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1. Predicting species distributions and community composition using satellite remote sensing predictors

   https://doi.org/10.1038/s41598-021-96047-7  

   Pinto-Ledezma, Jesús N. ; Cavender-Bares, Jeannine ( December 2021 , Scientific Reports)

   Abstract Biodiversity is rapidly changing due to changes in the climate and human related activities; thus, the accurate predictions of species composition and diversity are critical to developing conservation actions and management strategies. In this paper, using satellite remote sensing products as covariates, we constructed stacked species distribution models (S-SDMs) under a Bayesian framework to build next-generation biodiversity models. Model performance of these models was assessed using oak assemblages distributed across the continental United States obtained from the National Ecological Observatory Network (NEON). This study represents an attempt to evaluate the integrated predictions of biodiversity models—including assemblage diversity and composition—obtainedmore »by stacking next-generation SDMs. We found that applying constraints to assemblage predictions, such as using the probability ranking rule, does not improve biodiversity prediction models. Furthermore, we found that independent of the stacking procedure (bS-SDM versus pS-SDM versus cS-SDM), these kinds of next-generation biodiversity models do not accurately recover the observed species composition at the plot level or ecological-community scales (NEON plots are 400 m 2 ). However, these models do return reasonable predictions at macroecological scales, i.e., moderately to highly correct assignments of species identities at the scale of NEON sites (mean area ~ 27 km 2 ). Our results provide insights for advancing the accuracy of prediction of assemblage diversity and composition at different spatial scales globally. An important task for future studies is to evaluate the reliability of combining S-SDMs with direct detection of species using image spectroscopy to build a new generation of biodiversity models that accurately predict and monitor ecological assemblages through time and space.« less
2. Empirical Performance of Tree-Based Inference of Phylogenetic Networks

   https://doi.org/10.1101/693986  

   Cao, Zhen ; Zhu, Jiafan ; Nakhleh, Luay ( January 2019 , Leibniz international proceedings in informatics)

   Phylogenetic networks extend the phylogenetic tree structure and allow for modeling vertical and horizontal evolution in a single framework. Statistical inference of phylogenetic networks is prohibitive and currently limited to small networks. An approach that could significantly improve phylogenetic network space exploration is based on first inferring an evolutionary tree of the species under consideration, and then augmenting the tree into a network by adding a set of "horizontal" edges to better fit the data. In this paper, we study the performance of such an approach on networks generated under a birth-hybridization model and explore its feasibility as an alternativemore »to approaches that search the phylogenetic network space directly (without relying on a fixed underlying tree). We find that the concatenation method does poorly at obtaining a "backbone" tree that could be augmented into the correct network, whereas the popular species tree inference method ASTRAL does significantly better at such a task. We then evaluated the tree-to-network augmentation phase under the minimizing deep coalescence and pseudo-likelihood criteria. We find that even though this is a much faster approach than the direct search of the network space, the accuracy is much poorer, even when the backbone tree is a good starting tree. Our results show that tree-based inference of phylogenetic networks could yield very poor results. As exploration of the network space directly in search of maximum likelihood estimates or a representative sample of the posterior is very expensive, significant improvements to the computational complexity of phylogenetic network inference are imperative if analyses of large data sets are to be performed. We show that a recently developed divide-and-conquer approach significantly outperforms tree-based inference in terms of accuracy, albeit still at a higher computational cost.« less
3. Fusion neural networks for plant classification: learning to combine RGB, hyperspectral, and lidar data

   https://doi.org/10.7717/peerj.11790  

   Scholl, Victoria M. ; McGlinchy, Joseph ; Price-Broncucia, Teo ; Balch, Jennifer K. ; Joseph, Maxwell B. ( January 2021 , PeerJ)

   Airborne remote sensing offers unprecedented opportunities to efficiently monitor vegetation, but methods to delineate and classify individual plant species using the collected data are still actively being developed and improved. The Integrating Data science with Trees and Remote Sensing (IDTReeS) plant identification competition openly invited scientists to create and compare individual tree mapping methods. Participants were tasked with training taxon identification algorithms based on two sites, to then transfer their methods to a third unseen site, using field-based plant observations in combination with airborne remote sensing image data products from the National Ecological Observatory Network (NEON). These data were capturedmore »by a high resolution digital camera sensitive to red, green, blue (RGB) light, hyperspectral imaging spectrometer spanning the visible to shortwave infrared wavelengths, and lidar systems to capture the spectral and structural properties of vegetation. As participants in the IDTReeS competition, we developed a two-stage deep learning approach to integrate NEON remote sensing data from all three sensors and classify individual plant species and genera. The first stage was a convolutional neural network that generates taxon probabilities from RGB images, and the second stage was a fusion neural network that “learns” how to combine these probabilities with hyperspectral and lidar data. Our two-stage approach leverages the ability of neural networks to flexibly and automatically extract descriptive features from complex image data with high dimensionality. Our method achieved an overall classification accuracy of 0.51 based on the training set, and 0.32 based on the test set which contained data from an unseen site with unknown taxa classes. Although transferability of classification algorithms to unseen sites with unknown species and genus classes proved to be a challenging task, developing methods with openly available NEON data that will be collected in a standardized format for 30 years allows for continual improvements and major gains for members of the computational ecology community. We outline promising directions related to data preparation and processing techniques for further investigation, and provide our code to contribute to open reproducible science efforts.« less
4. Density estimation using deep generative neural networks

   https://doi.org/10.1073/pnas.2101344118  

   Liu, Qiao ; Xu, Jiaze ; Jiang, Rui ; Wong, Wing Hung ( April 2021 , Proceedings of the National Academy of Sciences)

   Density estimation is one of the fundamental problems in both statistics and machine learning. In this study, we propose Roundtrip, a computational framework for general-purpose density estimation based on deep generative neural networks. Roundtrip retains the generative power of deep generative models, such as generative adversarial networks (GANs) while it also provides estimates of density values, thus supporting both data generation and density estimation. Unlike previous neural density estimators that put stringent conditions on the transformation from the latent space to the data space, Roundtrip enables the use of much more general mappings where target density is modeled by learningmore »a manifold induced from a base density (e.g., Gaussian distribution). Roundtrip provides a statistical framework for GAN models where an explicit evaluation of density values is feasible. In numerical experiments, Roundtrip exceeds state-of-the-art performance in a diverse range of density estimation tasks.« less
5. Rethinking restoration targets for American chestnut using species distribution modeling

   https://doi.org/10.1007/s10531-019-01814-8  

   Barnes, Jessica Cavin ; Delborne, Jason A. ( July 2019 , Biodiversity and Conservation)

   Given the scale and speed of contemporary environmental changes, intensive conservation interventions are increasingly being proposed that would assist the evolution of adaptive traits in threatened species. The ambition of these projects is tempered by a number of concerns, including the potential maladaptation of manipulated organisms for contemporary and future climatic conditions in their historical ranges. Following the guidelines of the International Union for the Conservation of Nature, we use a species distribution model (SDM) to consider the potential impact of climate change on the distribution and quantity of suitable habitat for American chestnut (Castanea dentata), a functionally extinct forestmore »species that has been the focus of various restoration efforts for over 100 years. Consistent with other SDMs for North American trees, our model shows contraction of climatically suitable habitat for American chestnut within the species’ historical range and the expansion of climatically suitable habitat in regions to the north of it by 2080. These broad changes have significant implications for restoration practice. In particular, they highlight the importance of germplasm conservation, local adaptation, and addressing knowledge gaps about the interspecific interactions of American chestnut. More generally, this model demonstrates that the goals of assisted evolution projects, which often aim to maintain species in their native ranges, need to account for the uncertainty and novelty of future environmental conditions.« less