Data from: Genotype by sequencing identifies natural selection as a driver of intraspecific divergence in Atlantic populations of the high dispersal marine invertebrate, Macoma petalum

Mitochondrial DNA analyses indicate that the Bay of Fundy population of the intertidal tellinid bivalve Macoma petalum is genetically divergent from coastal populations in the Gulf of Maine and Nova Scotia. To further examine the evolutionary forces driving this genetic break, we performed double digest genotype by sequencing (GBS) to survey the nuclear genome for evidence of both neutral and selective processes shaping this pattern. The resulting reads were mapped to a partial transcriptome of its sister species, M. balthica, to identify single nucleotide polymorphisms (SNPs) in protein-coding genes. Population assignment tests, principle components analyses, analysis of molecular variance, and outlier tests all support differentiation between the Bay of Fundy genotype and the genotypes of the Gulf of Maine, Gulf of St. Lawrence, and Nova Scotia. Although both neutral and non-neutral patterns of genetic subdivision were significant, genetic structure among the regions was nearly 20 times higher for loci putatively under selection, suggesting a strong role for natural selection as a driver of genetic diversity in this species. Genetic differences were the greatest between the Bay of Fundy and all other population samples, and some outlier proteins were involved in immunity-related processes. Our results suggest that in combination with limited gene flow across the mouth of the Bay of Fundy, local adaptation is an important driver of intraspecific genetic variation in this marine species with high dispersal potential.

线粒体DNA（mitochondrial DNA）分析显示，潮间带樱蛤科双壳类（intertidal tellinid bivalve）Macoma petalum的芬迪湾（Bay of Fundy）种群，在遗传上与缅因湾（Gulf of Maine）及新斯科舍省（Nova Scotia）的沿岸种群存在显著分化。为进一步探究驱动这一遗传格局形成的进化动力，我们采用双酶切测序分型（double digest genotype by sequencing, GBS）技术对核基因组进行测序，以解析塑造该遗传分化的中性与选择过程。所得测序读段（reads）被比对至其姊妹种M. balthica的部分转录组，以此鉴定蛋白编码基因中的单核苷酸多态性（single nucleotide polymorphisms, SNPs）。群体分配检验、主成分分析、分子方差分析及离群位点检验均证实，芬迪湾种群的基因型与缅因湾、圣劳伦斯湾（Gulf of St. Lawrence）及新斯科舍省种群的基因型存在显著分化。尽管遗传分化的中性与非中性模式均具有统计学显著性，但候选受选择位点的区域间遗传结构差异程度较中性位点高出近20倍，这表明自然选择在该物种的遗传多样性塑造中发挥了关键作用。芬迪湾种群与其余所有采样种群间的遗传差异最为显著，且部分离群位点所编码的蛋白参与了免疫相关生理过程。本研究结果提示，结合芬迪湾湾口有限的基因流，局部适应是驱动这一具备高扩散潜力的海洋物种种内遗传变异的重要因素。