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多样化存在关联。这类观点曾被零星关联至鲑科鱼类类群基部发生的一次WGD事件，但始终未得到验证。本研究对覆盖鲑科主要演化支系（鲑亚科、茴鱼亚科与白鲑亚科）的多个物种中，由鲑科WGD所保留的大量基因旁系同源物（paralogue）进行了特征分析。通过结合数据开展校准松弛分子钟分析，我们首次得到了对鲑科WGD发生时间的精准约束与直接估算。研究结果显示，该事件的发生时间不晚于88百万年前，且在亚科类群分化前经过了4000万至5000万年的时间。我们还以最高支持度恢复了茴鱼亚科与白鲑亚科的姐妹群关系。比较系统发育分析表明，鲑科的物种多样化模式与始新世-渐新世过渡事件之后持续的气候降温在时间上高度契合，最高的物种多样化速率与近期冰期相吻合。进一步分析显示，演化出溯河洄游（anadromy）——即具备在淡水与海水间往返迁移的生理能力——的支系，其物种形成速率显著高于保留淡水定居祖先状态的姐妹群。溯河洄游习性大概率是为响应气候降温演化而来，该习性是公认的遗传隔离催化剂，尤其在环境扰动（如冰期旋回）期间。综上，我们认为驱动鲑科物种多样化的主要因素是与气候相关的生态生理因素，而非WGD事件。