Migration independently evolved numerous times in animals, with a myriad of ecological and evolutionary implications. In fishes, perhaps the most extreme form of migration is diadromy, the migration between marine and freshwater environments. Key and longstanding questions are: how many times has diadromy evolved in fishes, how frequently do diadromous clades give rise to non-diadromous species, and does diadromy influence lineage diversification rates? Many diadromous fishes have large geographic ranges with constituent populations that use isolated freshwater habitats. This may limit gene flow among some populations, increasing the likelihood of speciation in diadromous lineages relative to non-diadromous lineages. Alternatively, diadromy may reduce lineage diversification rates if migration is associated with enhanced dispersal capacity that facilitates gene flow within and between populations. Clupeiformes (herrings, sardines, shads and anchovies) is a model clade for testing hypotheses about the evolution of diadromy because it includes an exceptionally high proportion of diadromous species and several independent evolutionary origins of diadromy. However, relationships among major clupeiform lineages remain unresolved and existing phylogenies sparsely sampled diadromous species, limiting the resolution of phylogenetically-informed statistical analyses. We assembled a phylogenomic dataset and used multi-species coalescent and concatenation-based approaches to generate the most comprehensive, highly-resolved clupeiform phylogeny to date, clarifying associations among several major clades and identifying recalcitrant relationships needing further examination. We determined that variation in rates of sequence evolution (heterotachy) and base-composition (non-stationarity) had little impact on our results. Using this phylogeny, we characterized evolutionary patterns of diadromy and tested for differences in lineage diversification rates between diadromous, marine, and freshwater lineages. We identified thirteen transitions to diadromy, all during the Cenozoic Era (ten origins of anadromy, two origins of catadromy, and one origin of amphidromy), and seven losses of diadromy. Two diadromous lineages rapidly generated non-diadromous species, demonstrating that diadromy is not an evolutionary dead-end. We discovered considerably faster transition rates out of diadromy than to diadromy. The largest lineage diversification rate increase in Clupeiformes was associated with a transition to diadromy, but we uncovered little statistical support for categorically faster lineage diversification rates in diadromous versus non-diadromous fishes. We propose that diadromy may increase the potential for accelerated lineage diversification, particularly in species that migrate long distances. However, this potential may only be realized in certain biogeographic contexts, such as when diadromy allows access to ecosystems in which there is limited competition from incumbent species.

中文翻译：

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系统发育组学、谱系多样化率和 Clupeiformes（凤尾鱼、鲱鱼、沙丁鱼和近缘动物）的发育


迁徙在动物中独立进化了无数次，具有无数的生态和进化影响。在鱼类中，也许最极端的迁移形式是 diadromy，即海洋和淡水环境之间的迁移。关键和长期存在的问题是：鱼类的成岩进化了多少次，成因支系产生非成生物种的频率如何，成因学是否影响谱系多样化率？许多洄游鱼类的地理范围很广，其组成种群使用孤立的淡水栖息地。这可能会限制某些种群之间的基因流动，相对于非生菌谱系，增加生肖谱系中物种形成的可能性。或者，如果迁移与促进种群内部和种群之间基因流动的增强扩散能力相关，则谱系学可能会降低谱系多样化率。Clupeiformes（鲱鱼、沙丁鱼、鳀鱼和凤尾鱼）是检验有关生境进化假设的模型分支，因为它包括极高比例的生鱼物种和生相的几个独立进化起源。然而，主要 clupeiform 谱系之间的关系仍未解决，现有的系统发育对洄流性物种进行稀疏采样，限制了系统发育信息统计分析的分辨率。我们组装了一个系统发育数据集，并使用基于多物种合并和串联的方法生成了迄今为止最全面、高分辨率的 clupeiform 系统发育，阐明了几个主要分支之间的关联并确定了需要进一步检查的顽固关系。 我们确定序列进化速率 （异质性） 和碱基组成 （非平稳性） 的变化对我们的结果影响不大。利用这种系统发育，我们表征了沉积学的进化模式，并测试了洄游、海洋和淡水谱系之间谱系多样化率的差异。我们确定了 13 次向胎面的转变，均在新生代 （10 次离境起源，2 次起源于轮距，1 次起源于两面起源），以及 7 次起降的损失。两个生贯谱系迅速产生了非生贯物种，证明生贯性不是进化的死胡同。我们发现，从 diadromy 的转换率比从 diadromy 转换的转换率快得多。Clupeiformes 中最大的谱系多样化率增加与向成河性过渡有关，但我们发现对洄生鱼类与非洄生鱼类的谱系多样化率绝对更快的统计支持几乎没有。我们提出 diadromy 可能会增加加速谱系多样化的可能性，尤其是在长距离迁移的物种中。然而，这种潜力只能在某些生物地理背景下实现，例如当沉积学允许进入与现有物种竞争有限的生态系统时。