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.

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.

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.

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.

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.

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.

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.

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.

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.  

Arachnids are the most abundant land predators. Despite the importance of their functional roles as predators and the of necessity to understand their diet for conservation and nutrient fluxes, the trophic ecology of many arachnid species is not fully understood. In the case of the wandering spider, Phoneutria boliviensis F. O. Pickard-Cambridge, 1897, only selected field and laboratory observational studies about their diet exist. By using a DNA metabarcoding approach, we compared the prey found in the gut content of males and females from three distant Colombian populations of P. boliviensis. By DNA metabarcoding of the cytochrome c oxidase subunit I (COI), we detected and identified 234 prey records belonging to 96 operational taxonomic units (OTUs), as prey for this wandering predator. Our results broaden the known diet of P. boliviensis with at least 75 prey taxa not previously registered in fieldwork or laboratory experimental trials. These results suggest that P. boliviensis feeds predominantly on invertebrates (Diptera, Lepidoptera, Coleoptera and Orthoptera) and opportunistically on small squamates. Intersex and interpopulation differences are observed. Assuming that prey preference does not vary between populations, these differences are likely associated with a higher local prey availability. Finally, we suggest that DNA metabarcoding can be used for evaluating subtle differences in the diet of distinct populations of P. boliviensis, particularly when predation records in the field cannot be established or quantified using direct observation

This is the first study to document the genetic diversity of the white-tailed deer population on St. John, US Virgin Islands. The island population was founded by a small number of animals, has very limited hunting or predation, and recently experienced a reduction in size following an extended drought in 2015. DNA samples were collected from hair from 23 anesthetized adult deer (13 males, 10 females) ranging in age from 1-8 years (3.36+ 1.9 yr) and also from fecal DNA samples, for a total of 42 individuals analyzed for genetic diversity. The St. John deer data set averaged 4.19 alleles per marker and demonstrates the second lowest number of alleles (A) when compared to other populations of Odocoileus virginianus (4.19). Heterozygosity was similar to the other studies (0.54) with little evidence of inbreeding. To explain the level of heterogygosity and lack of inbreeding within the St. John population, three hypotheses are proposed, including the effect of intrinsic biological traits within the population, a recent infusion of highly heterogeneous loci from North American populations, and a consistent level of immigration from a nearby island. Additional work is needed to further understand the genetic history of the St. John and regional deer populations.

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.

Only a few studies on the nocturnal behavior of African ungulates exist so far, with mostly small sample sizes. For a comprehensive understanding of nocturnal behavior, this database needs to be expanded. Zoo animals offer a good opportunity to lay the corresponding foundations. The results can provide clues for the study of wild animals and furthermore contribute to a better understanding of animal welfare and better husbandry conditions in zoos. To tackle this open question, we developed a stand-alone open-source software based on deep learning techniques, named BOVIDS (Behavioral Observations by Videos and Images using a Deep-Learning Software). This software is used to identify ungulates in their enclosure and to determine crucial behavioral poses on video material with an accuracy of 99.4%. A case study on 25 Common Elands (Tragelaphus oryx) out of 5 EAZA zoos with a total of 11,411 hours video material out of 822 nights is conducted, yielding the first detailed description of the nightly behavior of Common Elands. Our results indicate that age and sex are influencing factors on the nocturnal activity budget, the length of behavioral phases as well as the number of phases per behavioral state during the night. Finally, the results suggest the existence of species-specific rhythms that open future research directions.

Oxford Nanopore Technologies (ONT) is a third-generation sequencing technology that is gaining popularity in ecological research for its portable and low-cost sequencing possibilities. Although the technology is primarily developed for long-read sequencing, it can also be applied to sequence amplicons. The downside of ONT is the low quality of the raw reads. Hence, generating a high-quality consensus sequence is still a challenge. We present Amplicon_sorter, a tool for reference-free sorting of ONT sequenced amplicons based on their similarity in sequence and length and for building solid consensus sequences.

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.

Aims: Amidst the Campos the Altitude (Highland Grasslands) in the Brazilian Atlantic Forest, woody communities grow either clustered in tree islands or interspersed within the herbaceous matrix. The functional ecology, diversity and biotic processes shaping these communities are largely unstudied. We characterised the functional assembly and diversity of these tropical montane woody communities and investigated how those communities fit within the Grime’s CSR (C – competitor, S – stress-tolerant, R – ruderal) scheme, what trade-offs they exhibit and how traits and functional diversity vary in response to bamboo invasion. Methods: We sampled five leaf traits and wood density along transects covering the woody communities both inside tree islands and outside (i.e. woody plants in the grasslands community) to characterise the functional ecology of the community. We used Kruskal-Wallis test, t-test and variation partitioning to determine effects of inside vs outside the tree island and bamboo invasion on traits, woody species diversity and functional diversity. Results: We found a general SC/S strategy with drought-related functional trade-offs. Woody plants in tree islands had more acquisitive traits, whereas woody plants within the grasslands had more conservative traits. Trait variation was mostly taxonomically driven, and species composition varied between inside and outside tree islands. Leaf thickness, wood density and foliar water uptake were unrelated to CSR-strategies, suggesting independent trait dimensions and multiple drought-coping strategies within the predominant S-strategy. Bamboo-invaded islands showed lower Simpson diversity, lower functional dispersion, lower foliar water uptake and greater leaf thickness than non-invaded tree islands. Conclusions: The observed functional assembly in response to bamboo and facilitation have implications for future forest expansion and response of the communities to climate change. Further studies on eco-physiological and establishment traits and the mechanisms behind biotic interactions are needed to better understand the response of these communities to future environmental changes.

Quantifying habitat quality is dependent on measuring a site’s relative contribution to population growth rate. This is challenging for studies of waterbirds, whose high mobility can decouple demographic rates from local habitat conditions and make sustained monitoring of individuals near-impossible. To overcome these challenges, biologists have used many direct and indirect proxies of waterbird habitat quality. However, consensus on what methods are most appropriate for a given scenario is lacking. We undertook a structured literature review of the methods used to quantify waterbird habitat quality, and provide a synthesis of the context-dependent strengths and limitations of those methods. Our structured search of the Web of Science database returned a sample of 398 studies, upon which our review was based. The reviewed studies assessed habitat quality by either measuring habitat attributes (e.g., food abundance, water quality, vegetation structure), or measuring attributes of the waterbirds themselves (e.g., demographic parameters, body condition, behaviour, distribution). Measuring habitat attributes, although they are only indirectly related to demographic rates, has the advantage of being unaffected by waterbird behavioural stochasticity. Conversely, waterbird-derived measures (e.g., body condition, peck rates) may be more directly related to demographic rates than habitat variables, but may be subject to greater stochastic variation (e.g., behavioural change due to presence of conspecifics). Therefore, caution is needed to ensure that the measured variable does influence waterbird demographic rates. This assumption was usually based on ecological theory rather than empirical evidence. Our review highlighted that there is no single best, universally applicable method to quantify waterbird habitat quality. Individual project specifics (e.g., time frame, spatial scale, funding) will influence the choice of variables measured. Where possible, practitioners should measure variables most directly related to demographic rates. Generally, measuring multiple variables yields a better chance of accurately capturing the relationship between habitat characteristics and demographic rates.

The host-associated microbiome plays a significant role in health. However, the roles of factors such as host genetics and microbial interactions in determining microbiome diversity remain unclear. We examined these factors using amplicon-based sequencing of 175 Thoropa taophora frog skin swabs collected from a naturally fragmented landscape in southeastern Brazil. Specifically, we examined (1) the effects of geography and host genetics on microbiome diversity and structure; (2) the structure of microbial eukaryotic and bacterial co-occurrence networks; and (3) co-occurrence between microeukaryotes with bacterial OTUs known to affect growth of the fungal frog pathogen Batrachochytrium dendrobatidis (including anti-Bd bacteria commonly referred to as “antifungal”). Microbiome structure correlated with geographic distance, and microbiome diversity varied with both overall host genetic diversity and diversity at the frog MHC IIB immunity locus. Our network analysis showed the highest connectivity when both eukaryotes and bacteria were included, implying that ecological interactions occur among Domains. Lastly, anti-Bd bacteria did not demonstrate broad negative co-occurrence with fungal OTUs in the microbiome, indicating that these bacteria are unlikely to be broadly antifungal. Our findings emphasize the importance of considering both Domains in microbiome research, and suggest that probiotic strategies for amphibian disease management should be considered with caution.