[论文解读] Nested interaction networks represent a missing link in the study of behavioural and community ecology

Pierre‐Olivier Montiglio, Kiyoko M. Gotanda+4 more|arXiv (Cornell University)|Apr 3, 2018

Plant and animal studies参考文献 56被引用 3

一句话总结

本文提出嵌套互作网络作为一种统一框架，通过建模层级生物系统（其中节点，如基因、个体、物种，彼此嵌套，且连接跨越不同层级），整合了行为生态学与群落生态学。它展示了嵌套性如何实现间接效应及跨层级的互作传播，为进化、生态与行为等尺度的跨学科研究提供了概念性支撑。

ABSTRACT

Interactions are ubiquitous across biological systems. These interactions can be abstracted as patterns of connections among distinct units such as genes, proteins, individual organisms, or species which form a hierarchy of biological organisation. Connections in this hierarchy are arranged in a nested structure: gene and protein networks shape phenotypic traits and together constitute individuals, individuals are embedded within populations, populations within communities, and communities within ecosystems. This pervasive "nestedness" of networks can result in propagation of the effects from within-level interactions at one level to units at higher or lower levels of organization. The concept of nested biological networks is implicit in a variety of disciplines ranging from the study of genetic circuits regulating phenotypic trait expression (Babu et al. 2004), to the study of predator-prey interactions influencing community composition (Poisot et al. 2016). However, studies typically only address interactions within and among directly neighbouring hierarchical levels, such as genotypes and phenotypic traits, or populations and communities. Here, we formalise nested networks as having nodes that can contain, or be embedded in, other nodes, and where edges can bridge connections between sets of embedded nodes. We then argue that explicitly accounting for network nestedness across levels of organization will encourage integrative thinking on new interdisciplinary research fronts. We focus on two phenomena in particular: (i) indirect connections among units can arise from the structure of connections at higher or lower levels of organisation, (ii) the propagation of effects across neighbouring hierarchical levels of organization. This framework of nested interaction networks provides a tool for researchers across disciplines to conceptualize their work as elements on a common scaffold.

研究动机与目标

• 为填补从基因到生态系统等生物组织层级间互作整合的空白。
• 形式化嵌套网络的概念，其中节点可嵌入其他节点中，边连接不同层级。
• 展示某一层次的网络结构如何生成跨层级的间接连接并传播影响。
• 通过提供共享的概念框架，促进整合性、跨学科研究。
• 将嵌套网络定位为理解复杂生物系统的关键缺失环节。

提出的方法

• 将嵌套网络定义为节点可包含或嵌入其他节点，形成层级结构的系统。
• 通过连接不同层级中嵌套节点的边来建模互作，实现跨层级连通性。
• 形式化通过网络结构从低层级互作向更高或更低层级传播影响的过程。
• 使用现有实证与理论案例（如基因回路、捕食者-猎物网）说明嵌套网络的动力学。
• 应用网络理论分析生物层级结构，研究嵌套性如何影响系统层面的特性。
• 通过整合基因组学、行为学、种群生态学与群落生态学的概念，提出跨学科研究的支撑框架。

实验结果

研究问题

• RQ1 生物单元之间的间接连接如何从更高或更低层级的互作结构组织中产生？
• RQ2 通过嵌套网络结构，某一层次的互作影响以何种方式传播到其他层次？
• RQ3 嵌套性对生物系统的稳定性、动态特性及进化有何影响？
• RQ4 嵌套互作网络如何作为跨多样化生物学科的统一框架？
• RQ5 自然系统中存在哪些机制反映或依赖于嵌套网络结构？

主要发现

• 嵌套互作网络提供了一个正式结构，其中节点嵌套于其他节点之中，支持生物系统的层级组织。
• 连接嵌套节点的边实现了跨层级连接，产生在单一层级上不明显的间接互作。
• 嵌套网络的结构促进了影响在层级之间的传播，例如从基因互作传播至群落水平的动力学。
• 该框架解释了为何单一层级上看似孤立的互作，可通过网络拓扑影响其他层级的结果。
• 该方法为整合行为生态学、群落生态学与进化生物学的研究提供了共同的概念支撑。
• 来自基因回路与捕食者-猎物互作的实证案例表明，嵌套网络结构具有普遍性与实用性。