Community and Conservation Ecology, Centre for Ecological and Evolutionary Studies, University of Groningen, The Netherlands.
Am Nat. 2012 Oct;180(4):E75-89. doi: 10.1086/667574. Epub 2012 Aug 24.
In this article we propose a new framework for studying adaptive radiations in the context of diversity-dependent diversification. Diversity dependence causes diversification to decelerate at the end of an adaptive radiation but also plays a key role in the initial pulse of diversification. In particular, key innovations (which in our definition include novel traits as well as new environments) may cause decoupling of the diversity-dependent dynamics of the innovative clade from the diversity-dependent dynamics of its ancestral clade. We present a likelihood-based inference method to test for decoupling of diversity dependence using molecular phylogenies. The method, which can handle incomplete phylogenies, identifies when the decoupling took place and which diversification parameters are affected. We illustrate our approach by applying it to the molecular phylogeny of the North American clade of the legume tribe Psoraleeae (47 extant species, of which 4 are missing). Two diversification rate shifts were previously identified for this clade; our analysis shows that the first, positive shift can be associated with decoupling of two Pediomelum subgenera from the other Psoraleeae lineages, while we argue that the second, negative shift can be attributed to speciation being protracted. The latter explanation yields nonzero extinction rates, in contrast to previous findings. Our framework offers a new perspective on macroevolution: new environments and novel traits (ecological opportunity) and diversity dependence (ecological limits) cannot be considered separately.
在本文中，我们提出了一个新的框架，用于在依赖多样性的多样化背景下研究适应性辐射。多样性依赖性导致多样化在适应性辐射结束时减速，但在多样化的初始脉冲中也起着关键作用。特别是，关键创新（在我们的定义中包括新的特征和新的环境）可能导致创新分支的多样性依赖性动态与祖先分支的多样性依赖性动态解耦。我们提出了一种基于似然的推断方法，使用分子系统发育来测试多样性依赖性的解耦。该方法可以处理不完整的系统发育，确定解耦发生的时间以及受影响的多样化参数。我们通过将其应用于豆科 Psoraleeae 北美分支的分子系统发育（47 个现存物种，其中 4 个缺失）来说明我们的方法。先前已经确定了这个分支的两个多样化率变化；我们的分析表明，第一个正的变化可以与两个 Pediomelum 亚属与其他 Psoraleeae 谱系的解耦相关，而我们认为第二个负的变化可以归因于物种形成的延长。后一种解释产生了非零灭绝率，与先前的发现相反。我们的框架为宏观进化提供了一个新的视角：新的环境和新的特征（生态机会）和多样性依赖性（生态限制）不能分开考虑。
