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使用随机森林和近似贝叶斯计算识别性状介导的群落组装模型。

Identifying models of trait-mediated community assembly using random forests and approximate Bayesian computation.

作者信息

Ruffley Megan, Peterson Katie, Week Bob, Tank David C, Harmon Luke J

机构信息

Department of Biological Sciences University of Idaho Moscow ID USA.

Institute for Bioinformatics and Evolutionary Studies (IBEST) Moscow ID USA.

出版信息

Ecol Evol. 2019 Nov 21;9(23):13218-13230. doi: 10.1002/ece3.5773. eCollection 2019 Dec.

Abstract

Ecologists often use dispersion metrics and statistical hypothesis testing to infer processes of community formation such as environmental filtering, competitive exclusion, and neutral species assembly. These metrics have limited power in inferring assembly models because they rely on often-violated assumptions. Here, we adapt a model of phenotypic similarity and repulsion to simulate the process of community assembly via environmental filtering and competitive exclusion, all while parameterizing the strength of the respective ecological processes. We then use random forests and approximate Bayesian computation to distinguish between these models given the simulated data. We find that our approach is more accurate than using dispersion metrics and accounts for uncertainty in model selection. We also demonstrate that the parameter determining the strength of the assembly processes can be accurately estimated. This approach is available in the R package CAMI; Community Assembly Model Inference. We demonstrate the effectiveness of CAMI using an example of plant communities living on lava flow islands.

摘要

生态学家经常使用分布指标和统计假设检验来推断群落形成过程,如环境过滤、竞争排斥和中性物种集合。这些指标在推断集合模型方面的能力有限,因为它们依赖于常常被违反的假设。在这里,我们采用一种表型相似性和排斥模型来模拟通过环境过滤和竞争排斥的群落集合过程,同时对各自生态过程的强度进行参数化。然后,我们使用随机森林和近似贝叶斯计算,根据模拟数据区分这些模型。我们发现,我们的方法比使用分布指标更准确,并且考虑了模型选择中的不确定性。我们还证明,可以准确估计决定集合过程强度的参数。这种方法可以在R包CAMI(群落集合模型推断)中获得。我们以生活在熔岩流岛屿上的植物群落为例,展示了CAMI的有效性。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/8b13/6912896/72b6d3f66ac9/ECE3-9-13218-g001.jpg

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