Fine scale prediction of ecological community composition using a two-step sequential Machine Learning ensemble

Prediction is one of the last frontiers in ecology. Indeed, predicting fine-scale species composition in natural systems is a complex challenge as multiple abiotic and biotic processes operate simultaneously to determine local species abundances. On the one hand, species intrinsic performance and their tolerance limits to different abiotic pressures modulate species abundances. On the other hand there is growing recognition that species interactions play an equally important role in limiting or promoting such abundances within ecological communities. Here, we present a joint effort between ecologists and data scientists to use data-driven models to predict species abundances using reasonably easy to obtain data. We propose a sequential data-driven modeling approach that in a first step predicts the potential species abundances based on abiotic variables, and in a second step uses these predictions to model the realized abundances once accounting for species competition. Using a curated data set over five years we predict fine-scale species abundances in a highly diverse annual plant community. Our models show a remarkable spatial predictive accuracy using only easy-to-measure variables in the field, yet such predictive power is lost when temporal dynamics are taken into account. This result suggests that predicting future abundances requires longer time series analysis to capture enough variability. In addition, we show that these data-driven models can also suggest how to improve mechanistic models by adding missing variables that affect species performance such as particular soil conditions (e.g. carbonate availability in our case). Robust models for predicting fine-scale species composition informed by the mechanistic understanding of the underlying abiotic and biotic processes can be a pivotal tool for conservation, especially given the human-induced rapid environmental changes we are experiencing. This objective can be achieved by promoting the knowledge gained with classic modelling approaches in ecology and recently developed data-driven models. Author summary Prediction is challenging but recently developed Machine Learning techniques allow to dramatically improve prediction accuracy in several domains. However, these tools are often of little application in ecology due to the hardship of gathering information on the needed explanatory variables, which often comprise not only physical variables such as temperature or soil nutrients, but also information about the complex network of species interactions that modulate species abundances. Here we present a two-step sequential modelling framework that overcomes these constraints. We first infer potential species abundances by training models just with easily obtained abiotic variables and then use this outcome to fine-tune the prediction of the realized species abundances when taking into account the rest of the predicted species in the community. Overall, our results show a promising way forward for fine scale prediction in ecology.
O.G. acknowledges support provided by the Ministerio de Ciencia, Innovacion y Universidades (RYC-2017-23666). O.G. and I.B. acknowledge financial support provided by the Secretaria de Estado de Investigacion, Desarrollo e Innovacion (CGL2017-92436-EXP, SIMPLEX and RTI2018-098888-A-I00, MeDiNaS). J.G. acknowledges financial support provided by the Ministerio de Ciencia, Innovacion y Universidades (PGC2018-093854-B-I00). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.