Duchêne D A, Hua X, Bromham L
Macroevolution & Macroecology, Research School of Biology, Australian National University, Canberra, ACT, Australia.
School of Life and Environmental Sciences, University of Sydney, Sydney, NSW, Australia.
J Evol Biol. 2017 Oct;30(10):1884-1897. doi: 10.1111/jeb.13148. Epub 2017 Aug 20.
Molecular phylogenies are increasingly being used to investigate the patterns and mechanisms of macroevolution. In particular, node heights in a phylogeny can be used to detect changes in rates of diversification over time. Such analyses rest on the assumption that node heights in a phylogeny represent the timing of diversification events, which in turn rests on the assumption that evolutionary time can be accurately predicted from DNA sequence divergence. But there are many influences on the rate of molecular evolution, which might also influence node heights in molecular phylogenies, and thus affect estimates of diversification rate. In particular, a growing number of studies have revealed an association between the net diversification rate estimated from phylogenies and the rate of molecular evolution. Such an association might, by influencing the relative position of node heights, systematically bias estimates of diversification time. We simulated the evolution of DNA sequences under several scenarios where rates of diversification and molecular evolution vary through time, including models where diversification and molecular evolutionary rates are linked. We show that commonly used methods, including metric-based, likelihood and Bayesian approaches, can have a low power to identify changes in diversification rate when molecular substitution rates vary. Furthermore, the association between the rates of speciation and molecular evolution rate can cause the signature of a slowdown or speedup in speciation rates to be lost or misidentified. These results suggest that the multiple sources of variation in molecular evolutionary rates need to be considered when inferring macroevolutionary processes from phylogenies.
分子系统发育学越来越多地被用于研究宏观进化的模式和机制。特别是，系统发育树中的节点高度可用于检测随时间变化的多样化速率。此类分析基于这样的假设：系统发育树中的节点高度代表多样化事件的时间，而这又基于可以从DNA序列分歧准确预测进化时间的假设。但是，分子进化速率受到多种因素影响，这些因素可能也会影响分子系统发育树中的节点高度，进而影响多样化速率的估计。特别是，越来越多的研究揭示了从系统发育树估计的净多样化速率与分子进化速率之间的关联。这种关联可能通过影响节点高度的相对位置，系统性地偏差多样化时间的估计。我们在多样化速率和分子进化速率随时间变化的几种情况下模拟了DNA序列的进化，包括多样化和分子进化速率相关联的模型。我们表明，常用方法，包括基于度量、似然和贝叶斯方法，在分子替换速率变化时识别多样化速率变化的能力可能较低。此外，物种形成速率与分子进化速率之间的关联可能导致物种形成速率放缓或加速的信号丢失或被误识别。这些结果表明，从系统发育树推断宏观进化过程时，需要考虑分子进化速率变化的多种来源。
