化。