The influence of gene flow on population viability in an isolated urban caracal population

Wildlife populations are becoming increasingly fragmented by anthropogenic development. Small and isolated populations often face an elevated risk of extinction, in part due to inbreeding depression. Here, we examine the genomic consequences of urbanization in a caracal (Caracal caracal) population that has become isolated in the Cape Peninsula region of the City of Cape Town, South Africa, and is thought to number ~50 individuals. We document low levels of migration into the population over the past ~75 years, with an estimated rate of 1.3 effective migrants per generation. As a consequence of this isolation and small population size, levels of inbreeding are elevated in the contemporary Cape Peninsula population (mean FROH = 0.20). Inbreeding primarily manifests as long runs of homozygosity >10 Mb, consistent with the effects of isolation due to the rapid recent growth of Cape Town. To explore how reduced migration and elevated inbreeding may impact future population dynamics, we parameterized an eco-evolutionary simulation model. We find that if migration rates do not change in the future, the population is expected to decline, though with a low projected risk of extinction. However, if migration rates decline or anthropogenic mortality rates increase, the potential risk of extinction is greatly elevated. To avert a population decline, we suggest that translocating migrants into the Cape Peninsula to initiate a genetic rescue may be warranted in the near future. Our analysis highlights the utility of genomic datasets coupled with computational simulation models for investigating the influence of gene flow on population viability.

An Allee-based distributed algorithm for microbial whole-cell sensors

Reliable detection of substances present at potentially low concentrations is a problem common to many biomedical applications. Complementary to well-established enzyme-, antibody-antigen-, and sequencing-based approaches, so-called microbial whole-cell sensors, i.e., synthetically engineered microbial cells that sense and report substances, have been proposed as alternatives. Typically these cells operate independently: a cell reports an analyte upon local detection.In this work, we analyze a distributed algorithm for microbial whole-cell sensors, where cells communicate to coordinate if an analyte has been detected. The algorithm, inspired by the Allee effect in biological populations, causes cells to alternate between a logical 0 and 1 state in response to reacting with the particle of interest. When the cells in the logical 1 state exceed a threshold, the algorithm converts the remaining cells to the logical 1 state, representing an easily-detectable output signal. We validate the algorithm through mathematical analysis and simulations, demonstrating that it works correctly even in noisy cellular environments.

Redefining 'state-of-the-art' for integrated population models with immigration

Research Highlight: Christian, M., Oosthuizen, W. C., Bester, M. N., & de Bruyn, P. N. (2024). Robustly estimating the demographic contribution of immigration: Simulation, sensitivity analysis and seals. Journal of Animal Ecology. https://doi.org/10.1111/1365-2656.14053. Immigration can have profound consequences for local population dynamics and demography, but collecting data to accurately quantifying it is challenging. The recent rise of integrated population models (IPMs) offers an alternative by making it possible to estimate immigration without the need for explicit data, and to quantify its contribution to population dynamics through transient Life Table Response Experiments (tLTREs). Simulation studies have, however, highlighted that this approach can be prone to bias and overestimation. In their new study, Christian et al. address one of the root causes of this issue by improving the estimation of time variation in vital rates and immigration using Gaussian processes in lieu of traditionally used temporal random effects. They demonstrate that IPM-tLTRE frameworks with Gaussian processes produce more accurate and less biased estimates of immigration and its contribution to population dynamics and illustrate the applicability of this approach using a long-term data set on elephant seals (Mirounga leonida). Results are validated with a simulation study and suggest that immigration of breeding females has been central for population recovery of elephant seals despite the species' high female site fidelity. Christian et al. thus present new insights into population regulation of long-lived marine mammals and highlight the potential for using Gaussian process priors in IPMs. They also illustrate a suite of 'best practices' for state-of-the-art IPM-tLTRE analyses and provide an inspirational example for the kind of ecological modelling workflow that can be invaluable not just as a starting point for fellow ecologists picking up or improving their own IPM-tLTRE analyses, but also for teaching and in contexts where model estimates are used for informing management and conservation decision-making.

Range-Wide Phylogeography and Ecological Niche Modeling Provide Insights into the Evolutionary History of the Mongolian Racerunner (Eremias argus) in Northeast Asia

The Mongolian racerunner, Eremias argus, is a small lizard endemic to Northeast Asia that can serve as an excellent model for investigating how geography and past climate change have jointly influenced the evolution of biodiversity in this region. To elucidate the processes underlying its diversification and demography, we reconstructed the range-wide phylogeographic pattern and evolutionary trajectory, using phylogenetic, population genetic, landscape genetic, Bayesian phylogeographic reconstruction and ecological niche modeling approaches. Phylogenetic analyses of the mtDNA cyt b gene revealed eight lineages that were unbounded by geographic region. The genetic structure of E. argus was mainly determined by geographic distance. Divergence dating indicated that E. argus and E. brenchleyi diverged during the Mid-Pliocene Warm Period. E. argus was estimated to have coalesced at~0.4351 Ma (Marine Isotope Stage 19). Bayesian phylogeographic diffusion analysis revealed out-of-Inner Mongolia and rapid colonization events from the end of the Last Interglacial to the Last Glacial Maximum, which is consistent with the expanded suitable range of the Last Glacial Maximum. Pre-Last Glacial Maximum growth of population is presented for most lineages of E. argus. The Glacial Maximum contraction model and the previous multiple glacial refugia hypotheses are rejected. This may be due to an increase in the amount of climatically favorable habitats in Northeast Asia. Furthermore, E. argus barbouri most likely represents an invalid taxon. The present study is the first to report a range-wide phylogeography of reptiles over such a large region in Northeast Asia. Our results make a significant contribution towards understanding the biogeography of the entire Northeast Asia.

Integrated bacterial transcriptome and host metabolome analysis reveals insights into "Candidatus Liberibacter asiaticus" population dynamics in the fruit pith of three citrus cultivars with different tolerance

"Candidatus Liberibacter asiaticus" (CLas), the causal agent of citrus Huanglongbing (HLB), is able to multiply to a high abundance in citrus fruit pith. However, little is known about the biological processes and phytochemical substances that are vital for CLas colonization and growth in fruit pith. In this study, CLas-infected fruit pith of three citrus cultivars ("Shatangju" mandarin, "Guanxi" pomelo, and "Shatian" pomelo) exhibiting different tolerance to CLas were collected and used for dual RNA-Seq and untargeted metabolome analysis. Comparative transcriptome analysis found that the activation of the CLas noncyclic TCA pathway and pathogenic-related effectors could contribute to the colonization and growth of CLas in fruit pith. The pre-established Type 2 prophage in the CLas genome and the induction of its CRISPR/cas system could enhance the phage resistance of CLas and, in turn, facilitate CLas population growth in fruit pith. CLas infection caused the accumulation of amino acids that were correlated with tolerance to CLas. The accumulation of most sugars and organic acids in CLas-infected fruit pith, which could be due to the phloem blockage caused by CLas infection, was thought to be beneficial for CLas growth in localized phloem tissue. The higher levels of flavonoids and terpenoids in the fruit pith of CLas-tolerant cultivars, particularly those known for their antimicrobial properties, could hinder the growth of CLas. This study advances our understanding of CLas multiplication in fruit pith and offers novel insight into metabolites that could be responsible for tolerance to CLas or essential to CLas population growth.IMPORTANCECitrus Huanglongbing (HLB, also called citrus greening disease) is a highly destructive disease currently threatening citrus production worldwide. HLB is caused by an unculturable bacterial pathogen, "Candidatus Liberibacter asiaticus" (CLas). However, the mechanism of CLas colonization and growth in citrus hosts is poorly understood. In this study, we utilized the fruit pith tissue, which was able to maintain the CLas at a high abundance, as the materials for dual RNA-Seq and untargeted metabolome analysis, aiming to reveal the biological processes and phytochemical substances that are vital for CLas colonization and growth. We provided a genome-wide CLas transcriptome landscape in the fruit pith of three citrus cultivars with different tolerance and identified the important genes/pathways that contribute to CLas colonization and growth in the fruit pith. Metabolome profiling identified the key metabolites, which were mainly affected by CLas infection and influenced the population dynamic of CLas in fruit pith.

Degeneration of foundation cushion species induced by ecological constraints can cause massive changes in alpine plant communities

Foundational cushion plants can re-organize community structures and sustain a prominent proportion of alpine biodiversity, but they are sensitive to climate change. The loss of cushion species can have broad consequences for associated biota. The potential plant community changes with the population dynamics of cushion plants remain, however, unclear. Using eight plant communities along a climatic and community successional gradient, we assessed cushion population dynamics, the underlying ecological constraints and hence associated plant community changes in alpine communities dominated by the foundational cushion plant Arenaria polytrichoides. The population dynamics of Arenaria are attributed to ecological constraints at a series of life history stages. Reproductive functions are constrained by increasing associated beneficiary plants; subsequent seedling establishment is constrained by temperature, water and light availability, extreme climate events, and interspecific competition; strong competitive exclusion may accelerate mortality and degeneration of cushion populations. Along with cushion dynamics, species composition, abundance and community structure gradually change. Once cushion plants completely degenerate, previously cushion-dominated communities shift to relatively stable communities that are overwhelmingly dominated by sedges. Climate warming may accelerate the degeneration process of A. polytrichoides. Degeneration of this foundational cushion plant will possibly induce massive changes in alpine plant communities and hence ecosystem functions in alpine ecosystems. The assessment of the population dynamics of foundation species is critical for an effective conservation of alpine biodiversity.

The angiogenic growth of cities

Describing the space-time evolution of urban population is a fundamental challenge in the science of cities, yet a complete theoretical treatment of the underlying dynamics is still missing. Here, we first reconstruct the evolution of London (UK) over 180 years and show that urban growth consists of an initial phase of diffusion-limited growth, followed by the development of the railway transport network and a consequential shift from central to suburban living. Such dynamics-which are analogous to angiogenesis in biological systems-can be described by a minimalist reaction-diffusion model coupled with economic constraints and an adaptive transport network. We then test the generality of our approach by reproducing the evolution of Sydney, Australia, from 1851 to 2011. We show that the rail system coevolves with urban population, displaying hierarchical characteristics that remain constant over time unless large-scale interventions are put in place to alter the modes of transport. These results demonstrate that transport schemes are first-order controls of long-term urbanization patterns and efforts aimed at creating more sustainable and healthier cities require careful consideration of population-transport feedbacks.

Harvest and decimation affect genetic drift and the effective population size in wild reindeer

Harvesting and culling are methods used to monitor and manage wildlife diseases. An important consequence of these practices is a change in the genetic dynamics of affected populations that may threaten their long-term viability. The effective population size (N e) is a fundamental parameter for describing such changes as it determines the amount of genetic drift in a population. Here, we estimate N e of a harvested wild reindeer population in Norway. Then we use simulations to investigate the genetic consequences of management efforts for handling a recent spread of chronic wasting disease, including increased adult male harvest and population decimation. The N e/N ratio in this population was found to be 0.124 at the end of the study period, compared to 0.239 in the preceding 14 years period. The difference was caused by increased harvest rates with a high proportion of adult males (older than 2.5 years) being shot (15.2% in 2005-2018 and 44.8% in 2021). Increased harvest rates decreased N e in the simulations, but less sex biased harvest strategies had a lower negative impact. For harvest strategies that yield stable population dynamics, shifting the harvest from calves to adult males and females increased N e. Population decimation always resulted in decreased genetic variation in the population, with higher loss of heterozygosity and rare alleles with more severe decimation or longer periods of low population size. A very high proportion of males in the harvest had the most severe consequences for the loss of genetic variation. This study clearly shows how the effects of harvest strategies and changes in population size interact to determine the genetic drift of a managed population. The long-term genetic viability of wildlife populations subject to a disease will also depend on population impacts of the disease and how these interact with management actions.

An integrated population model reveals source-sink dynamics for competitively subordinate African wild dogs linked to anthropogenic prey depletion

Many African large carnivore populations are declining due to decline of the herbivore populations on which they depend. The densities of apex carnivores like the lion and spotted hyena correlate strongly with prey density, but competitively subordinate carnivores like the African wild dog benefit from competitive release when the density of apex carnivores is low, so the expected effect of a simultaneous decrease in resources and dominant competitors is not obvious. Wild dogs in Zambia's South Luangwa Valley Ecosystem occupy four ecologically similar areas with well-described differences in the densities of prey and dominant competitors due to spatial variation in illegal offtake. We used long-term monitoring data to fit a Bayesian integrated population model (IPM) of the demography and dynamics of wild dogs in these four regions. The IPM used Leslie projection to link a Cormack-Jolly-Seber model of area-specific survival (allowing for individual heterogeneity in detection), a zero-inflated Poisson model of area-specific fecundity and a state-space model of population size that used estimates from a closed mark-capture model as the counts from which (latent) population size was estimated. The IPM showed that both survival and reproduction were lowest in the region with the lowest density of preferred prey (puku, Kobus vardonii and impala, Aepyceros melampus), despite little use of this area by lions. Survival and reproduction were highest in the region with the highest prey density and intermediate in the two regions with intermediate prey density. The population growth rate (λ ) was positive for the population as a whole, strongly positive in the region with the highest prey density and strongly negative in the region with the lowest prey density. It has long been thought that the benefits of competitive release protect African wild dogs from the costs of low prey density. Our results show that the costs of prey depletion overwhelm the benefits of competitive release and cause local population decline where anthropogenic prey depletion is strong. Because competition is important in many guilds and humans are affecting resources of many types, it is likely that similarly fundamental shifts in population limitation are arising in many systems.

Dispersal synchronizes giant kelp forests

Spatial synchrony is the tendency for population fluctuations to be correlated among different locations. This phenomenon is a ubiquitous feature of population dynamics and is important for ecosystem stability, but several aspects of synchrony remain unresolved. In particular, the extent to which any particular mechanism, such as dispersal, contributes to observed synchrony in natural populations has been difficult to determine. To address this gap, we leveraged recent methodological improvements to determine how dispersal structures synchrony in giant kelp (Macrocystis pyrifera), a global marine foundation species that has served as a useful system for understanding synchrony. We quantified population synchrony and fecundity with satellite imagery across 11 years and 880 km of coastline in southern California, USA, and estimated propagule dispersal probabilities using a high-resolution ocean circulation model. Using matrix regression models that control for the influence of geographic distance, resources (seawater nitrate), and disturbance (destructive waves), we discovered that dispersal was an important driver of synchrony. Our findings were robust to assumptions about propagule mortality during dispersal and consistent between two metrics of dispersal: (1) the individual probability of dispersal and (2) estimates of demographic connectivity that incorporate fecundity (the number of propagules dispersing). We also found that dispersal and environmental conditions resulted in geographic clusters with distinct patterns of synchrony. This study is among the few to statistically associate synchrony with dispersal in a natural population and the first to do so in a marine organism. The synchronizing effects of dispersal and environmental conditions on foundation species, such as giant kelp, likely have cascading effects on the spatial stability of biodiversity and ecosystem function.

Bringing traits back into the equation: A roadmap to understand species redistribution

Ecological and evolutionary theories have proposed that species traits should be important in mediating species responses to contemporary climate change; yet, empirical evidence has so far provided mixed evidence for the role of behavioral, life history, or ecological characteristics in facilitating or hindering species range shifts. As such, the utility of trait-based approaches to predict species redistribution under climate change has been called into question. We develop the perspective, supported by evidence, that trait variation, if used carefully can have high potential utility, but that past analyses have in many cases failed to identify an explanatory value for traits by not fully embracing the complexity of species range shifts. First, we discuss the relevant theory linking species traits to range shift processes at the leading (expansion) and trailing (contraction) edges of species distributions and highlight the need to clarify the mechanistic basis of trait-based approaches. Second, we provide a brief overview of range shift-trait studies and identify new opportunities for trait integration that consider range-specific processes and intraspecific variability. Third, we explore the circumstances under which environmental and biotic context dependencies are likely to affect our ability to identify the contribution of species traits to range shift processes. Finally, we propose that revealing the role of traits in shaping species redistribution may likely require accounting for methodological variation arising from the range shift estimation process as well as addressing existing functional, geographical, and phylogenetic biases. We provide a series of considerations for more effectively integrating traits as well as extrinsic and methodological factors into species redistribution research. Together, these analytical approaches promise stronger mechanistic and predictive understanding that can help society mitigate and adapt to the effects of climate change on biodiversity.

Estimated summer abundance and krill consumption of fin whales throughout the Scotia Sea during the 2018/2019 summer season

Among large cetaceans in the Southern Hemisphere, fin whales were the most heavily exploited in terms of numbers taken during the period of intense industrial whaling. Recent studies suggest that, whilst some humpback whale populations in the Southern Hemisphere appears to have almost completely recovered to their estimated pre-whaling abundance, much less is known about the status of Southern Hemisphere fin whales. Circumpolar estimates in the 1990s suggest an abundance of about 5500 animals south of 60° S, while the IDCR/SOWER-2000 survey for the Scotia Sea and Antarctic Peninsula areas estimated 4670 fin whales within this region in the year 2000. More recent studies in smaller regions indicate higher densities, suggesting that previous estimates are overly conservative and/or that fin whales are undergoing a substantial increase. Here we report findings from a recent multi-vessel single-platform sightings survey carried out as part of the 2019 Area 48 Survey for Antarctic krill. While fin whales were encountered throughout the entire survey area, which covered the majority of CCAMLR Management Area 48, they were particularly abundant around the South Orkney Islands and the eastern Bransfield Strait. Large feeding aggregations were also encountered within the central Scotia Sea between South Orkney Islands and South Georgia. Distance sampling analyses suggest an average fin whale density throughout the Scotia Sea of 0.0256 ( CV = 0.149 ) whales per km2, which agrees well with recent density estimates reported from smaller sub-regions within the Scotia Sea. Design-based distance sampling analyses resulted in an estimated total fin whale abundance of 53,873 (CV = 0.15, 95% CI 40,233-72,138), while a density surface model resulted in a slightly lower estimate of 50,837 (CV: 0.136, 95% CI 38,966-66,324). These estimates are at least an order of magnitude greater than the previous estimate from the same region based on the IDCR/SOWER-2000 data, suggesting that fin whales are undergoing a substantial abundance increase in the South Atlantic. This may have important implications for the assessment of cetacean population trends, but also for CCAMLRs spatial overlap analysis process and efforts to implement a Feedback Management system for Antarctic krill. Our abundance estimate suggests an annual summer krill consumption by fin whales in the Antarctic Peninsula and Scotia Sea area of 7.97 (95% CI 4.94-11.91) million tonnes, which would represent around 20 times the total krill catch taken by the commercial fishery in Area 48 in the same season, or about 12.7% of the 2019 summer krill standing stock estimated from data collected during the same survey. This highlights the crucial importance of including cetacean krill predators in assessment and management efforts for living marine resources in the Southern Ocean, and particularly stresses the urgent need for a re-appraisal of abundance, distribution and ecological role of Southern Hemisphere fin whales.

Population Structures and Dynamics of Rhododendron Communities with Different Stages of Succession in Northwest Guizhou, China

To explore the population structures and dynamics of Rhododendron shrub communities at different stages of succession in northwest Guizhou, China, this study examined the populations of Rhododendron annae and Rhododendron irroratum shrub with two different stages. A space-for-time substitution was employed to establish the diameter class/height structures, static life tables, and survival/mortality rate/disappearance rate curves of both Rhododendron populations with different orders of succession. Their structural and quantitative dynamics were analyzed, and their development trends were predicted. The results showed that, quantitatively, the populations of R. annae and R. irroratum in the two Rhododendron communities with different orders of succession were dominated by age classes one, two, and three as well as height classes i, ii, and iii. The number of Rhododendron plants at the three age classes and the three height classes accounted for 97.61-100% of the total. The quantitative dynamic indices of R. annae and R. irroratum were both greater than 0, with and without considering external interference. In terms of age class and height structures, both Rhododendron populations were expanding populations, presenting "inverted-J-shaped" and irregular pyramid patterns. There was a sufficient number of young individuals, but few or no old individuals. Both survival curves of the populations of R. annae and R. irroratum in the two Rhododendron communities with different orders of succession belonged to the Deevy-II type. In the late stage of succession, the mortality curves and disappearance curves of both Rhododendron populations in these communities presented a trend of increasing first and then decreasing with increasing age class. This result indicates that at each age class, R. annae and R. irroratum showed a trend of gradual increase after two, four, and six years. In brief, the populations of R. annae and R. irroratum have rich reserves of seedlings and saplings, but high mortality and disappearance rates. In this context, it is necessary to reduce human interference and implement targeted conservation measures to promote the natural renewal of Rhododendron populations.

Modeling time-varying phytoplankton subsidy reveals at-risk species in a Chilean intertidal ecosystem

The allometric trophic network (ATN) framework for modeling population dynamics has provided numerous insights into ecosystem functioning in recent years. Herein we extend ATN modeling of the intertidal ecosystem off central Chile to include empirical data on pelagic chlorophyll-a concentration. This intertidal community requires subsidy of primary productivity to support its rich ecosystem. Previous work models this subsidy using a constant rate of phytoplankton input to the system. However, data shows pelagic subsidies exhibit highly variable, pulse-like behavior. The primary contribution of our work is incorporating this variable input into ATN modeling to simulate how this ecosystem may respond to pulses of pelagic phytoplankton. Our model results show that: (1) closely related sea snails respond differently to phytoplankton variability, which is explained by the underlying network structure of the food web; (2) increasing the rate of pelagic-intertidal mixing increases fluctuations in species' biomasses that may increase the risk of local extirpation; (3) predators are the most sensitive species to phytoplankton biomass fluctuations, putting these species at greater risk of extirpation than others. Finally, our work provides a straightforward way to incorporate empirical, time-series data into the ATN framework that will expand this powerful methodology to new applications.

Changes in landscape and climate in Mexico and Texas reveal small effects on migratory habitat of monarch butterflies (Danaus plexippus)

The decline of the iconic monarch butterfly (Danaus plexippus) in North America has motivated research on the impacts of land use and land cover (LULC) change and climate variability on monarch habitat and population dynamics. We investigated spring and fall trends in LULC, milkweed and nectar resources over a 20-year period, and ~ 30 years of climate variables in Mexico and Texas, U.S. This region supports spring breeding, and spring and fall migration during the annual life cycle of the monarch. We estimated a - 2.9% decline in milkweed in Texas, but little to no change in Mexico. Fall and spring nectar resources declined < 1% in both study extents. Vegetation greenness increased in the fall and spring in Mexico while the other climate variables did not change in both Mexico and Texas. Monarch habitat in Mexico and Texas appears relatively more intact than in the midwestern, agricultural landscapes of the U.S. Given the relatively modest observed changes in nectar and milkweed, the relatively stable climate conditions, and increased vegetation greenness in Mexico, it seems unlikely that habitat loss (quantity or quality) in Mexico and Texas has caused large declines in population size or survival during migration.

7-day patterns in Black-White segregation in 49 metropolitan areas

While residential segregation is a persistent attribute of metropolitan areas, recent studies find segregation levels fluctuate throughout the day, reaching their lowest levels during daytime hours. This paper shows hourly variations in Black-White segregation from Monday through Sunday for the top 49 most populated metropolitan areas with Global Positioning System (GPS) data collected from mobile phones from October 2018. I find that segregation levels are higher on average over weekends compared to that of weekdays. I use models to identify the characteristics of neighborhoods with higher levels of segregation on weekends, which include all demographic variables and nearly a third of 35 sectors of businesses and organizations, such as retail, personal care, and religious organizations. I also find more than a third of the sectors are associated with higher levels of segregation during business hours on weekdays, including academic institutions, health care, manufacturing, and financial institutions. Findings from this paper display the significance in the distinction between weekdays and weekends with where people spend their time and how this relates to racial segregation. Specifically, Black people, on average, stay in their home census tracts and visit non-White neighborhoods for organizational resources more so than White people. Significant patterns of associations between racial segregation and the majority of businesses demonstrate the salience of race for more industries than previously understood.

Active microbial population dynamics and life strategies drive the enhanced carbon use efficiency in high-organic matter soils

Microbial carbon use efficiency (CUE) is a critical parameter that controls carbon storage in soil, but many uncertainties remain concerning adaptations of microbial communities to long-term fertilization that impact CUE. Based on H218O quantitative stable isotope probing coupled with metagenomic sequencing, we disentangled the roles of active microbial population dynamics and life strategies for CUE in soils after a long-term (35 years) mineral or organic fertilization. We found that the soils rich in organic matter supported high microbial CUE, indicating a more efficient microbial biomass formation and a greater carbon sequestration potential. Organic fertilizers supported active microbial communities characterized by high diversity and a relative increase in net growth rate, as well as an anabolic-biased carbon cycling, which likely explains the observed enhanced CUE. Overall, these results highlight the role of population dynamics and life strategies in understanding and predicting microbial CUE and sequestration in soil.IMPORTANCEMicrobial CUE is a major determinant of global soil organic carbon storage. Understanding the microbial processes underlying CUE can help to maintain soil sustainable productivity and mitigate climate change. Our findings indicated that active microbial communities, adapted to long-term organic fertilization, exhibited a relative increase in net growth rate and a preference for anabolic carbon cycling when compared to those subjected to chemical fertilization. These shifts in population dynamics and life strategies led the active microbes to allocate more carbon to biomass production rather than cellular respiration. Consequently, the more fertile soils may harbor a greater microbially mediated carbon sequestration potential. This finding is of great importance for manipulating microorganisms to increase soil C sequestration.

The prevalence of simian malaria in wild long-tailed macaques throughout Peninsular Malaysia

The parasite Plasmodium knowlesi has been the sole cause of malaria in Malaysia from 2018 to 2022. The persistence of this zoonotic species has hampered Malaysia's progress towards achieving the malaria-free status awarded by the World Health Organisation (WHO). Due to the zoonotic nature of P. knowlesi infections, it is important to study the prevalence of the parasite in the macaque host, the long-tailed macaque (Macaca fascicularis). Apart from P. knowlesi, the long-tailed macaque is also able to harbour Plasmodium cynomolgi, Plasmodium inui, Plasmodium caotneyi and Plasmodium fieldi. Here we report the prevalence of the 5 simian malaria parasites in the wild long-tailed macaque population in 12 out of the 13 states in Peninsular Malaysia using a nested PCR approach targeting the 18s ribosomal RNA (18s rRNA) gene. It was found that all five Plasmodium species were widely distributed throughout Peninsular Malaysia except for states with major cities such as Kuala Lumpur and Putrajaya. Of note, Pahang reported a malaria prevalence of 100% in the long-tailed macaque population, identifying it as a potential hotspot for zoonotic transmission. Overall, this study shows the distribution of the 5 simian malaria parasite species throughout Peninsular Malaysia, the data of which could be used to guide future malaria control interventions to target zoonotic malaria.

Post-settlement dynamics of Japanese flounder Paralichthys olivaceus in Tango Bay: Seasonal patterns in growth, mortality, and recruitment potential

Japanese flounder Paralichthys olivaceus is one of the most valuable coastal flatfish species in East Asia. To investigate post-settlement growth and mortality, juveniles were sampled in Tango Bay (Japan) weekly throughout the settlement period in 2007 and 2008. Otolith (lapillus) microstructure analysis enabled the categorization of juveniles into six biweekly cohorts each year. Later cohorts exhibited higher growth rates possibly because of higher water temperatures. A key observation was the direct relationship between high mortality and high density in mid-season cohorts in both years, pointing to density-dependent mortality. This increased mortality may be attributed to predation, including cannibalism by earlier cohorts. Furthermore, growth-selective mortality was evident soon after settlement, underscoring the vulnerability of slow growers to predation during the early juvenile stage. Although earlier and later cohorts were less abundant but showed promising recruitment potential, the prospective contribution of mid-season cohorts to the adult population remained uncertain. The results clearly highlight the importance of density-dependent mortality in population regulation in post-settlement Japanese flounder.

Application of machine learning with large-scale data for an effective vaccination against classical swine fever for wild boar in Japan

Classical swine fever has been spreading across the country since its re-emergence in Japan in 2018. Gifu Prefecture has been working diligently to control the disease through the oral vaccine dissemination targeting wild boars. Although vaccines were sprayed at 14,000 locations between 2019 and 2020, vaccine ingestion by wild boars was only confirmed at 30% of the locations. Here, we predicted the vaccine ingestion rate at each point by Random Forest modeling based on vaccine dissemination data and created prediction surfaces for the probability of vaccine ingestion by wild boar using spatial interpolation techniques. Consequently, the distance from the vaccination point to the water source was the most important variable, followed by elevation, season, road density, and slope. The area under the curve, model accuracy, sensitivity, and specificity for model evaluation were 0.760, 0.678, 0.661, and 0.685, respectively. Areas with high probability of wild boar vaccination were predicted in northern, eastern, and western part of Gifu. Leave-One-Out Cross Validation results showed that Kriging approach was more accurate than the Inverse distance weighting method. We emphasize that effective vaccination strategies based on epidemiological data are essential for disease control and that our proposed tool is also applicable for other wildlife diseases.

Concurrent threats and extinction risk in a long-lived, highly fecund vertebrate with parental care

Detecting declines and quantifying extinction risk of long-lived, highly fecund vertebrates, including fishes, reptiles, and amphibians, can be challenging. In addition to the false notion that large clutches always buffer against population declines, the imperiled status of long-lived species can often be masked by extinction debt, wherein adults persist on the landscape for several years after populations cease to be viable. Here we develop a demographic model for the eastern hellbender (Cryptobranchus alleganiensis), an imperiled aquatic salamander with paternal care. We examined the individual and interactive effects of three of the leading threats hypothesized to contribute to the species' demise: habitat loss due to siltation, high rates of nest failure, and excess adult mortality caused by fishing and harvest. We parameterized the model using data on their life history and reproductive ecology to model the fates of individual nests and address multiple sources of density-dependent mortality under both deterministic and stochastic environmental conditions. Our model suggests that high rates of nest failure observed in the field are sufficient to drive hellbender populations toward a geriatric age distribution and eventually to localized extinction but that this process takes decades. Moreover, the combination of limited nest site availability due to siltation, nest failure, and stochastic adult mortality can interact to increase the likelihood and pace of extinction, which was particularly evident under stochastic scenarios. Density dependence in larval survival and recruitment can severely hamper a population's ability to recover from declines. Our model helps to identify tipping points beyond which extinction becomes certain and management interventions become necessary. Our approach can be generalized to understand the interactive effects of various threats to the extinction risk of other long-lived vertebrates. As we face unprecedented rates of environmental change, holistic approaches incorporating multiple concurrent threats and their impacts on different aspects of life history will be necessary to proactively conserve long-lived species.

Climate change reduces long-term population benefits from no-take marine protected areas through selective pressures on species movement

Marine protected areas (MPAs) are important conservation tools that confer ecosystem benefits by removing fishing within their borders to allow stocks to rebuild. Fishing mortality outside a traditionally fixed MPA can exert selective pressure for low movement alleles, resulting in enhanced protection. While evolving to move less may be useful for conservation presently, it could be detrimental in the face of climate change for species that need to move to track their thermal optimum. Here, we build a spatially explicit simulation model to assess the impact of movement evolution in and around static MPAs resulting from both fishing mortality and temperature-dependent natural mortality on conservation benefits across five climate scenarios: (i) linear mean temperature shift, (ii) El Niño/La Niña conditions, (iii) heat waves, (iv) heatwaves with a mean temperature shift, and (v) no climate change. While movement evolution allows populations within MPAs to survive longer, we find that over time, climate change degrades the benefits by selecting for higher movement genotypes. Resulting population declines within MPAs are faster than expected based on climate mortality alone, even within the largest MPAs. Our findings suggest that while static MPAs may conserve species for a time, other strategies, such as dynamic MPA networks or assisted migration, may also be required to effectively incorporate climate change into conservation planning.

Population genomic evidence of structured and connected Plasmodium vivax populations under host selection in Latin America

Pathogen genomic epidemiology has the potential to provide a deep understanding of population dynamics, facilitating strategic planning of interventions, monitoring their impact, and enabling timely responses, and thereby supporting control and elimination efforts of parasitic tropical diseases. Plasmodium vivax, responsible for most malaria cases outside Africa, shows high genetic diversity at the population level, driven by factors like sub-patent infections, a hidden reservoir of hypnozoites, and early transmission to mosquitoes. While Latin America has made significant progress in controlling Plasmodium falciparum, it faces challenges with residual P. vivax. To characterize genetic diversity and population structure and dynamics, we have analyzed the largest collection of P. vivax genomes to date, including 1474 high-quality genomes from 31 countries across Asia, Africa, Oceania, and America. While P. vivax shows high genetic diversity globally, Latin American isolates form a distinctive population, which is further divided into sub-populations and occasional clonal pockets. Genetic diversity within the continent was associated with the intensity of transmission. Population differentiation exists between Central America and the North Coast of South America, vs. the Amazon Basin, with significant gene flow within the Amazon Basin, but limited connectivity between the Northwest Coast and the Amazon Basin. Shared genomic regions in these parasite populations indicate adaptive evolution, particularly in genes related to DNA replication, RNA processing, invasion, and motility - crucial for the parasite's survival in diverse environments. Understanding these population-level adaptations is crucial for effective control efforts, offering insights into potential mechanisms behind drug resistance, immune evasion, and transmission dynamics.

Microgeographic variation in demography and thermal regimes stabilize regional abundance of a widespread freshwater fish

Predicting the persistence of species under climate change is an increasingly important objective in ecological research and management. However, biotic and abiotic heterogeneity can drive asynchrony in population responses at small spatial scales, complicating species-level assessments. For widely distributed species consisting of many fragmented populations, such as brook trout (Salvelinus fontinalis), understanding the drivers of asynchrony in population dynamics can improve the predictions of range-wide climate impacts. We analyzed the demographic time series from mark-recapture surveys of 11 natural brook trout populations in eastern Canada over 13 years to examine the extent, drivers, and consequences of fine-scale population variation. The focal populations were genetically differentiated, occupied a small area (~25 km2 ) with few human impacts, and experienced similar climate conditions. Recruitment was highly asynchronous, weakly related to climate variables and showed population-specific relationships with other demographic processes, generating diverse population dynamics. In contrast, individual growth was mostly synchronized among populations and driven by a shared positive relationship with stream temperature. Outputs from population-specific models were unrelated to four of the five hypothesized drivers (recruitment, growth, reproductive success, phylogenetic distance), but variation in groundwater inputs strongly influenced stream temperature regimes and stock-recruitment relationships. Finally, population asynchrony generated a portfolio effect that stabilized regional species abundance. Our results demonstrated that population demographics and habitat diversity at microgeographic scales can play a significant role in moderating species responses to climate change. Moreover, we suggest that the absence of human activities within study streams preserved natural habitat variation and contributed to asynchrony in brook trout abundance, while the small study area eased monitoring and increased the likelihood of detecting asynchrony. Therefore, anthropogenic habitat degradation, landscape context, and spatial scale must be considered when developing management strategies to monitor and maintain populations that are diverse, stable, and resilient to climate change.

Evolution and emergence of Mycobacterium tuberculosis

Tuberculosis (TB) remains one of the deadliest infectious diseases in human history, prevailing even in the 21st century. The causative agents of TB are represented by a group of closely related bacteria belonging to the Mycobacterium tuberculosis complex (MTBC), which can be subdivided into several lineages of human- and animal-adapted strains, thought to have shared a last common ancestor emerged by clonal expansion from a pool of recombinogenic Mycobacterium canettii-like tubercle bacilli. A better understanding of how MTBC populations evolved from less virulent mycobacteria may allow for discovering improved TB control strategies and future epidemiologic trends. In this review, we highlight new insights into the evolution of mycobacteria at the genus level, describing different milestones in the evolution of mycobacteria, with a focus on the genomic events that have likely enabled the emergence and the dominance of the MTBC. We also review the recent literature describing the various MTBC lineages and highlight their particularities and differences with a focus on host preferences and geographic distribution. Finally, we discuss on putative mechanisms driving the evolution of tubercle bacilli and mycobacteria in general, by taking the mycobacteria-specific distributive conjugal transfer as an example.

A new trophic specialization buffers a top predator against climate-driven resource instability

Intraspecific phenotypic variability is key to respond to environmental changes and anomalies. However, documenting the emergence of behavioral diversification in natural populations has remained elusive due to the difficulty of observing such a phenomenon at the right time and place. Here, we investigated how the emergence of a new trophic strategy in a population subjected to high fluctuations in the availability of its main trophic resource (migrating songbirds) affected the breeding performance, population structure, and population fitness of a specialized color polymorphic predator, the Eleonora's falcon from the Canary Islands. Using long-term data (2007-2022), we found that the exploitation of an alternative prey (a local petrel species) was associated with the growth of a previously residual falcon colony. Pairs in this colony laid earlier and raised more fledglings than in the other established colonies. The specialization on petrels increased over time, independently of annual fluctuations in prey availability. Importantly, however, the positive effect of petrel consumption on productivity was stronger in years with lower food availability. This trophic diversification was further associated with the genetically determined color morph, with dark individuals preying more frequently on petrels than pale ones, which might promote the long-term maintenance of genotypic and phenotypic diversity. We empirically demonstrate how the emergence of an alternative trophic strategy can buffer populations against harsh environmental fluctuations by stabilizing their productivity.

Why so many polyploids? Accounting for environmental stochasticity in unreduced gamete formation lowers the perceived barriers to polyploid establishment

While polyploids are common in nature, existing models suggest that polyploid establishment should be difficult and rare. We explore this apparent paradox by focussing on the role of unreduced gametes, as their union is the main route for the formation of neopolyploids. Production of such gametes is affected by genetic and environmental factors, resulting in variation in the formation rate of unreduced gametes (u). Once formed, neopolyploids face minority cytotype exclusion (MCE) due to a lack of viable mating opportunities. More than a dozen theoretical models have explored factors that could permit neopolyploids to overcome MCE and become established. Until now, however, none have explored variability in u and its consequences for the rate of polyploid establishment. Here, we determine the distribution that best fits the available empirical data on u. We perform a global sensitivity analysis exploring the consequences of using empirical distributions of u to investigate effects on polyploid establishment. We determined that in many cases, u is best fit by a log-normal distribution. We found environmental stochasticity in u dramatically impacts model predictions when compared to a static u. Our results help reconcile previous modelling results suggesting high barriers to the polyploid establishment with the observation that polyploids are common in nature.

Global warming is projected to lead to increased freshwater growth potential and changes in pace of life in Atlantic salmon Salmo salar

Global warming has been implicated in widespread demographic changes in Atlantic salmon Salmo salar populations, but projections of life-history responses to future climate change are lacking. Here, we first exploit multiple decades of climate and biological data from the Burrishoole catchment in the west of Ireland to model statistical relationships between atmospheric variables, water temperature, and freshwater growth of juvenile Atlantic salmon. We then use this information to project potential changes in juvenile growth and life-history scheduling under three shared socioeconomic pathway and representative concentration pathway scenarios from 1961 to 2100, based on an ensemble of five climate models. Historical water temperatures were well predicted with a recurrent neural network, using observation-based atmospheric forcing data. Length-at-age was in turn also well predicted by cumulative growing degree days calculated from these water temperatures. Most juveniles in the Burrishoole population migrated to sea as 2-year-old smolts, but our future projections indicate that the system should start producing a greater proportion of 1-year-old smolts, as increasingly more juveniles cross a size-based threshold in their first summer for smoltification the following spring. Those failing to cross the size-based threshold will instead become 2-year-old smolts, but at a larger length relative to 2-year-old smolts observed currently, owing to greater overall freshwater growth opportunity. These changes in age- and size-at-seaward migration could have cascading effects on age- and size-at-maturity and reproductive output. Consequently, the seemingly small changes that our results demonstrate have the potential to cause significant shifts in population dynamics over the full life cycle. This workflow is highly applicable across the range of the Atlantic salmon, as well as to other anadromous species, as it uses openly accessible climate data and a length-at-age model with minimal input requirements, fostering improved general understanding of phenotypic and demographic responses to climate change and management implications.

Depth distribution of plant-parasitic nematodes on bentgrass golf greens in Missouri and Indiana

Control of plant-parasitic nematodes (PPNs) on golf putting greens with nematicides is dependent on the seasonal occurrence and depth distribution of target PPN populations. This study aimed to determine if plant-parasitic nematode populations on golf course putting greens in Missouri and Indiana peaked at a targetable depth at a specific time in the year, focusing primarily on lance (Hoplolaimus spp.) and root-knot (Meloidogyne spp.) nematodes. To elucidate species diversity in the region, rDNA from a subset of lance and root-knot nematodes was sequenced and analyzed, with additional micromorphology of a lance nematode assessed in scanning electron micrographs (SEM). Soil samples were taken to a depth of 25 cm and stratified into 5 cm increments during April, June, August and October at seven sites across Missouri, three in the Kansas City metro of Kansas in 2021 and in ten sites across Indiana in 2022. Samples were stratified in five-centimeter increments and aggregated for a total of 100 cm3 of soil at each depth for each sampling. Samples were processed using a semi-automatic elutriator followed by the sucrose-flotation method, and populations were counted using a hemocytometer and recorded. For molecular characterization, rDNA was extracted and analyzed from 31 individual lance nematodes from one site in Missouri and eight sites in Indiana, and 13 root-knot nematodes from nine sites across Indiana. A significant interaction occurred between sampling month and depth for lance and ring nematodes Missouri/KS, with both PPN populations peaking at the 0-5 cm depth during October, which is well after most targeted nematicide applications are applied. Ring nematodes in Indiana did not follow this trend and were most abundant in August at a depth of 0-5 cm. No significant interaction between depth and month occurred for lance or root-knot nematodes in Indiana, or root-knot nematodes in Missouri/KS. Hoplolaimus stephanus and H. magnistylus were the lance species identified on golf greens, and Meloidogyne naasi, M. graminicola and M. marylandi were the root-knot species identified. Scanning-electron micrographs confirmed morphological characteristics unique to H. stephanus.

Exploring the effects of competition and predation on the success of biological invasion through mathematical modeling

Biological invasions are a major cause of species extinction and biodiversity loss. Exotic predators are the type of introduced species that have the greatest negative impact, causing the extinction of hundreds of native species. Despite this, they continue to be intentionally introduced by humans. Understanding the causes that determine the success of these invasions is a challenge within the field of invasion biology. Mathematical models play a crucial role in understanding and predicting the behavior of exotic species in different ecosystems. This study examines the effect of predation and competition on the invasion success of an exotic generalist predator in a native predator-prey system. Considering that the exotic predator both consumes the native prey and competes with the native predator, it is necessary to study the interplay between predation and competition, as one of these interspecific interactions may either counteract or contribute to the impact of the other on the success of a biological invasion. Through a mathematical model, represented by a system of ordinary differential equations, it is possible to describe four different scenarios upon the arrival of the exotic predator in a native predator-prey system. The conditions for each of these scenarios are described analytically and numerically. The numerical simulations are performed considering the American mink (Mustela vison), an invasive generalist predator. The results highlight the importance of considering the interplay between interspecific interactions for understanding biological invasion success.

Seed traits and recruitment interact with habitats to generate patterns of local adaptation in a perennial grass

A fundamental challenge in the field of ecology involves understanding the adaptive traits and life history stages regulating the population dynamics of species across diverse habitats. Seed traits and early seedling vigor are thought to be key functional traits in plants with important consequences for recruitment, establishment, and population persistence. However, little is known about how diverse seed traits interact with seed and microsite availability to impact plant populations. Here, we performed a factorial experiment involving seed addition and surface soil disturbance to explore the combined effects of seed and site availability using genotypes characterized by varying seed mass and dormancy traits. Additionally, we included hybrids that exhibited recombined seed trait relationships compared to natural genotypes, allowing us to assess the impact of specific seed traits on establishment across different sites. We detected a significant three-way interaction between seed addition, site conditions, and soil surface disturbance, influencing both seedling establishment and adult recruitment in Panicum hallii, a perennial grass found in coastal mesic (lowland) and inland xeric (upland) habitats. This establishment/recruitment pattern suggests that mesic and xeric establishment at foreign sites is constrained by the interplay of seed and site limitations. Notably, soil surface disturbance facilitated establishment and recruitment of the xeric genotype while limiting the mesic genotype across all sites. Our results highlight the importance of seed size and dormancy as key factors impacting seedling establishment and adult recruitment, suggesting a potential interactive relationship between these traits.

Demographic patterns of two related desert shrubs with overlapping distributions in response to past climate changes

Numerous studies have revealed that past geological events and climatic fluctuations had profoundly affected the genetic structure and demographic patterns of species. However, related species with overlapping ranges may have responded to such environmental changes in different ways. In this study, we compared the genetic structure and population dynamics of two typical desert shrubs with overlapping distributions in northern China, Nitraria tangutorum and Nitraria sphaerocarpa, based on chloroplast DNA (cpDNA) variations and species distribution models. We sequenced two cpDNA fragments (trnH-trnA and atpH-atpI) in 633 individuals sampled from 52 natural populations. Twenty-four chlorotypes, including eight rare chlorotypes, were identified, and a single dominant haplotype (H4) widely occurred in the entire geographical ranges of the two species. There were also a few distinctive chlorotypes fixed in different geographical regions. Population structure analyses suggested that the two species had significantly different levels of total genetic diversity and interpopulation differentiation, which was highly likely correlated with the special habitat preferences of the two species. A clear phylogeographic structure was identified to exist among populations of N. sphaerocarpa, but not exist for N. tangutorum. The neutral tests, together with the distribution of pairwise differences revealed that N. tangutorum experienced a sudden demographic expansion, and its expansion approximately occurred between 21 and 7 Kya before present, while a rapid range expansion was not identified for N. sphaerocarpa. The ecological niche modeling (ENM) analysis indicated that the potential ranges of two species apparently fluctuated during the past and present periods, with obvious contraction in the Last Glacial Maximum (LGM) and recolonization in the present, respectively, comparing to the Last Interglacial (LIG). These findings suggest that the two species extensively occurred in the Northwest of China before the Quaternary, and the current populations of them originated from a few separated glacial refugia following their habitat fragmentation in the Quarternary. Our results provide new insights on the impact of past geological and climatic fluctuations on the population dynamics of desert plants in northwestern China, and further enforce the hypothesis that there were several independent glacial refugia for these species during the Quaternary glaciations.

Mass trapping of the diamondback moth (Plutella xylostella L.) by a combination of its sex pheromone and allyl isothiocyanate in cabbage fields in southern Vietnam

A lure composed of (Z)-11-hexadecenal, (Z)-11-hexadecenyl acetate, and (Z)-11-hexadecen-1-ol at a ratio of 5 : 5 : 1 at a dose of 0.01 mg was optimal for the attraction of the Vietnamese strain of the diamondback moth (DBM). The combination of the sex pheromone with a plant volatile, allyl isothiocyanate, significantly increased the attraction of the pheromone trap. Females were also attracted, but they were only about 2% of all moths captured. In plots with 120-130 traps per ha, mass trapping with the combined lures reduced the DBM larval densities in cabbage fields as effectively as the spraying of insecticides 6 to 8 times. The weekly trap catches indicated that DBM adult densities in the mass-trapping fields were low until 28 days after transplantation, and then were kept to a modest increase until day 49. This field study also shows that the trap catches were well correlated with the DBM larval densities.

Natural selection and genetic diversity maintenance in a parasitic wasp during continuous biological control application

Aphidius gifuensis is a parasitoid wasp and primary endoparasitoid enemy of the peach potato aphid, Myzus persicae. Artificially reared, captive wasps of this species have been extensively and effectively used to control populations of aphids and limit crop loss. However, the consequences of large-scale releasing of captive A. gifuensis, such as genetic erosion and reduced fitness in wild populations of this species, remains unclear. Here, we sequence the genomes of 542 A. gifuensis individuals collected across China, including 265 wild and 277 human-intervened samples. Population genetic analyses on wild individuals recovered Yunnan populations as the ancestral group with the most complex genetic structure. We also find genetic signature of environmental adaptation during the dispersal of wild populations from Yunnan to other regions. While comparative genomic analyses of captive wasps revealed a decrease in genetic diversity during long-term rearing, population genomic analyses revealed signatures of natural selection by several biotic (host plants) or abiotic (climate) factors, which support maintenance of the gene pool of wild populations in spite of the introduction of captive wasps. Therefore, the impact of large-scale release is reduced. Our study suggests that A. gifuensis is a good system for exploring the genetic and evolutionary effects of mass rearing and release on species commonly used as biocontrol agents.

Taking the beat of the Arctic: are lemming population cycles changing due to winter climate?

Reports of fading vole and lemming population cycles and persisting low populations in some parts of the Arctic have raised concerns about the spread of these fundamental changes to tundra food web dynamics. By compiling 24 unique time series of lemming population fluctuations across the circumpolar region, we show that virtually all populations displayed alternating periods of cyclic/non-cyclic fluctuations over the past four decades. Cyclic patterns were detected 55% of the time (n = 649 years pooled across sites) with a median periodicity of 3.7 years, and non-cyclic periods were not more frequent in recent years. Overall, there was an indication for a negative effect of warm spells occurring during the snow onset period of the preceding year on lemming abundance. However, winter duration or early winter climatic conditions did not differ on average between cyclic and non-cyclic periods. Analysis of the time series shows that there is presently no Arctic-wide collapse of lemming cycles, even though cycles have been sporadic at most sites during the last decades. Although non-stationary dynamics appears a common feature of lemming populations also in the past, continued warming in early winter may decrease the frequency of periodic irruptions with negative consequences for tundra ecosystems.

Airborne imagery does not preclude detectability issues in estimating bird colony size

Aerial images obtained by drones are increasingly used for ecological research such as wildlife monitoring. Yet detectability issues resulting from animal activity or visibility are rarely considered, although these may lead to biased population size and trend estimates. In this study, we investigated detectability in a census of Malagasy pond heron Ardeola idae colonies on the island of Mayotte. We conducted repeated drone flights over breeding colonies in mangrove habitats during two breeding seasons. We then identified individuals and nests in the images and fitted closed capture-recapture models on nest-detection histories. We observed seasonal variation in the relative abundance of individuals, and intra-daily variation in the relative abundance of individuals-especially immature birds-affecting the availability of nests for detection. The detection probability of nests estimated by capture-recapture varied between 0.58 and 0.74 depending on flyover days and decreased 25% from early to late morning. A simulation showed that three flyovers are necessary to detect a 5-6% decline in colonies of 50 to 200 nests. These results indicate that the detectability of nests of forest-canopy breeding species from airborne imagery can vary over space and time; we recommend the use of capture-recapture methods to control for this bias.

Breeding behavior analysis in a large captive colony of African penguins (Spheniscus demersus) and its implications for population management and conservation

The African penguin Spheniscus demersus, frequently housed in zoos, holds potential for future reintroduction efforts due to its declining wild population. This paper aims to explore various aspects of reproductive performance in African penguins within a large ex situ colony at Zoo Wrocław in Poland, covering 9 years of breeding behaviors. The analysis reveals parallels in colony growth and partner change patterns with those observed in the wild. Positive correlations were found between breeding success and pair-bond duration, with the increasing colony size influencing reproductive performance. Contrary to their wild counterparts, captive African penguins initiate breeding attempt and produce a fertilized egg at a younger age. However, successful breeding still requires gaining experience or forming pairs with more experienced partners. Our research indicates that providing captive African penguins with unlimited food resources and sufficient nesting space results in rapid colony growth. The increased colony size facilitates breeding behaviors that positively influence population dynamics, particularly through the maintenance of long-term pair bond relationships and the potential for partner changes when necessary or desirable to enhance breeding success. We present compelling case studies in pair fidelity, offering valuable insights and implications for the management of captive populations and conservation efforts.

Empirical dynamic modelling and enhanced causal analysis of short-length Culex abundance timeseries with vector correlation metrics

Employing Empirical Dynamic Modelling we investigate whether model free methods could be applied in the study of Culex mosquitoes in Northern Greece. Applying Simplex Projection and S-Map algorithms on yearly timeseries of maximum abundances from 2011 to 2020 we successfully predict the decreasing trend in the maximum number of mosquitoes which was observed in the rural area of Thessaloniki during 2021. Leveraging the use of vector correlation metrics we were able to deduce the main environmental factors driving mosquito abundance such as temperature, rain and wind during 2012 and study the causal interaction between neighbouring populations in the industrial area of Thessaloniki between 2019 and 2020. In all three cases a chaotic and non-linear behaviour of the underlying system was observed. Given the health risk associated with the presence of mosquitoes as vectors of viral diseases these results hint to the usefulness of EDM methods in entomological studies as guides for the construction of more accurate and realistic mechanistic models which are indispensable to public health authorities for the design of targeted control strategies and health prevention measures.

Population dynamics of Tribolium castaneum (Coleoptera: Tenebrionidae) in wheat and in wheat mixed with cracked wheat held in different types of containers

The population dynamics of Tribolium castaneum (Herbst), red flour beetle, was studied at 30 °C using long vertical columns (LVCs) (150 mm diameter and 1,020 mm long) and shallow containers (SCs) (460 mm long, 660 mm wide, and 150 mm high), containing 14 kg of whole wheat or a diet made of whole wheat and cracked wheat in 19:1 ratio by mass. The moisture content of the wheat or mixed diet was 14.5% (wb). Every 4 wk and up to 24 wk the live and dead adults were counted in the SCs or in each section of the LVCs. Each LVC was separated into 10 equal sections before removing grain from the LVC. After counting, the grains were incubated at 30 °C and 70% RH for 4 wk, and emerged adults after re-incubation were counted as offspring. The adults and offspring were mainly concentrated in the top section of the LVCs, which could be due to higher mortality in the lower sections and preference of T. castaneum for the surface of grain bulk. The diet influenced the population, and the insects developed better in the cracked wheat-based diet. Greater surface area of the container increased the multiplication and/ or survival of T. castaneum and insects inside SCs with larger surface area and with cracked wheat-based diet, had quicker population increase rate and larger carrying capacity than LVCs.

Exogenous salicylic acid induces defense responses in tea plants against Toxoptera aurantii (Hemiptera: Aphididae)

Toxoptera aurantii is one of the most destructive pests, threatening the yield and quality of tea plantations. The salicylic acid (SA)-mediated signaling pathway is vital for the induction of plant defense responses; however, its role in tea plant resistance to T. aurantii remains unclear. Thus, this study used and electrical penetration graph and monitoring of population dynamics to evaluate the effects of exogenous SA application on T. aurantii feeding behavior and population growth in tea seedlings. Moreover, the effects of SA treatment on the activities of defense-related enzymes were analyzed. Probe counts and the duration of xylem sap ingestion were significantly higher in SA-treated plants than those in the control group. The total duration of passive phloem ingestion was significantly decreased in 0.5 mmol/l SA-treated plants, and the application of 0.5, 1, and 4 mmol/l SA significantly inhibited T. aurantii population growth. In addition, the activities of polyphenol oxidase, peroxidase, and superoxide dismutase were significantly increased in the 0.5 mmol/l SA-treated plants. Overall, this study demonstrates the capacity of exogenous SA to activate defense responses against T. aurantii. These results have crucial implications for understanding the mechanisms of enhanced resistance, thereby providing a sustainable approach for managing T. aurantii.

Estimating blue mussel (Mytilus edulis) connectivity and settlement capacity in mid-latitude fjord regions

The mussel industry faces challenges such as low and inconsistent levels of larvae settlement and poor-quality spat, leading to variable production. However, mussel farming remains a vital sustainable and environmentally responsible method for producing protein, fostering ecological responsibility in the aquaculture sector. We investigate the population connectivity and larval dispersion of blue mussels (Mytilus edulis) in Scottish waters, as a case study, using a multidisciplinary approach that combined genetic data and particle modelling. This research allows us to develop a thorough understanding of blue mussel population dynamics in mid-latitude fjord regions, to infer gene-flow patterns, and to estimate population divergence. Our findings reveal a primary south-to-north particle transport direction and the presence of five genetic clusters. We discover a significant and continuous genetic material exchange among populations within the study area, with our biophysical model's outcomes aligning with our genetic observations. Additionally, our model reveals a robust connection between the southwest coast and the rest of the west coast. This study will guide the preservation of mussel farming regions, ensuring sustainable populations that contribute to marine ecosystem health and resilience.

Regional environmental differences significantly affect the genetic structure and genetic differentiation of Carpinus tientaiensis Cheng, an endemic and extremely endangered species from China

Differences in topography and environment greatly affect the genetic structure and genetic differentiation of species, and endemic or endangered species with limited geographic ranges seem to be more sensitive to changes in climate and other environmental factors. The complex topography of eastern China is likely to affect genetic differentiation of plants there. Carpinus tientaiensis Cheng is a native and endangered plants from China, and exploring its genetic diversity has profound significance for protection and the collection of germplasm resources. Based on AFLP markers, this study found that C. tientaiensis has low genetic diversity, which mainly came from within populations, while Shangshantou and Tiantai Mountain populations have relatively high genetic diversity. The Nei genetic distance was closely related to geographical distance, and temperature and precipitation notablely affected the genetic variation and genetic differentiation of C. tientaiensis. Based on cpDNA, this study indicated that C. tientaiensis exhibits a moderate level of genetic diversity, and which mainly came from among populations, while Tiantai Mountain population have the highest genetic diversity. It demonstrated that there was genetic differentiation between populations, which can be divided into two independent geographical groups, but there was no significant phylogeographic structure between them. The MaxEnt model showed that climate change significantly affects its distribution, and the suitable distribution areas in Zhejiang were primarily divided into two regions, eastern Zhejiang and southern Zhejiang, and there was niche differentiation in its suitable distribution areas. Therefore, this study speculated that the climate and the terrain of mountains and hills in East China jointly shape the genetic structure of C. tientaiensis, which gived rise to an obvious north-south differentiation trend of these species, and the populations located in the hilly areas of eastern Zhejiang and the mountainous areas of southern Zhejiang formed two genetic branches respectively.

Reduction in size-at-maturity in unprecedentedly strong cohorts of redfish (Sebastes mentella and S. fasciatus) in the Gulf of St. Lawrence and Laurentian Channel

Life-history traits, such as size-at-maturity, are key parameters to model population dynamics used to inform fisheries management. Fishery-induced evolution, density-dependent effects, and global warming have been shown to affect size- and age-at-maturity, and resulting spawning stock biomass (SSB) in a wide range of commercial fish stocks. Marked changes in redfish biomass and environmental conditions in the Gulf of St. Lawrence and Laurentian Channel over the past decade called for a review and update of size-at-maturity for commercially important deepwater redfish Sebastes mentella and Acadian redfish Sebastes fasciatus stocks. Following a 25-year moratorium, local redfish biomass has recently reached unprecedented levels, co-occurring with an overall warming of bottom water temperatures. Our objectives were (1) to perform a histological assessment of redfish reproduction stages, including the validation and fine-tuning of a robust visual chart to facilitate monitoring of size-at-maturity and SSB in a transforming environment, and (2) to evaluate changes in size-at-maturity in unprecedentedly strong cohorts of redfish, and consequences for stock status assessment and fisheries management. Each specimen was genetically identified to species, and gonad reproduction stages were determined by histology and macroscopic appearances. The present study enabled a robust visual chart for continued and cost-effective monitoring of redfish reproduction stages to be refined and validated, and has shown a large decrease in redfish length when 50% of the individuals are considered mature that led to an increase in estimates of SSB during the 2011-2021 period for S. mentella and S. fasciatus. These changes modified the perception of stock status, thus having significant implications for fisheries management. Given that fishery-induced evolution and community structure changes along with global warming are affecting numerous stocks worldwide, the present study outlines a major and global challenge for scientists and resources managers. As shown by our results, the monitoring and frequent updates of life-history traits in transforming environments are needed to provide reliable science advice for sustainable fisheries.

Movements and spatial distribution of an endangered fish (Sciaena umbra) within a marine protected area

The brown meagre (Sciaena umbra) is an endangered species, which requires specific protection measures to ensure its conservation. These measures need to be informed by high-quality scientific knowledge on their space use patterns. Here, we used acoustic telemetry to assess its seasonal movement patterns and habitat use within a marine protected area (MPA). Our results suggested that S. umbra is a highly sedentary species (home range < 1.0 km2) and, therefore, the MPA is extensive enough to protect the local population. Their population was discretely distributed in two main areas within the MPA, which was likely a result of habitat segregation and density-dependent movements. The temporal variability of their movements further uncovered when and where spawning occurs (mainly, but probably not only, in the fully protected area in June) and indicated that spillover of this species is limited but still possible. Overall, we highlight the importance of MPAs in the recovery of S. umbra, we advocate the need to perpetuate the current national fishing bans and extend it to other countries in the Mediterranean region, and we emphasize that considering the fine-scale movements of S. umbra in future management actions is key to achieving a successful recovery of their populations.

Longevity of companion dog breeds: those at risk from early death

The companion dog is one of the most phenotypically diverse species. Variability between breeds extends not only to morphology and aspects of behaviour, but also to longevity. Despite this fact, little research has been devoted to assessing variation in life expectancy between breeds or evaluating the potential for phylogenetic characterisation of longevity. Using a dataset of 584,734 unique dogs located within the UK, including 284,734 deceased, we present variation in longevity estimates within the following: parental lineage (purebred = 1 breed, crossbred ≥ 2 breeds), breed (n = 155), body size (large, medium, small), sex (male, female) and cephalic index (brachycephalic, mesocephalic, dolichocephalic). Survival estimates were then partitioned amongst phylogenetic clades: providing evidence that canine evolutionary history (via domestication and associated artificial selection) is associated with breed lifespan. This information provides evidence to inform discussions regarding pedigree health, whilst helping current/prospective owners, breeders, policy makers, funding bodies and welfare organisations improve decision making regarding canine welfare.

DEBBIES Dataset to study Life Histories across Ectotherms

Demographic models are used to explore how life history traits structure life history strategies across species. This study presents the DEBBIES dataset that contains estimates of eight life history traits (length at birth, puberty and maximum length, maximum reproduction rate, fraction energy allocated to respiration versus reproduction, von Bertalanffy growth rate, mortality rates) for 185 ectotherm species. The dataset can be used to parameterise dynamic energy budget integral projection models (DEB-IPMs) to calculate key demographic quantities like population growth rate and demographic resilience, but also link to conservation status or biogeographical characteristics. Our technical validation shows a satisfactory agreement between observed and predicted longevity, generation time, age at maturity across all species. Compared to existing datasets, DEBBIES accommodates (i) easy cross-taxonomical comparisons, (ii) many data-deficient species, and (iii) population forecasts to novel conditions because DEB-IPMs include a mechanistic description of the trade-off between growth and reproduction. This dataset has the potential for biologists to unlock general predictions on ectotherm population responses from only a few key life history traits.

Life table parameters and digestive physiology of Aulacophora lewisii Baly (Coleoptera: Chrysomelidae) on three Luffa acutangula (L.) Roxb. (Cucurbitaceae) cultivars

Aulacophora lewisii Baly (Coleoptera: Chrysomelidae) is an important pest of Luffa acutangula (L.) Roxb. (Cucurbitaceae) in India. Larvae of A. lewisii feed on the roots, while adults consume leaves of L. acutangula. In the current study, effects of three L. acutangula cultivars (Abhiskar, Debsundari, and Jaipur Long) on the life table parameters by age-stage, two-sex approach, and key digestive enzymatic activities (amylolytic, proteolytic, and lipolytic) of the larvae and adults of A. lewisii were determined. Further, nutrients (total carbohydrates, proteins, lipids, amino acids, and nitrogen content) and antinutrients (total phenols, flavonols, and tannins) present in the roots and leaves of three cultivars were estimated. The development time (egg to adult emergence) was fastest and slowest on Jaipur Long (31.80 days) and Abhiskar (40.91 days), respectively. Fecundity was highest and lowest on Jaipur Long (279.91 eggs) and Abhiskar (137.18 eggs), respectively. The intrinsic rate of increase (r) was lowest on Abhiskar (0.0511 day-1) and highest on Jaipur Long (0.0872 day-1). The net reproductive rate (R0) was lowest on Abhiskar (23.32 offspring female-1). The mean generation time (T) was shortest on Jaipur Long (52.59 days) and longest on Abhiskar (61.58 days). The amylolytic, proteolytic, and lipolytic activities of larvae and adults of A. lewisii were highest and lowest on Jaipur Long and Abhiskar, respectively. The lower level of nutrients and higher level of antinutrients influenced higher larval development time and lower fecundity of A. lewisii on Abhiskar than other cultivars. Our results suggest that Abhiskar cultivar could be promoted for cultivation.

Small rodent population cycles and plants - after 70 years, where do we go?

Small rodent population cycles characterise northern ecosystems, and the cause of these cycles has been a long-lasting central topic in ecology, with trophic interactions currently considered the most plausible cause. While some researchers have rejected plant-herbivore interactions as a cause of rodent cycles, others have continued to research their potential roles. Here, we present an overview of whether plants can cause rodent population cycles, dividing this idea into four different hypotheses with different pathways of plant impacts and related assumptions. Our systematic review of the existing literature identified 238 studies from 150 publications. This evidence base covered studies from the temperate biome to the tundra, but the studies were scattered across study systems and only a few specific topics were addressed in a replicated manner. Quantitative effects of rodents on vegetation was the best studied topic, and our evidence base suggests such that such effects may be most pronounced in winter. However, the regrowth of vegetation appears to take place too rapidly to maintain low rodent population densities over several years. The lack of studies prevented assessment of time lags in the qualitative responses of vegetation to rodent herbivory. We conclude that the literature is currently insufficient to discard with confidence any of the four potential hypotheses for plant-rodent cycles discussed herein. While new methods allow analyses of plant quality across more herbivore-relevant spatial scales than previously possible, we argue that the best way forward to rejecting any of the rodent-plant hypotheses is testing specific predictions of dietary variation. Indeed, all identified hypotheses make explicit assumptions on how rodent diet taxonomic composition and quality will change across the cycle. Passing this bottleneck could help pinpoint where, when, and how plant-herbivore interactions have - or do not have - plausible effects on rodent population dynamics.

Accounting for unobserved population dynamics and aging error in close-kin mark-recapture assessments

Obtaining robust estimates of population abundance is a central challenge hindering the conservation and management of many threatened and exploited species. Close-kin mark-recapture (CKMR) is a genetics-based approach that has strong potential to improve the monitoring of data-limited species by enabling estimates of abundance, survival, and other parameters for populations that are challenging to assess. However, CKMR models have received limited sensitivity testing under realistic population dynamics and sampling scenarios, impeding the application of the method in population monitoring programs and stock assessments. Here, we use individual-based simulation to examine how unmodeled population dynamics and aging uncertainty affect the accuracy and precision of CKMR parameter estimates under different sampling strategies. We then present adapted models that correct the biases that arise from model misspecification. Our results demonstrate that a simple base-case CKMR model produces robust estimates of population abundance with stable populations that breed annually; however, if a population trend or non-annual breeding dynamics are present, or if year-specific estimates of abundance are desired, a more complex CKMR model must be constructed. In addition, we show that CKMR can generate reliable abundance estimates for adults from a variety of sampling strategies, including juvenile-focused sampling where adults are never directly observed (and aging error is minimal). Finally, we apply a CKMR model that has been adapted for population growth and intermittent breeding to two decades of genetic data from juvenile lemon sharks (Negaprion brevirostris) in Bimini, Bahamas, to demonstrate how application of CKMR to samples drawn solely from juveniles can contribute to monitoring efforts for highly mobile populations. Overall, this study expands our understanding of the biological factors and sampling decisions that cause bias in CKMR models, identifies key areas for future inquiry, and provides recommendations that can aid biologists in planning and implementing an effective CKMR study, particularly for long-lived data-limited species.

Genomic variation in montane bumblebees in Scandinavia: High levels of intraspecific diversity despite population vulnerability

Populations of many bumblebee species are declining, with distributions shifting northwards to track suitable climates. Climate change is considered a major contributing factor. Arctic species are particularly vulnerable as they cannot shift further north, making assessment of their population viability important. Analysis of levels of whole-genome variation is a powerful way to analyse population declines and fragmentation. Here, we use genome sequencing to analyse genetic variation in seven species of bumblebee from the Scandinavian mountains, including two classified as vulnerable. We sequenced 333 samples from across the ranges of these species in Sweden. Estimates of effective population size (NE ) vary from ~55,000 for species with restricted high alpine distributions to 220,000 for more widespread species. Population fragmentation is generally very low or undetectable over large distances in the mountains, suggesting an absence of barriers to gene flow. The relatively high NE and low population structure indicate that none of the species are at immediate risk of negative genetic effects caused by high levels of genetic drift. However, reconstruction of historical fluctuations in NE indicates that the arctic specialist species Bombus hyperboreus has experienced population declines since the last ice age and we detected one highly inbred diploid male of this species close to the southern limit of its range, potentially indicating elevated genetic load. Although the levels of genetic variation in montane bumblebee populations are currently relatively high, their ranges are predicted to shrink drastically due to the effects of climate change and monitoring is essential to detect future population declines.