Data from: Evolutionary diversification of reef corals: a comparison of the molecular and fossil records

Understanding historical patterns of diversity dynamics is of paramount importance for many evolutionary questions. The fossil record has long been the only source of information on patterns of diversification, but the molecular record, derived from time-calibrated phylogenies, is becoming an important additional resource. Both fossil and molecular approaches have shortcomings and biases. These have been well studied for fossil data but much less so for molecular data and empirical comparisons between approaches are lacking. Here we compare the patterns of diversification derived from fossil and molecular data in scleractinian reef coral species. We also assess the robustness of molecular diversification rates to poor taxon sampling. We find that the temporal pattern of molecular diversification rates is robust to incomplete sampling when rates are calculated per interval. The major obstacle of molecular methods is that rate estimates are distorted because diversification rates can never be negative, whereas the fossil record suffers from incomplete preservation and inconsistent taxonomy. Nevertheless, the molecular pattern of diversification is comparable to the pattern we observe in the fossil record, with the timing of major diversification pulses coinciding in each dataset. For example, both agree that the end-Triassic coral extinction was a catastrophic bottleneck in scleractinian evolution.

探究多样化动态的历史模式，对于诸多演化生物学研究问题而言均具有核心重要性。长期以来，化石记录一直是获取多样化模式相关信息的唯一数据源，而基于时间校准系统发育树（time-calibrated phylogenies）构建的分子记录，正逐步成为另一重要的补充信息源。化石与分子两类研究方法均存在局限性与分析偏倚：针对化石数据的相关偏倚研究已较为充分，但针对分子数据的同类研究仍相对不足，且两类方法的实证对比研究仍付诸阙如。本研究以石珊瑚目造礁珊瑚（scleractinian reef coral）物种为研究对象，对比了基于化石与分子数据得到的多样化模式；同时还评估了分子多样化速率在类群采样不充分时的稳健性。研究结果表明：当按时间间隔计算多样化速率时，分子多样化速率的时间模式不受不完全采样的影响。分子方法的主要局限在于，由于多样化速率不可能为负值，导致速率估计结果出现偏差；而化石记录则面临保存不完全、分类标准不统一的问题。尽管存在上述局限，分子数据得到的多样化模式与化石记录所观测到的模式仍具有可比性——两类数据集的主要多样化脉冲发生时间高度吻合。例如，二者均证实三叠纪末期珊瑚灭绝事件是石珊瑚演化历程中的灾难性瓶颈效应。