Adaptive evolution across multi-scale biological systems: finding a bridge between molecular evolution and multi-species dynamics.

基因存在于物种中，物种存在于群落中，群落存在于生态系统中。考虑一下多物种群落的涌现复杂性;它是一个由其物种的联合活动形成的自组织系统，这些活动所需的信息存储在基因中的“较低水平”。在物种或群落内部发生的生物活动可以表现在外部（例如，改变生态系统），从而影响社区本身的性质和动态。这里的关键见解是，基因“感知”的适应性景观不能独立于这些基因如何影响更高层次的复杂性。因此，一个复杂的生物系统（例如，社区）可以在进化时间上发展出因果交互的复杂网络，具有水平之间的反馈（例如，基因，物种和社区）影响每个基因的适应性景观。然而，适应性基因进化的经典解释，如新达尔文理论所体现的，是还原论的，并且在很大程度上假设了单向因果途径。因此，经典的方法一直在努力提供一个完整的帐户如何进化可以建立和微调多尺度生物系统内的联系。这种多层次的因果关系促使备受推崇的生物学哲学家伊夫琳·福克斯·凯勒（Evelyn Fox Keller）质疑生物学家使用“基因”概念的方式。来解释复杂的生物系统如果伊夫林·福克斯·凯勒是正确的，那么如果我们坚持追求纯粹的还原解释，那么关于复杂性起源和进化的基本问题就无法解决。事实上，凯勒最近呼吁生物学家调整他们的分析和建模技术，以解决多尺度系统，并考虑不同策略的“多元化马赛克”。作为一名进化生物学家，我对凯勒的呼吁做出了回应。关于生物复杂性的基本问题，例如围绕多尺度系统的适应性进化的问题，已经从研究的裂缝中消失了，因为它们位于两个或更多领域的边界。适应性基因进化的传统方法是牢固地植根于人口遗传理论，虽然必要的，其范围是有限的高度还原的适应性景观的看法。对适应性进化的完整理解将要求我们考虑（i）多尺度动力学的影响（例如，多基因和多物种的相互作用）的适应性景观，（ii）基因型和表型的分散映射，以及（iii）生物学的多个领域。因为我们提出了新的问题，我们需要开发新的研究工具。因此，该项目旨在开发适合于理解跨多尺度生物系统的基因（和基因组）适应动力学的理论和方法。学员将获得适合广泛职业的数据科学和基因组学技能。

Genes exist within species, species exist within communities, and communities exist within ecosystems. Consider the emergent complexity of a multi-species community; it is a self-organizing system shaped by the combined activities of its species, with the information required for those activities stored at "lower levels" within genes. The biological activities occurring inside of the species, or the community, can manifest externally (e.g., changing the ecosystem), and thereby influence the properties and dynamics of the community itself. The key insight here is that the fitness landscape that genes "perceive" cannot be independent of how those genes affect higher levels of complexity. Therefore a complex biological system (e.g., a community) can develop a complex network of causal interactions over evolutionary time, with feedback between levels (e.g., genes, species and community) influencing each gene's adaptive landscape. However, the classical account of adaptive gene evolution, as embodied by neo-Darwinian theory, is reductionist and largely assumes unidirectional causal pathways. Thus, the classical approach has struggled to provide a full account of how evolution can establish and fine-tune links within multi-scale biological systems. Such multi-level causality motivated the highly-regarded philosopher of biology, Evelyn Fox Keller, to question the way biologists use the concept of "the gene for." to explain complex biological systems. If Evelyn Fox Keller is correct, then fundamental questions about the origin and evolution of complexity cannot be solved if we persist in pursuing purely reductive explanations. Indeed, Keller has recently called on biologists to adapt their analysis and modelling techniques to address multi-scale systems, and to consider a "pluralistic mosaic" of different strategies. The proposed research program is a response to Keller's call from my perspective as an evolutionary biologist. Fundamental questions about biological complexity, such as those surrounding adaptive evolution across multi-scale systems, have fallen through the cracks of investigation because they lie on the boundary of two or more fields. The traditional approach to adaptive gene evolution is firmly rooted in population genetic theory and, while necessary, its scope is limited by a highly reductive view of adaptive landscapes. A complete understanding of adaptive evolution will require us to consider (i) the effect of multi-scale dynamics (e.g., multi-gene and multi-species interactions) on adaptive landscapes, (ii) a de-centralized mapping of genotype and phenotype, and (iii) multiple fields of biology. Because we are asking new questions, we will need to develop new research tools. Hence, this project seeks to develop theory and methods appropriate for understanding adaptive dynamics of genes (and genomes) across multi-scale biological systems. Trainees will acquire data science and genomics skills suitable to a broad the range of careers.