Genomic divergence between the migratory and stationary ecotypes of Atlantic cod

Atlantic cod displays a range of phenotypic and genotypic variations, which includes the differentiation into coastal stationary and offshore migratory types of cod that co-occur in several parts of its distribution range and are often sympatric on the spawning grounds. Differentiation of these ecotypes may involve both historical separation and adaptation to ecologically distinct environments, the genetic basis of which is now beginning to be unravelled. Genomic analyses based on recent sequencing advances are able to document genomic divergence in more detail and may facilitate the exploration of causes and consequences of genome-wide patterns. We examined genomic divergence between the stationary and migratory types of cod in the Northeast Atlantic, using next-generation sequencing of pooled DNA from each of two population samples. Sequence data was mapped to the published cod genome sequence, arranged in more than 6000 scaffolds (611 Mb). We identified 25 divergent scaffolds (26 Mb) with a higher than average gene density, against a backdrop of overall moderate genomic differentiation. Previous findings of localized genomic divergence in three linkage groups were confirmed, including a large (15 Mb) genomic region, which seems to be uniquely involved in the divergence of migratory and stationary cod. The results of the pooled sequencing approach support and extend recent findings based on single-nucleotide polymorphism markers and suggest a high degree of reproductive isolation between stationary and migratory cod in the North-east Atlantic.

大西洋鳕鱼（Atlantic cod）展现出多样的表型与基因型变异，其中包括分化为沿岸定居型与近海洄游型两种生态型；二者在其分布范围的多个区域同域共存，且在产卵场常呈同域分布。这类生态型的分化可能同时涉及历史隔离与对不同生态环境的适应，其遗传基础目前正逐步得到解析。基于近年测序技术进步的基因组分析，能够更为细致地刻画基因组分化情况，并有助于探索全基因组模式的成因与后果。本研究以东北大西洋的定居型与洄游型鳕鱼为研究对象，对两个种群样本的混合DNA池开展下一代测序（next-generation sequencing）。测序数据被比对至已发表的鳕鱼基因组序列，该基因组组装得到6000余个支架序列（scaffolds），总长611 Mb。研究在整体中等程度的基因组分化背景下，鉴定出25个基因密度高于平均水平的分化支架（总长26 Mb）。此前在3个连锁群中发现的局部基因组分化得到验证，其中包含一个15 Mb的大型基因组区域，该区域似乎特异性参与定居型与洄游型鳕鱼的分化过程。本研究通过混合测序方法获得的结果，支持并拓展了此前基于单核苷酸多态性（single-nucleotide polymorphism, SNP）标记的研究发现，表明东北大西洋的定居型与洄游型鳕鱼之间存在高度的生殖隔离。