pyResearchInsights—An open‐source Python package for scientific text analysis

1. With an increasing number of scientific articles published each year, there is a need to synthesize and obtain insights across ever‐growing volumes of literature. Here, we present pyResearchInsights, a novel open‐source automated content analysis package that can be used to analyze scientific abstracts within a natural language processing framework.
2. The package collects abstracts from scientific repositories, identifies topics of research discussed in these abstracts, and presents interactive concept maps to visualize these research topics. To showcase the utilities of this package, we present two examples, specific to the field of ecology and conservation biology.
3. First, we demonstrate the end‐to‐end functionality of the package by presenting topics of research discussed in 1,131 abstracts pertaining to birds of the Tropical Andes. Our results suggest that a large proportion of avian research in this biodiversity hotspot pertains to species distributions, climate change, and plant ecology.
4. Second, we retrieved and analyzed 22,561 abstracts across eight journals in the field of conservation biology to identify twelve global topics of conservation research. Our analysis shows that conservation policy and landscape ecology are focal topics of research. We further examined how these conservation‐associated research topics varied across five biodiversity hotspots.
5. Lastly, we compared the utilities of this package with existing tools that carry out automated content analysis, and we show that our open‐source package has wider functionality and provides end‐to‐end utilities that seldom exist across other tools.

     

Age‐specific habitat preference,carrying capacity,and landscape structure determine the response of population spatial variability to fishing‐driven age truncation

1. Understanding the mechanisms underlying spatial variability of exploited fish is critical for the sustainable management of fish stocks. Empirical studies suggest that size‐selective fishing can elevate fish population spatial variability (i.e., more heterogeneous distribution) through age truncation, making the population less resilient to changing environment. However, species differ in how their spatial variability responds to age truncation and the underlying mechanisms remain unclear.
2. We hypothesize that age‐specific habitat preference, together with environmental carrying capacity and landscape structure, determines the response of population spatial variability to fishing‐induced age truncation. To test these hypotheses, we design an individual‐based model of an age‐structured fish population on a two‐dimensional landscape under size‐selective fishing. Individual fish reproduces and survives, and moves between habitats according to age‐specific habitat preference and density‐dependent habitat selection.
3. Population spatial variability elevates with increasing age truncation, and the response is stronger for populations with stronger age‐specific habitat preference. On a gradient landscape, reducing carrying capacity elevates the relative importance of density dependence in habitat selection, which weakens the response of spatial variability to age truncation for populations with strong age‐specific habitat preference. On a fragmented landscape, both populations with strong and weak age‐specific habitat preferences are restricted at local optimal habitats, and reducing carrying capacity weakens the responses of spatial variability to age truncation for both populations.
4. Synthesis and applications. We demonstrate that to track and predict the changes in population spatial variability under exploitation, it is essential to consider the interactive effects of age‐specific habitat preference, carrying capacity, and landscape structure. To improve spatial management in fisheries, it is crucial to enhance empirical and theoretical developments in the methodology to quantify age‐specific habitat preference of marine fish, and to understand how climatic change influences carrying capacity and landscape continuity.

     

Plant–herbivore interactions: Combined effect of groundwater level,root vole grazing,and sedge silicification

1. Accumulation of silica (Si) by plants can be driven by (1) herbivory pressure (and therefore plant–herbivore interactions), (2) geohydrological cycles, or (3) a combination of (1) and (2), with (1–3) possibly affecting Si concentration with a 1‐year delay.
2. To identify the relative significance of (1–3), we analyzed the concentration of Si in fibrous tussock sedge (Carex appropinquata), the population density of the root vole (Microtus oeconomus), and the groundwater level, over 11 years.
3. The largest influence of autumn Si concentration in leaves (Si_leaf) was on the level of the current‐year groundwater table, which was positive and accounted for 13.3% of its variance. The previous year''s vole population density was weakly positively correlated with Si_leaf, and it alone explained 9.5% of its variance.
4. The only variable found to have a positive, significant effect on autumn Si concentration in rhizomes (Si_rhiz) was the current‐year spring water level, explaining as much as 60.9% of its variance.
5. We conclude that the changes in Si concentration in fibrous tussock sedge are predominantly driven by hydrology, with vole population dynamics being secondary.
6. Our results provide only partial support for the existence of plant–herbivore interactions, as we did not detect the significant effects of Si tussock concentration on the vole density dynamics. This was mainly due to the low level of silicification of sedges, which was insufficient to impinge herbivores.
7. Future studies on plant–herbivore interactions should therefore aim at disentangling whether anti‐herbivore protection is dependent on threshold values of herbivore population dynamics. Furthermore, studies on Si accumulation should focus on the effect of water‐mediated Si availability.

     

Cross‐continental comparison of parasite communities in a wide‐ranging carnivore suggests associations with prey diversity and host density

1. Parasites are integral to ecosystem functioning yet often overlooked. Improved understanding of host–parasite associations is important, particularly for wide‐ranging species for which host range shifts and climate change could alter host–parasite interactions and their effects on ecosystem function.
2. Among the most widely distributed mammals with diverse diets, gray wolves (Canis lupus) host parasites that are transmitted among canids and via prey species. Wolf–parasite associations may therefore influence the population dynamics and ecological functions of both wolves and their prey. Our goal was to identify large‐scale processes that shape host–parasite interactions across populations, with the wolf as a model organism.
3. By compiling data from various studies, we examined the fecal prevalence of gastrointestinal parasites in six wolf populations from two continents in relation to wolf density, diet diversity, and other ecological conditions.
4. As expected, we found that the fecal prevalence of parasites transmitted directly to wolves via contact with other canids or their excreta was positively associated with wolf density. Contrary to our expectations, the fecal prevalence of parasites transmitted via prey was negatively associated with prey diversity. We also found that parasite communities reflected landscape characteristics and specific prey items available to wolves.
5. Several parasite taxa identified in this study, including hookworms and coccidian protozoans, can cause morbidity and mortality in canids, especially in pups, or in combination with other stressors. The density–prevalence relationship for parasites with simple life cycles may reflect a regulatory role of gastrointestinal parasites on wolf populations. Our result that fecal prevalence of parasites was lower in wolves with more diverse diets could provide insight into the mechanisms by which biodiversity may regulate disease. A diverse suite of predator–prey interactions could regulate the effects of parasitism on prey populations and mitigate the transmission of infectious agents, including zoonoses, spread via trophic interactions.

     

Diving deeper into the underlying white shark behaviors at Guadalupe Island,Mexico

1. Fine‐scale movement patterns are driven by both biotic (hunting, physiological needs) and abiotic (environmental conditions) factors. The energy balance governs all movement‐related strategic decisions.
2. Marine environments can be better understood by considering the vertical component. From 24 acoustic trackings of 10 white sharks in Guadalupe Island, this study linked, for the first time, horizontal and vertical movement data and inferred six different behavioral states along with movement states, through the use of hidden Markov models, which allowed to draw a comprehensive picture of white shark behavior.
3. Traveling was the most frequent state of behavior for white sharks, carried out mainly at night and twilight. In contrast, area‐restricted searching was the least used, occurring primarily in daylight hours.
4. Time of day, distance to shore, total shark length, and, to a lesser extent, tide phase affected behavioral states. Chumming activity reversed, in the short term and in a nonpermanent way, the behavioral pattern to a general diel vertical pattern.

     

SizeExtractR: A workflow for rapid reproducible extraction of object size metrics from scaled images

1. Size is a biological characteristic that drives ecological processes from microscopic to geographic spatial scales, influencing cellular energetics, species fitness, population dynamics, and ecological interactions. Methods to measure size from images (e.g., proxies of body size, leaf area, and cell area) occur along a gradient from manual approaches to fully automated technologies (e.g., machine learning). These methods differ in terms of time investment, expertise required, and data or resource availability. While manual methods can improve accuracy through human recognition, they can be labor intensive, highlighting the need for semi‐automated, and user‐friendly software or workflows to increase the efficiency of manual techniques.
2. Here, we present SizeExtractR, an open‐source workflow that enables faster extraction of size metrics from scaled images (e.g., each image includes a ruler) using semi‐automated protocols. It comprises a set of ImageJ macros to speed up size extraction and annotation, and an R‐package for the quality control of annotations, data collation, calibration, and visualization.
3. SizeExtractR extracts seven common size dimensions, including planar area, min/max diameter, and perimeter. Users can record additional categorical variables relating to their own study, for example species ID, by simply adding alphanumeric annotations to individual objects when prompted. Using a population size structure case study for hard corals as an example, we show how SizeExtractR was used to quantify the impact of mass coral bleaching on coral population dynamics. Lastly, the time saving benefit of using SizeExtractR was quantified during a series of timed image analyses, revealing up to a 49% reduction in image analysis time compared to a fully manual approach.
4. SizeExtractR automatically archives results, allowing re‐analysis of size extraction and promoting quality control and reproducibility. It has already been employed in marine and terrestrial sciences to assess population dynamics and demography, energy investment in eggs, and growth of nursery reared corals, with potential to be applied to a wide range of other research fields.

     

How do King Cobras move across a major highway? Unintentional wildlife crossing structures may facilitate movement

1. Global road networks continue to expand, and the wildlife responses to these landscape‐level changes need to be understood to advise long‐term management decisions. Roads have high mortality risk to snakes because snakes typically move slowly and can be intentionally targeted by drivers.
2. We investigated how radio‐tracked King Cobras (Ophiophagus hannah) traverse a major highway in northeast Thailand, and if reproductive cycles were associated with road hazards.
3. We surveyed a 15.3 km stretch of Highway 304 to determine if there were any locations where snakes could safely move across the road (e.g., culverts and bridges). We used recurse analyses to detect possible road‐crossing events, and used dynamic Brownian Bridge Movement Models (dBBMMs) to show movement pathways association with possible unintentional crossing structures. We further used Integrated Step Selection Functions (ISSF) to assess seasonal differences in avoidance of major roads for adult King Cobras in relation to reproductive state.
4. We discovered 32 unintentional wildlife crossing locations capable of facilitating King Cobra movement across the highway. While our dBBMMs broadly revealed underpasses as possible crossing points, they failed to identify specific underpasses used by telemetered individuals; however, the tracking locations pre‐ and post‐crossing and photographs provided strong evidence of underpass use. Our ISSF suggested a lower avoidance of roads during the breeding season, although the results were inconclusive. With the high volume of traffic, large size of King Cobras, and a 98.8% success rate of crossing the road in our study (nine individuals: 84 crossing attempts with one fatality), we strongly suspect that individuals are using the unintentional crossing structures to safely traverse the road.
5. Further research is needed to determine the extent of wildlife underpass use at our study site. We propose that more consistent integration of drainage culverts and bridges could help mitigate the impacts of roads on some terrestrial wildlife.

     

Population dynamics of the glacial relict amphipods in a subarctic lake: role of density‐dependent and density‐independent factors

Relative role of intrinsic density‐dependent factors (such as inter‐ and intraspecific competition, predation) and extrinsic density‐independent factors (environmental changes) in population dynamics is a key issue in ecology. Density‐dependent mechanisms are considered as important drivers of population dynamics in many vertebrate and insect species; however, their influence on the population dynamics of freshwater invertebrates is not clearly understood. In this study, I examined interannual variations in the abundance of the glacial relict amphipod Monoporeia affinis in a small subarctic lake based on long‐term (2002–2019) monitoring data. The results suggest that the population dynamics of amphipods in the lake is influenced by the combined effects of both intrinsic and extrinsic factors. The reproductive success of amphipod cohorts was inversely related to its initial abundance, indicating it is influenced by density‐dependent factors. M. affinis recruitment was negatively correlated with population density and near‐bottom temperature but positively correlated with food availability, which is defined as the concentration of chlorophyll a. Multiple regression with chlorophyll, temperature, and abundance of parent cohort as independent factors explained about 80% of the variation in the reproductive success of amphipods. The negative correlation between amphipod recruitment and water temperature indicates that the current climate conditions adversely affect the populations of glacial relict amphipods even in cold‐water lakes of the subarctic zone. Results of this study can be useful in environmental assessments to separate population oscillations connected with density‐dependent mechanisms from human‐mediated changes.     

Classifying behavior from short‐interval biologging data: An example with GPS tracking of birds

1. Recent advances in digital data collection have spurred accumulation of immense quantities of data that have potential to lead to remarkable ecological insight, but that also present analytic challenges. In the case of biologging data from birds, common analytical approaches to classifying movement behaviors are largely inappropriate for these massive data sets.
2. We apply a framework for using K‐means clustering to classify bird behavior using points from short time interval GPS tracks. K‐means clustering is a well‐known and computationally efficient statistical tool that has been used in animal movement studies primarily for clustering segments of consecutive points. To illustrate the utility of our approach, we apply K‐means clustering to six focal variables derived from GPS data collected at 1–11 s intervals from free‐flying bald eagles (Haliaeetus leucocephalus) throughout the state of Iowa, USA. We illustrate how these data can be used to identify behaviors and life‐stage‐ and age‐related variation in behavior.
3. After filtering for data quality, the K‐means algorithm identified four clusters in >2 million GPS telemetry data points. These four clusters corresponded to three movement states: ascending, flapping, and gliding flight; and one non‐moving state: perching. Mapping these states illustrated how they corresponded tightly to expectations derived from natural history observations; for example, long periods of ascending flight were often followed by long gliding descents, birds alternated between flapping and gliding flight.
4. The K‐means clustering approach we applied is both an efficient and effective mechanism to classify and interpret short‐interval biologging data to understand movement behaviors. Furthermore, because it can apply to an abundance of very short, irregular, and high‐dimensional movement data, it provides insight into small‐scale variation in behavior that would not be possible with many other analytical approaches.

     

Is negative density‐dependent reproduction regulated by density‐induced stress in root voles? Two field experiments

Density dependence in reproduction plays an important role in stabilizing population dynamics via immediate negative feedback from population density to reproductive output. Although previous studies have shown that negative density‐dependent reproduction is associated with strong spacing behavior and social interaction between individuals, the proximal mechanism for generating negative density‐dependent reproduction remains unclear. In this study, we investigated the effects of density‐induced stress on reproduction in root voles. Enclosed founder populations were established by introducing 6 (low density) and 30 (high density) adults per sex into per enclosure (four enclosures per density in total) during the breeding season from April to July 2012 and from May to August 2015. Fecal corticosterone metabolite (FCM) levels, reproductive traits (recruitment rate and the proportion of reproductively active individuals), and founder population numbers were measured following repeated live trapping in both years. The number of founders was negatively associated with recruitment rates and the proportion of reproductively active individuals, displaying a negative density‐dependent reproduction. FCM level was positively associated with the number of founders. The number of founder females directly affected the proportion of reproductive females, and directly and indirectly through their FCM levels affected the recruitment rate; the effect of the number of male founders on the proportion of reproductive males was mediated by their FCM level. Our results showed that density‐induced stress negatively affected reproductive traits and that density‐induced stress is one ecological factor generating negative density‐dependent reproduction.     

Test of theory of foraging mode: Goldcrests,Regulus regulus,forage by high‐yield,energy‐expensive hovering flight when food is abundant but use low‐yield,low‐cost methods when food is scarce

1. Here, I describe foraging behavior of goldcrests, Regulus regulus, based on eight years of field observation in a coniferous forest dominated by Norway spruce Picea abies in southwestern Sweden. The aim was to test predictions from theory on the choice of optimal foraging modes in relation to food availability.
2. Mortality from early November to early March amounts to 70–86% among goldcrests in the resident population, suggesting they are food‐limited in winter. Food‐limitation manifests itself as a shortage of time for foraging. It promotes the use of foraging methods that minimize the daily foraging time by maximizing the rate of net energy gain. It increases both individual survival and competitiveness. Elimination of competitors by exploitation occurs when an individual is able to support itself, while food density in the habitat is reduced to levels at which others cannot.
3. Theory shows that when food is abundant, high‐efficiency energy‐expensive search and capture methods give shorter daily foraging times than low‐efficiency low‐cost methods, whereas the latter gives shorter daily foraging times at food shortages (Norberg 2021). Hovering flight is extremely expensive in energy but results in high foraging efficiency. Hover‐foraging should therefore be used when food is abundant.
4. In autumn, there were 85.3 arthropods per kilogram of branch mass, as opposed to 12.9 in spring. The numerical decline of arthropods, their fat metabolism, and size‐biased predation by birds reduced the spring density of food for goldcrests to less than 15.1% of the autumn density.
5. Hover‐foraging occurred 5.29 times per minute in autumn but only 0.23 times per minute in spring, which is 4.4% of the autumn frequency.
6. Foraging conditions are favorable at midsummer because of long days, high temperatures, and an abundance of arthropod prey. Parent birds that were feeding fledglings gathered food at a high rate and hovered 5.42 times per minute. But adults with no young to feed were not compelled to maximize the rate of net energy gain and only hover‐foraged 0.52 times per minute, which is 10% of that of providers.
7. These results are highly consistent from year to year and in qualitative agreement with theory.

Goldcrests minimize daily foraging time by using high‐efficiency energy‐expensive hover‐foraging when food is abundant but low‐efficiency low‐cost methods at food shortages.     

Shotgun metagenomics of soil invertebrate communities reflects taxonomy,biomass, and reference genome properties

• Metagenomics – shotgun sequencing of all DNA fragments from a community DNA extract – is routinely used to describe the composition, structure, and function of microorganism communities. Advances in DNA sequencing and the availability of genome databases increasingly allow the use of shotgun metagenomics on eukaryotic communities. Metagenomics offers major advances in the recovery of biomass relationships in a sample, in comparison to taxonomic marker gene‐based approaches (metabarcoding). However, little is known about the factors which influence metagenomics data from eukaryotic communities, such as differences among organism groups, the properties of reference genomes, and genome assemblies.
• We evaluated how shotgun metagenomics records composition and biomass in artificial soil invertebrate communities at different sequencing efforts. We generated mock communities of controlled biomass ratios from 28 species from all major soil mesofauna groups: mites, springtails, nematodes, tardigrades, and potworms. We shotgun sequenced these communities and taxonomically assigned them with a database of over 270 soil invertebrate genomes.
• We recovered over 95% of the species, and observed relatively high false‐positive detection rates. We found strong differences in reads assigned to different taxa, with some groups (e.g., springtails) consistently attracting more hits than others (e.g., enchytraeids). Original biomass could be predicted from read counts after considering these taxon‐specific differences. Species with larger genomes, and with more complete assemblies, consistently attracted more reads than species with smaller genomes. The GC content of the genome assemblies had no effect on the biomass–read relationships. Results were similar among different sequencing efforts.
• The results show considerable differences in taxon recovery and taxon specificity of biomass recovery from metagenomic sequence data. The properties of reference genomes and genome assemblies also influence biomass recovery, and they should be considered in metagenomic studies of eukaryotes. We show that low‐ and high‐sequencing efforts yield similar results, suggesting high cost‐efficiency of metagenomics for eukaryotic communities. We provide a brief roadmap for investigating factors which influence metagenomics‐based eukaryotic community reconstructions. Understanding these factors is timely as accessibility of DNA sequencing and momentum for reference genomes projects show a future where the taxonomic assignment of DNA from any community sample becomes a reality.

     

Favorable spring conditions can buffer the impact of winter carryover effects on a key breeding decision in an Arctic‐breeding seabird

1. The availability and investment of energy among successive life‐history stages is a key feature of carryover effects. In migratory organisms, examining how both winter and spring experiences carryover to affect breeding activity is difficult due to the challenges in tracking individuals through these periods without impacting their behavior, thereby biasing results.
2. Using common eiders Somateria mollissima, we examined whether spring conditions at an Arctic breeding colony (East Bay Island, Nunavut, Canada) can buffer the impacts of winter temperatures on body mass and breeding decisions in birds that winter at different locations (Nuuk and Disko Bay, Greenland, and Newfoundland, Canada; assessed by analyzing stable isotopes of 13‐carbon in winter‐grown claw samples). Specifically, we used path analysis to examine how wintering and spring environmental conditions interact to affect breeding propensity (a key reproductive decision influencing lifetime fitness in female eiders) within the contexts of the timing of colony arrival, pre‐breeding body mass (body condition), and a physiological proxy for foraging effort (baseline corticosterone).
3. We demonstrate that warmer winter temperatures predicted lower body mass at arrival to the nesting colony, whereas warmer spring temperatures predicted earlier arrival dates and higher arrival body mass. Both higher body mass and earlier arrival dates of eider hens increased the probability that birds would initiate laying (i.e., higher breeding propensity). However, variation in baseline corticosterone was not linked to either winter or spring temperatures, and it had no additional downstream effects on breeding propensity.
4. Overall, we demonstrate that favorable pre‐breeding conditions in Arctic‐breeding common eiders can compensate for the impact that unfavorable wintering conditions can have on breeding investment, perhaps due to greater access to foraging areas prior to laying.

     

Localizing wild chimpanzees with passive acoustics

1. Localizing wildlife contributes in multiple ways to species conservation. Data on animal locations can reveal elements of social behavior, habitat use, population dynamics, and be useful in calculating population density. Acoustic localization systems (ALS) are a non‐invasive method widely used in the marine sciences but not well established and rarely employed for terrestrial species.
2. We deployed an acoustic array in a mountainous environment with heterogeneous vegetation, comprised of four custom‐built GPS synchronized acoustic sensors at about 500 m intervals in Issa Valley, western Tanzania, covering an area of nearly 2 km². Our goal was to assess the precision and error of the estimated locations by conducting playback tests, but also by comparing the estimated locations of wild chimpanzee calls with their true locations obtained in parallel during follows of individual chimpanzees. We assessed the factors influencing localization error, such as wind speed and temperature, which fluctuate during the day and are known to affect sound transmission.
3. We localized 282 playback sounds and found that the mean localization error was 27 ± 21.8 m. Localization was less prone to error and more precise during early mornings (6:30 h) compared to other periods. We further localized 22 wild chimpanzee loud calls within 52 m of the location of a researcher closely following the calling individuals.
4. We demonstrate that acoustic localization is a powerful tool for chimpanzee monitoring, with multiple behavioral and conservation applications. Its applicability in studying social dynamics and revealing density estimation among many others, especially but not exclusively for loud calling species, provides an efficient way of monitoring populations and informing conservation plans to mediate species loss.

     

Drivers and consequences of partial migration in an alpine bird species

1. Partial migration, where a portion of the population migrates between winter and summer (breeding) areas and the rest remain year‐round resident, is a common phenomenon across several taxonomic groups. Several hypotheses have been put forward to explain why some individuals migrate while others stay resident, as well as the fitness consequences of the different strategies. Yet, the drivers and consequences of the decision to migrate or not are poorly understood.
2. We used data from radio‐tagged female (n = 73) willow ptarmigan Lagopus lagopus in an alpine study area in Central Norway to test if (i) the decision to migrate was dependent on individual state variables (age and body weight), (ii) individuals repeated migratory decisions between seasons, and (iii) the choice of migratory strategy was related to reproductive success.
3. Partially supporting our prediction that migratory strategy depends on individual state, we found that juvenile birds with small body sizes were more likely to migrate, whereas large juveniles remained resident. For adult females, we found no relationship between the decision to migrate or stay resident and body weight. We found evidence for high individual repeatability of migratory decision between seasons. Migratory strategy did not explain variation in clutch size or nest fate among individuals, suggesting no direct influence of the chosen strategy on reproductive success.
4. Our results indicate that partial migration in willow ptarmigan is related to juvenile body weight, and that migratory behavior becomes a part of the individual life history as a fixed strategy. Nesting success was not affected by migratory strategy in our study population, but future studies should assess other traits to further test potential fitness consequences.

     

Conventional wisdom on roosting behavior of Australian flying‐foxes—A critical review,and evaluation using new data

1. Fruit bats (Family: Pteropodidae) are animals of great ecological and economic importance, yet their populations are threatened by ongoing habitat loss and human persecution. A lack of ecological knowledge for the vast majority of Pteropodid species presents additional challenges for their conservation and management.
2. In Australia, populations of flying‐fox species (Genus: Pteropus) are declining and management approaches are highly contentious. Australian flying‐fox roosts are exposed to management regimes involving habitat modification, through human–wildlife conflict management policies, or vegetation restoration programs. Details on the fine‐scale roosting ecology of flying‐foxes are not sufficiently known to provide evidence‐based guidance for these regimes, and the impact on flying‐foxes of these habitat modifications is poorly understood.
3. We seek to identify and test commonly held understandings about the roosting ecology of Australian flying‐foxes to inform practical recommendations and guide and refine management practices at flying‐fox roosts.
4. We identify 31 statements relevant to understanding of flying‐fox roosting structure and synthesize these in the context of existing literature. We then contribute a contemporary, fine‐scale dataset on within‐roost structure to further evaluate 11 of these statements. The new dataset encompasses 13‐monthly repeat measures from 2,522 spatially referenced roost trees across eight sites in southeastern Queensland and northeastern New South Wales.
5. We show evidence of sympatry and indirect competition between species, including spatial segregation of black and grey‐headed flying‐foxes within roosts and seasonal displacement of both species by little red flying‐foxes. We demonstrate roost‐specific annual trends in occupancy and abundance and provide updated demographic information including the spatial and temporal distributions of males and females within roosts.
6. Insights from our systematic and quantitative study will be important to guide evidence‐based recommendations on restoration and management and will be crucial for the implementation of priority recovery actions for the preservation of these species in the future.

     

Density‐dependent demography and movements in a cyclic brown lemming population

Theoretical modeling predicts that both direct and delayed density‐dependence are key factors to generate population cycles. Deciphering density‐dependent processes that lead to variable population growth characterizing different phases of the cycles remains challenging. This is particularly the case for the period of prolonged low densities, which is inherently data deficient. However, demographic analyses based on long‐term capture–mark–recapture datasets can help resolve this question. We relied on a 16‐year (2004–2019) live‐trapping program to analyze the summer demography and movements of a cyclic brown lemming population in the Canadian Arctic. More specifically, we examined if inversely density‐dependent processes could explain why population growth can remain low during the prolonged low phase. We found that the proportion of females in the population was inversely density‐dependent with a strong male‐biased sex ratio at low densities but not at high densities. However, survival of adult females was higher than adult males, but both had lower survival at low densities than at high ones. Distances moved by both adult males and females were density‐dependent, and proportion of females in reproductive condition was weakly density‐dependent as it tended to increase at low density. Individual body condition, measured as monthly change in body mass, was not density‐dependent. Overall, the strong male‐biased sex ratio at very low densities suggests a loss of reproductive potential due to the rarity of females and appears to be the most susceptible demographic factor that could contribute to the prolonged low phase in cyclic brown lemmings. What leads to this sex‐bias in the first place is still unclear, potentially owing to our trapping period limited to the summer, but we suggest that it could be due to high predation rate on breeding females in winter.     

The forestecology R package for fitting and assessing neighborhood models of the effect of interspecific competition on the growth of trees

1. Neighborhood competition models are powerful tools to measure the effect of interspecific competition. Statistical methods to ease the application of these models are currently lacking.
2. We present the forestecology package providing methods to (a) specify neighborhood competition models, (b) evaluate the effect of competitor species identity using permutation tests, and (cs) measure model performance using spatial cross‐validation. Following Allen and Kim (PLoS One, 15, 2020, e0229930), we implement a Bayesian linear regression neighborhood competition model.
3. We demonstrate the package''s functionality using data from the Smithsonian Conservation Biology Institute''s large forest dynamics plot, part of the ForestGEO global network of research sites. Given ForestGEO’s data collection protocols and data formatting standards, the package was designed with cross‐site compatibility in mind. We highlight the importance of spatial cross‐validation when interpreting model results.
4. The package features (a) tidyverse‐like structure whereby verb‐named functions can be modularly “piped” in sequence, (b) functions with standardized inputs/outputs of simple features sf package class, and (c) an S3 object‐oriented implementation of the Bayesian linear regression model. These three facts allow for clear articulation of all the steps in the sequence of analysis and easy wrangling and visualization of the geospatial data. Furthermore, while the package only has Bayesian linear regression implemented, the package was designed with extensibility to other methods in mind.

     

The use of trail cameras to monitor species inhabiting artificial nest boxes

1. Artificial boxes are commonly used in studies of cavity‐dwelling animals of various taxa. One advantage of nest boxes is that cameras can be used to monitor animals inside the cavity, however, most cameras used today have to be built de novo or modified or are expensive.
2. Here, we describe a method for monitoring nest boxes using off‐the‐shelf models of trail cameras that can record photographs and videos in daylight and darkness (TCM; Trail Camera Method). The cameras can record sequentially within a given time lapse or an infra‐red motion sensor can be triggered by activity in the nest box.
3. Using TCM in a Great Tit (Parus major) nest box population, we studied the hourly pattern of the first egg laying and the first egg hatching. We found that Great Tits laid eggs within 2 h of the sunrise while the timing of hatching spanned the 24‐h day. Moreover, we found that the hour of hatching affects the nestlings’ mass on the 2nd day of life, but not on the 12th day of life.
4. Comparing to traditional nest box checks, TMC requires about 75% less time to obtain data on the timing of egg laying and hatching. Moreover, the hour estimation error was several orders of magnitude greater with the traditional method.
5. Our data demonstrate that commercially available trail cameras are an affordable and convenient method of monitoring artificial cavities. Trail cameras are small, standalone, weather‐proof devices with integrated powering, memory storage, lighting, and recording systems. They could be easily swapped between boxes or removed. After small modifications of the box, they could be used to monitor a wide variety of behaviors of many animal taxa.