1. Describing and explaining patterns of individual animal behaviors in situ, and their repeatability over the annual cycle, is an emerging field in ecology owing largely to advances in tagging technology. 2. We describe individual movements of adult Sakhalin taimen Parahucho perryi, an endangered salmonid fish, in the headwaters of a river in northern Japan during the spring spawning season over two years. 3. Migration timing, separated into stages prior to, during, and following the spawning period, was found to be more consistent and repeatable for females than males. 4. We hypothesized that the observed coordinated movement within seasons, and repeatability in migration timing across seasons, could result from 1) individual-specific responsiveness resulting from endogenous, biological traits that are mediated by environmental factors, or 2) social interactions among comigrating individuals. 5. We found that water temperature and water level experienced by fish near the river mouth approximately a week before arrival at the spawning ground explained variability in run timing between years for females but not males. 6. We found no evidence of conspecific attraction or repulsion resulting from social interactions among the spawners and post-spawners. 7. We conclude that individual-specific responsiveness to environmental cues was the likely mechanism underpinning the observed migration timing and movement patterns. 8. Determining the importance of these environmental and social factors not only during spawning but also during non-breeding life-history stages would contribute to a more comprehensive understanding of migratory connectivity in this species.
Myriad ecological and evolutionary factors can influence whether a particular parasite successfully transmits to a new host during a disease outbreak, with consequences for the structure and diversity of parasite populations. However, even though the diversity and evolution of parasite populations is of clear fundamental and applied importance, we have surprisingly few studies that track how genetic structure of parasites changes during naturally occurring outbreaks in non-human populations. Here, we used population genetic approaches to reveal how genotypes of a bacterial parasite, Pasteuria ramosa, change over time, focusing on how infecting P. ramosa genotypes change during the course of epidemics in Daphnia populations in two lakes. We found evidence for genetic change – and, therefore, evolution – of the parasite during outbreaks. In one lake, P. ramosa genotypes structured by sampling date; in both lakes, genetic distance between groups of P. ramosa isolates increased with time between sampling. Diversity in parasite populations remained constant over epidemics, though one epidemic (which was large) had low genetic diversity while the other epidemic (which was small) had high genetic diversity. Our findings demonstrate that patterns of parasite evolution differ between outbreaks; future studies exploring the feedbacks between epidemic size, host diversity, and parasite genetic diversity would improve our understanding of parasite dynamics and evolution.
Automated 3D-image based tracking systems are new and promising devices to investigate the foraging behaviour of flying animals with great accuracy and precision. 3D analyses can provide accurate assessments of flight performance in regard to speed, curvature, and hovering. However, there have been few applications of this technology in ecology, particularly for insects. We used this technology to analyse the behavioural interactions between the Western honey bee Apis melifera and its invasive predator the Asian hornet, Vespa velutina nigrithorax. We investigated whether predation success could be affected by flight speed, flight curvature, and hovering of the Asian hornet and honey bees in front of one beehive. We recorded a total of 603,259 flight trajectories and 5,175 predator-prey flight interactions leading to 126 successful predation events, representing 2.4% predation success. Flight speeds of hornets in front of hive entrances were much lower than that of their bee prey; in contrast to hovering capacity, while curvature range overlapped between the two species. There were large differences in speed, curvature and hovering between the exit and entrance flights of honey bees. Interestingly, we found hornet density affected flight performance of both honey bees and hornets. Higher hornet density led to a decrease in the speed of honey bees leaving the hive, and an increase in the speed of honey bees entering the hive, together with more curved flight trajectories. These effects suggest some predator avoidance behaviour by the bees. Higher honey bee flight curvature resulted in lower hornet predation success. Results showed an increase of predation success when hornet number increased up to 8 individuals, above which predation success decreased, likely due to competition among predators. Although based on a single colony, this study reveals interesting outcomes derived from the use of automated 3D tracking to derive accurate measures of individual behaviour and behavioural interactions among flying species.
1. The Environmental Data Initiative (EDI) is a trustworthy, stable data repository and data management support organization for the environmental scientist. In a bottom-up community process EDI was built with the premise that freely and easily available data are necessary to advance the understanding of complex environmental processes and change, to improve transparency of research results, and to democratize ecological research. 2. EDI provides tools and support that allow the environmental researcher to easily integrate data publishing into the research workflow. 3. Almost ten years since going into production, we analyze metadata to provide a general description of EDI’s collection of data and its data management philosophy and placement in the repository landscape. We discuss how comprehensive metadata and the repository infrastructure lead to highly findable, accessible, interoperable, and reusable (FAIR) data by evaluating compliance with specific community proposed FAIR criteria. 4. Finally, we review measures and patterns of data (re)use, assuring that EDI is fulfilling its stated premise.
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 National Forestry Commission of Mexico continuously monitors forest structure within the country’s continental territory by the implementation of the National Forest and Soils Inventory (INFyS). Due to the challenges involved in collecting data exclusively from field surveys, there are spatial information gaps for important forest attributes. This can produce bias or increase uncertainty when generating estimates required to support forest management decisions. Our objective is to predict the spatial distribution of tree height and tree density in all Mexican forests. We performed wall-to-wall spatial predictions of both attributes in 1-km grids, using ensemble machine learning across each forest type in Mexico. Predictor variables include remote sensing imagery and other geospatial data (e.g., vegetation indexes, surface temperature). Training data is from the 2009-2014 cycle (n>26,000 sampling plots). Spatial cross validation suggested that the model had a better performance when predicting tree height r2=0.4 [0.15,0.55] (mean[min, max]) than for tree density r2=0.2[0.10,0.31]. Maximum values of tree height were for coniferous forests, coniferous-broadleaf forests and cloud mountain forest (~36 m, 30 m and 21 m, respectively). Tropical forests had maximum values of tree density (~1370 trees/ha), followed by tropical dry forest (1006 trees/ha) and coniferous forest (988 trees/ha). Although most forests had relatively low values of uncertainty, e.g., values <40%, arid and semiarid ecosystems had high uncertainty in both tree height and tree density predictions, e.g., values >60%. The applied open science approach we present is easily replicable and scalable, thus it is helpful to assist in the decision-making and future of the National Forest and Soils Inventory. This work highlights the need for technical capabilities aimed to use and resignify all the effort done by the Mexican Forestry Commission in implementing the INFyS.
Designing appropriate management plans requires knowledge of both the dispersal ability and what has shaped the current distribution of the species under consideration. Here we investigated the evolutionary history of the endangered grey reef shark (Carcharhinus amblyrhynchos) across its range by sequencing thousands of RAD-seq loci in 173 individuals in the Indo-Pacific (IP) . We first bring evidence of the occurrence of a range expansion (RE) originating close to the Indo-Australian Archipelago (IAA) where two stepping-stone waves (east and westward) colonized almost the entire IP. Coalescent modeling additionally highlighted a homogenous connectivity (Nm~10 per generation) throughout the range, and an isolation by distance model suggested the absence of barriers to dispersal despite the affinity of C. amblyrhynchos to coral reefs. This coincides with long-distance swims previously recorded, suggesting that the strong genetic structure at the IP scale (FST ~ 0.56 between its ends) is the consequence of its broad current distribution and organization in a large number of demes. Our results strongly suggest that management plans for the grey reef shark should be designed on a range-wide rather than a local scale due to its continuous genetic structure. We further contrasted these results with those obtained previously for the sympatric but strictly lagoon-associated Carcharhinus melanopterus, known for its restricted dispersal ability. C. melanopterus exhibits similar RE dynamic, but is characterized by stronger genetic structure and a non-homogeneous connectivity largely dependent on local coral reefs availability. This sheds new light on shark evolution, emphasizing the roles of IAA as source of biodiversity and of life history traits in shaping the extent of genetic structure and diversity.
Terrestrial resource pulses can significantly affect the community dynamics of freshwater ecosystems. Previously, its effect on the river community is considered to be stronger in summer, while weaker in winter when terrestrial invertebrates are less abundant. The movement of the terrestrial earthworms are triggered in winter, so they may be supplied to winter rivers as terrestrial resource pulse, but little is known about it. Here, we report that the massive numbers of the terrestrial earthworms were supplied intensively to an upstream of the small river in early winter. In particular, we found large numbers of Megascolecidae earthworms were supplied in an upstream of the small river in Northern Japan. Furthermore, we observed that supplied earthworms were consumed by salmonid fish species (masu salmon, white spotted char and rainbow trout) and aquatic invertebrates (gammarid amphipod, planarian flatworm and stonefly larvae). These findings suggests that the terrestrial earthworms may play a key role in ecosystem functioning in winter when severe and other resources are scarce.
In many species, offspring display conspicuous adult-like colouration already early in life, even though they might be very vulnerable to predation at this stage. Yet, the signalling function of adult-like traits in nestlings has been little explored to date. Here, we investigated whether the yellow breast plumage of blue tit (Cyanistes caeruleus) nestlings shows patterns of condition-dependence and hence signals individual quality, as has been described for adult birds. During three consecutive breeding seasons, we therefore explored the association between nestling body mass and three colour components of the yellow breast plumage (i.e., UV chroma, carotenoid chroma and total brightness), considering both within and among nest effects. Carotenoid chroma was not affected by body mass. However, UV chroma and total brightness showed an among-nest effect of body mass, suggesting that they might signal aspects of genetic quality or parental rearing capacity. Interestingly, we also found a within-nest effect of body mass on total brightness, suggesting that this is a good candidate for a condition-dependent signal within the family. Thus, other family members could rely on brightness to adjust their behavioural strategies, such as feeding behaviour in parents. Our study thus reveals that certain colour components of the yellow breast plumage signal different aspects of offspring quality and suggest that they might have a correlated signalling value across life-history stages.
Resource fluctuation is a major driver of animal movement, influencing strategic choices such as residency vs nomadism, or social dynamics. The Arctic tundra is characterized by strong seasonality: resources are abundant during the short summers but scarce in winters. Therefore, expansion of boreal-forest species onto the tundra raises questions on how they cope with winter-resource scarcity. We examined a recent incursion by red foxes (Vulpes vulpes) onto the coastal tundra of western Hudson Bay, an area historically occupied by Arctic foxes (Vulpes lagopus) that lacks access to anthropogenic foods, and compared seasonal shifts in space use of the two species. We used 4 years of telemetry data following 8 red foxes and 11 Arctic foxes to test the hypothesis that the movement strategies of both species are primarily driven by temporal variability of resources. We also predicted that the harsh tundra conditions in winter affect red foxes more than Arctic foxes, which are adapted to this environment. Dispersal was the most frequent winter movement strategy in both fox species, despite its association with high mortality (winter mortality was 9.4 times higher in dispersers than residents). Red foxes consistently dispersed towards the boreal forest, whereas Arctic foxes primarily used sea ice to disperse. Home range size of red and Arctic foxes did not differ in summer, but resident red foxes substantially increased their home range size in winter, whereas home range size of resident Arctic foxes did not change seasonally. As climate changes, abiotic constraints on some species may relax, but associated declines in prey communities may lead to local extirpation of many predators, notably by favoring dispersal during resource scarcity.
Aim: Species’ environmental requirements and large-scale spatial and evolutionary processes are known to determine the structure and composition of local communities. However, ecological interactions and historical processes also have major effects on community assembly at landscape and local scales. In this work we evaluate whether two xerophytic shrub communities follow fixed ecological assembly dynamics throughout large geographical extents, or their composition is rather driven by species individualistic responses to environmental and macroecological constraints. Location: SW Iberian Peninsula (Portugal and Spain) Taxa: Stauracanthus genistoides agg. and Ulex australis agg (Fabaceae). Methods:Inland dune xerophytic shrub communities were sampled in 95 plots distributed within their potential area of occurrence. Then, we described the main gradients of vegetation composition and assess the relevance of biotic interactions. We also characterized the habitat suitability of the dominant species, S. genistoides and U. australis, to map the potential distribution of the xerophytic shrub communities. Finally, to identify the relative importance of each factor driving changes in community composition, we examined the relationships between the vegetation gradients and a broad set of explanatory variables. Results: Our results show that xerophytic shrubs follow uniform successional patterns throughout the whole geographical area, but also that these communities respond differently to the main environmental gradients in each region. Soil organic matter is the main determinant of community variations in the northern regions, Setúbal Peninsula and Comporta, while in the South/South-Western region most of the variation between both types of communities is explained by temperature seasonality. Main conclusions: The relative importance of the main factors causing community-level responses varies according to regional processes and the suitability of the environmental conditions for the dominant species in these communities. These responses are also determined by intrinsic community mechanisms that result in a high degree of similarity in the gradient-driven community stages in different regions.
Whole-genome sequencing for generating SNP data is increasingly used in population genetic studies. However, obtaining genomes for massive numbers of samples is still not within the budgets of many researchers. It is thus imperative to select an appropriate reference genome and sequencing coverage to ensure the accuracy of the results for a specific research question, while balancing cost and feasibility. To evaluate the effect of the choice of the reference genome and sequencing coverage on downstream analyses, we used five confamilial reference genomes of variable relatedness and three levels of sequencing coverage (3.5x, 7.5x and 12x) in a population genomic study on two caddisfly species: Himalopsyche digitata and H. tibetana. Using these 30 datasets (five reference genomes × three coverages × two target species), we estimated population genetic indices (inbreeding coefficient, nucleotide diversity, pairwise and genome-wide FST) based on variants and population structure (PCA and admixture) based on genotype likelihood estimates. The results showed that both distantly related reference genomes and lower sequencing coverage lead to degradation of resolution. In addition, choosing a more closely related reference genome may significantly remedy the defects caused by low coverage. Therefore, we conclude that population genetic studies would benefit from closely related reference genomes, especially as the costs of obtaining a high-quality reference genome continue to decrease. However, to determine a cost-efficient strategy for a specific population genomic study, a trade-off between reference genome relatedness and sequencing depth can be considered.
Species distribution patterns are essential for the conservation of biodiversity. The aim of this study was to evaluate the influence of multiple ecological hypotheses on the spatial patterns of rodent species richness in China. First, we divided the geographic region of China into 80 × 80 km2 grid cells and mapped the distribution ranges of the 237 rodent species. Rodent taxa were separated into three response variables based on their distribution: (a) all species, (b) non-endemic species, and (c) endemic species. The predictors were divided into four factor sets: (a) energy-water, (b) climatic seasonality, (c) habitat heterogeneity, and (d) human factors, which were used to represent four different ecological hypotheses. We then performed multiple regression analysis (OLS), spatial autoregressive models (SAR), and variation partitioning analyses to determine the effects of predictors on the spatial patterns of rodent species. The Hengduan Mountains and surrounding mountains in southwest China showed the highest species richness and endemism. Habitat heterogeneity is the most important factor explaining the species richness distribution patterns across all species and non-endemic species. Endemic species richness patterns are most susceptible to seasonal changes in climate and least affected by human factors. The effects of energy and water on the three response variables showed consistent levels of importance.
The eastern tree hyrax is thought to be a solitarily living arboreal species of the forests of East Africa. However, in the coast of Kenya, indigenous forests have been almost entirely cleared, and some of the last tree hyrax populations live in limestone rocky formations and caves. Interestingly, they seem to be living in social groups. Here, we describe and document photographically these unique tree hyrax populations. We also describe their acoustical communication and their calling activity in three different habitats. Based on these animals' physical appearance and acoustic analyses of their calls, they represent the species eastern tree hyrax, Dendrohyrax validus. Due to immence pressure from humans, the future of these small and isolated, cave-living tree hyrax populations does not seem bright.
1. Our understanding of how bees (Apoidea) use temperate forests is largely limited to sampling the understory and forest floor. Studies over the last decade have demonstrated that bee communities are vertically stratified within forests, yet the ecology of bee assemblages immediately above the canopy, the canopy-aerosphere interface, remains unexplored. 2. We sampled and compared bee communities above the canopy of a temperate forest to the understory (1 m), midstory (10 m), and canopy (20 m) on the campus of the University of Massachusetts, in Amherst, Massachusetts, USA from April – August, 2021. 3. Overall, we found that assemblages above the canopy had more bees than in the understory, were distinct in composition from all other strata, and included the greatest proportion of unique species. Bee abundance and species richness were highest in the understory throughout the spring (April and May) and decreased as the season progressed, while bee abundance and species richness at higher strata increased into the summer months. We also found that bees with preferences to nest in moist and rotting wood were largely restricted to canopy and midstory strata. 4. We conclude that bee assemblages occupying the space above the forest canopy are abundant and diverse, and their unique composition suggests that this canopy-aerosphere interface plays an additional role in the bee community of temperate forests. Alternatively, our findings question how forest bee communities should be defined while highlighting the need for research on fundamental processes governing species stratification in and above the canopy.
Species distribution models (SDMs) are practical tools to assess the habitat suitability of species with numerous applications in environmental management and conservation planning. The manipulation of the input data to deal with their spatial bias is one of the advantageous methods to enhance the performance of SDMs. However, the development of a model parameterization approach covering different SDMs to achieve well-performing models has never been implemented. We integrated input data manipulation and model tuning for four commonly-used SDMs; generalized linear model (GLM), gradient boosted model (GBM), random forest (RF), and maximum entropy (MaxEnt), and compared their predictive performance to model geographically imbalanced biased data of a rare species complex of mountain vipers. Models were tuned up based on a range of model-specific parameters considering two background selection methods; random and background weighting schemes. The performance of the fine-tuned models was assessed based on a recently identified localities of the species. The results indicated that although the fine-tuned version of all models shows great performance in predicting training data (AUC > 0.9 and TSS > 0.5), they produce different results in classifying out-of-bag data. The GBM and RF with higher sensitivity of training data showed more different performances. The GLM, despite having high predictive performance for test data, showed lower specificity. It was only the MaxEnt model that showed high predictive performance and comparable results for identifying test data in both random and background weighting procedures. Our results highlight that while GBM and RF are prone to overfitting training data and GLM over-predict non-sampled areas MaxEnt is capable of producing results that are both predictable (extrapolative) and complex (interpolative). We discuss the assumptions of each model and conclude that MaxEnt could be considered as a practical method to cope with imbalanced-biased data in species distribution modeling approaches.
1. Animal abundance estimation is increasingly based on drone or aerial survey photography. Manual post-processing has been used extensively, however volumes of such data are increasing, necessitating some level of automation, either for complete counting, or as a labour-saving tool. Any automated processing can be challenging when using the tools on species that nest in close formation such as Pygoscelid penguins. 2. We present here an adaptation of state-of-the-art crowd-counting methodologies for counting of penguins from aerial photography. 3. The crowd-counting model performed significantly better in terms of model performance and computational efficiency than standard Faster RCNN deep-learning approaches and gave an error rate of only 0.8 percent. 4. Crowd-counting techniques as demonstrated here have the ability to vastly improve our ability to count animals in tight aggregations, which will demonstrably improve monitoring efforts from aerial imagery.