Population Ecology Research Articles

Population dynamics of sympatric Phortica spp. and first record of stable presence of Phortica oldenbergi in a Thelazia callipaeda-endemic area of Italy.

Five species of the Phortica genus (Diptera: Drosophilidae) are known in Europe and the Middle East. Among these, Phortica variegata and Phortica okadai are better known for their role as vectors of the zoonotic eyeworm Thelazia callipaeda. Other species, such as Phortica semivirgo and Phortica oldenbergi, have been studied less. Given the paucity of data about these Phortica spp. vectors, we explored the population dynamics and ecology of Phortica spp. in an area highly endemic for T. callipeada (Manziana, Rome, Central Italy). Phortica spp. flies were collected over a 3-year period (2018-2020) during their active season (April-October) with a sweep net while hovering around fermenting fruits or a human operator acting as baits. Collected flies were morphologically identified and tested for a T. callipeada infection and for the presence of Wolbachia, by polymerase chain reaction (PCR). Population dynamics of species collected was associated to environmental drivers through generalized additive models. Of the 5564 flies collected, 90.8% were P. variegata, 9.1% were P. oldenbergi, 0.05% were P. semivirgo, and one specimen was P. okadai. Only P. variegata scored molecularly infected with T. callipeada throughout the 3-year sampling period (1.8%). Phortica oldenbergi, observed consistently during the entire sampling period, exhibited a marked preference for fruit traps, contrasting with the lachryphagous activity of P. variegata. Analysis of environmental drivers of P. oldenbergi and P. variegata population dynamics indicated temperature, wind speed, and pressure as significant factors. In addition, Wolbachia pipientis endosymbiont was detected in P. oldenbergi and P. okadai. For the first time, this study analysed several ecological aspects of Phortica species coexisting in a T. callipeada endemic area, highlighting different behaviors in the same environment and their vectorial role. Notably, this is also the first report of the presence of P. oldenbergi in Italy and P. okadai in Europe, underscoring the importance of extensive sampling for detecting potential vectors and alien species with direct implications for vector-borne disease epidemiology.

Bacterial population-level trade-offs between drought tolerance and resource acquisition traits impact decomposition.

Microbes drive fundamental ecosystem processes such as decomposition. Environmental stressors are known to affect microbes, their fitness, and the ecosystem functions that they perform, yet understanding the causal mechanisms behind this influence has been difficult. We used leaf litter on soil surface as a model in situ system to assess changes in bacterial genomic traits and decomposition rates over 18months with drought as a stressor. We hypothesized that genome-scale trade-offs due to investment in stress tolerance traits under drought reduce the capacity for bacterial populations to carry out decomposition, and that these population-level trade-offs scale up to impact emergent community traits thereby reducing decomposition rates. We observed drought tolerance mechanisms that were heightened in bacterial populations under drought, identified as higher gene copy numbers in metagenome-assembled genomes. A subset of populations under drought had reduced carbohydrate-active enzyme genes which suggested - as a trade-off - a decline in decomposition capabilities. These trade-offs were driven by community succession and taxonomic shifts as distinct patterns appeared in populations. We show that trait-tradeoffs in bacterial populations under drought could scale up to reduce overall decomposition capabilities and litter decay rates. Using a trait-based approach to assess the population ecology of soil bacteria, we demonstrate genome-level trade-offs in response to drought with consequences for decomposition rates.

Linear infrastructure and associated wildlife accidents create an ecological trap for an apex predator and scavenger

Animals may fall into an ‘ecological trap’ when they select seemingly attractive habitats at the expense of their fitness. This maladaptive behavior is often the result of rapid, human-induced changes in their natal environment, such as the construction of energy and transportation infrastructure. We tested the ecological trap hypothesis regarding human-created linear infrastructure on a widely distributed apex predator and scavenger—the Golden Eagle (Aquila chrysaetos), whose range spans the entire Northern Hemisphere. Roads and railways offer novel and attractive feeding opportunities through traffic-induced mortality of other species, while powerline areas provide perching or nesting sites and scavenging opportunities from electrocuted or collision-killed birds. These conditions may have negative demographic consequences for eagles if these apparent opportunities turn into traps. Using step selection functions, we analyzed habitat selection of 74 GPS-tracked Golden Eagles (37 adults and 37 immatures) during eleven years in Fennoscandia. To assess habitat attractiveness, we used wildlife traffic accident statistics for dominant wild species, and to evaluate demographic consequences, we used mortality data from the GPS-tagged eagles. Our analysis revealed that eagles selected linear features such as roads, railways and powerlines at both the population and individual levels. Both adult and immature eagles consistently selected these features, and the strength of selection for linear features increased with age in immature eagles. The linear features however had 5.5 times higher mortality risk for eagles than other selected habitats indicating the presence of an ecological trap. We discuss the implications of these findings for the conservation and population ecology of apex predators and scavengers, as well as their potential demographic consequences. To mitigate this issue, we urgently recommend the removal of carcasses from roads and tracks to prevent ecological traps for raptors and scavenger species worldwide. Additionally, we advocate for the development of methods and strategies to reduce wildlife traffic accidents.

What in Earth? Analyses of Canadian soil populations of Aspergillus fumigatus

Aspergillus fumigatus is a globally distributed mold and a major cause of opportunistic infections in humans. Because most infections are from environmental exposure, it’s critical to understand environmental populations of A. fumigatus. Soil is a major ecological niche for A. fumigatus. Here we analyzed 748 soil isolates from 21 locations in six provinces and one territory in Canada. All isolates were genotyped using nine microsatellite markers. Due to small sample size and/or close proximities for some local samples, these isolates were grouped into 16 local geographic and ecological populations. Our results indicated high allelic and genotypic diversities within most local and provincial populations. Interestingly, low but statistically significant genetic differentiations were found among geographic populations within Canada, with relatively similar proportions of strains and genotypes belonging to two large genetic clusters. In Hamilton, Ontario and Vancouver, BC, where two and three ecological populations were analyzed respectively, we found limited genetic difference among them. Most local and provincial populations showed evidence of both clonality and recombination, with no population showing random recombination. Of the 748 soil isolates analyzed here, two were resistant to triazole antifungals. We discuss the implications of our results to the evolution and epidemiology of A. fumigatus.

Manipulating a host-native microbial strain compensates for low microbial diversity by increasing weight gain in a wild bird population

Empirical studies from laboratory systems and humans show that the gut microbiota is linked to host health. Similar evidence for effects on traits linked to fitness in nature is rare, not least because experimentally manipulating the gut microbiota is challenging. We isolated, characterized, and cultured a bacterial strain, Lactobacillus kimchicus APC4233, directly from a wild bird (the great tit Parus major) and provided it as a self-administered dietary supplement. We assessed the impact of the treatment on the host microbiota community, on weight, and tested whether the treatment affected a previous result linking microbiota alpha diversity to weight in nestlings. The treatment dramatically increased L. kimchicus abundance in the gut microbiota and increased alpha diversity. This effect was strongest in the youngest birds, validating earlier findings pointing to a brief developmental window when the gut microbiota are most sensitive. In time-lagged models, nestling weight was higher in the treatment birds suggesting L. kimchicus may have probiotic potential. There was also a positive time-lagged relationship between diversity and weight in control birds but not in the treatment birds, suggesting L. kimchicus helped birds compensate for low alpha diversity. We discuss why ecological context is likely key when predicting impacts of the microbiome. The manipulation of the gut microbiota with a host native strain in this wild population provides direct evidence for the role of the microbiota in the ecology and evolution of natural populations.

Management considerations of moose life‐history characteristics in Colorado, USA

Wildlife management agencies are obliged to provide evidence‐based management recommendations to stakeholders. However, allocation of resources towards the management of species is rarely uniform. The consideration of life‐history characteristics of moose offers wildlife managers a more robust understanding of population ecology, while also providing insight into potential limiting factors for long‐term management. From 2014–2020 we simultaneously measured survival of adult female moose, as well as calf productivity, in relation to the nutritional condition of adult females, in Colorado. Mean annual adult survival was high (93% and 95% confidence interval: 91–95%). Human hunter harvest was the leading source of mortality and lowered annual adult survival to 88%. Malnutrition was the leading source of natural mortality. Mean annual pregnancy rates were relatively low (77%) and highly variable (95% confidence interval: 65–88%). However, low pregnancy rates were compensated for by high apparent calf survival. The best predictor of moose pregnancy was nutritional condition. Our data suggest that bottom‐up ecological processes were affecting moose population growth, but populations were likely increasing during our study, with a simulated population growth rate of 1.04 (95% confidence interval: 0.94–1.17).

Population Composition, Physiology and Ecology of Filamentous Bacteria in Activated Sludge

Population Composition, Physiology and Ecology of Filamentous Bacteria in Activated Sludge

Tracking Small Animals in Complex Landscapes: AComparison of Localisation Workflows for Automated Radio Telemetry Systems.

Automated radio telemetry systems (ARTS) have the potential to revolutionise our understanding of animal movement by providing a near-continuous record of individual locations in the wild. However, localisation errors in ARTS data can be very high, especially in natural landscapes with complex vegetation structure and topography. This curtails the research questions that may be addressed with this technology. We set up an ARTS grid in a valley with heterogeneous vegetation cover in the Colombian high Andes and applied an analytical pipeline to test the effectiveness of localisation methods. We performed calibration trials to simulate animal movement in high- or low-flight, or walking on the ground, and compared workflows with varying decisions related to signal cleaning, selection, smoothing, and interpretation, along with four multilateration approaches. We also quantified the influence of spatial features on the system's accuracy. Results showed large variation in localisation error, ranging between 0.4-43.4 m and 474-1929 m, depending on the localisation method used. We found that the selection of higher radio signal strengths and data smoothing based on the temporal autocorrelation are useful tools to improve accuracy. Moreover, terrain ruggedness, height of movement, vegetation type, and the location of animals inside or outside the grid area influence localisation error. In the case of our study system, thousands of location points were successfully estimated for two high-altitude hummingbird species that previously lacked movement data. Our case study on hummingbirds suggests ARTS grids can be used to estimate small animals' home ranges, associations with vegetation types, and seasonality in occurrence. We present a comparative localisation pipeline, highlighting the variety of possible decisions while processing radio signal data. Overall, this study provides guidance to improve the resolution of location estimates, broadening the application of this tracking technology in the study of the spatial ecology of wild populations.

Announcement of the 5th Population Ecology Awards

Announcement of the 5th Population Ecology Awards

Fitness and Survival of the Fall Armyworm, Spodoptera Frugiperda (Lepidoptera: Noctuidae) on Maize in West Java, Indonesia

An important pest of maize is a new invasive species called Spodoptera frugiperda, also known as the fall armyworm (FAW), causing a considerable economic impact in Indonesia since 2019. This insect has a large host range, a quick generation time at the right temperature, a high rate of reproduction, and a high dispersal capacity. In population ecology and pest management, fitness and survival are crucial. This research was aimed to determine some biological aspects and demographic statistics of three FAW populations (lowland, midland, and highland) in a laboratory setting with 25 ± 2 °C, 75 ± 5% relative humidity, and a 12:12 (L:D) hour photoperiod. Findings indicated no variation in the length of the FAW life stage or its reproductive capacity. Nonetheless, notable variations were noted in the average fecundity of females, with FAW of the highland population laying the most eggs (1242.1 eggs). FAW had the shortest mean generation time (T), the highest intrinsic rate of increase (rm), the finite rate of increase (λ), and the highest net reproductive rate (R0) of the highland population. Overall FAW collected from highland, midland, and lowland can adapt well when brought to a laboratory with a constant temperature at 25 ± 2 °C without detriment to the parameters of the life table. The knowledge gained from this study is crucial for managing FAW because it improves comprehension of its life cycle and adaptability to various altitudes, enabling us to take appropriate action to stop its spread.

Genetic analysis of key agronomic traits of local sheep breeds in Xinjiang, China

The formation of sheep (Ovis aries) breeds is influenced by different ecological environments and populations with different living habits, resulting in the development of germplasm resources with stable genetic key agronomic traits. Thus, investigating the genetic mechanisms behind various agronomic traits can enhance the conservation and utilization of diverse sheep breeds. Here, we explored the sheep variome and selection signatures using the Ovine Infinium HD SNP BeadChip (600 K SNPs) from 23 sheep breeds, comprising a total of 1215 sheep. The genetic mechanisms of wool quality and tail morphology were analyzed by selective sweep and genome-wide association study. Based on the results of within-population selective sweep analysis, we performed gene network analysis and divided them into 6 gene communities. We identified genetic regions containing genes linked to sheep wool and tail, which have been and may continue to be important targets for breeding and selection. Furthermore, our results revealed the expression profiles of genes in these regions across different biological systems. Our study provides insights into categorizing sheep breeds into distinct gene communities, as well as references for constructing genetic network pathways related to key agronomic traits in sheep and other domestic animals.

Retrodiction of forest demography: Backward simulation with reverse matrix models

Abstract Reconstructing past ecological population dynamics and demographic events is crucial for understanding the dynamics of ecological processes, evaluating the impact of environmental changes and making informed conservation decisions. In forest ecosystems, retrodiction (i.e. the backward projection of ecological populations) plays a pivotal role in understanding historical forest carbon levels and the factors that have influenced their variation over time, because forest demography is a major determinant of the amount of carbon stored in forest ecosystems. The persistent lack of quantitative methods has been a significant obstacle in retrodicting forest demography, especially in applications of a broad geographical scale. While there is a wealth of models for predicting future forest conditions, models that can project these conditions backward in time are scarce. This study presents reverse matrix model (RMM), an innovative retrodiction modelling approach grounded in the principles of transition matrix models. RMM is designed to deduce past demographic characteristics of ecological populations using current data, making it one of the first models capable of projecting the fine‐scale dynamics of forest demography into the past. We assessed the retrodictive performance of RMM by fitting it to a dataset of a disturbed tropical rainforest in French Guiana in 2001–2023, then comparing the retrodictions to observations back to 1983 when the disturbance occurred. We further empirically evaluated the viability of retrodiction over a defined duration by inverting the density‐dependent matrix model by Lin et al. (1996), which predicts the dynamics of northern hardwoods in the United States. The case studies demonstrate significant potential for RMM application in various domains of forestry and conservation, including ecosystem management and conservation planning, global change impact assessment and biodiversity monitoring.

Population ecology of the red-winged grasshopper, Celes skalozubovi akitanus (Orthoptera, Acrididae), in Japan

Population ecology of the red-winged grasshopper, Celes skalozubovi akitanus (Orthoptera, Acrididae), in Japan

Quantifying attributes of boring bivalve populations in corals using micro-computed tomography

Bioerosion plays a crucial factor in shaping the structure and function of coral reef ecosystems, with bioeroders actively altering both the physical and ecological dynamics of coral substrates. Despite their importance, studying internal bioeroders in corals presents significant challenges owing to their cryptic nature within the skeletal structures. Additionally, invasive methods are often required to reveal the subtle and microscopic bioerosive alterations they induce in calcium carbonate substrates. Here, we demonstrate the effectiveness of high-resolution micro-computed tomography (μCT) in quantifying the abundance, size, distribution, and growth directions of coral bioeroders such as cryptic calcareous bivalves in the northern Red Sea. We scanned three coral species inhabited by bioeroders, followed by the utilization of three-dimensional image analysis software to identify, count, and measure each bivalve within the coral skeleton, along with quantifying boring cavity volumes. We revealed that μCT captures small boring cavities (< 1mm), providing more accurate abundance estimates of live and dead boring bivalves than the skeleton decalcification technique, with the added benefits of being rapid and non-destructive in contrast to traditional methods. Furthermore, measurements of empty cavity volumes enabled the estimations of the contribution of bioeroders to the overall coral skeletal porosity. Overall, our study highlights μCT as a practical and effective tool for studying cryptic coral bioeroders, providing novel ecological insights into bioeroder population ecology and coral-bioeroder interactions.

Bayesian estimation of spatially varying mortality risk using tagged animal data

Abstract The survival of animals is impacted by landscapes of spatially varying mortality factors including habitat type, predation risk or harvest risk, among others. Characterization of these spatial mortality processes is important for managing animal populations and their habitats, yet this information has proved challenging to capture. Advances in telemetry now make it possible to monitor tagged individuals' locations through time for a wide range of taxa, providing opportunity to assess movement and mortality simultaneously through spatial time‐to‐event data. Existing time‐to‐event modelling frameworks have largely ignored spatially varying mortality processes or have treated an animal's location as fixed at a regional level. Here we present a general spatial survival model for analysing time‐to‐event data arising from animal telemetry. Our model has a flexible Cox regression form and can estimate the effects of conventional non‐spatial risk factors (size, seasonality, etc.), spatial covariates (e.g. habitat type) and spatial variation in risk not explained by covariates on mortality. We show how to fit our model using Bayesian methods and demonstrate applications of our model with several simulated examples and two animal telemetry case studies. Our model produced consistent and unbiased parameter estimates throughout simulations with a variety of spatial and non‐spatial hazards. In the first case study, data from 147 tagged caribou in British Columbia, Canada, revealed a spatially heterogeneous mortality landscape with caribou survival varying by elevation, likely in response to space use by predators. Our second case study involved a dataset of 390 acoustically tagged Atlantic cod in a southern Norwegian fjord where a marine protected area (MPA) was established during the study. We found that the MPA led to a shift from mostly fishing mortality to mostly natural mortality within the fjord and that these risks had markedly different spatial hazard patterns. Our spatial time‐to‐event model can make use of data from a variety of widely used telemetry technologies to characterize landscapes of mortality risks for different taxa. Our work provides new opportunities to inform the spatial ecology and management of fish and wildlife populations.

Modeling and dynamical analysis of an ecological population with the Allee effect

Modeling and dynamical analysis of an ecological population with the Allee effect

Growth rate as a link between microbial diversity and soil biogeochemistry.

Measuring the growth rate of a microorganism is a simple yet profound way to quantify its effect on the world. The absolute growth rate of a microbial population reflects rates of resource assimilation, biomass production and element transformation-some of the many ways in which organisms affect Earth's ecosystems and climate. Microbial fitness in the environment depends on the ability to reproduce quickly when conditions are favourable and adopt a survival physiology when conditions worsen, which cells coordinate by adjusting their relative growth rate. At the population level, relative growth rate is a sensitive metric of fitness, linking survival and reproduction to the ecology and evolution of populations. Techniques combining omics and stable isotope probing enable sensitive measurements of the growth rates of microbial assemblages and individual taxa in soil. Microbial ecologists can explore how the growth rates of taxa with known traits and evolutionary histories respond to changes in resource availability, environmental conditions and interactions with other organisms. We anticipate that quantitative and scalable data on the growth rates of soil microorganisms, coupled with measurements of biogeochemical fluxes, will allow scientists to test and refine ecological theory and advance process-based models of carbon flux, nutrient uptake and ecosystem productivity. Measurements of in situ microbial growth rates provide insights into the ecology of populations and can be used to quantitatively link microbial diversity to soil biogeochemistry.

Population status and ecology of the globally threatened liverwort Marsupella profunda Lindb. in Britain

ABSTRACT Introduction Marsupella profunda Lindb. is known from Britain, Portugal and Macaronesia. Its population status and ecology in Britain were investigated. Methods An inventory of records of Marsupella profunda was prepared, and surveys were conducted at a subset of sites. Population size was measured by counts of ‘individual-equivalents’, defined as occupied 1 m grid cells. Habitat and community composition were recorded by relevés. Key results and conclusions Marsupella profunda is confined to habitat created by china clay quarrying, and mostly occurs on kaolinised granite. It is one of the earliest colonists of this substrate. The longevity of habitat patches is limited mainly by competitive exclusion by other bryophytes and excessive shade from scrub development. It has been recorded from six sites in West Cornwall but presently survives at only one of these, where it will likely become extinct within the next 20 years due to vegetation succession. In East Cornwall, an enormous complex of active and disused quarries within the St Austell China Clay Region supports a large population (10,000–20,000 individual-equivalents), but this is declining because china clay production has decreased greatly over the past 30 years. Attempts to conserve the species by the special protection of areas of land have failed because the quarrying process that originally supplied fresh suitable substrate no longer operates in these areas, habitat management measures have been insufficient, and scrub development has progressed. The future of the species in Britain depends on the uncertain future of commercial quarrying in areas of kaolinised granite in Cornwall.

Recombinase-aid amplification combined with lateral flow detection assay for sex identification of the great white pelican (Pelecanus onocrotalus)

Sex identification in avian species is essential for biodiversity conservation and ecological studies. However, the sex of nearly half of the birds could not be identified based on their external appearance. It is difficult to visually identify sex to monitor the ecology and conservation of wild populations. In this study, we designed primer pairs for large white pelican using recombinase-based isothermal amplification combined with a lateral flow dipstick (RAA-LFD) assay for chromo-helicase-DNA binding protein (CHD) genes mapped to W chromosomes and an ultra-conserved element (UCE) located on chromosome 6, respectively. Our result showed that the raaW4-RAA-LFD can detect up to 0.1 ng of genomic DNA (gDNA) templates of female pelicans in 30 min at 39 ℃ and accurately distinguish female from male without any cross reactivity. RaaUCE2-RAA-LFD can amplify both male and female pelicans with a detection limit of 25 pg. To further evaluate the assay, 15 white pelicans of unknown sex were tested using the RAA-LFD assay and conventional polymerase chain reaction (PCR). The results of the raaW4-RAA-LFD assay were consistent with those of the conventional PCR. The developed RAA-LFD assay is equipped with field-deployable instruments and offers a field platform for rapid and reliable sex identification in pelicans.

Accurately estimating correlations between demographic parameters: A comment on Deane etal. (2023).

Estimating correlations among demographic parameters is an important method in population ecology. A recent paper by Deane etal. (Ecology and Evolution 13:e9847, 2023) attempted to explore the effects of different priors for covariance matrices on inference when using mark-recovery data. Unfortunately, Deane etal. (2023) made a mistake when parameterizing some of their models. Rather than exploring the effects of different priors, they examined the effects of the use of incorrect equations on inference. In this manuscript, we clearly describe the mistake in Deane etal. (2023). We then demonstrate the use of an alternative and appropriate method and reach different conclusions regarding the effects of priors on inference. Consistent with other recent literature, informative inverse Wishart priors can lead to flawed inference, while vague priors on covariance matrix components have little impact when sample sizes are adequate.