Rüber Lukas, Zardoya Rafael
Departamento de Biodiversidad y Biología Evolutiva, Museo Nacional de Ciencias Naturales, José Gutiérrez Abascal 2, 28006 Madrid, Spain.
Evolution. 2005 May;59(5):1119-27.
Lineages that underwent rapid cladogenesis are attractive systems for the study of mechanisms underlying taxonomic, ecological, morphological, and behavioral diversification. Recently developed statistical methods provide insights into historical patterns of diversity and allow distinguishing bursts of cladogenesis from stochastic background rates in the presence of confounding factors such as extinction and incomplete taxon sampling. Here, we compare the dynamics of speciation in several marine fish lineages some of which were previously proposed to have undergone significant changes of cladogenesis through time. We tested for evidence of episodes of rapid cladogenesis using the constant rate and Monte Carlo constant rate tests that are robust to incomplete taxon sampling. These tests employ the statistic gamma to measure the relative position of internal node in a chronogram. For the first time, we conducted a comparative analysis to address the behavior of the statistic under different chronogram-constructing methods (Langley-Fitch, nonparametric rate smoothing, and penalized likelihood). Although estimates of gamma sometimes differ widely among methods, acceptance or rejection of the constant rate model within a particular clade appears to be robust to the choice of method. Bursts of cladogenesis were detected in 14 of 34 studied datasets. Some of these were previously proposed to represent marine fish "radiations," whereas others are identified anew. Our results indicate that the wider application of tree shape methods that are able to detect significantly elevated rates of speciation is useful to more precisely define clades that underwent episodes of rapid cladogenesis in marine fish clades. Contrasting the patterns of phylogenetic diversification in marine fish lineages may facilitate the identification of common evolutionary trajectories versus idiosyncrasies, and ultimately help towards a better understanding of the factors and processes underlying speciation in the marine realm.
经历快速分支形成的谱系是研究分类学、生态学、形态学和行为多样化潜在机制的有吸引力的系统。最近开发的统计方法为多样性的历史模式提供了见解，并允许在存在灭绝和分类单元采样不完整等混杂因素的情况下，将分支形成的爆发与随机背景速率区分开来。在这里，我们比较了几种海洋鱼类谱系的物种形成动态，其中一些谱系之前被认为随着时间的推移经历了显著的分支形成变化。我们使用对分类单元采样不完整具有鲁棒性的恒定速率检验和蒙特卡洛恒定速率检验，来检验快速分支形成事件的证据。这些检验使用统计量γ来测量时间树中内部节点的相对位置。我们首次进行了一项比较分析，以研究该统计量在不同时间树构建方法（兰利 - 费奇法、非参数速率平滑法和惩罚似然法）下的表现。尽管γ的估计值有时在不同方法之间差异很大，但在特定分支内对恒定速率模型的接受或拒绝似乎对方法的选择具有鲁棒性。在34个研究数据集中的14个中检测到了分支形成的爆发。其中一些之前被认为代表海洋鱼类“辐射”，而其他一些则是新发现的。我们的结果表明，能够检测到显著升高的物种形成速率的树形方法的更广泛应用，有助于更精确地定义在海洋鱼类分支中经历快速分支形成事件的类群。对比海洋鱼类谱系中的系统发育多样化模式，可能有助于识别共同的进化轨迹与特质，并最终有助于更好地理解海洋领域物种形成的因素和过程。
