From microevolutionary processes to macroevolutionary patterns: modelling long-term evolution driven by ecological adaptation

几个世纪以来，长期的进化模式一直吸引着生物学家的想象力，而理解“生命之树”是科学中的一个基本问题。人们对停滞和适应性辐射等宏观进化模式进行了广泛的分析，普遍认为生态适应对长期进化起着重要作用。然而，对宏观进化模式的生态学解释仍然大多基于言语理论。宏观进化模式最终产生于微观进化过程。通过这里提出的研究，我打算为宏观进化动力学和系统发育分析发展一个数学理论，这是从生态生灭过程衍生出来的。我建议将这一理论作为现有比较系统发育方法的试验场。最后，我建议应用新的计算工具来研究大型系统发育树上生态重要性状的宏观进化。具体地说：1)我建议使用包含多样性和灭绝的自适应动力学模型来分类由不同类型的生态相互作用产生的宏观进化动力学的显著模式，针对不同维度的表型空间，以及关于进化群落的生物地理的不同假设。这将产生对长期进化的机械论模型所产生的宏观进化模式类型的一般分类。特别是，它将使对宏观进化的重要语言理论的批判性评估成为可能。2)自适应动力学模型产生了人工系统发育树，我建议使用各种比较的系统发育方法进行分析，以测试其中哪种方法最能解释系统发育。这将允许比较方法作出的推论与产生系统发育的实际生态过程进行比较。这项工作还将对宏观演化的机制模型的统计性质提供重要的见解。3)微生物塑造了地球生态系统的化学结构，确定原核生物生命树代谢功能的宏观进化模式是一个重要的问题。原核生物的系统发育可能非常庞大，它们的分析需要新的计算工具。我建议将这些工具应用到沿着微生物生命树的蛋白质超家族的进化问题上。

Long-term patterns of evolution have captured the imagination of biologists for centuries, and understanding the “tree of life” is a fundamental problem in science. Macroevolutionary patterns such as stasis and adaptive radiations have been extensively analyzed, and it is generally thought that ecological adaptations play an important role for long-term evolution. However, ecological explanations for macroevolutionary patters are still mostly based on verbal theories. Macroevolutionary patterns ultimately result from microevolutionary processes. With the research proposed here, I intend to develop a mathematical theory for macroevolutionary dynamics and phylogenetic analysis that is derived from ecological birth-death processes. I propose to use this theory as a testing ground for existing comparative phylogenetic methods. Finally, I propose to apply novel computational tools to study macroevolution of ecologically important traits on large phylogenetic trees. Specifically: 1) I propose to use adaptive dynamics models incorporating diversification and extinction to classify salient patterns of macroevolutionary dynamics generated by different types of ecological interactions, for varying dimensions of phenotype space, and for different assumptions about the biogeography of the evolving communities. This will yield a general classification of the types of macroevolutionary patterns generated by mechanistic models for long-term evolution. In particular, it will enable a critical evaluation of salient verbal theories for macroevolution. 2) The adaptive dynamics models yield artificial phylogenetic trees that I propose to analyze using a variety of comparative phylogenetic methods in order to test which of these can best explain the phylogenies. This will allow for a comparison of inferences made from comparative methods with the actual ecological processes that generated the phylogenies. This work will also give important insights into the statistical properties of mechanistic models for macroevolution. 3) Microorganisms have shaped the chemistry of Earth's ecosystems, and determining the macroevolutionary patterns of metabolic functions in the prokaryotic tree of life is an important problem. Prokaryotic phylogenies can be extremely large, and their analysis requires novel computational tools. I propose to apply such tools to the problem of the evolution of protein superfamilies along the microbial tree of life.