Ecological Informatics最新文献

Tropical dry forests are highly threatened at a global scale. Long-term monitoring of remaining stands is needed to assess forest health, efficacy of management practices, and potential impacts of climate change. Using a multi-seasonal Landsat time series, we examined Normalized Difference Vegetation Index (NDVI) patterns in native dry forest, non-native vegetation types, and dry forest restoration sites from 1999 to 2022 in the Hawaiian Islands. We calculated trends in median NDVI and robust coefficient of variation of NDVI for dry and wet seasons, and used Breaks for Additive Seasonal and Trend analysis to detect trend departures. To assess the impact of regional drying trends, NDVI trends were compared to the seasonal long-term precipitation anomaly and cumulative precipitation anomaly. We found that native dry forest was less green than non-native forest, particularly during the dry season, and that median NDVI increased in both native and non-native dry forests over the study period despite negative precipitation anomaly trends. This result differs from coarser-scale studies in Hawaii, but is supported by trends in other dry forest regions. Greening was also observed in restoration study sites, especially larger sites where native species establishment and recruitment has been reported. Non-native grassland NDVI exhibited a strong positive link to precipitation anomalies, suggesting that drier climate scenarios may exacerbate the invasive grass-wildfire cycle that threatens native dry forest. These results demonstrate that Landsat time series may be used to detect seasonal variation in dry forest plots and to support restoration site monitoring in a highly fragmented ecosystem.

Accurate estimation of fractional vegetation coverage (FVC) is essential for assessing the ecological environment and acquiring ecological information. However, under natural lighting conditions, shadows in vegetation scenes can easily lead to confusion between shadowed vegetation and shadowed soil, leading to misclassification and omission errors. This issue limits the precision of both vegetation extraction and FVC estimation. To address this challenge, this study introduces a novel deep learning model, the Mixture of Modality Transformer (MoMFormer), which is specifically designed to mitigate shadow interference in vegetation extraction. Our model uses the Swin-transformer V2 as a feature extractor, effectively capturing vegetation features from a dual-modality (regular-exposure RGB and high dynamic range HDR) dataset. A dynamic aggregation module (DAM) is integrated to adaptively blend the most relevant vegetation features. We selected several state-of-the-art (SOTA) methods and conducted extensive experiments using a self-annotated dataset featuring diverse vegetation–soil scenes and compare our model with several state-of-the-art methods. The results demonstrate that MoMFormer achieves an accuracy of 89.43 % on the HDR-RGB dual-modality dataset, with an FVC accuracy of 87.57 %, outperforming other algorithms and demonstrating high vegetation extraction accuracy and adaptability under natural lighting conditions. This research offers new insights into accurate vegetation information extraction in naturally lit environments with shadows, providing robust technical support for high-precision validation of vegetation coverage products and algorithms based on multimodal data. The code and datasets used in this study are publicly available at https://github.com/hhhxiaohe/MoMFormer.

Near-term iterative ecological forecasting has great potential for providing new insights into our ability to predict multiple ecological variables. However, true, out-of-sample probabilistic forecasts remain rare, and variability in forecast performance has largely been unexamined in process-based forecasts which predict multiple ecosystem variables. To explore how forecast performance varies for water temperature and dissolved oxygen, two freshwater variables important for lake ecosystem functioning, we produced probabilistic forecasts at multiple depths over two open-water seasons in Lake Sunapee, NH, USA. Our forecasting system, FLARE (Forecasting Lake And Reservoir Ecosystems), uses a 1-D coupled hydrodynamic-biogeochemical process model, which we assessed relative to both climatology and persistence null models to quantify how much information process-based FLARE forecasts provide over null models across varying environmental conditions. We found that FLARE water temperature forecasts were always more skillful than FLARE oxygen forecasts. Specifically, temperature forecasts outperformed both null models up to 11 days into the future, as compared to only two days for oxygen. Across different years, we observed variable forecast skill, with performance generally decreasing with depth for both variables. Overall, all temperature forecasts and surface oxygen, but not deep oxygen, forecasts were more skillful than at least one null model >80 % of the forecasted period, indicating that our process-based model was able to reproduce the dynamics of these two variables with greater reliability than the null models. However, process-based oxygen forecasts from deeper waters were less skillful than both null models during a majority of the forecasted period, which suggests that deep-water oxygen dynamics are dominated by autocorrelation and seasonal change, which are inherently captured by the null forecasts. Our results highlight that forecast performance varies among lake water quality metrics and that process-based forecasts can provide important information in conjunction with null models in varying environmental conditions. Altogether, these process-based forecasts can be used to develop quantitative tools which inform our understanding of future ecosystem change.

Perusal of the environmental modelling literature reveals that the Lin's concordance correlation coefficient is a popular validation statistic to characterise model or map quality. In this communication, we illustrate with synthetic examples three undesirable statistical properties of this coefficient. We argue that ignorance of these properties have led to a frequent misuse of this coefficient in modelling and mapping studies. The stand-alone use of the concordance correlation coefficient is insufficient because i) it does not inform on the relative contribution of bias and correlation, ii) the values cannot be compared across different datasets or studies and iii) it is prone to the same problems as other linear correlation statistics. The concordance coefficient was, in fact, thought initially for evaluating reproducibility studies over repeated trials of the same variable, not for characterising model accuracy. For the validation of models and maps, we recommend calculating statistics that, combined with the concordance correlation coefficient, represent various aspects of the model or map quality, which can be visualised together in a single figure with a Taylor or solar diagram.

We present a comprehensive, customizable workflow for inferring prokaryotic phenotypic traits from marker gene sequences and modelling the relationships between these traits and environmental factors, thus overcoming the limited ecological interpretability of marker gene sequencing data. We created the trait sequence database ampliconTraits, constructed by cross-mapping species from a phenotypic trait database to the SILVA sequence database and formatted to enable seamless classification of environmental sequences using the SINAPS algorithm. The R package MicEnvMod enables modelling of trait – environment relationships, combining the strengths of different model types and integrating an approach to evaluate the models' predictive performance in a single framework. Traits could be accurately predicted even for sequences with low sequence identity (80 %) with the reference sequences, indicating that our approach is suitable to classify a wide range of environmental sequences. Validating our approach in a large trans-continental soil dataset, we showed that trait distributions were robust to classification settings such as the bootstrap cutoff for classification and the number of discrete intervals for continuous traits. Using functions from MicEnvMod, we revealed precipitation seasonality and land cover as the most important predictors of genome size. We found Pearson correlation coefficients between observed and predicted values up to 0.70 using repeated split sampling cross validation, corroborating the predictive ability of our models beyond the training data. Predicting genome size across the Iberian Peninsula, we found the largest genomes in the northern part. Potential limitations of our trait inference approach include dependence on the phylogenetic conservation of traits and limited database coverage of environmental prokaryotes. Overall, our approach enables robust inference of ecologically interpretable traits combined with environmental modelling allowing to harness traits as bioindicators of soil ecosystem functioning.

Effective evidence synthesis is important for the integration of scientific research into decision-making. However, fully depicting the vast mosaic of concepts and applications in environmental sciences and ecology often entails a substantial workload. New Artificial Intelligence (AI) tools present an attractive option for addressing this challenge but require sufficient validation to match the vigorous standards of a systematic review. This article demonstrates the use of generative AI in the selection of relevant literature as part of a systematic review on indicators of ecosystem condition. We highlight, through the development of an optimal prompt to communicate inclusion and exclusion criteria, the need to describe ecosystem condition as a multidimensional concept whilst also maintaining clarity on what does not meet the criteria of comprehensiveness. We show that, although not completely infallible, the GPT-3.5 model significantly outperforms traditional literature screening processes in terms of speed and efficiency whilst correctly selecting 83 % of relevant literature for review. Our study highlights the importance of precision in prompt design and the setting of query parameters for the AI model and opens the perspective for future work using language models to contextualize complex concepts in the environmental sciences. Future development of this methodology in tandem with the continued evolution of the accessibility and capacity of AI tools presents a great potential to improve evidence synthesis through gains in efficiency and possible scope.