Data from: RAD sequencing reveals genomewide divergence between independent invasions of the European green crab (Carcinus maenas) in the Northwest Atlantic

Genomic studies of invasive species can reveal both invasive pathways and functional differences underpinning patterns of colonization success. The European green crab (Carcinus maenas) was initially introduced to eastern North America nearly 200 years ago where it expanded northwards to eastern Nova Scotia. A subsequent invasion to Nova Scotia from a northern European source allowed further range expansion, providing a unique opportunity to study the invasion genomics of a species with multiple invasions. Here, we use restriction-site-associated DNA sequencing-derived SNPs to explore fine-scale genomewide differentiation between these two invasions. We identified 9137 loci from green crab sampled from 11 locations along eastern North America and compared spatial variation to mitochondrial COI sequence variation used previously to characterize these invasions. Overall spatial divergence among invasions was high (pairwise FST ~0.001 to 0.15) and spread across many loci, with a mean FST ~0.052 and 52% of loci examined characterized by FST values >0.05. The majority of the most divergent loci (i.e., outliers, ~1.2%) displayed latitudinal clines in allele frequency highlighting extensive genomic divergence among the invasions. Discriminant analysis of principal components (both neutral and outlier loci) clearly resolved the two invasions spatially and was highly correlated with mitochondrial divergence. Our results reveal extensive cryptic intraspecific genomic diversity associated with differing patterns of colonization success and demonstrates clear utility for genomic approaches to delineating the distribution and colonization success of aquatic invasive species.

入侵物种的基因组研究既可揭示其入侵路径，也可解析支撑定殖成功模式的功能差异。欧洲绿蟹（Carcinus maenas）于近200年前首次被引入北美东部，随后向北扩张至新斯科舍省东部。后续又有源自北欧的入侵种群抵达新斯科舍省，进一步拓展了其分布范围，这为研究具有多次入侵事件的物种的入侵基因组学提供了独特契机。本研究利用限制性酶切位点相关DNA测序（restriction-site-associated DNA sequencing, RAD-seq）获得的单核苷酸多态性（Single Nucleotide Polymorphisms, SNPs），探究这两次入侵种群间的精细全基因组分化。我们对北美东部11个采样位点的绿蟹进行测序，共鉴定得到9137个基因座，并将空间遗传变异与此前用于表征这些入侵种群的线粒体细胞色素氧化酶I亚基（mitochondrial cytochrome c oxidase subunit I, COI）序列变异进行了比较。整体而言，入侵种群间的空间遗传分化程度较高（两两遗传分化系数（fixation index, FST）约为0.001至0.15），且分化信号广泛分布于众多基因座中，平均FST约为0.052，其中52%的检测基因座的FST值大于0.05。多数分化程度最高的基因座（即异常位点，约占1.2%）呈现出等位基因频率的纬度梯度，这表明两次入侵种群间存在广泛的基因组分化。主成分判别分析（Discriminant Analysis of Principal Components, DAPC，涵盖中性位点与异常位点）可清晰地从空间上区分这两次入侵种群，且其结果与线粒体分化程度高度相关。本研究结果揭示了与不同定殖成功模式相关的广泛隐蔽种内基因组多样性，并证明了基因组学方法在阐明水生入侵物种分布与定殖成功机制方面的显著应用价值。