Leaf venation networks of Bornean trees: images and hand-traced segmentations.

The data set contains images of leaf venation networks obtained from tree species in Malaysian Borneo. The data set contains 726 leaves from 295 species comprising 50 families, sampled from eight forest plots in Sabah. Image extents are approximately 1 × 1 cm, or 50 megapixels. All images contain a region of interest in which all veins have been hand traced. The complete data set includes over 30 billion pixels, of which more than 600 million have been validated by hand tracing. These images are suitable for morphological characterization of these species, as well as for training of machine-learning algorithms that segment biological networks from images. Data are made available under the Open Data Commons Attribution License. You are free to copy, distribute, and use the database; to produce works from the database; and to modify, transform, and build upon the database. You must attribute any public use of the database, or works produced from the database, in the manner specified in the license. For any use or redistribution of the database, or works produced from it, you must make clear to others the license of the database and keep intact any notices on the original database

Navigation between states in ecological communities by taking shortcuts, with application to control

Many community ecology problems can be framed in terms of controlling the transition from an initial state to a desired state. However, it is often unclear what action sequence (if any) would yield the desired state. Here we develop a simple approach for navigating to desired states, applicable when the costs and outcomes of actions are known. We find lowest-cost action sequences (adding a species, removing a species, changing the environment, waiting) via A* search on a state diagram. Lowest-cost sequences usually are indirect and leverage waiting for natural transitions caused by competitive exclusion. In tests on simulated and empirical data across taxa, our approach provides ~50% probability of substantial cost improvement relative to nominal approaches. As an example, numerous successes are predicted in gut microbial communities for removing the pathogen Clostridium difficile. This work thus provides a conceptual foundation for efficient state transitions in species-rich communities

Empirical Predictability of Community Responses to Climate Change

Robust predictions of ecosystem responses to climate change are challenging. To achieve such predictions, ecology has extensively relied on the assumption that community states and dynamics are at equilibrium with climate. However, empirical evidence from Quaternary and contemporary data suggest that species communities rarely follow equilibrium dynamics with climate change. This discrepancy between the conceptual foundation of many predictive models and observed community dynamics casts doubts on our ability to successfully predict future community states. Here we used community response diagrams (CRDs) to empirically investigate the occurrence of different classes of disequilibrium responses in plant communities during the Late Quaternary, and bird communities during modern climate warming in North America. We documented a large variability in types of responses including alternate states, suggesting that equilibrium dynamics are not the most common type of response to climate change. Bird responses appeared less predictable to modern climate warming than plant responses to Late Quaternary climate warming. Furthermore, we showed that baseline climate gradients were a strong predictor of disequilibrium states, while ecological factors such as species’ traits had a substantial, but inconsistent effect on the deviation from equilibrium. We conclude that (1) complex temporal community dynamics including stochastic responses, lags, and alternate states are common; (2) assuming equilibrium dynamics to predict biodiversity responses to future climate changes may lead to unsuccessful predictions

Linking functional traits to multiscale statistics of leaf venation networks

Funding Information UK Natural Environment Research Council. Grant Number: NE/M019160/1 US National Science Foundation. Grant Number: DEB‐2025282 NERC Human‐modified Tropical Forest Programme. Grant Number: NE/M017508/1 Biodiversity And Land‐use Impacts on Tropical Ecosystem Function (BALI). Grant Numbers: NE/K016253/1, NE/K016253/1 Sime Darby Foundation Stability of Altered Forest Ecosystems (SAFE) Project Sabah Biodiversity Council Institute for Tropical Biology and Conservation (ITBC) at the University of Malaysia, Sabah (UMS) Sabah Forest Research Centre (FRC) at Sepilok Sabah Forestry Department SEARRP, Yayasan Sabah (Maliau Basin Conservation Area) Maliau Basin and Danum Valley Management Committees Acknowledgements Fieldwork was supported by Unding Jami, Matheus Henrique Nuñes, Rudi Saul Cruz Chino, Milenka Ximena Montoya, and South East Asia Rainforest Research Program (SEARRP) staff. Research was facilitated by Rob Ewers, Laura Kruitbos, Reuben Nilus, Glen Reynolds, and Charles Vairappan. Species identifications were made by Bernadus Bala Ola, Bill McDonald, Alexander Karolus, and MinSheng Khoo. This work also was supported by the UK Natural Environment Research Council (NERC; no. NE/M019160/1, to BB) and the US National Science Foundation (no. DEB‐2025282, to BB). This publication is a contribution from the NERC Human‐modified Tropical Forest Programme (no. NE/M017508/1, to YAT) and Biodiversity And Land‐use Impacts on Tropical Ecosystem Function (BALI) consortium (no. NE/K016253/1, to YM and no. NE/K016253/1, to YAT). The SAFE Project was funded by the Sime Darby Foundation and the UK NERC. The study areas are part of the Global Ecosystems Monitoring Network (GEM) via an ERC Advanced Investigator Award to YM (no. 321131). The project also was supported by the Stability of Altered Forest Ecosystems (SAFE) Project, the Sabah Biodiversity Council (SaBC, permits JKM/MBS.1000‐2/2 JLD.3‐126 and ‐154), the Institute for Tropical Biology and Conservation (ITBC) at the University of Malaysia, Sabah (UMS), the Sabah Forest Research Centre (FRC) at Sepilok, the Sabah Forestry Department, the SEARRP, Yayasan Sabah (Maliau Basin Conservation Area), and the Maliau Basin and Danum Valley Management Committees. Sean Gleason and several anonymous reviewers provided constructive feedback on the manuscript.Peer reviewedPublisher PD

Late Quaternary climate legacies in contemporary plant functional composition

The functional composition of plant communities is commonly thought to be determined by contemporary climate. However, if rates of climate‐driven immigration and/or exclusion of species are slow, then contemporary functional composition may be explained by paleoclimate as well as by contemporary climate. We tested this idea by coupling contemporary maps of plant functional trait composition across North and South America to paleoclimate means and temporal variation in temperature and precipitation from the Last Interglacial (120 ka) to the present. Paleoclimate predictors strongly improved prediction of contemporary functional composition compared to contemporary climate predictors, with a stronger influence of temperature in North America (especially during periods of ice melting) and of precipitation in South America (across all times). Thus, climate from tens of thousands of years ago influences contemporary functional composition via slow assemblage dynamics

Empirical Predictability of Community Responses to Climate Change

Robust predictions of ecosystem responses to climate change are challenging. To achieve such predictions, ecology has extensively relied on the assumption that community states and dynamics are at equilibrium with climate. However, empirical evidence from Quaternary and contemporary data suggest that species communities rarely follow equilibrium dynamics with climate change. This discrepancy between the conceptual foundation of many predictive models and observed community dynamics casts doubts on our ability to successfully predict future community states. Here we used community response diagrams (CRDs) to empirically investigate the occurrence of different classes of disequilibrium responses in plant communities during the Late Quaternary, and bird communities during modern climate warming in North America. We documented a large variability in types of responses including alternate states, suggesting that equilibrium dynamics are not the most common type of response to climate change. Bird responses appeared less predictable to modern climate warming than plant responses to Late Quaternary climate warming. Furthermore, we showed that baseline climate gradients were a strong predictor of disequilibrium states, while ecological factors such as species' traits had a substantial, but inconsistent effect on the deviation from equilibrium. We conclude that (1) complex temporal community dynamics including stochastic responses, lags, and alternate states are common; (2) assuming equilibrium dynamics to predict biodiversity responses to future climate changes may lead to unsuccessful predictions