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Predicting the effects of warming temperatures on the abundance and distribution of organisms under future climate scenarios often requires extrapolating species-environment correlations to climatic conditions not currently experienced by a species, which can result in unrealistic predictions. For poikilotherms, incorporating species' thermal physiology to inform extrapolations under novel thermal conditions can result in more realistic predictions. Furthermore, models that incorporate species and spatial dependencies may improve predictions by capturing correlations present in ecological data that are not accounted for by predictor variables. Here, we present a joint species, spatially dependent physiologically guided abundance (jsPGA) model for predicting multispecies responses to climate warming. The jsPGA model uses a basis function approach to capture both species and spatial dependencies. We apply the jsPGA model to predict the response of eight fish species to projected climate warming in thousands of lakes in Minnesota, USA. By the end of the century, the cold-adapted species was predicted to have high probabilities of extirpation across its current range-with 10% of lakes currently inhabited by this species having an extirpation probability >0.90. The remaining species had varying levels of predicted changes in abundance, reflecting differences in their thermal physiology. Though the model did not identify many strong species dependencies, the variation in estimated spatial dependence across species suggested that accounting for both dependencies was important for predicting the abundance of these fishes. The jsPGA model provides a new tool for predicting changes in the abundance, distribution, and extirpation probability of poikilotherms under novel thermal conditions.

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.

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.

The coexistence of obligate mutualists is often precariously close to tipping points where small environmental changes can drive catastrophic shifts in species composition. For example, microbial ecosystems can collapse by the decline of a strain that provides an essential resource on which other strains cross-feed. Here, we show that tipping points, ecosystem collapse, bistability and hysteresis arise even with very weak (non-obligate) mutualism provided the population is spatially structured. Based on numeric solutions of a metacommunity model and mean-field analyses, we demonstrate that weak mutualism lowers the minimal dispersal rate necessary to avoid stochastic extinction, while species need to overcome a mean threshold density to survive in this low dispersal rate regime. Our results allow us to make numerous predictions for mutualistic metacommunities regarding tipping points, hysteresis effects, and recovery from external perturbations, and let us draw general conclusions for ecosystems even with random, not necessarily mutualistic, interactions and systems with density-dependent dispersal rather than direct mutualistic interactions.

In this paper we study the permanence and impermanence for continuous-time competitive Kolmogorov systems via the carrying simplex. We first give an extension to attractors of V. Hutson's results on the existence of repellors in continuous-time dynamical systems that have found wide use in the study of permanence via average Liapunov functions. We then give a general criterion for the stability of the boundary of carrying simplex for competitive Kolmogorov systems of differential equations, which determines the permanence and impermanence of such systems. Based on the criterion, we present a complete classification of the permanence and impermanence in terms of inequalities on parameters for all three-dimensional competitive systems which have linearly determined nullclines. The results are applied to many classical models in population dynamics including the Lotka-Volterra system, Gompertz system, Leslie-Gower system and Ricker system. [ABSTRACT FROM AUTHOR]

High-throughput sequencing (HTS) has revolutionized microbiology, but many microbes exist at low abundance in their natural environment and/or are difficult, if not impossible, to culture in the laboratory. This makes it challenging to use HTS to study the genomes of many important microbes and pathogens. In this review, we discuss the development and application of selective whole genome amplification (SWGA) to allow whole or partial genomes to be sequenced for low abundance microbes directly from complex biological samples. We highlight ways in which genomic data generated by SWGA have been used to elucidate the population dynamics of important human pathogens and monitor development of antimicrobial resistance and the emergence of potential outbreaks. We also describe the limitations of this method and propose some potential innovations that could be used to improve the quality of SWGA and lower the barriers to using this method across a wider range of infectious pathogens. [ABSTRACT FROM AUTHOR]

Pathogens such as bacteria, fungi and viruses are important components of soil and aquatic communities, where they can benefit from decaying and living organic matter, and may opportunistically infect human and animal hosts. One-third of human infectious diseases is constituted by sapronotic disease agents that are natural inhabitants of soil or aquatic ecosystems. They are capable of existing and reproducing in the environment outside of the host for extended periods of time. However, as ecological research on sapronosis is infrequent and epidemiological models are even rarer, very little information is currently available. Their importance is overlooked in medical and veterinary research, as well as the relationships between free environmental forms and those that are pathogenic. Here, using dynamical models in realistic aquatic metacommunity systems, we analyze sapronosis transmission, using the human pathogen Mycobacterium ulcerans that is responsible for Buruli ulcer. We show that the persistence of bacilli in aquatic ecosystems is driven by a seasonal upstream supply, and that the attachment and development of cells to aquatic living forms is essential for such pathogen persistence and population dynamics. Our work constitutes the first set of metacommunity models of sapronotic disease transmission, and is highly flexible for adaptation to other types of sapronosis. The importance of sapronotic agents on animal and human disease burden needs better understanding and new models of sapronosis disease ecology to guide the management and prevention of this important group of pathogens. Author summary: Bacterial pathogens responsible for sapronotic diseases represent a threat to public health, accounting for one-third of human infections. However, little is known about variations in infection risk in time and space, hence limiting control strategies development, due to a lack of research on these pathogens. In this study, we developed a first realistic mathematical model to describe the spatial and temporal dynamics of sapronotic bacteria and their interactions with wildlife in aquatic ecosystems. Our model allows identifying the characteristics of wildlife-sapronotic bacteria interactions that play the most important role in determining disease risks in animals and humans. [ABSTRACT FROM AUTHOR]

Thalamic brain areas play an important role in adaptive behaviors. Nevertheless, the population dynamics of thalamic relays during learning across sensory modalities remain unknown. Using a cross-modal sensory reward-associative learning paradigm combined with deep brain two-photon calcium imaging of large populations of auditory thalamus (medial geniculate body, MGB) neurons in male mice, we identified that MGB neurons are biased towards reward predictors independent of modality. Additionally, functional classes of MGB neurons aligned with distinct task periods and behavioral outcomes, both dependent and independent of sensory modality. During non-sensory delay periods, MGB ensembles developed coherent neuronal representation as well as distinct co-activity network states reflecting predicted task outcome. These results demonstrate flexible cross-modal ensemble coding in auditory thalamus during adaptive learning and highlight its importance in brain-wide cross-modal computations during complex behavior. The computational role of individual sensory thalamic nuclei in flexible encoding during adaptive behaviors is not fully understood. Here authors, using longitudinal deep brain two-photon calcium imaging, show that changes in mouse auditory thalamus single cell and neuronal population dynamics are predictive of task outcome in cross-modal associative learning. [ABSTRACT FROM AUTHOR]

ABSTRACT The L‐tryptophan–derived purple pigment violacein (VIO) is produced in recombinant bacteria and studied for its versatile applications. Microbial synthetic co‐cultures are gaining more importance as efficient factories for synthesizing high‐value compounds. In this work, a mutualistic and cross‐feeding Escherichia coli co‐culture is metabolically engineered to produce VIO. The strains are genetically modified by auxotrophies in the tryptophan (TRP) pathway to enable a metabolic division of labor. Therein, one strain produces anthranilate (ANT) and the other transforms it into TRP and further to VIO. Population dynamics and stability depend on the choice of carbon source, impacting the presence and thus exchange of metabolites as well as overall VIO productivity. Four carbon sources (D‐glucose, glycerol, D‐galactose, and D‐xylose) were compared. D‐Xylose led to co‐cultures which showed stable growth and VIO production, ANT‐TRP exchange, and enhanced VIO production. Best titers were ∼126 mg L–1 in shake flasks. The study demonstrates the importance and advantages of a mutualistic approach in VIO synthesis and highlights the carbon source's role in co‐culture stability and productivity. Transferring this knowledge into an up‐scaled bioreactor system has great potential in improving the overall VIO production. [ABSTRACT FROM AUTHOR]

We consider a general impulsive reaction-diffusion equation with shifting environment and birth pulse, both induced by climate changes, to capture essential features of the dynamics of species exhibiting distinct stages of reproduction and dispersal. We convert this model into a discrete-time semiflow, and hence to a discrete-time recursion system. We establish the existence of forced waves and asymptotic spreading properties of solutions, and obtain sufficient conditions for the global asymptotic stability of the forced waves. [ABSTRACT FROM AUTHOR]

Traditional assays for counting bacteriophages and their lysogens are labor-intensive and perturbative to the host cells. Here, we present a high-throughput infection method in a microplate reader, where the growth dynamics of the infected culture is measured using the optical density (OD). We find that the OD at which the culture lyses scales linearly with the logarithm of the initial phage concentration, providing a way of measuring phage numbers over nine orders of magnitude and down to single-phage sensitivity. Interpreting the measured dynamics using a mathematical model allows us to infer the phage growth rate, which is a function of the phage-cell encounter rate, latent period, and burst size. Adding antibiotic selection provides the ability to measure the rate of host lysogenization. Using this method, we found that when E. coli growth slows down, the lytic growth rate of lambda phages decreases, and the propensity for lysogeny increases, demonstrating how host physiology influences the viral developmental program. Traditional assays for counting bacteriophages and their lysogens are labor-intensive and perturbative to the host cells. Here, the authors present a high-throughput method that can be used to estimate the number of phages in a sample, by measuring growth dynamics of the infected culture in a microplate reader. [ABSTRACT FROM AUTHOR]

Rabies is a neglected disease primarily related to dog-mediated transmission to humans. Accurate dog demographic and dynamic data are essential for effectively planning and evaluating population management strategies when designing interventions to prevent rabies. However, in Thailand, longitudinal survey data regarding dog population size are scarce. A school-based participatory research (SBPR) approach was conducted to survey owned dogs for one year in four high-risk provinces (Chiang Rai, Surin, Chonburi, and Songkhla) of Thailand, aiming to understand dog population dynamics and raise awareness about rabies. 'Pupify' mobile application was developed to collect data on dog population and observe the long-term population dynamics in this study. At the end of the data collection period, telephone interviews were conducted to gain insight into contextual perceptions and awareness regarding both animal and human rabies, as well as the social responsibility of dog owners in disease prevention and control. Among 303 high school students who registered in our study, 218 students reported at least one update of their dog information throughout the one-year period. Of 322 owned dogs from our survey, the updates of dog status over one year showed approximately 7.5 newborns per 100-dog-year, while deaths and missing dogs were 6.2 and 2.7 per 100-dog-year, respectively. The male to female ratio was approximately 1.8:1. Twenty-three students (10%) voluntarily participated and were interviewed in the qualitative study. The levels of rabies awareness and precautions among high-school students were relatively low. The high dropout rate of the survey was due to discontinuity in communication between the researcher and the students over the year. In conclusion, this study focused on using the SBPR approach via mobile application to collect data informing dog population dynamics and raising awareness regarding rabies in Thailand Other engaging platforms (e.g. Facebook, Instagram, Twitter, and other popular applications) is necessary to enhance communication and engagement, thereby sustaining and maintaining data collection. Further health education on rabies vaccination and animal-care practices via social media platforms would be highly beneficial. For sustainable disease control, engaging communities to raise awareness of rabies and increase dog owners' understanding of their responsibilities should be encouraged. [ABSTRACT FROM AUTHOR]

Freshwater mussels preserve valuable information about hydrology, climate, and population dynamics, but developing seasonal chronologies can be problematic. Using clumped isotope thermometry, we produced high-resolution reconstructions of modern and historic (~ 1900) temperatures and δ18Owater from mussel shells collected from an impounded river, the Brazos in Texas, before and after damming. We also performed high-resolution growth band analyses to investigate relationships between mussel growth rate, rainfall, and seasonal temperature. Reconstructed δ18Owater and temperature vary little between the modern (3R5) and historic shell (H3R). However, a positive relationship between reconstructed δ18Owater and growth rate in H3R indicates that aside from diminished growth in winter, precipitation and flow rate are the strongest controls on mussel growth in both modern and pre-dam times. Overall, our results demonstrate (1) the impact, both positive and negative, of environmental factors such as flow alteration and temperature on mussel growth and (2) the potential for clumped isotopes in freshwater mussels as a paleohydrology and paleoclimate proxies in terrestrial environments. [ABSTRACT FROM AUTHOR]

Morphometric characteristics of fishes were observable characteristics that are set of largely statistical methods used for examining variations in body size and shape. The objectives taken for the current study were to examine the complete morpho-biology of Schizothorax richardsonii from three major snow-fed rivers of the Kumaun Himalaya in Uttarakhand, India, and to establish the statistical relationship among various morphological characteristics related to body size and fin shape. In this study 120 fish specimen including 66 male and 54 female were studied for one year. Twelve distinct morphometric and five meristic counts had been examined in percentage of their body length and head length respectively. For biostatistics, the data was analysed by using various statistical methods including summary statistics, correlation, PCA analysis, Barlett’s test of sphericity, and multiple linear regression. Fish samples studied were found within the range of 17.7 – 42.2 cm in TL and BW from 60 - 780 gm. Morphological characteristics had high coefficient of correlation (r ≥ 0.90), indicating the characters' strong relationship, with the highest correlation (r = 0.99). Additionally, the coefficient of determination (R² ) value was found within the range of 0.62 to 0.99, which shows a significant relationship between the morphometric characteristics. PCA analysis revealed the major significance found among parameters, together with regression analysis. This study will provide a baseline data and a valuable insight into the population dynamics, and may contribute to the development of more effective strategies for the management. [ABSTRACT FROM AUTHOR]

Predation has direct effects on prey population dynamics through mortality, and it can induce indirect effects through fear. The indirect effects of predation have been documented experimentally, but few studies have quantified them in nature so that their role in prey population dynamics remains controversial. Given the expanding or reintroduced populations of large predators in many areas, the quantification of indirect effects of predation is crucial. We sought to evaluate the direct and indirect fitness effects of intense cougar (Puma concolor) predation using 48 years of data on marked bighorn sheep (Ovis canadensis) on Ram Mountain, Alberta, Canada. We compared years of intense cougar predation with years with no or occasional cougar predation. We first quantified the effects of predation on neonatal, weaning, and overwinter lamb survival, three metrics potentially affected by direct and indirect effects. We then investigated the possible indirect effects of intense cougar predation on lamb production, female summer mass gain, and lamb mass at weaning. We found strong effects of cougar predation on lamb survival, lamb production, and seasonal mass gain of lambs and adult females. In years with high predation, neonatal, weaning, and overwinter lamb survival declined by 18.4%, 19.7% and 20.8%, respectively. Indirect effects included a 14.2% decline in lamb production. Female summer mass gain decreased by 15.6% and lamb mass at weaning declined by 8.0% in years of intense cougar predation. Our findings bring key insights on the impacts of predation on prey fitness by reporting moderate to large effects on recruitment and illustrate the importance of indirect effects of predation on population dynamics. [ABSTRACT FROM AUTHOR]

Mangrove clam is the most sought-after bivalve in the Philippines due to its taste, size, and nutrition. Due to its economic importance, this paper aims to determine the population dynamics of mangrove clam P. philippiana harvested in gleaning sites in the Davao region using the FAO ICLARM Stock Assessment Tool (FISAT II). A total of 2493 clams collected from December 2018-December 2020 with sizes ranging from 14-84 mm SL and 2.2-178.6 g were classified according to size classes with 5 mm intervals. The length-weight relationship was computed and showed negative allometry (a = 0.002, b = 2.6205, R² = 0.89). The estimated growth parameters using ELEFAN I was L∞ = 98.64 mm, K = 1.33 year-1, t0 = -1.07. Length converted catch curve routine estimated Z = 10.27year-1, M = 1.52 year-1, F = 8.75 year-1, E = 0.85, and backward extrapolation generated Lc50 = 34.83 mm SL which is below Lm = 65.76 mm SL. Recruitment patterns were highest during July and August 2020, and VPA showed a high F at 60 mm SL. Beverton and Holt Y/R analysis showed E0.5 = 0.328 and Emax = 0.551, yield isopleths derived from plotted Lc50/L∞ = 0.353 and E = 0.85 values were within quadrant D. The result revealed that Lm>Lc50 implies that mangrove clams gleaned in the area were small and immature. Moreover, F>Fopt and E>Emax and E>E0.5 suggest that mangrove clam fishery in the region was heavily exploited. The study concluded that the mangrove clam Pegophysema philippiana was overexploited and that a management strategy was needed in the Davao Region, Philippines. [ABSTRACT FROM AUTHOR]

Conservation decisions are often based on population models that rely on underlying assumptions made about species' demographic parameters. The Rio Grande Cooter (Pseudemys gorzugi) is a conservation-dependent riverine turtle, but our understanding of its population dynamics has been limited due to the absence of long-term surveys. We used mark-recapture data collected between 2016 and 2022 from the Black River, New Mexico, USA, to evaluate P. gorzugi somatic growth parameters. Females reached larger maximum size than males but exhibited a slower growth rate. We observed only a slight difference in maximum length and Brody growth coefficient of turtles from different locations, but the growth coefficients were overall significantly lower than any other Pseudemys species. Turtles on the Black River represent the northernmost robust population of P. gorzugi. In light of the intense human use of the river and riparian areas coupled with the impacts of climate change, it is imperative to maintain commitment to conservation efforts to resist population declines given the slow somatic growth rate of the population. [ABSTRACT FROM AUTHOR]

Aim: This study investigates the biogeographic patterns of Pacific white‐sided dolphins (Lagenorhynchus obliquidens) in the Eastern North Pacific based on long‐term passive acoustic records. We aim to elucidate the ecological and behavioural significance of distinct echolocation click types and their implications for population delineation, geographic distribution, environmental adaptation and management. Location: Eastern North Pacific Ocean. Time Period: 2005–2021. Major Taxa Studied: Pacific white‐sided dolphin. Methods: Over 50 cumulative years of passive acoustic monitoring (PAM) data from 14 locations were analyzed using a deep neural network to classify two distinct Pacific white‐sided dolphin echolocation click types. The study assessed spatial, diel, seasonal and interannual patterns of the two click types, correlating them with major environmental drivers such as the El Niño Southern Oscillation and the North Pacific Gyre Oscillation, and modeling long‐term spatial‐seasonal patterns. Results: Distinct spatial, diel and seasonal patterns were observed for each click type. Significant biogeographical shifts in presence were observed following the 2014–2016 marine heatwave event. Main Conclusions: Distinct spatial distributions of the two click types support the hypothesis that Pacific white‐sided dolphins produce population‐specific echolocation clicks. Seasonal and diel patterns suggest spatiotemporal niche partitioning between the populations in Southern California. Interannual changes, notably initiated during the 2014–2016 marine heatwave, indicate climate‐driven range expansions and contractions related to gradual tropicalization of the Southern California Bight. [ABSTRACT FROM AUTHOR]

Species interaction effects on populations can vary in both magnitude (i.e. strong vs. weak) and sign (positive, negative, or no effect). Context‐dependent effects of species interactions occur when the sign or strength of the interaction's effect on population growth rate changes across abiotic gradients. We know that species can vary substantially in the degree of context dependence they exhibit, even across similar abiotic gradients. However, few studies have characterised context dependence of co‐occurring species, limiting our ability to understand the implications of context dependence for species interaction effects on community composition. Using over three decades of data collected for 13 tallgrass prairie forbs at the Konza Prairie Biological Station, we parameterise density structured population models that predict population dynamics as functions of abiotic conditions and bison herbivory. We use these models to estimate the degree of context dependence in responses to bison herbivory for 13 species across three abiotic gradients: weather, fire frequency and soil type. All species showed significant context dependence for fire frequency in the same direction, though with variable magnitude, such that herbivory increased cover with more frequent fires. Context dependence with weather and soil type varied dramatically across species in both direction and magnitude. For example, herbivory effects on 3/13 species were stronger in wet conditions, but herbivory effects on 5/13 species were stronger in dry conditions. Thus, context dependence exhibited by individual species, as opposed to effects of abiotic conditions on the relative abundances of species, could generate much of the weather‐dependent effects of herbivory on community composition. Synthesis: Our work suggests that species can vary dramatically in the presence, direction and magnitude of context dependence, even when occurring in the same community and when considering the same species interaction (i.e. response to a herbivore). In addition, we find that context dependence could drive substantial variation in the effect of species interactions on community characteristics (e.g. composition) across multiple abiotic gradients. [ABSTRACT FROM AUTHOR]

Studying the mechanisms shaping age-related changes in behavior ("behavioral aging") is important for understanding population dynamics in our changing world. Yet, studies that capture within-individual behavioral changes in wild populations of long-lived animals are still scarce. Here, we used a 15-y GPS-tracking dataset of a social obligate scavenger, the griffon vulture (Gyps fulvus), to investigate age-related changes in movement and social behaviors, and disentangle the role of behavioral plasticity and selective disappearance in shaping such patterns. We tracked 142 individuals for up to 12 y and found a nonlinear increase in site fidelity with age: a sharp increase in site fidelity before sexual maturity (<5 y old), stabilization during adulthood (6 to 15 y), and a further increase at old age (>15 y). This pattern resulted from individuals changing behavior throughout their life (behavioral plasticity) and not from selective disappearance. Mature vultures increased the predictability of their movement routines and spent more nights at the most popular roosting sites compared to younger individuals. Thus, adults likely have a competitive advantage over younger conspecifics. These changes in site fidelity and movement routines were mirrored in changes to social behavior. Older individuals interacted less with their associates (decreasing average strength with age), particularly during the breeding season. Our results reveal a variety of behavioral aging patterns in long-lived species and underscore the importance of behavioral plasticity in shaping such patterns. Comprehensive longitudinal studies are imperative for understanding how plasticity and selection shape the persistence of wild animal populations facing human-induced environmental changes. [ABSTRACT FROM AUTHOR]

The fluid movement of an arm requires multiple spatiotemporal parameters to be set independently. Recent studies have argued that arm movements are generated by the collective dynamics of neurons in motor cortex. An untested prediction of this hypothesis is that independent parameters of movement must map to independent components of the neural dynamics. Using a task where three male monkeys made a sequence of reaching movements to randomly placed targets, we show that the spatial and temporal parameters of arm movements are independently encoded in the low-dimensional trajectories of population activity in motor cortex: each movement’s direction corresponds to a fixed neural trajectory through neural state space and its speed to how quickly that trajectory is traversed. Recurrent neural network models show that this coding allows independent control over the spatial and temporal parameters of movement by separate network parameters. Our results support a key prediction of the dynamical systems view of motor cortex, and also argue that not all parameters of movement are defined by different trajectories of population activity [ABSTRACT FROM AUTHOR]

Donkeys (Equus asinus) have been used extensively in agriculture and transportations since their domestication, ca. 5000–7000 years ago, but the increased mechanization of the last century has largely spoiled their role as burden animals, particularly in developed countries. Consequently, donkey breeds and population sizes have been declining for decades, and the diversity contributed by autochthonous gene pools has been eroded. Here, we examined coding-region data extracted from 164 complete mitogenomes and 1392 donkey mitochondrial DNA (mtDNA) control-region sequences to (i) assess worldwide diversity, (ii) evaluate geographical patterns of variation, and (iii) provide a new nomenclature of mtDNA haplogroups. The topology of the Maximum Parsimony tree confirmed the two previously identified major clades, i.e. Clades 1 and 2, but also highlighted the occurrence of a deep-diverging lineage within Clade 2 that left a marginal trace in modern donkeys. Thanks to the identification of stable and highly diagnostic coding-region mutational motifs, the two lineages were renamed as haplogroup A and haplogroup B, respectively, to harmonize clade nomenclature with the standard currently adopted for other livestock species. Control-region diversity and population expansion metrics varied considerably between geographical areas but confirmed North-eastern Africa as the likely domestication center. The patterns of geographical distribution of variation analyzed through phylogenetic networks and AMOVA confirmed the co-occurrence of both haplogroups in all sampled populations, while differences at the regional level point to the joint effects of demography, past human migrations and trade following the spread of donkeys out of the domestication center. Despite the strong decline that donkey populations have undergone for decades in many areas of the world, the sizeable mtDNA variability we scored, and the possible identification of a new early radiating lineage further stress the need for an extensive and large-scale characterization of donkey nuclear genome diversity to identify hotspots of variation and aid the conservation of local breeds worldwide. [ABSTRACT FROM AUTHOR]

Species‐specific phenological responses to changing climate are reshuffling the timing of species interactions, however we do not fully understand the consequences of these changes for species' population dynamics and community composition. In this study, we experimentally manipulated the timing of germination for five annual plant species from southern California and used pairwise competition experiments and coexistence theory to quantify how phenological shifts may impact species interactions and coexistence. We found that phenological shifts may help promote coexistence when they confer an advantage for competitively inferior species, but in other cases promote dominance by competitively superior species. Earlier germination generally increased species' performance relative to competitors, but the relative changes in intra‐and inter‐specific interactions caused more complex effects on niche and fitness differences. Phenological differences tended to reduce stabilising niche differences for many species pairs and reduced overall coexistence probabilities. Synthesis. While phenological differences among species have typically been considered a form of niche partitioning, it seems increasingly likely that phenological offsets could destabilise species coexistence. The net effects of changing phenology on species coexistence will depend on the complex combinations of effects on intra‐ and inter‐specific interactions, which remain challenging to predict. [ABSTRACT FROM AUTHOR]

Background: Sequential population-based household serosurveys of SARS-CoV-2 covering the COVID-19 pre- and post-vaccination periods are scarce in Brazil. This study investigated seropositivity trends in the municipality of São Paulo. Methods: We conducted seven cross-sectional surveys of adult population-representative samples between June 2020 and April 2022. The study design included probabilistic sampling, test for SARS-CoV-2 antibodies using the Roche Elecsys anti-nucleocapsid assay, and statistical adjustments for population demographics and non-response. The weighted seroprevalences with 95% confidence intervals (CI) were estimated by sex, age group, race, schooling, and mean income study strata. Time trends in seropositivity were assessed using the Joinpoint model. We compared infection-induced seroprevalences with COVID-19 reported cases in the pre-vaccination period. Results: The study sample comprised 8,134 adults. The overall SARS-CoV-2 seroprevalence increased from 11.4% (95%CI: 9.2–13.6) in June 2020 to 24.9% (95%CI: 21.0–28.7) in January 2021; from 38.1% (95%CI: 34.3–41.9) in April 2021 to 77.7% (95%CI: 74.4–81.0) in April 2022. The prevalence over time was higher in the subgroup 18–39 years old than in the older groups from Survey 3 onwards. The self-declared Black or mixed (Pardo) group showed a higher prevalence in all surveys compared to the White group. Monthly prevalence rose steeply from January 2021 onwards, particularly among those aged 60 years or older. The infection-to-case ratios ranged from 8.9 in June 2020 to 4.3 in January 2021. Conclusions: The overall seroprevalence rose significantly over time and with age and race subgroup variations. Increases in the 60 years or older age and the White groups were faster than in younger ages and Black or mixed (Pardo) race groups in the post-vaccination period. Our data may add to the understanding of the complex and changing population dynamics of the SARS-CoV-2 infection, including the impact of vaccination strategies and the modelling of future epidemiological scenarios. [ABSTRACT FROM AUTHOR]

Over-summering of shorebirds refers to the phenomenon where certain species of shorebirds, primarily migratory, remain on their non-breeding grounds during the summer months for one or more years instead of migrating to their breeding grounds. The present study investigates the presence and abundance of over-summering shorebird species at four distinct sites covering 24 scanning points along the southeastern coasts of Tamil Nadu for 2017-2023. A total of 13 species were observed over-summering, with Lesser Sand Plover being the most dominant species, followed by Greater Sand Plover. Notably, 10 species were found across all four sites, while three species--Black-tailed Godwit, Bar-tailed Godwit, and Common Sandpiper--were exclusive to Dhanushkodi Lagoon, observed only during 2023. The study examined the year-wise abundance of these species, revealing a decline in over-summering shorebirds across all study sites. The Eurasian Curlew, Curlew Sandpiper, Bar-tailed & Black-tailed Godwits are the 'Near Threatened' species observed during the study. Furthermore, the research highlighted variations in Shannon species diversity index (H) location-wise and year-wise - Manoli Island (H = 2.25) in 2023; Dhanushkodi Lagoon (H = 1.8) in 2023; Valinokkam Lagoon (H = 1.63), and Pillaimadam Lagoon (H = 2.08) in 2017. Key findings are that among the study sites, in Pillaimadam Lagoon all 10 species' abundance declined; in Valinokkam Lagoon, Greater Sand Plover and Little Stint marginally increased, and eight species declined; Common Redshank and Ruddy Turnstone marginally increased in Manoli Island, while other eight species declined; Grey Plover population increased in Dhanushkodi Lagoon along with a marginal decrease in Common Redshank and Ruddy Turnstone as other species declined, over the years of study. [ABSTRACT FROM AUTHOR]

During learning of a sensory discrimination task, the cortical and subcortical regions display complex spatiotemporal dynamics. During learning, both the amygdala and cortex link stimulus information to its appropriate association, for example, a reward. In addition, both structures are also related to nonsensory parameters such as body movements and licking during the reward period. However, the emergence of the cortico-amygdala relationships during learning is largely unknown. To study this, we combined wide-field cortical imaging with fiber photometry to simultaneously record cortico-amygdala population dynamics as male mice learn a whisker-dependent go/no-go task. We were able to simultaneously record neuronal populations from the posterior cortex and either the basolateral amygdala (BLA) or central/medial amygdala (CEM). Prior to learning, the somatosensory and associative cortex responded during sensation, while amygdala areas did not show significant responses. As mice became experts, amygdala responses emerged early during the sensation period, increasing in the CEM, while decreasing in the BLA. Interestingly, amygdala and cortical responses were associated with task-related body movement, displaying significant responses ∼200 ms before movement initiation which led to licking for the reward. A correlation analysis between the cortex and amygdala revealed negative and positive correlation with the BLA and CEM, respectively, only in the expert case. These results imply that learning induces an involvement of the cortex and amygdala which may aid to link sensory stimuli with appropriate associations. [ABSTRACT FROM AUTHOR]

When biological populations expand into new territory, the evolutionary outcomes can be strongly influenced by genetic drift, the random fluctuations in allele frequencies. Meanwhile, spatial variability in the environment can also significantly influence the competition between subpopulations vying for space. Little is known about the interplay of these intrinsic and extrinsic sources of noise in population dynamics: When does environmental heterogeneity dominate over genetic drift or vice versa, and what distinguishes their population genetics signatures? Here, in the context of neutral evolution, we examine the interplay between a population's intrinsic, demographic noise and an extrinsic, quenched random noise provided by a heterogeneous environment. Using a multispecies Eden model, we simulate a population expanding over a landscape with random variations in local growth rates and measure how this variability affects genealogical tree structure, and thus genetic diversity. We find that, for strong heterogeneity, the genetic makeup of the expansion front is to a great extent predetermined by the set of fastest paths through the environment. The landscapedependent statistics of these optimal paths then supersede those of the population's intrinsic noise as the main determinant of evolutionary dynamics. Remarkably, the statistics for coalescence of genealogical lineages, derived from those deterministic paths, strongly resemble the statistics emerging from demographic noise alone in uniform landscapes. This cautions interpretations of coalescence statistics and raises new challenges for inferring past population dynamics. [ABSTRACT FROM AUTHOR]

In Chile, Piscirickettsia salmonis contains two genetically isolated genogroups, LF-89 and EM-90. However, the impact of a potential co-infection with these two variants on Salmonid Rickettsial Septicemia (SRS) in Atlantic salmon (Salmo salar) remains largely unexplored. In our study, we evaluated the effect of P. salmonis LF-89-like and EM-90-like co-infection on post-smolt Atlantic salmon after an intraperitoneal challenge to compare changes in disease dynamics and host immune response. Co-infected fish had a significantly lower survival rate (24.1%) at 21 days post-challenge (dpc), compared with EM-90-like single-infected fish (40.3%). In contrast, all the LF-89-like single-infected fish survived. In addition, co-infected fish presented a higher presence of clinical lesions than any of the single-infected fish. The gene expression of salmon immune-related biomarkers evaluated in the head kidney, spleen, and liver showed that the EM-90-like isolate and the co-infection induced the up-regulation of cytokines (e.g., il-1β, ifnγ, il8, il10), antimicrobial peptides (hepdicin) and pattern recognition receptors (PRRs), such as TLR5s. Furthermore, in serum samples from EM-90-like and co-infected fish, an increase in the total IgM level was observed. Interestingly, specific IgM against P. salmonis showed greater detection of EM-90-like antigens in LF-89-like infected fish serum (cross-reaction). These data provide evidence that P. salmonis LF-89-like and EM-90-like interactions can modulate SRS disease dynamics in Atlantic salmon, causing a synergistic effect that increases the severity of the disease and the mortality rate of the fish. Overall, this study contributes to achieving a better understanding of P. salmonis population dynamics. [ABSTRACT FROM AUTHOR]

Colonization of the infant gut is an important developmental process characterized by high carriage of antimicrobial resistance genes (ARGs) and high abundances of pathobionts. The horizontal transfer of ARGs to pathogenic bacteria represents a major public health concern. However, there is still a paucity of longitudinal studies surveilling ARGs in healthy infant guts at high temporal resolution. Furthermore, we do not yet have a clear view of how temporal variation in ARG carriage relates to the dynamics of specific bacterial populations, as well as community virulence potential. Here, we performed deep shotgun metagenomic sequencing of monthly fecal samples from a cohort of 12 infants, covering the first year of life to interrogate the infant gut microbiome for ARG content. We further relate ARG dynamics to the dynamics of taxa, virulence potential, as well as the potential for ARG mobilization. We identify a core resistome dominated by efflux systems typically associated with Enterobacteriaceae. Overall ARG carriage declined over the first year of life and showed strong contemporaneous correlation with the population dynamics of Proteobacteria. Furthermore, the majority of ARGs could be further mapped to metagenome-assembled genomes (MAGs) classified to this phylum. We were able to assign a large number of ARGs to E. coli by correlating the temporal dynamics of individual genes with species dynamics, and we show that the temporal dynamics of ARGs and virulence factors are highly correlated, suggesting close taxonomic associations between these two gene classes. Finally, we identify ARGs linked with various categories of mobile genetic elements, demonstrating preferential linkage among mobility categories and resistance to different drug classes. While individual variation in ARG carriage is substantial during infancy there is a clear reduction over the first year of life. With few exceptions, ARG abundances closely track the dynamics of pathobionts and community virulence potential. These findings emphasize the potential for development of resistant pathogens in the developing infant gut, and the importance of effective surveillance in order to detect such events. [ABSTRACT FROM AUTHOR]

Wheat starch fermentation slurry is the main substrate for producing Ganmianpi, a traditional Chinese fermented wheat starch-based noodle. In the present work, the microbial population dynamics and metabolite changes in wheat starch fermentation slurry at different fermentation times (0, 1, 2, 3, and 4 days) were measured by using high-throughput sequencing analysis and headspace solid-phase microextraction gas chromatography–mass spectrometry (HS-SPME/GC-MS) methods. The texture and sensory properties of Ganmianpi made from fermented starch slurry are also evaluated. The results showed that Latilactobacillus curvatus and Leuconostoc citreum were the dominant bacteria in wheat starch fermentation slurry, while Saccharomyces cerevisiae and Kazachstania wufongensis were identified as the main species of fungi. With the extension of fermentation time, the reducing sugar content first increased and then decreased, when the titratable acidity content showed an increasing trend, and the nonvolatile acid was significantly higher than the volatile acid. A total of 62 volatile flavor compounds were identified, and the highest content is alcohols, followed by acids. Fermentation significantly reduced the hardness and chewiness of Ganmianpi, and increased its resilience and cohesiveness. Ganmianpi made from fermented starch slurry for two and three days showed a higher sensory score than other samples. The present study is expected to provide a theoretical basis for exploiting the strains with potential for commercial application as starter cultures and quality improvement of Ganmianpi. [ABSTRACT FROM AUTHOR]

Introduction: Although estimate models have been proposed to determine free-roaming (both stray and semi-domiciled) dog populations, to date, no study has focused on the three major border areas of Brazil. Therefore, the present study assessed the free-roaming dog population of Foz do Iguaçu, a major far-west Brazilian city located in a three-border area (Brazil, Argentina, and Paraguay), which is considered among the top five Brazilian tourist destinations. Methods: Capture-release sampling was performed in three phases with a 6-month interval and 10-day duration of each phase, totaling 18 months, between 2018 and 2019. Results: A total of 1,273 dogs were estimated in the first [95% confidence interval (CI), 468-2,078 dogs], 904 in the second (95%CI, 452-1,355 dogs), and 1,564 in the third (95%CI, 521-2,607 dogs) capture phases in this area, suggesting a population density of 18.4 dogs/km² (6.1-30.6 dogs/km², 95% CI). Of all free-roaming dogs, 452/1,125 (40.2%) were stray with no confirmed ownership or household, whereas 672/1,125 (59.8%) had a known origin, among which 625/1,125 (55.6%) were semi-domiciled with ownership or a household, 36/1,125 (3.2%) were neighborhood dogs with maintainers, and 11/1,125 (1.0%) were owned by recycling material collectors and homeless individuals. The majority of the 1,125 dogs (862/1,125; 76.6%) had an ideal body condition score. The high outdoor access of owned dogs is likely caused by cultural behavior. However, because 533/1,125 (47.4%) of the free-roaming dogs presented with clinical abnormalities, irresponsible ownership may have negatively impacted dog health and welfare. Discussion: This study was the first to establish the density of free-roaming dogs, the ratio of stray and semi-domiciled dogs, and their dynamics over time in Foz do Iguaçu. The findings may serve as a warning for the high level of dog outdoor access and irresponsible guardianship, whichmay negatively a [ABSTRACT FROM AUTHOR]

Responding to threats in the real world demands a sophisticated orchestration of freeze and flight behaviors dynamically modulated by the neural activity. While the medial prefrontal cortex-basolateral amygdala (mPFC-BLA) network is known to play a pivotal role in coordinating these responses, the mechanisms underlying its population dynamics remain vague. As traditional Pavlovian fear conditioning models fall short in encapsulating the breadth of natural escape behaviors, we introduce a novel dataset to bridge this gap, capturing the defensive strategies of mice against a spider robot in a natural-like environment. The adaptive escape behaviors and concurrent mPFC-BLA activity in eight mice were monitored using wireless local field potential (LFP) and video recordings, both individually and in groups. Our data offers a unique avenue to explore the neural dynamics that govern fear- and vigilance-induced threat responses in isolated and social contexts. Supplemented by detailed methodologies and validation, the dataset allows for the analysis of the transient neural oscillatory dynamics, with prospective implications for the fields of neuroscience, robotics, and artificial intelligence. [ABSTRACT FROM AUTHOR]

Across the globe, many species of insects are facing population decline. This is largely driven by anthropogenic changes to the environment, including the widespread exposure of invertebrates to endocrine disrupting chemicals (EDCs), which impair fertility. To test whether generations of Drosophila melanogaster born from parents exposed to a common dietary EDC, equol, could recover reproductive function, we quantified the reproductive capacity of the two subsequent generations. Using a novel suite of flow cytometry assays to assess sperm functionality in real time, we find that sperm function is compromised across three generations, even after non-exposed in individuals contribute to the breeding population. Though the sex ratio alters in response to EDC exposure, favouring the survival of female offspring, most lineages with ancestral EDC exposure exhibit persistent subfertility in both the male and female. Male offspring with ancestral EDC exposure present with reduced fertility and dysfunctional spermatozoa, whereby spermatozoa are metabolically stressed, lack DNA integrity and present with permanent epigenetic alterations. Across generations, male and female offspring demonstrate distinct patterns of reproductive characteristics, depending upon the specific lineage of EDC exposure. Our results illustrate how dietary EDCs present in agricultural plants could promote transgenerational subfertility and contribute to declining insect populations. [ABSTRACT FROM AUTHOR]

East African countries accounted for ~ 10% of all malaria prevalence worldwide in 2022, with an estimated 23.8 million cases and > 53,000 deaths. Despite recent increases in malaria incidence, high-resolution genome-wide analyses of Plasmodium parasite populations are sparse in Kenya, Tanzania, and Uganda. The Kenyan-Ugandan border region is a particular concern, with Uganda confirming the emergence and spread of artemisinin resistant P. falciparum parasites. To establish genomic surveillance along the Kenyan-Ugandan border and analyse P. falciparum population dynamics within East Africa, we generated whole-genome sequencing (WGS) data for 38 parasites from Bungoma, Western Kenya. These sequences were integrated into a genomic analysis of available East African isolate data (n = 599) and revealed parasite subpopulations with distinct genetic structure and diverse ancestral origins. Ancestral admixture analysis of these subpopulations alongside isolates from across Africa (n = 365) suggested potential independent ancestral populations from other major African populations. Within isolates from Western Kenya, the prevalence of biomarkers associated with chloroquine resistance (e.g. Pfcrt K76T) were significantly reduced compared to wider East African populations and a single isolate contained the PfK13 V568I variant, potentially linked to reduced susceptibility to artemisinin. Overall, our work provides baseline WGS data and analysis for future malaria genomic surveillance in the region. [ABSTRACT FROM AUTHOR]

In this work, we study the invasion dynamics of a stage-structured population located in a one-dimensional periodic lattice. With a biologically relevant hypothesis that the population diffuses in its immature stage, we derive a novel spatially heterogeneous population model with coupled local and nonlocal effects. Assuming a KPP-type structure, we obtain the existence and variational characterization of spreading speed by appealing to monotone dynamical system theories. Further, we study the dependence of the spreading speed on the dispersal rate of immature population; it turns out that there exists an optimal dispersal strategy to maximize the speed. Numerical simulations further suggest that such an optimal strategy is unique. [ABSTRACT FROM AUTHOR]

General anesthesia can impact a patient's memory and cognition by influencing hippocampal function. The CA1 and dentate gyrus (DG), serving as the primary efferent and gateway of the hippocampal trisynaptic circuit facilitating cognitive learning and memory functions, exhibit significant differences in cellular composition, molecular makeup, and responses to various stimuli. However, the effects of isoflurane-induced general anesthesia on CA1 and DG neuronal activity in mice are not well understood. In this study, utilizing electrophysiological recordings, we examined neuronal population dynamics and single-unit activity (SUA) of CA1 and DG in freely behaving mice during natural sleep and general anesthesia. Our findings reveal that isoflurane anesthesia shifts local field potential (LFP) to delta frequency and reduces the firing rate of SUA in both CA1 and DG, compared to wakefulness. Additionally, the firing rates of DG neurons are significantly lower than CA1 neurons during isoflurane anesthesia, and the recovery of theta power is slower in DG than in CA1 during the transition from anesthesia to wakefulness, indicating a stronger and more prolonged impact of isoflurane anesthesia on DG. This work presents a suitable approach for studying brain activities during general anesthesia and provides evidence for distinct effects of isoflurane anesthesia on hippocampal subregions. [ABSTRACT FROM AUTHOR]

Motivation The knowledge of protein dynamics, or turnover, in patients provides invaluable information related to certain diseases, drug efficacy, or biological processes. A great corpus of experimental and computational methods has been developed, including by us, in the case of human patients followed in vivo. Moving one step further, we propose a novel modeling approach to capture population protein dynamics using Bayesian methods. Results Using two datasets, we demonstrate that models inspired by population pharmacokinetics can accurately capture protein turnover within a cohort and account for inter-individual variability. Such models pave the way for comparative studies searching for altered dynamics or biomarkers in diseases. Availability and implementation R code and preprocessed data are available from zenodo.org. Raw data are available from panoramaweb.org. [ABSTRACT FROM AUTHOR]

Despite the high diversity of elasmobranch fishes in the Balearic Islands, knowledge of their biology and population dynamics is still scarce. A recent mark-and-recapture experiment off the Balearic Islands tagged 3738 individuals of 23 shark and batoid species during MEDITS and CANAL bottom trawl scientific surveys from June 2021 to August 2023. Retrieval was reported for the sharks Scyliorhinus canicula and Mustelus mustelus, revealing relatively small home ranges for these species (0.2–38.5 km and 7.8–15.3 km for S. canicula and M. mustelus, respectively). Recapture efficiency was higher from scientific surveys than from commercial catches, highlighting potential challenges in collaboration with fishermen and recapture reports. Density estimates obtained from the MEDITS bottom trawl survey suggest a much larger population for S. canicula than estimates from the mark–recapture data, indicating MEDITS density estimates for this species may be overestimated due to its scavenger behavior perhaps favoring individuals searching for discards aggregated in the fishing grounds. This study emphasizes the importance of monitoring, collaborative efforts, and improved reporting mechanisms to enhance our understanding of elasmobranch populations and provide support for sustainable management of these vulnerable marine species. [ABSTRACT FROM AUTHOR]

The pine marten (Martes martes) occupies the northernmost extent of its distribution in Norway, where microtine rodents are an important food item. The relationship between microtine rodent abundance and pine marten population dynamics is not well understood. In this paper, we examined this relationship and tested if environmental factors (e.g. snow depth, elevation, mature spruce forest density and agricultural land density) modulate pine marten population dynamics. We calculated pine marten abundance indices using data collected from 593 unique snow transects surveyed between 2003 and 2014 in Hedmark, Norway. We employed a Partial Rate Correlation Function to identify potential cyclicity in pine marten populations. We did not observe any cyclical patterns in pine marten populations within our short time series. Instead, their population appeared to be directly density‐dependent. Although the population growth rate of pine marten tended to increase with increasing elevation, it was not affected by individual variables including a microtine rodent abundance index and snow depth. However, the annual growth rate of pine marten populations was positively affected by the interaction between the microtine rodent abundance index and increasing elevation. Pine marten abundance increased with microtine rodent abundance, elevation, snow depth and density of mature spruce forest, but decreased with increasing agricultural land density. Pine martens are opportunistic diet generalists that can switch between prey and cache food for later consumption. They are also strongly territorial with delayed implantation and are slow to respond to environmental changes due to their relatively low reproductive potential. These life‐history traits may mitigate the effects of fluctuating microtine rodent abundance on pine marten reproduction and survival. Nevertheless, our findings suggest that microtine rodents still serve as important prey which can influence the population dynamics of pine martens in higher elevation habitats where alternative prey may be less available. [ABSTRACT FROM AUTHOR]

Species experience a variety of environmental and anthropogenic conditions across their ranges leading to spatial variation in population dynamics. Understanding population dynamics under different conditions is important but it is challenging to allocate limited effort to spatial and temporal subpopulation monitoring. Using GLMMs, we analyze survey data of a metapopulation of coconut crabs spanning 7 years and 15 sites in and near the Pemba archipelago, Zanzibar, to estimate trends in population size (based on catch per unit effort), weight and sex ratio at the meta‐ and subpopulation level and investigate anthropogenic drivers of these trends. We found that the overall metapopulation has remained stable in terms of size and composition over the survey period, but observed diverging trends in population size and sex ratio at some subpopulations. Formal protection of sites was associated with positive population trends. Of nine sites for which we could estimate site‐specific trends, three showed increasing and two decreasing trends, whereas four sites had stable subpopulations. Although anthropogenic factors affected the average weight, and the incidence of small and large individuals, we found no temporal trends in any weight‐related measures. Furthermore, there were no apparent patterns between weight‐related measures and subpopulation trends. The metapopulation was biased toward males, and exploitation appeared to be associated with declining trends in the proportion of females, likely an artifact of a strong decline in the proportion of females in one of only two exploited sites in the dataset. Educational campaigns implemented in 2020 at six sites were not related to higher population sizes in later surveys. The variable trends in subpopulation sizes and composition highlight the need for spatially replicated monitoring in metapopulations. The analyses further provide a detailed baseline for future subpopulation studies of this vulnerable species in one of its last remaining metapopulations in the Western Indian Ocean. [ABSTRACT FROM AUTHOR]

Predators impose top‐down forces on prey populations, with the strength of those effects often varying over space and time and among demographic groups. In ungulates, predation risk is typically greatest for neonatal offspring, with some suggesting that predators can key in on adult activity to locate hidden neonates. However, few field studies to date have been able to directly assess the influence of maternal care on ungulate neonate survival. Using a population of white‐tailed deer under heavy coyote predation pressure, we tested the maternal dispersion hypothesis, which suggests the dispersion of maternal activity temporally and spatially attenuates risk of predation for ungulate neonates during this vulnerable altricial phase. We compared support for this hypothesis with more commonly tested hypotheses regarding the influence of habitat conditions and intrinsic factors on neonatal survival. Fawn survival to 16 weeks was 27.7%, with coyotes accounting for 59% of fawn mortalities. In support of our maternal temporal diffusion hypothesis, we found that neonatal survival decreased as more maternal visits (proportionally) occurred at night. The only other significant (p <.1) predictor of fawn survival was birth timing, with fawn survival decreasing as the season progressed. Given that fawn survival declined as the proportion of nighttime visits increased, and that wild pig presence and human disturbance can push doe and fawn activity toward nocturnal hours, additional research is needed to determine whether managing pig and human disturbance can decrease fawn mortality. More broadly, given the importance of recruitment in ungulate population dynamics, our finding opens a potentially important new line of inquiry on how maternal behaviors influence predation risk in large animal predator–prey ecology. [ABSTRACT FROM AUTHOR]

Understanding the dynamics of population recovery in threatened species requires robust longitudinal monitoring datasets. However, evidence‐based decision‐making is often impeded by variable data collection approaches, necessitating critical evaluation of restricted available baselines. The Hainan gibbon, the world's rarest primate, had possibly declined to only seven or eight individuals in 1978 at Bawangling National Nature Reserve but has experienced subsequent population growth. Past population estimates lack detailed reporting of survey effort, and multiple conflicting estimates are available, hindering assessment of gibbon recovery. We investigated all reported estimates of Bawangling gibbon population size from 1978 to 2022, to evaluate the biological signal of population trends and the extent to which noise associated with varying survey effort, reporting and estimation may mask or misrepresent any underlying signal. This longitudinal dataset demonstrates that the Bawangling population experienced a series of bottlenecks and recoveries, with three successive periods of growth interspersed by population crashes (1978–1989, 1989–2000 and 2000–2022). The rate of gibbon population recovery was progressively slower over time in each successive period of growth, and this potential decline in recovery rate following serial bottlenecks suggests that additional management strategies may be required alongside "nature‐based solutions" for this species. However, population viability analysis suggests the 1978 founder population is unlikely to have been as low as seven individuals, raising concerns for interpreting reported historical population counts and understanding the dynamics of the species' recovery. We caution against overinterpreting potential signals within "messy" conservation datasets, and we emphasise the crucial importance of standardised replicable survey methods and transparent reporting of data and effort in all future surveys of Hainan gibbons and other highly threatened species. [ABSTRACT FROM AUTHOR]

Population dynamics are driven by stochastic and density‐dependent processes acting on demographic rates. Individuals differ demographically, and to capture these differences, models of population dynamics are usually structured by age and stage, rarely by sex. An effect of sex on population dynamics is expected if the dynamics of males and females differ, requiring an unequal sex ratio at birth and/or sex‐specific survival probabilities. Goshawks (Accipiter gentilis) show large sexual size dimorphism and differential survival, but it is unknown whether males and females contribute differently to population dynamics. We studied a goshawk population in northern Germany over 47 years using brood monitoring data, collected feathers and nestling ringing data. We jointly analyzed the data using a two‐sex integrated population model and performed retrospective and prospective population analyses to understand whether the demographic drivers of population change differ between the sexes. The population showed large fluctuations, during which the number of breeding pairs doubled, but the long‐term trend of the population was slightly negative. Female survival exceeded male survival during the first year of life. Females started to reproduce at a younger age than males, productivity increased with female age, the sex ratio of nestlings was male biased and there was moderate male immigration. Despite these differences, temporal variation in sex ratio did not contribute to population dynamics and the contribution of temporal variation in survival was similar for both sexes. Variation in first‐year survival was the strongest driver in this population, regulated by a weak density‐dependent feedback acting through female first‐year survival. Overall, the contributions of the two sexes to population dynamics were similar in this monogamous species with strong sexual size dimorphism. [ABSTRACT FROM AUTHOR]

Biased sex ratios among reproductive individuals are common in plants, but the underlying mechanisms, as well as the evolutionary consequences, are not well understood. The classical theory of Düsing and Fisher predicts an equal primary sex ratio at seed production, based on the selective advantage of the rare sex. Biased sex ratios among reproductive plants can arise from sexual dimorphism in survival and flowering. Sex ratio biases can also be present from the seed stage; in these cases, assumptions of Düsing's and Fisher's theory, for example, random mating or demographic equilibrium, are thought to be violated.We investigated mechanisms leading to female‐biased sex ratios in the arctic‐alpine dwarf willow Salix herbacea L. We studied sex ratios in three natural populations over 3 years as well as in 29 crosses (full‐sib families) under controlled conditions over four growth periods. We tested whether sex ratio was associated with habitat parameters (elevation and snowmelt time), or with germination, survival or flowering, and whether females and males differed in size or flowering that may cause observation bias.We detected a strong and consistent female bias, both in natural populations (sex ratio [proportion of females]: 0.71–0.82) and in our controlled experiment (overall sex ratio: 0.70–0‐72). Female bias became more pronounced with increasing elevation. Our data did not support sexual dimorphism in size or flowering. Family sex ratios varied largely (from 0.25 to 1), including many female‐biased families, unbiased families and two male‐biased families. Families with lower germination, seedling establishment, survival or flowering did not have stronger female bias, indicating that intrinsically higher survival or flowering in females does not explain overall female bias.Synthesis. Our results suggest that sex ratio bias in S. herbacea is already present in seeds and does not arise through intrinsic differences between sexes. Candidate mechanisms that can lead to both overall female bias and variation in sex ratio among families are meiotic drive or cyto‐nuclear interactions. The pioneer habit of Salix may lead to non‐equilibrium population dynamics that allow for the long‐term persistence of variable genetic sex ratio distortion systems that arise from genetic conflict. [ABSTRACT FROM AUTHOR]

Although repetitive DNA forms much of the human genome, its study is challenging due to limitations in assembly and alignment of repetitive short-reads. We have deployed k-Seek , software that detects tandem repeats embedded in single reads, on 2,504 human genomes from the 1,000 Genomes Project to quantify the variation and abundance of simple satellites (repeat units <20 bp). We find that the ancestral monomer of Human Satellite 3 makes up the largest portion of simple satellite content in humans (mean of ∼8 Mb). We discovered ∼50,000 rare tandem repeats that are not detected in the T2T-CHM13v2.0 assembly, including undescribed variants of telomericand pericentromeric repeats. We find broad homogeneity of the most abundant repeats across populations, except for AG-rich repeats which are more abundant in African individuals. We also find cliques of highly similar AG- and AT-rich satellites that are interspersed and form higher-order structures that covary in copy number across individuals, likely through concerted amplification via unequal exchange. Finally, we use pericentromeric polymorphisms to estimate centromeric genetic relatedness between individuals and find a strong predictive relationship between centromeric lineages and pericentromeric simple satellite abundances. In particular, ancestral monomers of Human Satellite 2 and Human Satellite 3 abundances correlate with clusters of centromeric ancestry on chromosome 16 and chromosome 9, with some clusters structured by population. These results provide new descriptions of the population dynamics that underlie the evolution of simple satellites in humans. [ABSTRACT FROM AUTHOR]

Simple Summary: Bactrocera dorsalis (Hendel) is a serious threat to the fruit industry. Implementing monitoring procedures is essential for effective pest control. The monitoring of B. dorsalis is predominantly conducted through the use of yellow sticky traps and baited traps, followed by manual counting. However, this approach is both time consuming and labor intensive. In this study, we employed automated identification and counting devices for monitoring the adult population dynamics of B. dorsalis in four counties with disparate climatic types in Yunnan. The differing climatic types and temperature fluctuations resulted in disparate population dynamics of B. dorsalis in the four counties, yet there were two peaks of adult emergence in each year. Furthermore, the population of B. dorsalis was correlated with temperature. The automated monitoring system employed in the study permitted the daily monitoring of adult B. dorsalis populations, thereby facilitating the tracking of the daily dynamics of B. dorsalis by farmers and researchers alike. Bactrocera dorsalis (Hendel) (Diptera: Tephritidae) is a global economic pest that poses a serious threat to the fruit industry. In the southwest of China, Yunnan Province sustains a severe infestation of B. dorsalis. An automated monitoring system designed for B. dorsalis was employed in this study to elucidate the annual population dynamics of B. dorsalis in four counties: Yuanjiang, Huaping, Guangnan, and Ludian in Yunnan. The system utilizes sex parapheromone and image recognition technology. The data uploaded by the device are used to analyze the annual population dynamics of B. dorsalis in different regions. The results showed that the populations of adult B. dorsalis in all four counties peaked twice annually, with Yuanjiang experiencing the earliest peak periods, followed by Huaping, Guangnan, and Ludian. Adult B. dorsalis occurred in Yuanjiang throughout the year, and Yuanjiang had the highest number of B. dorsalis monitored. In Huaping, adult B. dorsalis occurred in March–December and was highly active, with a high population density in 2019. Bactrocera dorsalis did not occur in December in Guangnan but only in May–October in Ludian. Bactrocera dorsalis abundance was correlated with temperature in all four areas. The outcomes of this experiment provide a practical foundation for developing control strategies targeting B. dorsalis in various orchards across each county. [ABSTRACT FROM AUTHOR]

Simple Summary: Longhorn beetles of the genus Monochamus are vectors of the pine wood nematode, which causes incurable pine wilt disease in coniferous trees. We developed temperature-dependent models to describe the oviposition of Monochamus saltuarius, a significant species within this genus. Our study demonstrated that these models effectively capture the nonlinear effects of temperature on the oviposition and aging of M. saltuarius adults. We compared two simulation approaches: one that separately accounted for the sexual maturation phase of adults and another that did not. Both methods proved capable of accurately describing oviposition patterns across various temperature conditions. The insights gained from this study have potential applications beyond estimating oviposition and predicting population dynamics of M. saltuarius. This modeling framework could be adapted to forecast population changes in a diverse range of pest species, offering a versatile tool for pest management strategies. Monochamus saltuarius Gebler is a serious insect pest in Europe and East Asia regions, including Portugal, Spain, China, Japan, and Korea. It transfers the pine wood nematode Bursaphelenchus xylophilus to conifer trees, resulting in pine wilt disease (PWD). As temperature is a key factor influencing insect population dynamics, temperature-dependent models describing M. saltuarius oviposition could estimate population growth potential and evaluate outbreak risks. In this study, the longevity and fecundity of M. saltuarius females were measured under constant temperature conditions ranging from 20 to 32 °C, and temperature-dependent models were constructed. The longevity of M. saltuarius females ranged from 83.36 days to 22.92 days, with a total fecundity of 141 eggs and 52.77 eggs at 20 °C and 32 °C, respectively. To describe oviposition, we used a single-phase simulation describing oviposition as a single model and a two-phase simulation describing sexual maturation and oviposition as two separate models. These models effectively described M. saltuarius oviposition (r2 > 0.96) under constant temperature conditions, with the two-phase simulation demonstrating greater accuracy overall. Such models could facilitate assessments of PWD risks. The modeling framework of this study shows potential for predicting threats from various forestry and agricultural pests. [ABSTRACT FROM AUTHOR]

In many European countries over the last few decades, arable fields dominate agricultural landscapes, leading to very intensive land-use practices. This seems to be the main cause of population declines for numerous farmland species, including the European brown hare (Lepus europaeus Pallas, 1778). The Research Institute for Animal Production (National Agricultural and Food Centre—NPPC, Luzianky, Slovakia) has been engaged in a long monitoring project (a project currently running), collecting certain indicators of brown hare population dynamics during hunting season from 1987 to 2023 in the Slovak Danubian Lowland. In the same macro-area (Čiližská Radvaň and Lehnice), a study was conducted on the influence of permanent semi-natural vegetation in relation to recruitment, population density and production. The entire monitored period was aggregated into 5-year intervals (for a total of seven time intervals), with the aim of analyzing the brown hare population dynamics. Spring hare density in the Danubian Lowland is currently 20.8 hares/km2, with harvests of 4.6 hares/km2. During the monitoring period, bag animals have been examined following the regular hunting operations for the purpose of age determination (weight of eye lenses), sex ratio and productivity. There was a large positive effect of set-aside with special mixtures created for hares in large-scale farmed agrarian landscapes on brown hare density, bag and recruitment. In-model hunting grounds with such set-asides increased the spring stock by 25%, bag by 100% and recruitment by 20%. This study reveals that the management of European brown hare is not sustainable in the Slovak Danubian Lowland, and the population is decreasing. This is proven through the decline in harvest brown hares and by population dynamic parameters. Our data suggest that improvements in the habitat quality of arable landscapes by the adoption of permanent semi-natural vegetation may be more effective in the increase in the brown hare population. [ABSTRACT FROM AUTHOR]

Aim: Temporal variability in population growth rates is a fundamental property of natural populations with implications for almost any facet in ecology and evolution. Using the framework of nonlinear averaging, we test the hypothesis that the magnitude of short‐term variability in population growth rates is influenced by the long‐term means of climatic conditions. Location: The contiguous United States. Time period: 1970–2019. Major taxa studied: Birds. Methods: Our study encompassed 3941 populations of resident birds in 1335 localities across the contiguous United States. For each population, we quantified the standard deviation of annual growth rates over the relevant period and the corresponding long‐term mean values of annual temperature and precipitation. We further considered the effects of covariates known to influence temporal variability in population growth, namely the standard deviations of climatic variables, the lifespan and the preferred habitat (forest vs. non‐forest) of each species. The effects of climate and species traits on the variability in population growth rates were analysed using linear mixed‐effects models. Results: The magnitude of variability in population growth rate decreased with increasing the long‐term mean of annual precipitation and had a U‐shaped dependence on mean annual temperature. Variability in climatic conditions increased population growth variability, but this effect was weaker than the effect of the corresponding long‐term means. A long lifespan reduced the impact of climatic variability on the variability in population growth rates. Main conclusions: Our finding that the magnitude of variability in population growth rates is influenced by the long‐term characteristics of climatic conditions and species traits extends our perspective on the relationship between climate and population dynamics and should be taken into account in future assessments of spatial and temporal population responses to climate change. [ABSTRACT FROM AUTHOR]