Data from: Bayesian phylogenetic estimation of clade ages supports trans-atlantic dispersal of cichlid fishes

Divergence-time estimation based on molecular phylogenies and the fossil record has provided insights into fundamental questions of evolutionary biology. In Bayesian node dating, phylogenies are commonly time calibrated through the specification of calibration densities on nodes representing clades with known fossil occurrences. Unfortunately, the optimal shape of these calibration densities is usually unknown and they are therefore often chosen arbitrarily, which directly impacts the reliability of the resulting age estimates. As possible solutions to this problem, two non-exclusive alternative approaches have recently been developed, the “fossilized birth-death” model and “total-evidence dating”. While these approaches have been shown to perform well under certain conditions, they require including all (or a random subset) of the fossils of each clade in the analysis, rather than just relying on the oldest fossils of clades. In addition, both approaches assume that fossil records of different clades in the phylogeny are all the product of the same underlying fossil sampling rate, even though this rate has been shown to differ strongly between higher-level taxa. We here develop a flexible new approach to Bayesian age estimation that combines advantages of node dating and the fossilized birth-death model. In our new approach, calibration densities are defined on the basis of first fossil occurrences and sampling rate estimates that can be specified separately for all clades. We verify our approach with a large number of simulated datasets, and compare its performance to that of the fossilized birth-death model. We find that our approach produces reliable age estimates that are robust to model violation, on par with the fossilized birth-death model. By applying our approach to a large dataset including sequence data from over 1000 species of teleost fishes as well as 147 carefully selected fossil constraints, we recover a timeline of teleost diversification that is incompatible with previously assumed vicariant divergences of freshwater fishes. Our results instead provide strong evidence for trans-oceanic dispersal of cichlids and other groups of teleost fishes.基于分子系统发育（molecular phylogenies）与化石记录的分化时间估算，已为进化生物学的基础性问题提供了关键洞见。在贝叶斯节点定年（Bayesian node dating）中，系统发育树通常通过对代表已知化石记录支系的节点指定校准密度来完成时间校准。遗憾的是，这类校准密度的最优形态通常未知，因此往往被随意指定，这直接影响了后续年代估算结果的可靠性。针对这一问题，近年来已开发出两种非排他性替代方案：『化石出生-死亡模型（fossilized birth-death model）』与『总证据定年（total-evidence dating）』。已有研究表明，这两种方法在特定条件下表现优异，但二者均要求在分析中纳入每个支系的全部化石（或随机选取的子集），而非仅依赖各支系的最古老化石。此外，两类方法均假设：系统发育中不同支系的化石记录均源自同一恒定的化石采样速率——尽管已有研究证实，该速率在高阶类群（higher-level taxa）间存在显著差异。本研究提出了一种灵活的贝叶斯年代估算新方法，整合了节点定年与化石出生-死亡模型的优势。在该新方法中，校准密度基于首现化石记录与可针对所有支系单独指定的采样速率估算值进行定义。我们通过大量模拟数据集验证了本方法，并将其性能与化石出生-死亡模型进行了对比。研究结果显示，本方法可生成可靠的年代估算结果，对模型误设具有鲁棒性，且性能与化石出生-死亡模型不相上下。我们将本方法应用于一组大型数据集，该数据集包含超过1000种真骨鱼类（teleost fishes）的序列数据，以及147个经过精心筛选的化石约束条件。最终我们重建了真骨鱼类的分化时间线，该时间线与此前学界公认的淡水鱼类地理隔离分化假说相悖。我们的研究结果反而为慈鲷（cichlids）及其他真骨鱼类类群的跨洋扩散提供了强有力的证据。