Data from: Genomic footprints of speciation in Atlantic eels (Anguilla anguilla and A. rostrata)

The importance of speciation-with-gene-flow scenarios is increasingly appreciated. However, the specific processes and the resulting genomic footprints of selection are subject to much discussion. We studied the genomics of speciation between the two panmictic, sympatrically spawning sister-species; European (Anguilla anguilla) and American eel (A. rostrata). Divergence is assumed to have initiated more than 3 million years ago, and although low gene flow still occurs strong postzygotic barriers are present. Restriction-site Associated DNA (RAD) sequencing identified 328,300 SNPs for subsequent analysis. However, despite the presence of 3,757 strongly differentiated SNPs (FST > 0.8), sliding window analyses of FST showed no larger genomic regions (i.e. hundreds of thousands to millions of bases) of elevated differentiation. Overall FST was 0.041 and linkage disequilibrium was virtually absent for SNPs separated by more than 1000 bp. We suggest this to reflect a case of genomic hitchhiking, where multiple regions are under directional selection between the species. However, low but biologically significant gene flow and high effective population sizes leading to very low genetic drift preclude accumulation of strong background differentiation. Genes containing candidate SNPs for positive selection showed significant enrichment for gene ontology (GO) terms relating to developmental processes and phosphorylation, which seems consistent with assumptions that differences in larval phase duration and migratory distances underlie speciation. Most SNPs under putative selection were found outside coding regions, lending support to emerging views that non-coding regions may be more functionally important than previously assumed. In total, the results demonstrate the necessity of interpreting genomic footprints of selection in the context of demographic parameters and life-history features of the studied species.

物种形成伴基因流情景（speciation-with-gene-flow scenarios）的重要性日益受到学界重视。然而，其背后的具体演化过程以及选择作用所留下的基因组印记，仍存在广泛讨论。我们针对两种随机交配、同域产卵的姊妹物种——欧洲鳗鲡（Anguilla anguilla）与美洲鳗鲡（A. rostrata）的物种形成基因组学展开了探究。一般认为二者的分化始于300多万年前，尽管目前仍存在低水平基因流，但二者已形成了较强的合子后生殖隔离屏障（postzygotic barriers）。通过限制性酶切位点相关DNA（Restriction-site Associated DNA, RAD）测序，我们共鉴定出328300个单核苷酸多态性（Single Nucleotide Polymorphism, SNP）位点用于后续分析。尽管鉴定得到3757个分化程度极高的SNP位点（固定指数Fixation Index, FST > 0.8），但对FST值的滑动窗口分析显示，并未存在分化程度升高的较大基因组区域（即数十万至数百万碱基对范围）。整体FST均值为0.041，且对于间距超过1000bp的SNP位点而言，几乎不存在连锁不平衡（Linkage Disequilibrium）现象。我们认为这一结果反映了基因组搭车效应（genomic hitchhiking）的典型案例：即两个物种间存在多个受定向选择作用的基因组区域。不过，低水平但具备生物学意义的基因流，以及极高的有效种群大小（effective population size）所带来的极低遗传漂变（genetic drift），阻碍了较强本底分化的积累。携带正向选择（positive selection）候选SNP位点的基因，在与发育过程及磷酸化作用相关的基因本体（Gene Ontology, GO）术语上呈现显著富集，这与"幼体发育期时长与迁徙距离差异是物种形成基础"的假说相符。绝大多数受推测选择作用的SNP位点均位于编码区之外，这为"非编码区可能比此前认知的更具功能重要性"这一新兴学术观点提供了有力支撑。总体而言，本研究结果证实，在解读选择作用的基因组印记时，必须结合研究物种的种群动态参数与生活史特征进行综合研判。