The mirid bugs Stenotus rubrovittatus and Trigonotylus caelestialium, which cause pecky rice, have become a threat to rice cultivation in Asia. Damage caused by these pests has rapidly become frequent since around 2000 in Japan. Their expansion pattern is not simple, making it difficult to manage them by prediction. Some insects with wide distributions have locally adapted variations in life-history traits. We performed laboratory rearing experiments to assess the geographical scale of intraspecific variations in life-history traits of S. rubrovittatus and T. caelestialium. These were aimed at increasing the accuracy of occurrence estimates and the number of generations per year. These results were compared with previous research, and differences in development rates were observed between populations of different latitudes, but not of the same latitude. Finally, plotting the timing of adult emergence and the potential number of generations per year on maps with a 5-km grid revealed that they differed greatly locally at the same latitude. These maps can be used for developing more efficient methods of managing mirid bugs in integrated pest management.

1. Restoration ecology has historically focused on reconstructing communities of highly visible taxa whilst less visible taxa, such as invertebrates and microbes, are ignored. This is problematic as invertebrates and microbes make up the vast bulk of biodiversity and drive many key ecosystem processes, yet they are rarely actively reintroduced following restoration, potentially limiting ecosystem function and biodiversity in these areas. 2. In this review, we discuss the current (limited) incorporation of invertebrates and microbes in restoration and rewilding projects. We argue that these groups should be actively rewilded during restoration to improve biodiversity and ecosystem function outcomes and highlight how they can be used to greater effect in the future. For example, invertebrates and microbes are easily manipulated, meaning whole communities can potentially be rewilded through habitat transplants in a practice that we refer to as “whole-of-community” rewilding. 3. We provide a framework for whole-of-community rewilding and describe empirical case studies as practical applications of this under-researched restoration tool that land managers can use to improve restoration outcomes. 4. We hope this new perspective on whole-of-community restoration will promote applied research into restoration that incorporates all biota, irrespective of size, whilst also enabling a better understanding of fundamental ecological theory, such as colonisation- competition trade-offs. This may be a necessary consideration as invertebrates that are important in providing ecosystem services are declining globally; targeting invertebrate communities during restoration may be crucial in stemming this decline.

In boreal landscapes, emphasis is currently placed on close-to-nature management strategies, which aim to maintain the biodiversity and ecosystem services related to old-growth forests. The success of these strategies, however, depends on an accurate understanding of the dynamics within these forests. This study aims to reconstruct the disturbance and post-disturbance dynamics in boreal old-growth forests that are driven by recurrent moderate-severity disturbances. We studied eight old-growth forests in Québec, Canada, that has recorded recurrent and moderate to severe spruce budworm (Choristoneura fumiferana [Clem.]) outbreaks over the 20th century. To reconstruct the disturbance history and the post-disturbance dynamics of the study sites, we used dendrochronological data and k-means clustering to identify growth releases and growth patterns in the studied trees. We identified nine growth patterns; these patterns represented trees differing in age, size, and canopy layer, and indicated different tree histories. Spruce budworm outbreaks caused recurrent moderate-severity disturbances within the study sites. The canopy gaps created by these disturbances were filled mainly by understorey trees, which responded by single and significant increases in radial growth and height. In contrast, overstorey trees had little influence on gap filling; thus, trees were mostly from the dominant and codominant canopy layers. Our study underlines the resistance of boreal old-growth forests to recurrent and moderate-severity disturbances, as understorey trees can rapidly fill the resulting gaps. However, trees that are unable to attain the canopy following the disturbance then tend to remain in the lower canopy layers. Therefore, reaching the canopy represents a once-in-a-lifetime opportunity, where success or failure depends on a relatively short window of time. This gap-filling dynamic produces, however, a vertical structure that is often similar to the expected structure in even-aged forests. Our results highlight the efficacy of identifying tree growth patterns to reconstruct stand disturbance dynamics and contribute to developing closer to nature forest management strategies.

Accurately estimating abundance is a critical component of monitoring and recovery of rare and elusive species. Spatial capture-recapture (SCR) models are an increasingly popular method for robust estimation of ecological parameters. We provide a maximum likelihood analytical framework to assess results from empirical studies to inform SCR sampling design, using both simulated and empirical data from non-invasive genetic sampling of seven boreal caribou populations (Rangifer tarandus caribou) which varied in range size and estimated population density. We use simulated population data with varying levels of clustered distributions to quantify the impact of non-independence of detections on density estimates, and empirical datasets to explore the influence of varied sampling intensity on the relative bias and precision of density estimates. Simulations revealed that clustered distributions of detections did not significantly impact relative bias or precision of density estimates. The empirical genotyping success rate was 95.1%. Empirical results indicated that reduced sampling intensity had a greater impact on density estimates in smaller ranges. The number of captures and spatial recaptures were strongly correlated with precision, but not relative bias. The best sampling designs did not differ with estimated population density but differed between large and small ranges. We provide an efficient framework implemented in R to estimate the detection parameters required when designing SCR studies. The framework can be used when designing a monitoring program to minimize effort and cost while maximizing effectiveness, which is critical for informing wildlife management and conservation.

1. In many social species, reproductive success varies between individuals within a population, resulting in socially structured populations. Social network analyses of familial relationships may provide insights on how fitness influences population-level demographic patterns. These methods have however rarely been applied to genetically-derived pedigree data from wild populations. 2. Here we use social networks to reconstruct parent-offspring relationships and create a familial network from polygamous boreal woodland caribou (Rangifer tarandus caribou) in Saskatchewan, Canada, to inform recovery efforts. We collected samples from 933 individuals at 15 variable microsatellite loci along with caribou-specific primers for sex identification. Using social network metrics, we assess the contribution of individual caribou to the population with several centrality metrics and then determine which metrics are best suited to inform on the population demographic structure. We look at the centrality of individuals from eighteen different local areas, along with the entire population. 3. We found substantial differences in centrality of individuals in different local areas, that in turn contributed differently to the full network, highlighting the importance of analyzing social networks at different scales. The full network revealed that boreal caribou in Saskatchewan form a complex, interconnected social network with strong familial ties, as the removal of edges with high betweenness did not result in distinct subgroups. Alpha, betweenness, and eccentricity centrality were the most informative metrics to characterize the population demographic structure and for spatially identifying areas of highest fitness levels and social cohesion across the range. 4. Synthesis and applications: Our results demonstrate the value of different network metrics in assessing genetically-derived familial networks. The spatial application of the familial networks identified areas of higher fitness levels and social cohesion across the range in support of population monitoring and recovery efforts.

1. The reduction of plant diversity following eutrophication threatens many ecosystems worldwide. Yet, the mechanisms by which species are lost following nutrient enrichment are still not completely understood, nor are the details of when such mechanisms act during the growing season, which hampers understanding and the development of mitigation strategies. 2. Using a common garden competition experiment, we found that early-season differences in growth rates among five perennial grass species measured in monoculture predicted short-term competitive dominance in pairwise combinations and that this effect was stronger under a fertilisation treatment. 3. We also examined the role of early-season growth rate in determining the outcome of competition along an experimental nutrient gradient in an alpine meadow. Early differences in growth rate between species predicted short-term competitive dominance under both ambient and fertilized conditions and competitive exclusion under fertilized conditions. 4. The results of these two studies suggests that plant species growing faster during the early stage of the growing season gain a competitive advantage over species that initially grow more slowly, and that this advantage is magnified under fertilisation. This finding is consistent with the theory of asymmetric competition for light in which fast-growing species can intercept incident light and hence outcompete and exclude slower-growing (and hence shorter) species. We predict that the current chronic nutrient inputs into many terrestrial ecosystems worldwide will reduce plant diversity and maintain low biodiversity state by continuously favouring fast-growing species. Biodiversity management strategies should focus on controlling nutrient inputs and reducing the growth of fast-growing species early in the season.

The mass die-off of Caribbean corals has transformed many of this region’s reefs to macroalgal-dominated habitats since systematic monitoring began in the 1970s. Although attributed to a combination of local and global human stressors, the lack of long-term data on Caribbean reef coral communities has prevented a clear understanding of the causes and consequences of coral declines. We integrated paleoecological, historical, and modern survey data to track the prevalence of major coral species and life history groups throughout the Caribbean from the pre-human period to present. The regional loss of Acropora corals beginning by the 1960s from local human disturbances resulted in increases in the prevalence of formerly subdominant stress-tolerant and weedy scleractinian corals and the competitive hydrozoan Millepora beginning in the 1970s and 1980s. These transformations have resulted in the homogenization of coral communities within individual countries. However, increases in stress-tolerant and weedy corals have slowed or reversed since the 1980s and 1990s in tandem with intensified coral bleaching. These patterns reveal the long history of increasingly stressful environmental conditions on Caribbean reefs that began with widespread local human disturbances and have recently culminated in the combined effects of local and global change.

Plasmids are extra-chromosomal genetic elements that encode a wide variety of phenotypes and can be maintained in bacterial populations through vertical and horizontal transmission, thus increasing bacterial adaptation to hostile environmental conditions like those imposed by antimicrobial substances. To circumvent the segregational instability resulting from randomly distributing plasmids between daughter cells upon division, non-transmissible plasmids tend to be carried in multiple copies per cell, which also results in a metabolic burden to the bacterial host, therefore reducing the overall fitness. This trade-off poses an existential question for plasmids: What is the optimal plasmid copy number? We address this question using a combination of population genetics modeling with microbiology experiments consisting of Escherichia coli K12 bearing a multi-copy plasmid encoding for blaTEM-1, a gene conferring resistance to b-lactam antibiotics. We use a Wright-Fisher model to evaluate the interaction between the above mentioned opposing forces. By numerically determining the optimal plasmid copy number for constant and fluctuating selection regimes, we conclude that plasmid copy number is an optimized evolutionary trait that depends on the rate of environmental fluctuation and balances the benefit between increased stability in the absence of selection with the burden associated with carrying multiple copies of the plasmid.

The construction of morphological character matrices is central to paleontological systematic study, which extracts paleontological information from fossils. Although the word information has been repeatedly mentioned in a wide array of paleontological systematic studies, its meaning has rarely been clarified and there has not been a standard to measure paleontological information due to the incompleteness of fossils, difficulty of recognizing homologous and homoplastic structures, etc. Here, based on information theory, we show the deep connections between paleontological systematic study and communication system engineering. It is information, the decrease of uncertainty, in morphological characters that distinguishes operational taxonomic units (OTUs) and reconstructs evolutionary history. We propose that concepts in communication system engineering such as source coding and channel coding correspond in paleontological studies to the construction of diagnostic features and the entire character matrices, which should be distinguished as how typical communication systems are engineered because these two steps serve dual purposes. With character matrices from six different vertebrate groups, we analyzed their information properties including source entropy, mutual information, and channel capacity. Estimation of channel capacity shows upper limits of all matrices in transmitting paleontological information, indicating that, due to the presence of noise, too many characters not only increase the burden in character scoring, but also may decrease quality of matrices. Information entropy, which measure how informative a variable is, of each character is tested as a weighting criterion in parsimony-based systematic studies, the results show high consistence with existing knowledge with both good resolution and interpretability.

1) Food web models explain and predict the trophic interactions in a food web, and they can infer missing interactions among the organisms. The allometric diet breadth model (ADBM) is a food web model based on the foraging theory. In the ADBM the foraging parameters are allometrically scaled to body sizes of predators and prey. In Petchey et al. (2008), the parameterisation of the ADBM had two limitations: (a) the model parameters were point estimates, and (b) food web connectance was not estimated. 2) The novelty of our current approach is: (a) we consider multiple predictions from the ADBM by parameterising it with approximate Bayesian computation, to estimate parameter distributions and not point estimates. (b) Connectance emerges from the parameterisation, by measuring model fit using the true skill statistic, which takes into account prediction of both the presences and absences of links. 3) We fit the ADBM using approximate Bayesian computation to 16 observed food webs from a wide variety of ecosystems. Connectance was consistently overestimated in the new parameterisation method. In some of the food webs, considerable variation in estimated parameter distributions occurred, and resulted in considerable variation (i.e. uncertainty) in predicted food web structure. 4) We conclude that the observed food web data is likely missing some trophic links that do actually occur, and that the ADBM likely predicts some links that do not exist. The latter could be addressed by accounting in the ADBM for additional traits other than body size. Further work could also address the significance of uncertainty in parameter estimates for predicted food web responses to environmental change.

Insect pollinators are important means for a stable ecosystem. The habitat types play a crucial role in the community composition, abundance, diversity, and species richness of the pollinators. The present study in Shivapuri–Nagarjun National Park explored the species richness and abundances of insect pollinators in four different habitats and different environmental variables in determining the community composition of the pollinators. Data were collected from 1500 m–2700 m using pan traps and hand sweeping methods. Non–metric multidimensional scaling (NMDS) and redundancy analysis (RDA) were conducted to show the association between insect pollinators and environmental variables. The results firmly demonstrated that species richness and abundances were higher in open trails compared to other habitats. The distribution of the pollinator species was more uniform in the open trail followed by the grassland. Similarly, a strong positive correlation between flower resources and pollinator’s abundance was found. In conclusion, the open trail harbor rich insect pollinators in lower elevation. The community structure of the pollinators was strongly influenced by the presence of flowers in the trails.

Aim: Threats faced by narrowly distributed endemic plant species in the face of the Earth’s sixth mass extinction and climate change exposure are especially severe for taxa on islands. We investigated the current and projected distribution and range changes of Cochemiea halei, an island endemic cactus. This taxon is of conservation concern, currently listed as vulnerable on the International Union for the Conservation of Nature Red List and as a species of special concern under Mexican federal law. The goals of this study are to 1). identify the correlations between climate variables and current suitable habitat for C. halei; 2). determine if the species is a serpentine endemic or has a facultative relationship with ultramafic soils; 3). predict range changes of the species based on climate change scenarios. Location: The island archipelago in Bahía Magdalena on the Pacific coast, Baja California Sur, Mexico. Methods: We used temperature and precipitation variables at 30 arcsecond resolution and soil type, employing multiple species distribution modeling methods, to identify important climate and soil conditions driving current habitat suitability. The best model of current suitability is used to predict possible effects of four climate change scenarios based on best case to worst case representative concentration pathways, with projected climate data from two general circulation models, over two time periods. Main conclusions: The occurrence of the species is found to be strongly correlated with ultramafic soils. The most important climate predictor for habitat suitability is annual temperature range. The species is predicted to undergo range contractions from 21% to 53%, depending on the severity and duration of exposure to climate change. The broader implications for a wide range of narrowly adapted, threatened and endemic plant species indicate an urgent need for threat assessment based on habitat suitability and climate change modeling.

The coronavirus disease 2019 (COVID-19) pandemic introduced an abrupt change in human behavior globally. Here, we discuss unique insights into the eco-evolutionary role of pathogens in ecosystems and present data that indicates the pandemic can fundamentally change our learning choices. This pathogen has indirectly affected many organisms and processes by globally changing the behavior of humans to avoid being infected. The pandemic also changed our learning behavior by affecting the relative importance of information and forcing teaching and learning into a framework that accommodates human behavioral measures to avoid disease transmission. Not only are these indirect effects on the environment occurring through a unique mechanistic pathway in ecology, the pandemic along with its effects on us provides a profound example of the role risk can play in the transmission of information between the at-risk. Ultimately, these changes in our learning behavior led to this special issue “Taking learning online in Ecology and Evolution.” The special issue was a call to the community to take learning in new directions, including online and distributed experiences. The topics examined include a significant component of DIY ecology and evolution that is experiential and but done individually, opportunities to use online tools and apps to be more inclusive, student-focused strategies for teaching online, how to reinvent conferences, strategies to retain experiential learning safely, emerging forms of teaching such as citizen science, apps and podcasting, and ideas on how to accommodate ever changing constraints in the college classroom, to name a few. The collective consensus in our fields is that these times are challenging but we can continue to improve and innovate on existing developments, and more broadly and importantly, this situation may provide an opportunity to reset some of the existing practices that fail to promote an effective and inclusive learning environment.

1. Plant leaf stomata are the gatekeepers of the atmosphere-plant interface and are essential building blocks of land surface models as they control transpiration and photosynthesis. Although more stomatal trait data is needed to significantly reduce the error in these model predictions, recording these traits is time-consuming and no standardized protocol is currently available. Some attempts were made to automate stomatal detection from photomicrographs, however, these approaches have the disadvantage of using classic image processing or targeting a narrow taxonomic entity which makes these technologies less robust and generalizable to other plant species. We propose an easy-to-use and adaptable workflow from leaf to label. A methodology for automatic stomata detection was developed using deep neural networks according to the state-of-the-art and its applicability demonstrated across the phylogeny of the angiosperms. 2. We used a patch-based approach for training/tuning three different deep learning architectures. For training, we used 431 micrographs taken from leaf prints made according the nail polish method from herbarium specimens of 19 species. The best performing architecture was tested on 595 images of 16 additional species spread across the angiosperm phylogeny. 3. The nail polish method was successfully applied in 78% of the species sampled here. The VGG19 architecture slightly outperformed the basic shallow and deep architectures, with a confidence threshold equal to 0.7 resulting in an optimal trade-off between precision and recall. Applying this threshold the VGG19 architecture obtained an average F-score of 0.87, 0.89 and 0.67 on the training, validation and unseen test set, respectively. The average accuracy was very high (94%) for computed stomatal counts on unseen images of species used for training. 4. The leaf-to-label pipeline is an easy-to-use workflow for researchers of different areas of expertise interested in detecting stomata more efficiently. The described methodology was based on multiple species and well-established methods so that it can serve as a reference for future work.

Ecosystems wherein social and solitary predators share space, complex asymmetric intraguild interactions actively shape the group size of social carnivores. Intense intraguild predation has been known to result in reduced group size and low recruitment rates in subordinate social carnivores. In South and South-east Asia, Dhole, tiger and leopard form a widely distributed sympatric guild of large carnivores. In this paper we attempted to understand the pack size dynamics of a subordinate social predator, the dhole, by investigating factors underlying pack size variation at two neighbouring sites. We further evaluated our local-scale patterns of pack size variation at a larger scale by doing a distribution-wide assessment of pack size across dhole ranging countries. Across study sites, we found an inverse relationship between the local abundance of a top predator and group size of a subordinate predator while accounting for variability in resources and habitat heterogeneity. Tiger density was low (0.71/100 Km2) at the site having large dhole packs (16.8 ± 3.1) whereas, a relatively smaller average dhole pack size (6.4 ± 1.3) was observed in a higher tiger density (5.67/100 Km2) area. Our results on distribution-wide assessment are concurrent with local-scale results, showing a positive association between prey abundance and pack size and a negative association between tiger densities and dhole pack size. Our study takes us one step closer to trying to answer the age-old question of what drives the pack size of social predators in a multi-predator system. Linking behaviour to population dynamics and carnivore interactions is another highlight of the study. Often helpful while optimizing conservation triage and formulation of management implications like recovery and translocations.

Spatial and temporal distribution of seabird transiting and foraging at sea is an important consideration for marine conservation planning. Using at-sea observations of seabirds (n = 317), collected during the breeding season from 2012 to 2016, we built boosted regression tree (BRT) models to identify relationships between numerically dominant seabird species (red-footed booby, brown noddy, white tern and wedge-tailed shearwater), geomorphology, oceanographic variability, and climate oscillation in the Chagos Archipelago. We documented positive relationships between red-footed booby and wedge-tailed shearwater abundance with the strength in the Indian Ocean Dipole, as represented by the Dipole Mode Index (6.7% and 23.7% contribution respectively). The abundance of red-footed boobies, brown noddies and white terns declined abruptly with greater distance to island (17.6%, 34.1% and 41.1% contribution respectively). We further quantified the effects of proximity to rat-free and rat-invaded islands on seabird distribution at sea, and identify breaking point distribution thresholds. We identified areas of increased abundance at sea and habitat use-age under a scenario where rats are eradicated from invaded nearby islands and recolonised by seabirds. Following rat eradication, abundance at sea of red-footed booby, brown noddy, and white terns increased by 14%, 17% and 3% respectively, with no important increase detected for shearwaters. Our results have implication for seabird conservation and island restoration. Climate oscillations may cause shifts in seabird distribution, possibly through changes in regional productivity and prey distribution. Invasive species eradications and subsequent island recolonization can lead to greater access for seabirds to areas at-sea, due to increased foraging or transiting through, potentially leading to distribution gains and increased competition. Our approach predicting distribution after successful eradications enables anticipatory threat-mitigation in these areas, minimising competition between colonies and thereby maximising the risk of success and the conservation impact of eradication programmes.  

Ancient DNA research has developed rapidly over the past few decades due to the improvement in PCR and next-generation sequencing (NGS) technologies, but challenges still exist. One major challenge in relation to ancient DNA research is to recover genuine endogenous ancient DNA sequences from the raw sequencing data. This is often difficult due to the degradation of ancient DNA and high levels of contamination, especially homologous contamination. In this study, we collected whole genome sequencing (WGS) data from 6 ancient samples to compare different mapping algorithms. To further explore more effective methods to separate endogenous DNA from the homologous contaminations, we attempted to recover reads based on the ancient DNA specific characteristics of deamination, depurination, and DNA fragmentation with different parameters. We propose a quick and improved pipeline for separating endogenous ancient DNA while simultaneously decreasing the homologous contaminations to a very low proportion. Overall, these recommendations for ancient DNA mapping and separation of endogenous DNA in this study could facilitate future studies of ancient DNA.

For procellariiform seabirds, wind and body morphology are crucial determinants of flight costs and flight speeds. During chick-rearing, parental seabirds commute frequently to provision their chicks, and their body mass changes between outbound and return legs. In Antarctica, the typical diurnal katabatic winds which blow stronger in the mornings, form al natural experiment to investigate flight behaviours in response to wind conditions. We GPS-tracked three closely related species of sympatrically breeding Antarctic fulmarine petrels which differ in wing loading and aspect ratio and investigated their flight behaviour in response to wind and changes in body mass. All three species reached higher flight speeds under stronger tailwinds, especially on return legs from foraging, when wing loading was increased since birds carried food for their chicks. Flight speeds decreased under stronger headwinds. Antarctic petrels (Thalassoica antarctica; intermediate body mass, highest wind loading and aspect ratio) responded stronger to changes in wind speed and direction than cape petrels (Daption capense; lowest body mass, wing loading and aspect ratio) or southern fulmars (Fulmarus glacialoides; highest body mass, intermediate wing loading and aspect ratio). Birds did not adjust their flight direction in relation to wind direction nor maximum distance to nest when they encountered strong headwinds on their outbound commutes. However, birds appeared to adjust the timing of commutes to those hours of the day when headwinds were weakest and they were more likely to encounter favourable tail- and crosswinds. Despite these adaptations to the predictable diurnal wind conditions, birds frequently encountered unfavourably strong headwinds, possibly as a result of weather systems disrupting the katabatics coupled with the need to feed. How the predicted decrease in Antarctic near-coastal wind speeds over the remainder of the century will affect flight costs and breeding success which ultimately drives population trajectories remains to be seen.