Search

In this paper, we introduce the Floquet mean-field dynamics and Floquet surface hopping approaches to study the nonadiabatic dynamics in periodically driven solid systems. We demonstrate that these two approaches can be formulated in both real and reciprocal spaces. Using the two approaches, we are able to simulate the interaction between electronic carriers and phonons under periodic drivings, such as strong light–matter interactions. Employing the Holstein and Peierls models, we show that strong light–matter interactions can effectively modulate the dynamics of electronic population and mobility. Notably, our study demonstrates the feasibility and effectiveness of modeling low-momentum carriers' interactions with phonons using a truncated reciprocal space basis, an approach impractical in real space frameworks. Moreover, we reveal that even with a significant truncation, carrier populations derived from surface hopping maintain greater accuracy compared to those obtained via mean-field dynamics. These results underscore the potential of our proposed methods in advancing the understanding of carrier–phonon interactions in various periodically driven materials. [ABSTRACT FROM AUTHOR]

Understanding the dynamics of excited-state vibrational energy relaxation in photosynthetic pigments is crucial for elucidating the mechanisms underlying energy transfer processes in light-harvesting complexes. Utilizing advanced femtosecond broadband transient fluorescence (TF) spectroscopy, we explored the excited-state vibrational dynamics of Chlorophyll-a (Chl-a) both in solution and within the light-harvesting complex II (LHCII). We discovered a vibrational cooling (VC) process occurring over ∼6 ps in Chl-a in ethanol solution following Soret band excitation, marked by a notable ultrafast TF blueshift and spectral narrowing. This VC process, crucial for regulating the vibronic lifetimes, was further elucidated through the direct observation of the population dynamics of higher vibrational states within the Qy electronic state. Notably, Chl-a within LHCII demonstrated significantly faster VC dynamics, unfolding within a few hundred femtoseconds and aligning with the ultrafast energy transfer processes observed within the complex. Our findings shed light on the complex interaction between electronic and vibrational states in photosynthetic pigments, underscoring the pivotal role of vibrational dynamics in enabling efficient energy transfer within light-harvesting complexes. [ABSTRACT FROM AUTHOR]

The dynamics of the sub-Ohmic spin-boson model under polarized initial conditions at finite temperatures is investigated by employing both analytical tools and the numerically accurate hierarchical equations of motion-tensor train method. By analyzing the features of nonequilibrium dynamics, we discovered a bifurcation phenomenon, which separates two regimes of the dynamics. It is found that before the bifurcation time, increasing temperature slows down the population dynamics, while the opposite effect occurs after the bifurcation time. The dynamics is highly sensitive to both initial preparation of the bath and thermal effects. [ABSTRACT FROM AUTHOR]

As an emerging technology in liquid inactivation, one of the main challenges of pulsed electric fields (PEFs) inactivation lies in quantitatively describing and predicting its lethality to microorganisms. However, due to its cross-scaled complexity and the consequent numerous regulatory factors, there is currently still no unified framework to understand the PEF dose–response relationship and the population dynamics theoretically. In this study, a simple yet powerful model from multiscale coarse-graining method is proposed to simulate the bacterial inactivation in suspensions during PEF processing. The complex dose–response effects at the macroscale are successfully reconstructed from simple evolution rules and several coarse-graining parameters, while considering the damage and death of a single bacterium at the microscale. Our model uncovers the seemingly chaotic and even controversial dose–response relationship of PEF in literatures and systematically explores the regulatory effect of experimental parameters in a unified framework. One of the interesting findings is that PEF with shorter pulsed width enhances lethality and reduces the minimal inhibitory time at a constant energy output per pulse, owing to the phase transitions in three bacterial population dynamics (Bistability mode, Avalanche mode, and Hybrid mode). Our study provides a new insight for numerically modeling PEF lethality in liquid inactivation and could serve as a guide for dosage management in practical applications. [ABSTRACT FROM AUTHOR]

By employing the numerically accurate multiple Davydov Ansatz (mDA) formalism in combination with the thermo-field dynamics (TFD) representation of quantum mechanics, we systematically explore the influence of three parameters—temperature, photonic-mode detuning, and qubit–phonon coupling—on population dynamics and absorption spectra of the Holstein–Tavis–Cummings (HTC) model. It is found that elevated qubit–phonon couplings and/or temperatures have a similar impact on all dynamic observables: they suppress the amplitudes of Rabi oscillations in photonic populations as well as broaden the peaks and decrease their intensities in the absorption spectra. Our results unequivocally demonstrate that the HTC dynamics is very sensitive to the concerted variation of the three aforementioned parameters, and this finding can be used for fine-tuning polaritonic transport. The developed mDA-TFD methodology can be efficiently applied for modeling, predicting, optimizing, and comprehensively understanding dynamic and spectroscopic responses of actual molecular systems in microcavities. [ABSTRACT FROM AUTHOR]

Scaffolded molecular networks are important building blocks in biological pigment–protein complexes, and DNA nanotechnology allows analogous systems to be designed and synthesized. System–environment interactions in these systems are responsible for important processes, such as the dissipation of heat and quantum information. This study investigates the role of nanoscale molecular parameters in tuning these vibronic system–environment dynamics. Here, genetic algorithm methods are used to obtain nanoscale parameters for a DNA-scaffolded chromophore network based on comparisons between its calculated and measured optical spectra. These parameters include the positions, orientations, and energy level characteristics within the network. This information is then used to compute the dynamics, including the vibronic population dynamics and system–environment heat currents, using the hierarchical equations of motion. The dissipation of quantum information is identified by the system's transient change in entropy, which is proportional to the heat currents according to the second law of thermodynamics. These results indicate that the dissipation of quantum information is highly dependent on the particular nanoscale characteristics of the molecular network, which is a necessary first step before gleaning the systematic optimization rules. Subsequently, the I-concurrence dynamics are calculated to understand the evolution of the vibronic system's quantum entanglement, which are found to be long-lived compared to these system–bath dissipation processes. [ABSTRACT FROM AUTHOR]

Stochastic chemical kinetics is a widely used formalism for studying stochasticity of chemical reactions inside single cells. Experimental studies of reaction networks are generally performed with cells that are part of a growing population, yet the population context is rarely taken into account when models are developed. Models that neglect the population context lose their validity whenever the studied system influences traits of cells that can be selected in the population, a property that naturally arises in the complex interplay between single-cell and population dynamics of cell fate decision systems. Here, we represent such systems as absorbing continuous-time Markov chains. We show that conditioning on non-absorption allows one to derive a modified master equation that tracks the time evolution of the expected population composition within a growing population. This allows us to derive consistent population dynamics models from a specification of the single-cell process. We use this approach to classify cell fate decision systems into two types that lead to different characteristic phases in emerging population dynamics. Subsequently, we deploy the gained insights to experimentally study a recurrent problem in biology: how to link plasmid copy number fluctuations and plasmid loss events inside single cells to growth of cell populations in dynamically changing environments. [ABSTRACT FROM AUTHOR]

We develop a theory of singlet fission in carotenoid dimers. Following photoexcitation of the "bright" state (i.e., a singlet electron–hole pair) in a single carotenoid, the first step in the singlet fission process is ultrafast intramolecular conversion into the highly correlated "dark" (or 2Ag) state. This state has both entangled singlet triplet-pair and charge-transfer character. Our theory is predicated on the assumption that it is the singlet triplet-pair component of the "dark" state that undergoes bimolecular singlet fission. We use valence bond theory to develop a minimal two-chain model of the triplet-pair states. The single and double chain triplet-pair spectra are described, as this helps explain the dynamics and the equilibrated populations. We simulate the dynamics of the initial entangled pair state using the quantum Liouville equation, including both spin-conserving and spin-nonconserving dephasing processes. By computing the intrachain and interchain singlet, triplet, and quintet triplet-pair populations, we show that singlet fission critically depends on the interchain coupling and the driving potential (that determines endothermic vs exothermic fission). [ABSTRACT FROM AUTHOR]

We investigate the dynamics of Landau–Zener (LZ) transitions in an anisotropic, dissipative three-level LZ model (3-LZM) using the numerically accurate multiple Davydov D2Ansatz in the framework of the time-dependent variational principle. It is demonstrated that a non-monotonic relationship exists between the Landau–Zener transition probability and the phonon coupling strength when the 3-LZM is driven by a linear external field. Under the influence of a periodic driving field, phonon coupling may induce peaks in contour plots of the transition probability when the magnitude of the system anisotropy matches the phonon frequency. The 3-LZM coupled to a super-Ohmic phonon bath and driven by a periodic external field exhibits periodic population dynamics in which the period and amplitude of the oscillations decrease with the bath coupling strength. [ABSTRACT FROM AUTHOR]

In this work, using the theory of first-order macroscopic crowd models, we introduce a compartmental advection–diffusion model, describing the spatio-temporal dynamics of a population in different human behaviors (alert, panic and control) during a catastrophic event. For this model, we prove the local existence, uniqueness and regularity of a solution, as well as the positivity and L 1 -boundedness of this solution. Then, in order to study the spatio-temporal propagation of these behavioral reactions within a population during a catastrophic event, we present several numerical simulations for different evacuation scenarios. [ABSTRACT FROM AUTHOR]

Background: Salinity, exacerbated by rising sea levels, is a critical environmental cue affecting freshwater ecosystems. Predicting ecosystem structure in response to such changes and their implications for the geographical distribution of arthropod disease vectors requires further insights into the plasticity and adaptability of lower trophic level species in freshwater systems. Our study investigated whether populations of the mosquito Culex pipiens, typically considered sensitive to salt, have adapted due to gradual exposure. Methods: Mesocosm experiments were conducted to evaluate responses in life history traits to increasing levels of salinity in three populations along a gradient perpendicular to the North Sea coast. Salt concentrations up to the brackish–marine transition zone (8 g/l chloride) were used, upon which no survival was expected. To determine how this process affects oviposition, a colonization experiment was performed by exposing the coastal population to the same concentrations. Results: While concentrations up to the currently described median lethal dose (LD50) (4 g/l) were surprisingly favored during egg laying, even the treatment with the highest salt concentration was incidentally colonized. Differences in development rates among populations were observed, but the influence of salinity was evident only at 4 g/l and higher, resulting in only a 1-day delay. Mortality rates were lower than expected, reaching only 20% for coastal and inland populations and 41% for the intermediate population at the highest salinity. Sex ratios remained unaffected across the tested range. Conclusions: The high tolerance to salinity for all key life history parameters across populations suggests that Cx. pipiens is unlikely to shift its distribution in the foreseeable future, with potential implications for the disease risk of associated pathogens. [ABSTRACT FROM AUTHOR]

Background: The influence of native secondary succession associated with anthropogenic disturbance on the biodiversity of the forests in subtropical China remains uncertain. In particular, the evolutionary response of small understory shrubs, particularly pioneer species inhabiting continuously disturbed habitats, to topographic heterogeneity and climate change is poorly understood. This study aimed to address this knowledge gap by focusing on the Gaultheria crenulata group, a clade of small pioneer shrubs in subtropical China. Results: We examined the genetic structure and demographic history of all five species of the G. crenulata group with two maternally inherited chloroplast DNA (cpDNA) fragments and two biparentally inherited low-copy nuclear genes (LCG) over 89 natural populations. We found that the genetic differentiation of this group was influenced by the geomorphological boundary between different regions of China in association with Quaternary climatic events. Despite low overall genetic diversity, we observed an isolation-by-distance (IBD) pattern at a regional scale, rather than isolation-by-environment (IBE), which was attributed to ongoing human disturbance in the region. Conclusion: Our findings suggest that the genetic structure of the G. crenulata group reflects the interplay of geological topography, historical climates, and anthropogenic disturbance during the Pliocene–Pleistocene-Holocene periods in subtropical China. The observed IBD pattern, particularly prominent in western China, highlights the role of limited dispersal and gene flow, possibly influenced by physical barriers or decreased connectivity over geographic distance. Furthermore, the east-to-west trend of gene flow, potentially facilitated by the East Asian monsoon system, underscores the complex interplay of biotic and abiotic factors shaping the genetic dynamics of pioneer species in subtropical China's secondary forests. These findings can be used to assess the impact of environmental changes on the adaptation and persistence of biodiversity in subtropical forest ecosystems. [ABSTRACT FROM AUTHOR]

Compelling evidence from around the world suggests that ethnic diversity is detrimental to neighborhood trust and cohesion. Much of this evidence derives from empirical associations found with static indicators of diversity, measuring the mix of ethnic groups at a single point in time, and controlling for a varied mix of individual and community‐level covariates. Less attention though has sought to understand how dynamic processes of migration and residential settlement both create diversity and influence trust and cohesion. In this study, census and survey data are used to analyze the demographic and economic characteristics and dynamics coinciding with diversity in local communities in Australia, and the implications for neighborhood trust and cohesion. Diverse communities are heavily concentrated in moderately and highly disadvantaged communities in large immigrant gateway cities. Highly diverse communities experience continual high levels of immigration and population turnover and contain young age structures and more diverse and transient housing and household structures. Survey analyses reveal that these characteristics substantially explain observed negative associations between diversity and neighborhood trust and cohesion. The results point to the near‐intractable difficulties in isolating the effects of diversity and the importance of understanding the dynamic demographic processes in the construction of neighborhood diversity, trust, and cohesion. [ABSTRACT FROM AUTHOR]

Background: Sarcoptic mange is a skin disease caused by the contagious ectoparasite Sarcoptes scabiei, capable of suppressing and extirpating wild canid populations. Starting in 2015, we observed a multi-year epizootic of sarcoptic mange affecting a red fox (Vulpes vulpes) population on Fire Island, NY, USA. We explored the ecological factors that contributed to the spread of sarcoptic mange and characterized the epizootic in a landscape where red foxes are geographically constrained. Methods: We tested for the presence of S. scabiei DNA in skin samples collected from deceased red foxes with lesions visibly consistent with sarcoptic mange disease. We deployed 96–100 remote trail camera stations each year to capture red fox occurrences and used generalized linear mixed-effects models to assess the affects of red fox ecology, human and other wildlife activity, and island geography on the frequency of detecting diseased red foxes. We rated the extent of visual lesions in diseased individuals and mapped the severity and variability of the sarcoptic mange disease. Results: Skin samples that we analyzed demonstrated 99.8% similarity to S. scabiei sequences in GenBank. Our top-ranked model (weight = 0.94) showed that diseased red foxes were detected more frequently close to roadways, close to territories of other diseased red foxes, away from human shelters, and in areas with more mammal activity. There was no evidence that detection rates in humans and their dogs or distance to the nearest red fox den explained the detection rates of diseased red foxes. Although detected infrequently, we observed the most severe signs of sarcoptic mange at the periphery of residential villages. The spread of visual signs of the disease was approximately 7.3 ha/week in 2015 and 12.1 ha/week in 2017. Conclusions: We quantified two separate outbreaks of sarcoptic mange disease that occurred > 40 km apart and were separated by a year. Sarcoptic mange revealed an unfettered spread across the red fox population. The transmission of S. scabiei mites in this system was likely driven by red fox behaviors and contact between individuals, in line with previous studies. Sarcoptic mange is likely an important contributor to red fox population dynamics within barrier island systems. [ABSTRACT FROM AUTHOR]

Pyropia nereocystis is an annual northeastern Pacific‐bladed bangialean species whose macroscopic stage epiphytized the annual canopy forming bull kelp Nereocystis luetkeana. I examined three in situ facets of these epiphyte‐host dynamics in the central California region: (1) spatial and temporal variation in the presence of P. nereocystis epiphytes as a function of host density, (2) the relationship between individual host morphology and epiphytic P. nereocystis biomass, and (3) the ecophysiological growth ramifications for subtidal transplants of both life stages of P. nereocystis. Swath canopy surveys and whole host collections were conducted at five sites between November 2017 and February 2019. Additionally, transplants of P. nereocystis gametophytes and sporophytes were conducted across multiple subtidal depths. I observed temporal changes in the proportions of hosts epiphytized by P. nereocystis, with differences in seasonal persistence of P. nereocystis among sites and between years. Biomass of P. nereocystis was positively correlated with individual host stipe length, stipe surface area, and the primary principal component (PC) of stipe morphometrics denoted by principal component analysis (PCA). Gametogenesis in P. nereocystis epiphytes was spatially heterogeneous and limited for the 2018–2019 cohort due to comprehensive removal of hosts by the February 2019 sampling period. Transplants of P. nereocystis gametophytes yielded similar growth responses among depths, and sporophyte (conchocelis) transplant areal growth was positively correlated with transplant depth. These findings detail spatiotemporal complexity and multi‐scale (individual, site, and whole region) phenological nuances for central Californian P. nereocystis epiphytes. [ABSTRACT FROM AUTHOR]

We study the Bolker–Pacala–Dieckmann–Law (BPDL) model of population dynamics in the regime of large population density. The BPDL model is a particle system in which particles reproduce, move randomly in space and compete with each other locally. We rigorously prove global survival as well as a shape theorem describing the asymptotic spread of the population, when the population density is sufficiently large. In contrast to most previous studies, we allow the competition kernel to have an arbitrary, even infinite range, whence the term non‐local competition. This makes the particle system non‐monotone and of infinite‐range dependence, meaning that the usual comparison arguments break down and have to be replaced by a more hands‐on approach. Some ideas in the proof are inspired by works on the non‐local Fisher‐KPP equation, but the stochasticity of the model creates new difficulties. [ABSTRACT FROM AUTHOR]

• Chancelloriids from the Balang Biota are revised as a new and an undetermined taxa. • Archiasterella acuminata had an acuminate basal end and a pronounced apical tuft. • Chancelloriids likely reached a high diversification in the early Cambrian. Chancelloriids are an enigmatic group of Cambrian animals characterized by radially symmetrical bodies equipped with spiny sclerites. Although they were major components of many benthic communities, current understanding on how this group diversified during the Cambrian remains limited. Clarifying these confusions about the diversification of chancelloriids requires new information provided by new studies of previously described and/or new material. Considering the emerging scenario of chancelloriids, the sack-like chancelloriids from the Stage 4 Balang Lagerstätte are restudied on the basis of previous collections, which are herein separated from Chancelloria eros Walcott, 1920, and revised as Archiasterella acuminata nov. sp. and Chancelloriidae gen. et sp. indet. The Ar. acuminata specimen is well preserved and does show its scleritome and sclerite characters, while the Chancelloriidae gen. et sp. indet. specimen is poorly preserved and its scleritome and sclerite characters are difficult to distinguish. By combining information from previous studies and the present research, data on chancelloriid occurrences in South China indicate that chancelloriids had once diversified in the Cambrian South China, evidenced by high-level richness of sclerite-based taxa during the late Fortunian to the middle Stage 3, and of sclerite formulas during the late Stage 2 to the Wuliuan. The result is inconsistent with the recent viewpoint that there were two flourishing ages of chancelloriids in South China. Although more evidence is needed to support our results, the present study offers insights in understanding the evolutionary dynamics of chancelloriids. [ABSTRACT FROM AUTHOR]

Leafless Bossiaea species are a unique group of plants endemic to Australia that present intriguing challenges in taxonomy and conservation because of their morphological simplicity and often small, disjunct populations. We employed whole genome reduced representation sequencing (DArTseq) to enhance our understanding of the population dynamics, diversity and taxonomy of leafless Bossiaea species. Our dataset comprised 52,539 single-nucleotide polymorphisms across 283 samples from 7 leafless Bossiaea species, including 6 listed threatened species. We examined population structure, phylogenetic relationships, kinship and gene flow within and among populations. On the basis of our population-genomic analyses, we propose recognition of the novel taxon Bossiaea vombata subsp. orientalis and a change in status from species (B. milesiae) to subspecies for B. fragrans subsp. milesiae. Additionally, we show extensive clonal reproduction across species and limited gene flow at distances of >1 km, shedding light on the challenges faced by these species. We advocate a coordinated approach to conservation, focusing on restoring self-sustaining populations and leveraging genetic rescue strategies. By addressing the population dynamics of multiple species simultaneously in taxonomically challenging lineages, we can make informed choices to safeguard biodiversity and evolutionary potential. This study investigates the population dynamics, diversity and taxonomy of leafless Bossiaea species, a distinctive group of Australian plants, by using whole-genome single-nucleotide polymorphism data. The findings suggest recognition of a new subspecies, Bossiaea vombata subsp. orientalis , and a change in status for B. milesiae to B. fragrans subsp. milesiae. We also highlight challenges in reproduction and gene flow among Bossiaea populations, emphasising the need for coordinated conservation efforts. (Image credit: Keith McDougall.) [ABSTRACT FROM AUTHOR]

The rostral ventromedial medulla (RVM) is the key output node of the descending pain-modulating system. Intrinsic and extrinsic factors contribute to the pain experience by influencing the activity of two functional types of RVM neurons, OFF-cells and ON-cells, which respectively exert inhibitory and facilitatory control over nociceptive transmission and pain. Dysfunction in descending control, which alters the distinct inhibitory and facilitatory outputs of RVM, contributes to persistent pain states. Characterizing the function(s) of genetically defined RVM populations has been challenging and conflicting results have emerged, stressing the need for rigorous interpretation of experiments based on candidate molecular markers. Further investigation of interactions within and between functional RVM populations are a critical next step in improving our understanding of descending control of pain. The descending-pain modulating circuit controls the experience of pain by modulating transmission of sensory signals through the dorsal horn. This circuit's key output node, the rostral ventromedial medulla (RVM), integrates 'top-down' and 'bottom-up' inputs that regulate functionally defined RVM cell types, 'OFF-cells' and 'ON-cells', which respectively suppress or facilitate pain-related sensory processing. While recent advances have sought molecular definition of RVM cell types, conflicting behavioral findings highlight challenges involved in aligning functional and molecularly defined types. This review summarizes current understanding, derived primarily from rodent studies but with corroborating evidence from human imaging, of the role of RVM populations in pain modulation and persistent pain states and explores recent advances outlining inputs to, and outputs from, RVM pain-modulating neurons. [ABSTRACT FROM AUTHOR]

Kaniatarowanenneh (the St. Lawrence River) is the outflow of one of the world's largest freshwater ecosystems and its ecological health has implications for resource management. The population dynamics of an ecologically and economically important fish, the Wa hia hé:ta, Mohawk for yellow perch (Perca flavescens), are considered by including data that extend to the past century to redress temporal gaps in comparative literature. We found both a significant top-down effect from piscivorous fish as well as a significant bottom-up effect related to total phosphorus on yellow perch relative abundance in the Lake Ontario–Upper St. Lawrence system. Regarding the bottom-up effect, the current state of yellow perch reflects the population size prior to cultural eutrophication (pre-1940s/50s) likely responding to the re-oligotrophication of the system. These findings emphasize the importance of considering historical records in fish population dynamics research to incorporate shifting population baselines into fisheries management. The study also demonstrates the need for collaborative approaches that bring critical new insights and multivocality. [ABSTRACT FROM AUTHOR]

Many population statistics describe the characteristics of populations within and among species. These are useful for describing population dynamics, understanding how environmental factors alter demographic patterns, testing hypotheses related to the evolution of life history characteristics and informing the effective management of populations.In this study, we propose a population statistic: the interstage flow. The interstage flow is defined as the product of the element in the ith row, the jth column of the population projection matrix and the jth element of the normalized stable stage distribution.The sum of the interstage flow matrix elements is equal to the population growth rate (PGR), which is the dominant eigenvalue of the population projection matrix. The interstage flow matrix elements allow decomposition of PGR into component contributions made by transitions between developmental stages.We demonstrate the utility of interstage flow matrices using matrix population models from the COMPADRE plant matrix database. We compared interstage flows among four life history/functional groups (FGs) (semelparous herbs, iteroparous herbs, shrubs and trees) and described how PGR reflected individual transitions related to stasis, fecundity and growth. We found that the individual flows are different among FGs.Synthesis. The proposed population statistic, the interstage flow matrix, describes the contribution of individual developmental stage transitions to the PGR. The flow of individuals between developmental stages differs in distinctive ways among different life histories and FGs. The interstage flow matrix is a valuable statistic for describing these differences. [ABSTRACT FROM AUTHOR]

Conservation policy for the high mountains of Asia increasingly recognises the need to encompass large multi‐use landscapes beyond the protected area network. Due to limited long‐term research in this region, our understanding of even fundamental processes, such as factors regulating large mammal populations is poor.Understanding the factors that regulate animal populations, especially those generating cyclicity, is a long‐standing problem in ecology. Long‐term research across multiple taxa (mainly from Europe and North America) has focussed on the relative roles of food and predation in generating cyclicity in population dynamics. It remains unclear how trophic interactions that are influenced by anthropogenic stressors can affect population dynamics in human‐modified landscapes.We present a 10‐year study to compare the effects of livestock grazing on density‐dependent dynamics in two populations of bharal, Pseudois nayaur, in the Himalayas. We combine this with a mechanistic understanding of whether density dependence in these two sites acts predominantly by affecting adult survival or recruitment. We compared and quantified density dependence in the bharal population by fitting Bayesian Gompertz state‐space models.We found evidence for negative density dependence which indicates possible cyclic dynamics in the bharal population of the site (Tabo) with low livestock density. The population dynamics of this site were driven by recruited offspring—with a 2‐year density‐dependent lag effect—rather than adult survival. In the site with high livestock density (Kibber), this density dependence was not detected. We postulate the potential role of excessive grazing by livestock in affecting offspring recruitment, thereby affecting the bharal population in Kibber.Synthesis and applications: Our results suggest that conservation action to facilitate wild herbivore population recovery, such as the development of protected areas and village reserves, needs to account for density‐dependent regulation. Sites with trophy hunting require continuous monitoring to understand the effects of density dependence so that appropriate hunting quotas can be formulated. [ABSTRACT FROM AUTHOR]

Plants and insect herbivores are two of the most diverse multicellular groups in the world, and both are strongly influenced by interactions with the belowground soil microbiome. Effects of reciprocal rapid evolution on ecological interactions between herbivores and plants have been repeatedly demonstrated, but it is unknown if (and how) the soil microbiome could mediate these eco‐evolutionary processes on a shared host plant. We tested the role of a plant‐beneficial soil bacterium Acidovorax radicis in altering eco‐evolutionary interactions between different aphid genotypes (Sitobion avenae, genotypes Sickte and Fescue) feeding on barley Hordeum vulgare. We measured fecundity, longevity and population growth of two aphid genotypes reared separately or together (population mixture) on three different barley varieties that were inoculated with or without A. radicis. Results showed that across all plant varieties A. radicis increased plant growth and suppressed aphid populations via reduced longevity and fecundity. The strength of effect was dependent on aphid genotype and barley variety, while the direction of effect was altered by aphid population mixture. Using Lotka–Volterra modelling, we demonstrated that while A. radicis inoculation decreased growth rates for both aphid genotypes it increased the competitiveness of one genotype against the other. In general, in the presence of A. radicis, the Fescue aphid genotype became more inhibitory of Sickte aphids, while Sickte aphids facilitated the growth of Fescue aphids. Our work demonstrates that plant rhizosphere microbiomes exert community‐level influences by mediating eco‐evolutionary interactions between herbivores and host plants. By altering competitive interaction outcomes among aphids and thus impacting processes such as rapid evolution, soil microbes contribute to the short‐ and long‐term structure and functioning of terrestrial habitats. [ABSTRACT FROM AUTHOR]

Landscapes of fear can determine the dynamics of entire ecosystems. In response to perceived predation risk, prey can show physiological, behavioral, or morphological trait changes to avoid predation. This in turn can indirectly affect other species by modifying species interactions (e.g., altered feeding), with knock‐on effects, such as trophic cascades, on the wider ecosystem. While such indirect effects stemming from the fear of predation have received extensive attention for herbivore–plant and predator–prey interactions, much less is known about how they alter parasite–host interactions and wildlife diseases. In this synthesis, we present a conceptual framework for how predation risk—as perceived by organisms that serve as hosts—can affect parasite–host interactions, with implications for infectious disease dynamics. By basing our approach on recent conceptual advances with respect to predation risk effects, we aim to expand this general framework to include parasite–host interactions and diseases. We further identify pathways through which parasite–host interactions can be affected, for example, through altered parasite avoidance behavior or tolerance of hosts to infections, and discuss the wider relevance of predation risk for parasite and host populations, including heuristic projections to population‐level dynamics. Finally, we highlight the current unknowns, specifically the quantitative links from individual‐level processes to population dynamics and community structure, and emphasize approaches to address these knowledge gaps. [ABSTRACT FROM AUTHOR]

Accounting for intraspecific and interspecific competition when assessing the effects of chemical and nonchemical stressors is an important uncertainty in ecological risk assessments. We developed novel projection of interspecific competition (PIC) matrices that allow for analysis of population dynamics of two or more species exposed to a given stressor(s) that compete for shared resources within a landscape. We demonstrate the application of PIC matrices to investigate the population dynamics of two hypothetical fish species that compete with one another and have differences in net reproductive rate and intrinsic rate of population increase. Population status predictions were made under scenarios that included exposure to a chemical stressor that reduced fecundity for one or both species. The results of our simulations demonstrated that measures obtained from the life table and Leslie matrix of an organism, including net reproductive rate and intrinsic rate of increase, can result in erroneous conclusions of population status and viability in the absence of a consideration of resource limitation and interspecific competition. This modeling approach can be used in conjunction with field monitoring efforts and/or laboratory testing to link effects due to stressors to possible outcomes within an ecosystem. In addition, PIC matrices could be combined with adverse outcome pathways to allow for ecosystem projection based on taxonomic conservation of molecular targets of chemicals to predict the likelihood of relative cross‐species susceptibility. Overall, the present study shows how PIC matrices can integrate effects across the life cycles of multiple species, provide a linkage between endpoints observed in individual and population‐level responses, and project outcomes at the community level for multiple generations for multiple species that compete for limited resources. Environ Toxicol Chem 2024;43:1406–1422. Published 2024. This article is a U.S. Government work and is in the public domain in the USA. [ABSTRACT FROM AUTHOR]

Stalk rot disease is a major constraint in maize production and till date reported to be caused by two to three species of phytopathogenic fungi but, in our present study, we disclose the first report of stalk rot is caused by complex species of phytopathogens, which belongs to five different genera. Therefore, to substantiate these findings, a total of 105 diseased samples of maize were collected from 21 different locations in six different geographical locations of India from which 48 isolates were used for the research study. Morphological features such as pigmentation, colony color, type of mycelium and pattern of mycelium was examined using macro and microscopic methods. A total of 11 different spp. of pathogens belonging to the five different genera: Fusarium verticillioides (56.25%), F. equiseti (14.5%), F. andiyazi (6.25%), F. solani (2.08%), F. proliferatum (2.08%), F. incarnatum (2.08%), Lasidioplodia theobrame (6.25%), Exserohilum rostrtum (4.16%), Nigrospora spp. (4.16%). and Schizophyllum commune (2.08%) were identified by different housekeeping genes (ITS, TEF-1α, RPB2 and Actin). Fusarium verticillioides, F. equiseti and F. andiyazi were major pathogens involved in stalk rot. This is the first report on F. proliferatum, F. solani, F. incarnatum, Lasidioplodia theobrame, Exserohilum rostrtum, Nigrospora spp. and Schizophyllum commune causing stalk rot of maize and their distribution in the different states of India. Studies on population dynamics of PFSR will enhance the understanding of pathogen behavior, virulence, or its association with different pathogens across India, which will facilitate the development of resistant maize genotypes against the PFSR. [ABSTRACT FROM AUTHOR]

Ramularia collo‐cygni (Rcc) is a major barley pathogen that causes yield and grain quality losses worldwide. The main sources of Rcc inoculum are the seed and asexual airborne spores. In Argentina, Rcc is considered to be an emerging threat to barley crops, especially as most varieties are susceptible to Rcc and have a European genetic background. Here, we describe the population genetic diversity and structure of the Argentinian Rcc population, based on 10 simple‐sequence repeat (SSR) markers, in order to compare it with Rcc populations from the Czech Republic and Scotland. The Argentinian Rcc population showed lower genetic diversity, higher level of structuring and higher number of clonal isolates than European populations. Significant differentiation at population origin (country) and region (Europe and South America) level suggests the occurrence of a genetic bottleneck and/or a founder effect on Rcc entry to Argentina and that this population could still be in a state of establishment and emergence. Further research on Rcc genetic structure at local and global scale will be crucial for the understanding of Rcc population dynamics for disease management. [ABSTRACT FROM AUTHOR]

Molecular tools are an indispensable part of ecology and biodiversity sciences and implemented across all biomes. About a decade ago, the use and implementation of environmental DNA (eDNA) to detect biodiversity signals extracted from environmental samples opened new avenues of research. Initial eDNA research focused on understanding population dynamics of target species. Its scope thereafter broadened, uncovering previously unrecorded biodiversity via metabarcoding in both well‐studied and understudied ecosystems across all taxonomic groups. The application of eDNA rapidly became an established part of biodiversity research, and a research field by its own. Here, we revisit key expectations made in a land‐mark special issue on eDNA in Molecular Ecology in 2012 to frame the development in six key areas: (1) sample collection, (2) primer development, (3) biomonitoring, (4) quantification, (5) behaviour of DNA in the environment and (6) reference database development. We pinpoint the success of eDNA, yet also discuss shortfalls and expectations not met, highlighting areas of research priority and identify the unexpected developments. In parallel, our retrospective couples a screening of the peer‐reviewed literature with a survey of eDNA users including academics, end‐users and commercial providers, in which we address the priority areas to focus research efforts to advance the field of eDNA. With the rapid and ever‐increasing pace of new technical advances, the future of eDNA looks bright, yet successful applications and best practices must become more interdisciplinary to reach its full potential. Our retrospect gives the tools and expectations towards concretely moving the field forward. [ABSTRACT FROM AUTHOR]

The compositional data are interrelated, and analyzing the evolution of each component is crucial for understanding population dynamics. However, the complex structure and tedious process of modeling pose challenges to the reasonable construction of grey compositional models for analyzing multi-trend mixed data. To address this, a novel enriched nonlinear grey compositional model with global multi-parameter combinatorial optimization is firstly proposed. Secondly, two types of Monte Carlo simulations are designed to validate the performances, modeling characteristics and noise levels of our model. Finally, using the bioenergy power generation structure of China as a case study, the practicability of our approach is verified. The results demonstrate that our model significantly outperforms traditional mainstream models in multi-trend mixed sequences, and the interrelationships among components are effectively verified. Our model not only enriches the methodological base but also broadens the application scope of grey compositional model. • A novel non-linear dynamic GM-Markov compositional model is constructed. • Our model is capable of achieving global multi-parameter combinatorial optimization. • Our model can accurately fit compositional data exhibiting fluctuations and multi-trend. • Our model might be useful in forecasting bioenergy power generation structures. [ABSTRACT FROM AUTHOR]

The mealybug (Paracoccus marginatus) is one of the most important pests of papaya (Carica papaya L.). The high potential damage of this pest threatens papaya production. The objective of this paper is to explore the impact of biocontrol and temperature variations on the population dynamics of Paracoccus marginatus (P. marginatus). We first propose and study a mathematical model for the dynamics of P. marginatus within a papaya field. This model consists of a time-delayed non-autonomous system of differential equations that takes into account the egg incubation period, temperature variations, plant compensation and predators that are natural enemies of the papaya pest. We provide the basic properties of the model, compute the basic offspring number N 0 and show that there exists two threshold parameters N _ 0 and ξ 0 such that N _ 0 ≤ N 0 ≤ ξ 0 ≤ 1 and N 0 ≥ N _ 0 > 1 provide conditions for the extinction and persistence of the pest within the papaya field, respectively. After, we investigate the impact of biocontrol on the pest population. We found that the use of a control strategy based on constant releases of predators could reduce the pest population by 35.62 percent and increase the biomass by 77.50 percent, while the use of impulsive releases of predators result in a decrease of 96.31 percent of the pest population and an increases of 55.74 percent of the biomass. We also combine the use of continuous predator releases and bio-pesticides and discovered that a spray applied 90 days after germination could completely eliminate the pest population and boost the biomass by 81.58 percent. • The population dynamics of Paracoccus marginatus , papaya pest is modeled. • The model includes the egg incubation period, temperature variations and biocontrol. • The warm temperatures are favorable to the development and survival of the pest. • The use of impulsive releases of predators can reduce the pest by 96.31%. • The use of continuous releases of predators and bio-pesticides can eradicate the pest. [ABSTRACT FROM AUTHOR]

Augmentative release of predators is used in agriculture to suppress pest populations and minimise crop damage. However, predators affect prey populations not only through consumption but by inducing changes to prey morphology, physiology, behaviour and life history. These risk‐induced trait responses can increase prey fitness, potentially reducing the efficacy of certain predators as biocontrol agents.We investigated how non‐consumptive effects contribute to the overall influence of predators by modelling the effect of the predator Podisus maculiventris on the population dynamics of a major agricultural pest, the Colorado potato beetle (Leptinotarsa decemlineata). We developed a demographic model incorporating both consumption and non‐consumptive Podisus‐induced shifts in beetle reproductive strategy. Our model combines data from multiple mechanistic experiments showing that predator‐exposed beetles produce fewer offspring but increase offspring provisioning, and that provisioned larvae have increased survival when predators are present. We simulated beetle densities across multiple beetle generations and a range of predator densities.The influence of non‐consumptive effects depended on predator density. At low predator densities, non‐consumptive effects strengthened the negative effect of predators by up to 45%, and risk‐induced changes to offspring provisioning had a stronger effect on prey densities than reduced offspring quantity. In contrast, at high predator densities, non‐consumptive effects changed the effect of predators by <5%, likely because beetle densities were very low both with and without non‐consumptive effects.Our results suggest that even adaptive responses to predation risk by prey do not necessarily reduce the ability of predators to suppress pest populations. [ABSTRACT FROM AUTHOR]

A change to a population's social network is a change to the substrate of cultural transmission, affecting behavioral diversity and adaptive cultural evolution. While features of network structure such as population size and density have been well studied, less is understood about the influence of social processes such as population turnover—or the repeated replacement of individuals by naive individuals. Experimental data have led to the hypothesis that naive learners can drive cultural evolution by better assessing the relative value of behaviors, although this hypothesis has been expressed only verbally. We conducted a formal exploration of this hypothesis using a generative model that concurrently simulated its two key ingredients: social transmission and reinforcement learning. We simulated competition between high- and low-reward behaviors while varying turnover magnitude and tempo. Variation in turnover influenced changes in the distributions of cultural behaviors, irrespective of initial knowledge-state conditions. We found optimal turnover regimes that amplified the production of higher reward behaviors through two key mechanisms: repertoire composition and enhanced valuation by agents that knew both behaviors. These effects depended on network and learning parameters. Our model provides formal theoretical support for, and predictions about, the hypothesis that naive learners can shape cultural change through their enhanced sampling ability. By moving from experimental data to theory, we illuminate an underdiscussed generative process that can lead to changes in cultural behavior, arising from an interaction between social dynamics and learning. [ABSTRACT FROM AUTHOR]

Detectability poses a common challenge faced by studies of small mammals. Traditional sampling methods use traps placed exclusively on the ground, which makes them less effective for monitoring species with climbing habits. The bias arising from imperfect detection may have important implications in pest assessment, epidemiological studies involving reservoirs, and conservation studies. In this study, we added above ground level (AGL) traps in the bushy or arboreal stratum to the conventional sampling protocol. Our objective was to evaluate whether the location of the traps influences the seasonal abundance pattern of Oligoryzomys flavescens, a scansorial rodent species identified as an orthohantavirus reservoir in the study area. Additionally, we evaluated the potential impact of various environmental variables on the capture probability of O. flavescens in different strata. Detectability of this rodent was significantly increased in traps placed AGL than at ground level (GL). However, trap placement level did not influence seasonal variation in O. flavescens abundance. Furthermore, the increase in herbaceous cover at ground level positively influenced the probability of capturing O. flavescens in traps placed AGL. Traditional sampling designs relying solely on GL traps may perform well for studies focused on the population dynamics of O. flavescens. Conversely, in areas where herbaceous vegetation facilitates connectivity between the ground and shrub layers, adding AGL traps in the sampling strategy can guarantee better results for studies that need to capture a large number of O. flavescens individuals (i.e., seroprevalence studies or investigations on movements). [ABSTRACT FROM AUTHOR]

Hourly, year‐round flow cytometry has made it possible to relate seasonal environmental variability to the population dynamics of the smallest, most abundant phytoplankton on the Northeast US Shelf. To evaluate whether the insights from these data extend to Synechococcus farther from shore, we analyze flow cytometry measurements made continuously from the underway systems on 21 cruises traveling between the Martha's Vineyard Coastal Observatory (MVCO) and the continental shelf break. We describe how seasonal patterns in Synechococcus, which have been documented in detail at MVCO, occur across the region with subtle variation. We find that the underlying relationship between temperature and division rate is consistent across the shelf and can explain much of the observed spatial variability in concentration. Connecting individual cell properties to annual and regional patterns in environmental conditions, these results demonstrate the value of autonomous monitoring and create an improved picture of picophytoplankton dynamics within an economically important ecosystem. [ABSTRACT FROM AUTHOR]

Freshwater mussel declines range from dramatic to subtle, but there are few methods for quantifying the extent of decline and overall assemblage health. Available assessment tools are specific to particular streams or regions and depend on untested assumptions or subjective assessments of species' tolerance to various factors. We developed a broadly applicable, objective mussel assemblage health index (MAHI). We compiled a dataset of mussel survey data from 50 streams across eastern North America and evaluated the ability of 19 candidate metrics to discriminate healthy and degraded assemblages. MAHI includes 4 metrics representing fundamental aspects of assemblage or population health (species loss, recruitment, abundance, and population growth). Metrics are scaled from 0 to 10 (representing increasing health), and the composite score is the unweighted mean of the 4 metrics. MAHI effectively discriminated healthy (median score = 8.3) and degraded (3.2) assemblages. The composite score is robust to missing values—omitting any single metric resulted in a median score change of ≤0.7. Composite scores were similar to independent scores provided by experts, but MAHI eliminates variation due to differences in individual perception or experience. MAHI can be applied to streams across eastern North America using commonly collected mussel survey data, and it may be adapted to other regions. MAHI is free of untested assumptions or subjective assessments, and it accounts for expected differences in mussel assemblages due to stream size, biogeographic region, and other intrinsic factors. MAHI will be a valuable tool for early detection of mussel declines, better understanding the causes of declines, and evaluating the effectiveness of conservation strategies and management actions. We developed a Microsoft Excel application that calculates MAHI scores, and we provide a link to that resource. [ABSTRACT FROM AUTHOR]

We extend the piecewise orthogonal collocation method to computing periodic solutions of coupled renewal and delay differential equations. Through a rigorous error analysis, we prove convergence of the relevant finite-element method and provide a theoretical estimate of the error. We conclude with some numerical experiments to further support the theoretical results. [ABSTRACT FROM AUTHOR]

Individuals delay natal dispersal for many reasons. There may be no place to disperse to; immediate dispersal or reproduction may be too costly; immediate dispersal may mean that the individual and their relatives miss the benefits of group living. Understanding the factors that lead to the evolution of delayed dispersal is important because delayed dispersal sets the stage for complex social groups and social behavior. Here, we study the evolution of delayed dispersal when the quality of the local environment is improved by greater numbers of individuals (e. g. , safety in numbers). We assume that individuals who delay natal dispersal also expect to delay personal reproduction. In addition, we assume that improved environmental quality benefits manifest as changes to fecundity and survival. We are interested in how do the changes in these life-history features affect delayed dispersal. We use a model that ties evolution to population dynamics. We also aim to understand the relationship between levels of delayed dispersal and the probability of establishing as an independent breeder (a population-level feature) in response to changes in life-history details. Our model emphasizes kin selection and considers a sexual organism, which allows us to study parent–offspring conflict over delayed dispersal. At evolutionary equilibrium, fecundity and survival benefits of group size or quality promote higher levels of delayed dispersal over a larger set of life histories with one exception. The exception is for benefits of increased group size or quality reaped by the individuals who delay dispersal. There, the increased benefit does not change the life histories supporting delay dispersal. Next, in contrast to previous predictions, we find that a low probability of establishing in a new location is not always associated with a higher incidence of delayed dispersal. Finally, we find that increased personal benefits of delayed dispersal exacerbate the conflict between parents and their offspring. We discuss our findings in relation to previous theoretical and empirical work, especially work related to cooperative breeding. • We study the evolution of delayed natal dispersal. • We assume delayed dispersal brings benefits to the natal group. • The number of delayed-dispersers is independent of the group quality. • Habitat saturation is not always associated with delayed dispersal. • Increased group benefits exacerbate conflict within the natal group. [ABSTRACT FROM AUTHOR]

Agonistic behavior, a critical component of territoriality, is widespread throughout terrestrial plethodontid salamanders, though geographic variation in this behavior is poorly understood. Using color polymorphic Eastern Red-backed Salamanders (Plethodon cinereus), we conducted same-sex laboratory trials to compare aggressive and submissive behaviors between two genetically distinct groups in northern Ohio. For each group, we tested 120 individuals from 3 populations. We predicted that the genetic group with a single color morph would exhibit a higher degree of agonistic and territorial behavior compared to the genetic group with two morphs as an adaptive consequence of altered social dynamics in monomorphic populations. Contrary to our prediction, laboratory trials demonstrated that residents from the polymorphic group were significantly more aggressive than residents from the monomorphic group. This finding was corroborated by a strong residency effect in the polymorphic group, an effect that was weaker in the monomorphic group. Our results suggest that individuals in the polymorphic group are more aggressive and territorial than individuals in the monomorphic group, signifying a greater propensity to secure a territory and defend it against intruders. Our results add important insight into how geographic variation and differences in morph frequency can be attributed to behavioral differences. [ABSTRACT FROM AUTHOR]

Īnanga (Galaxias maculatus) is a widespread freshwater fish, found around coastal New Zealand, Chatham Islands, southern Australia and southern South America, exhibiting both diadromous and land-locked life history patterns. We assessed population size structure, size at maturity, timing of reproduction, and post-reproductive survival in the Waikouaiti and Kakanui rivers, two regionally important G. maculatus populations in southern New Zealand. Size at maturity varied between rivers and sexes, with males generally maturing at smaller sizes than females. The timing of reproduction and recruitment was observed to vary across a relatively small spatial scale. Population length-frequencies indicated that both populations exhibited annual population dynamics, with most individuals spawning in their first year, then apparently dying soon afterwards (as indicated by a marked drop in post-spawning abundance). However, a few individuals with recently spent or resting gonads were present over the winter months, indicating some post-spawning survival. There was a lower frequency of exceptionally large (putatively 1+) individuals than reported for other populations around New Zealand and elsewhere, suggesting over-winter survival following spawning varies. Based on the variation in life history characters over small spatial scales, we suggest that management of regionally important G. maculatus populations should be based on catchment level information. [ABSTRACT FROM AUTHOR]

The taxonomic classification of Picea meyeri and P. mongolica has long been controversial. To investigate the genetic relatedness, evolutionary history, and population history dynamics of these species, genotyping-by-sequencing (GBS) technology was utilized to acquire whole-genome single nucleotide polymorphism (SNP) markers, which were subsequently used to assess population structure, population dynamics, and adaptive differentiation. Phylogenetic and population structural analyses at the genomic level indicated that although the ancestor of P. mongolica was a hybrid of P. meyeri and P. koraiensis, P. mongolica is an independent Picea species. Additionally, P. mongolica is more closely related to P. meyeri than to P. koraiensis, which is consistent with its geographic distribution. There were up to eight instances of interspecific and intraspecific gene flow between P. meyeri and P. mongolica. The P. meyeri and P. mongolica effective population sizes generally decreased, and Maxent modeling revealed that from the Last Glacial Maximum (LGM) to the present, their habitat areas decreased initially and then increased. However, under future climate scenarios, the habitat areas of both species were projected to decrease, especially under high-emission scenarios, which would place P. mongolica at risk of extinction and in urgent need of protection. Local adaptation has promoted differentiation between P. meyeri and P. mongolica. Genotype‒environment association analysis revealed 96,543 SNPs associated with environmental factors, mainly related to plant adaptations to moisture and temperature. Selective sweeps revealed that the selected genes among P. meyeri, P. mongolica and P. koraiensis are primarily associated in vascular plants with flowering, fruit development, and stress resistance. This research enhances our understanding of Picea species classification and provides a basis for future genetic improvement and species conservation efforts. [ABSTRACT FROM AUTHOR]

Predators can strongly influence prey populations not only through consumptive effects (CE) but also through non‐consumptive effects (NCE) imposed by predation risk. Yet, the impact of NCE on bioenergetic and stoichiometric body contents of prey, traits that are shaping life histories, population and food web dynamics, is largely unknown. Moreover, the degree to which NCE can evolve and can drive evolution in prey populations is rarely studied. A 6‐week outdoor mesocosm experiment with Caged‐Fish (NCE) and Free‐Ranging‐Fish (CE and NCE) treatments was conducted to quantify and compare the effects of CE and NCE on population densities, bioenergetic and stoichiometric body contents of Daphnia magna, a keystone species in freshwater ecosystems. We tested for evolution of CE and NCE by using experimental populations consisting of D. magna clones from two periods of a resurrected natural pond population: a pre‐fish period without fish and a high‐fish period with high predation pressure. Both Caged‐Fish and Free‐Ranging‐Fish treatments decreased the body size and population densities, especially in Daphnia from the high‐fish period. Only the Free‐Ranging‐Fish treatment affected bioenergetic variables, while both the Caged‐Fish and Free‐Ranging‐Fish treatments shaped body stoichiometry. The effects of CE and NCE were different between both periods indicating their rapid evolution in the natural resurrected population. Both the Caged‐Fish and Free‐Ranging‐Fish treatments changed the clonal frequencies of the experimental Daphnia populations of the pre‐fish as well as the high‐fish period, indicating that not only CE but also NCE induced clonal sorting, hence rapid evolution during the mesocosm experiment in both periods. Our results demonstrate that CE as well as NCE have the potential to change not only the body size and population density but also the bioenergetic and stoichiometric characteristics of prey populations. Moreover, we show that these responses not only evolved in the studied resurrected population, but that CE and NCE also caused differential rapid evolution in a time frame of 6 weeks (ca. four to six generations). As NCE can evolve as well as can drive evolution, they may play an important role in shaping eco‐evolutionary dynamics in predator–prey interactions. [ABSTRACT FROM AUTHOR]

Novel mosquito genetic control tools, such as CRISPR-based gene drives, hold great promise in reducing the global burden of vector-borne diseases. As these technologies advance through the research and development pipeline, there is a growing need for modeling frameworks incorporating increasing levels of entomological and epidemiological detail in order to address questions regarding logistics and biosafety. Epidemiological predictions are becoming increasingly relevant to the development of target product profiles and the design of field trials and interventions, while entomological surveillance is becoming increasingly important to regulation and biosafety. We present MGDrivE 3 (Mosquito Gene Drive Explorer 3), a new version of a previously-developed framework, MGDrivE 2, that investigates the spatial population dynamics of mosquito genetic control systems and their epidemiological implications. The new framework incorporates three major developments: i) a decoupled sampling algorithm allowing the vector portion of the MGDrivE framework to be paired with a more detailed epidemiological framework, ii) a version of the Imperial College London malaria transmission model, which incorporates age structure, various forms of immunity, and human and vector interventions, and iii) a surveillance module that tracks mosquitoes captured by traps throughout the simulation. Example MGDrivE 3 simulations are presented demonstrating the application of the framework to a CRISPR-based homing gene drive linked to dual disease-refractory genes and their potential to interrupt local malaria transmission. Simulations are also presented demonstrating surveillance of such a system by a network of mosquito traps. MGDrivE 3 is freely available as an open-source R package on CRAN (https://cran.r-project.org/package=MGDrivE2) (version 2.1.0), and extensive examples and vignettes are provided. We intend the software to aid in understanding of human health impacts and biosafety of mosquito genetic control tools, and continue to iterate per feedback from the genetic control community. [ABSTRACT FROM AUTHOR]

Davidia involucrata is a woody perennial and the only living species in the Genus Davidia. It is native to southern China where it holds cultural and scientific importance. However, D. involucrata is now an endangered species and its natural range includes low pH soils which are increasingly impacted by acid rain, nitrogen deposition and imbalanced nutrient cycling. The combination of these stresses also poses the additional risk of aluminum (Al) toxicity. Since the responses of D. involucrata to low pH and aluminum toxicity have not been investigated previously, a hydroponic experiment was conducted to examine the growth of one year old D. involucrata saplings after 50 d growth in a range of pH and Al conditions. Plant biomass, morphology, antioxidant enzyme activity, mineral concentrations and plant ecological strategy were compared at pH 5.8 and pH 4.0 without added Al (AlCl3) and in 0.1, 0.2 and 0.5 mM Al at pH 4.0. Our results showed that compared with pH 5.8, pH 4.0 (without added Al) not only inhibited root and shoot growth but also limited accumulation of nitrogen (N) and phosphorus (P) in leaves of D. involucrate. However, low Al concentrations (0.1 and 0.2 mM Al) at pH 4.0 partially restored the aboveground growth and leaf N concentrations, suggesting an alleviation of H+ toxicity by low Al concentrations. Compared with low Al concentrations, 0.5 mM Al treatment decreased plant growth and concentrations of N, P, and magnesium (Mg) in the leaves, which demonstrated the toxicity of high Al concentration. The results based on plant ecological strategy showed that D. involucrate decreased the competitiveness and favored its stress tolerance as pH changed from 5.8 to 4.0. Meanwhile, the competitiveness and stress tolerance of D. involucrata increased and decreased at low Al concentrations, respectively, and decreased and increased at high Al concentration, respectively. These trade-offs in ecological strategy were consistent with the responses of growth and antioxidant enzyme activity, reflecting a sensitive adaptation of D. involucrata to acid and Al stresses, which may aid in sustaining population dynamics. These findings are meaningful for understanding the population dynamics of D. involucrata in response to aluminum toxicity in acid soils. [ABSTRACT FROM AUTHOR]

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 with 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. [ABSTRACT FROM AUTHOR]

Background: The identification of low-frequency haplotypes, never observed in homozygous state in a population, is considered informative on the presence of potentially harmful alleles (candidate alleles), putatively involved in inbreeding depression. Although identification of candidate alleles is challenging, studies analyzing the dynamics of potentially harmful alleles are lacking. A pedigree of the highly endangered Gochu Asturcelta pig breed, including 471 individuals belonging to 51 different families with at least 5 offspring each, was genotyped using the Axiom PigHDv1 Array (658,692 SNPs). Analyses were carried out on four different cohorts defined according to pedigree depth and at the whole population (WP) level. Results: The 4,470 Linkage Blocks (LB) identified in the Base Population (10 individuals), gathered a total of 16,981 alleles in the WP. Up to 5,466 (32%) haplotypes were statistically considered candidate alleles, 3,995 of them (73%) having one copy only. The number of alleles and candidate alleles varied across cohorts according to sample size. Up to 4,610 of the alleles identified in the WP (27% of the total) were present in one cohort only. Parentage analysis identified a total of 67,742 parent-offspring incompatibilities. The number of mismatches varied according to family size. Parent-offspring inconsistencies were identified in 98.2% of the candidate alleles and 100% of the LB in which they were located. Segregation analyses informed that most potential candidate alleles appeared de novo in the pedigree. Only 17 candidate alleles were identified in the boar, sow, and paternal and maternal grandparents and were considered segregants. Conclusions: Our results suggest that neither mutation nor recombination are the major forces causing the apparition of candidate alleles. Their occurrence is more likely caused by Allele-Drop-In events due to SNP calling errors. New alleles appear when wrongly called SNPs are used to construct haplotypes. The presence of candidate alleles in either parents or grandparents of the carrier individuals does not ensure that they are true alleles. Minimum Allele Frequency thresholds may remove informative alleles. Only fully segregant candidate alleles should be considered potentially harmful alleles. A set of 16 candidate genes, potentially involved in inbreeding depression, is described. [ABSTRACT FROM AUTHOR]

The long-term dynamics of production of the glacial relict amphipod Monoporeia affinis was examined in a small subarctic lake. The aims of this study were: (1) to compare the production of amphipods with their biomass; (2) to relate the changes in amphipod population with environmental variables. I hypothesized secondary production could provide better insight into M. affinis population dynamics, than abundance and biomass alone. Production (increment-summation method) and its standard error were estimated based on benthic samples taken at a sublittoral site from June 2002 to May 2019 (as a rule, 4–5 times a year). Production and biomass were highly correlated with each other. The annual P/B ratio varied twofold. However, the majority of estimates did not differ significantly from the mean P/B value for the study period. Effects of environmental variables (water temperature and chlorophyll-a concentration) were pronounced for offspring and juvenile amphipods only. The older amphipods showed no significant correlation with any environmental variables. Despite the initial prediction, no reliable evidence was found that production revealed greater insight into population dynamics of M. affinis. This long-term study confirms that benthic production is mainly a function of biomass. [ABSTRACT FROM AUTHOR]

The grey rockcod, Lepidonotothen squamifrons is an important prey species for seals, penguins and Patagonian toothfish (Dissostichus eleginoides) in the Southern Ocean. Across the Kerguelen Plateau, the species was fished to commercial extinction (ca. 152 000 tonnes between 1971 and 1978) prior to the declaration of the French Exclusive Economic Zone in 1979 and the Australian Fishing Zone in 1981. In this study we estimate; age, growth, maturity, sex ratio, body condition (weight-at-length), and population density of grey rockcod using data from 19 trawl surveys from 1990 to 2014. There appeared to be three distinct geographical populations, with differences in biological parameters within each population. This study has identified separate metapopulations within the southern region of the Kerguelen Plateau and we recommend that management should take into account the different characteristics of these populations, and that this meta-population structure may be a factor in why this species required several decades to show signs of recovery. [ABSTRACT FROM AUTHOR]

Multispecies bacterial populations often inhabit confined and densely packed environments where spatial competition determines the ecological diversity of the community. However, the role of mechanical interactions in shaping the ecology is still poorly understood. Here, we study a model system consisting of two populations of nonmotile Escherichia coli bacteria competing within open, monolayer microchannels. The competitive dynamics is observed to be biphasic: After seeding, either one strain rapidly fixates or both strains orient into spatially stratified, stable communities. We find that mechanical interactions with other cells and local spatial constraints influence the resulting community ecology in unexpected ways, severely limiting the overall diversity of the communities while simultaneously allowing for the establishment of stable, heterogeneous populations of bacteria displaying disparate growth rates. Surprisingly, the populations have a high probability of coexisting even when one strain has a significant growth advantage. A more coccus morphology is shown to provide a selective advantage, but agent-based simulations indicate this is due to hydrodynamic and adhesion effects within the microchannel and not from breaking of the nematic ordering. Our observations are qualitatively reproduced by a simple Pólya urn model, which suggests the generality of our findings for confined population dynamics and highlights the importance of early colonization conditions on the resulting diversity and ecology of bacterial communities. These results provide fundamental insights into the determinants of community diversity in dense confined ecosystems where spatial exclusion is central to competition as in organized biofilms or intestinal crypts. [ABSTRACT FROM AUTHOR]

Habitat loss and isolation caused by landscape fragmentation represent a growing threat to global biodiversity. Existing theory suggests that the process will lead to a decline in metapopulation viability. However, since most metapopulation models are restricted to simple networks of discrete habitat patches, the effects of real landscape fragmentation, particularly in stochastic environments, are not well understood. To close this major gap in ecological theory, we developed a spatially explicit, individual-based model applicable to realistic landscape structures, bridging metapopulation ecology and landscape ecology. This model reproduced classical metapopulation dynamics under conventional model assumptions, but on fragmented landscapes, it uncovered general dynamics that are in stark contradiction to the prevailing views in the ecological and conservation literature. Notably, fragmentation can give rise to a series of dualities: a) positive and negative responses to environmental noise, b) relative slowdown and acceleration in density decline, and c) synchronization and desynchronization of local population dynamics. Furthermore, counter to common intuition, species that interact locally ("residents") were often more resilient to fragmentation than long-ranging "migrants." This set of findings signals a need to fundamentally reconsider our approach to ecosystem management in a noisy and fragmented world. [ABSTRACT FROM AUTHOR]