Centre for Ecological and Evolutionary Synthesis, Department of Biology, University of Oslo, Oslo, Norway.
Syst Biol. 2010 Dec;59(6):646-59. doi: 10.1093/sysbio/syq052. Epub 2010 Sep 22.
Traditionally, patterns and processes of diversification could only be inferred from the fossil record. However, there are an increasing number of tools that enable diversification dynamics to be inferred from molecular phylogenies. The application of these tools to new data sets has renewed interest in the question of the prevalence of diversity-dependent diversification. However, there is growing recognition that the absence of extinct species in molecular phylogenies may prevent accurate inferences about the underlying diversification dynamics. On the other hand, even though the fossil record provides direct data on extinct species, its incompleteness can also mask true diversification processes. Here, using computer-generated diversity-dependent phylogenies, we mimicked molecular phylogenies by eliminating extinct lineages. We also simulated the fossil record by converting the temporal axis into discrete intervals and imposing a variety of preservation processes on the lineages. Given the lack of reliable phylogenies for many fossil marine taxa, we also stripped away phylogenetic information from the computer-generated phylogenies. For the simulated molecular phylogenies, we examined the efficacy of the standard metric (the γ statistic) for identifying decreasing rates of diversification. We find that the underlying decreasing rate of diversification is detected only when the rate of change in the diversification rate is high, and if the molecular phylogeny happens to capture the diversification process as the equilibrium diversity is first reached or shortly thereafter. In contrast, estimating rates of diversification from the simulated fossil record captures the expected zero rate of diversification after equilibrium is reached under a wide range of preservation scenarios. The ability to detect the initial decreasing rate of diversification is lost as the temporal resolution of the fossil record drops and with a decreased quality of preservation. When the rate of change of the diversification rate is low, the γ statistic will typically fail to detect the decreasing rate of diversification, as will the fossil record, although the fossil record still retains the signature of the diversity dependence in yielding approximately zero diversification rates. Thus, although a significantly negative γ value for a molecular phylogeny indicates a decreasing rate of diversification, a nonsignificantly negative or positive γ value might mean exponential diversification, or a slowly decreasing rate of diversification, or simply species turnover at a constant diversity. The fossil record can be of assistance in helping choose among these possibilities.
传统上，多样化的模式和过程只能从化石记录中推断出来。然而，越来越多的工具使我们能够从分子系统发育中推断出多样化动态。这些工具在新数据集上的应用重新引起了人们对多样性依赖多样化的普遍性问题的兴趣。然而，人们越来越认识到，分子系统发育中没有灭绝物种可能会阻止对潜在多样化动态的准确推断。另一方面，尽管化石记录提供了关于灭绝物种的直接数据，但它的不完整性也可能掩盖真正的多样化过程。在这里，我们使用计算机生成的多样性依赖系统发育来模拟分子系统发育，通过消除灭绝谱系。我们还通过将时间轴转换为离散间隔并对谱系施加各种保存过程来模拟化石记录。考虑到许多化石海洋分类群缺乏可靠的系统发育，我们还从计算机生成的系统发育中去除了系统发育信息。对于模拟的分子系统发育，我们检查了标准度量（γ统计量）识别多样化率下降的功效。我们发现，只有当多样化率的变化率很高时，才会检测到潜在的多样化率下降，并且如果分子系统发育恰好在达到平衡多样性时或之后不久捕捉到多样化过程。相比之下，在广泛的保存情景下，在达到平衡后，从模拟化石记录中估计多样化率会捕获预期的零多样化率。随着化石记录的时间分辨率下降和保存质量下降，检测初始多样化率下降的能力将会丧失。当多样化率的变化率较低时，γ统计量通常无法检测到多样化率的下降，化石记录也是如此，尽管化石记录仍然保留了多样性依赖性的特征，导致大约为零的多样化率。因此，尽管分子系统发育的γ值显著为负表明多样化率下降，但γ值非显著负或正可能意味着指数多样化，或多样化率缓慢下降，或只是在恒定多样性下的物种更替。化石记录可以帮助我们在这些可能性之间做出选择。
