Data from: Repeated invasions into the twilight zone: evolutionary origins of a novel assemblage of fishes from deep Caribbean reefs

Mesophotic and deeper reefs of the tropics are poorly known and underexplored ecosystems worldwide. Collectively referred to as the ‘twilight zone,’ depths below ~30-40 m are home to many species of reef fishes that are absent from shallower depths, including many undescribed and endemic species. We currently lack even a basic understanding of the diversity and evolutionary origins of fishes on tropical mesophotic reefs. Recent submersible collections in the Caribbean have provided new specimens that are enabling phylogenetic reconstructions that incorporate deep-reef representatives of tropical-fish genera. Here, we investigate evolutionary depth transitions in the family Gobiidae (gobies), the most diverse group of tropical marine fishes. Using divergence-time estimation coupled with stochastic character mapping to infer the timing of shallow-to-deep habitat transitions in gobies, we demonstrate at least four transitions from shallow to mesophotic depths. Habitat transitions occurred in two broad time periods (Miocene, Pliocene-Pleistocene), and may have been linked to the availability of underutilized niches, as well as the evolution of morphological/behavioral adaptations for life on deep reefs. Further, our analysis shows that at least three evolutionary lineages that invaded deep habitats subsequently underwent speciation, reflecting another unique mode of radiation within the Gobiidae. Lastly, we synthesize depth distributions for 95 species of Caribbean gobies, which reveal major bathymetric faunal breaks at the boundary between euphotic and mesophotic reefs. Ultimately our study is the first rigorous investigation into the origin of Caribbean deep-reef fishes, and provides a framework for future studies that utilize rare, deep-reef specimens.全球范围内的热带中光礁（mesophotic reef）及更深海域珊瑚礁，仍是鲜为人知且勘探不足的生态系统。这类海域通常被统称为"暮光带"，约30至40米以下的水深栖息着诸多浅海珊瑚礁海域不存在的礁栖鱼类物种，其中包含大量尚未被描述的特有物种。目前我们甚至对热带中光礁海域鱼类的多样性及其演化起源都缺乏基础认知。近期加勒比海海域的载人潜水器采集工作获得了全新标本，得以开展包含热带鱼类属群深海礁代表性物种在内的系统发育重建研究。本研究聚焦于热带海洋鱼类中物种多样性最高的类群——鰕虎鱼科（Gobiidae，鰕虎鱼）的栖息深度演化转变现象。通过结合分化时间估计与随机特征映射的方法，推断鰕虎鱼从浅海到深海生境的转变时机，本研究证实至少存在四次由浅海向中光礁海域的生境转变事件。这类生境转变主要发生在两个大的地质时期（中新世、上新世-更新世），其成因或与未被充分利用的生态位可获得性，以及适应深海礁生活的形态/行为演化有关。此外，本研究分析显示，至少有三个侵入深海生境的演化支后续发生了物种形成事件，这反映出鰕虎鱼科内另一种独特的辐射演化模式。最后，本研究整合了加勒比海95种鰕虎鱼的深度分布数据，结果显示在透光礁（euphotic reef）与中光礁的分界处存在显著的水深动物区系分界。本研究最终是首个针对加勒比海深海礁鱼类起源开展的严谨调查，同时为未来利用珍稀深海礁标本的相关研究提供了研究框架。