Data from: A well-constrained estimate for the timing of the salmonid whole genome duplication reveals major decoupling from species diversification

Whole genome duplication (WGD) is often considered to be mechanistically associated with species diversification. Such ideas have been anecdotally attached to a WGD at the stem of the salmonid fish family, but remain untested. Here, we characterized an extensive set of gene paralogues retained from the salmonid WGD, in species covering the major lineages (subfamilies Salmoninae, Thymallinae and Coregoninae). By combining the data in calibrated relaxed molecular clock analyses, we provide the first well-constrained and direct estimate for the timing of the salmonid WGD. Our results suggest that the event occurred no later in time than 88 Ma and that 40–50 Myr passed subsequently until the subfamilies diverged. We also recovered a Thymallinae–Coregoninae sister relationship with maximal support. Comparative phylogenetic tests demonstrated that salmonid diversification patterns are closely allied in time with the continuous climatic cooling that followed the Eocene–Oligocene transition, with the highest diversification rates coinciding with recent ice ages. Further tests revealed considerably higher speciation rates in lineages that evolved anadromy—the physiological capacity to migrate between fresh and seawater—than in sister groups that retained the ancestral state of freshwater residency. Anadromy, which probably evolved in response to climatic cooling, is an established catalyst of genetic isolation, particularly during environmental perturbations (for example, glaciation cycles). We thus conclude that climate-linked ecophysiological factors, rather than WGD, were the primary drivers of salmonid diversification.

全基因组复制（whole genome duplication, WGD）通常被认为在机制上与物种分化密切相关。这类观点曾被轶事性地关联至鲑科（Salmonidae）鱼类类群起源节点处发生的一次全基因组复制事件，但始终未得到实证检验。本研究针对覆盖鲑科三大主要演化支系（鲑亚科Salmoninae、茴鱼亚科Thymallinae与白鲑亚科Coregoninae）的多个物种，系统鉴定了由鲑科全基因组复制事件保留下来的大量基因旁系同源物。通过整合上述数据开展校准宽松分子钟分析，我们首次获得了对鲑科全基因组复制事件发生时间的严谨约束且直接的定量估算。研究结果显示，该事件的发生时间不晚于88 Ma，且在此后的4000万至5000万年间，鲑科的三个亚科才逐步完成分化。本研究还得到了具有最高支持度的系统发育拓扑结构，证实茴鱼亚科与白鲑亚科构成姊妹群关系。比较系统发育检验结果表明，鲑科的物种分化模式在时间维度上与始新世-渐新世过渡事件之后持续的气候变冷过程高度契合，其中峰值物种分化速率与近代冰期恰好重合。进一步的检验还发现，演化出溯河洄游（anadromy）——即具备在淡水与海水间往复迁移的生理能力——的演化支系，其物种形成速率显著高于保留淡水栖息祖先状态的姊妹支系。溯河洄游这一性状极可能是对气候变冷的适应性演化结果，现已被证实是遗传隔离的重要催化因子，在环境扰动（如冰期循环）期间的作用尤为显著。综上，我们认为驱动鲑科物种分化的核心因素是与气候相关的生理生态因子，而非全基因组复制事件。