Huang Yuangeng, Roopnarine Peter D, Chen Zhong-Qiang
State Key Laboratory of Geomicrobiology and Environmental Changes, China University of Geosciences, Wuhan, China.
Department of Invertebrate Zoology and Geology, California Academy of Sciences, San Francisco, CA, USA.
Nat Protoc. 2025 Jun 16. doi: 10.1038/s41596-025-01201-4.
Fossils preserve crucial information about the underlying biological and ecological processes of past ecosystems. Models built on paleontological and paleoecological data can help to elucidate the factors influencing ecosystem health, stability, resilience and function, offering a unique perspective on the long-term ecological impacts of the ongoing human-induced biodiversity crisis and ecosystem degradation. Substantial advances have been made in quantifying the ecological dynamics and functional structures of paleocommunities. However, the effective reconstruction of paleo-food webs and the quantitative evaluation of paleocommunity dynamics are still challenging tasks. Here we present a detailed protocol for reconstructing paleo-food webs using fossil data and for modeling the stability and structures of these paleocommunities using the cascading extinction on graphs model. The procedure includes (1) selecting an appropriate geological time range and geographic scope, collecting fossil data and reconstructing paleocommunities; (2) assigning species to guilds on the basis of shared prey-predator relationships and connecting the guilds that interacted trophically; (3) measuring the functional structures and modeling their dynamics using species-level networks and cascading extinction on graphs models; and (4) analyzing the results to understand the community evolution and identify tipping points that predict ecosystem collapse. Organismal expertise is needed in the reconstruction of paleo-food webs. The resulting comparisons of the paleocommunity stability and structure can help calibrate the timing and patterns of ecological changes during critical intervals in Earth history. This Protocol aims to enhance the utilization of ecological modeling in understanding the evolution of ancient ecosystems. The time required for the protocol is community size dependent - for example, ~5 months for communities containing ~1,000 species.
化石保存了有关过去生态系统潜在生物和生态过程的关键信息。基于古生物学和古生态学数据构建的模型有助于阐明影响生态系统健康、稳定性、恢复力和功能的因素，为当前人类引发的生物多样性危机和生态系统退化的长期生态影响提供独特视角。在量化古群落的生态动态和功能结构方面已经取得了重大进展。然而，古食物网的有效重建和古群落动态的定量评估仍然是具有挑战性的任务。在此，我们提出了一个详细的方案，用于利用化石数据重建古食物网，并使用图上的级联灭绝模型对这些古群落的稳定性和结构进行建模。该过程包括：（1）选择合适的地质时间范围和地理范围，收集化石数据并重建古群落；（2）根据共享的捕食 - 被捕食关系将物种分配到功能群，并连接营养相互作用的功能群；（3）使用物种水平的网络和图上的级联灭绝模型测量功能结构并对其动态进行建模；（4）分析结果以了解群落演化并识别预测生态系统崩溃的临界点。重建古食物网需要生物体专业知识。古群落稳定性和结构的比较结果有助于校准地球历史关键时期生态变化的时间和模式。本方案旨在提高生态建模在理解古代生态系统演化中的应用。该方案所需时间取决于群落规模——例如，对于包含约1000个物种的群落，大约需要5个月。
