Population Structure Dynamics Research Articles

Phylogeographic Structure and Population Dynamics of Baoxing Osmanthus (Osmanthus serrulatus), an Endemic Species from the Southwest Sichuan Basin, China.

The mountainous regions of southwest China are recognized as pivotal centers for the origin and evolution of Osmanthus species. Baoxing Osmanthus (Osmanthus serrulatus Rehder), a rare and endemic species known for its spring blooms, is sparsely distributed within the high altitude evergreen broad-leaved forests surrounding the southwestern Sichuan Basin. However, persistent anthropogenic disturbances and habitat fragmentation have precipitated a significant decline in its natural population size, leading to the erosion of genetic resources. To assess the genetic status of O. serrulatus and formulate effective conservation strategies, we conducted sampling across ten wild populations, totaling 148 individuals in their natural habitats. We employed two cpDNA fragments (matK and trnS-trnG) to elucidate the phylogeographic structure and historical population dynamics. The results revealed low species-level genetic diversity, alongside pronounced regional differentiation among populations (FST = 0.812, p < 0.05) and a notable phylogeographic structure (NST = 0.698 > GST = 0.396, p < 0.05). Notably, genetic variation was predominantly observed among populations (81.23%), with no evidence of recent demographic expansion across the O. serrulatus distribution range. Furthermore, divergence dating indicated a timeline of approximately 4.85 Mya, corresponding to the late Miocene to early Pleistocene. This temporal correlation coincided with localized uplift events in the southwestern mountains and heightened Asian monsoons, suggesting pivotal roles for these factors in shaping the current phylogeographic pattern of O. serrulatus. These findings support the effective conservation of O. serrulatus germplasm and offer insights into the impact of Quaternary climate oscillations on companion species within evergreen broad-leaved forests. They also enhance our understanding of the origin and evolution of these forests in the southwestern mountains, aiding biodiversity conservation efforts in the region.

Microfluidic Ecology Unravels the Genetic and Ecological Drivers of T4r Bacteriophage Resistance in E. coli: Insights into Biofilm-Mediated Evolution.

We use a microfluidic ecology which generates non-uniform phage concentration gradients and micro-ecological niches to reveal the importance of time, spatial population structure and collective population dynamics in the de novo evolution of T4r bacteriophage resistant motile E. coli. An insensitive bacterial population against T4r phage occurs within 20 hours in small interconnected population niches created by a gradient of phage virions, driven by evolution in transient biofilm patches. Sequencing of the resistant bacteria reveals mutations at the receptor site of bacteriophage T4r as expected but also in genes associated with biofilm formation and surface adhesion, supporting the hypothesis that evolution within transient biofilms drives de novo phage resistance.

Characteristics of phytoplankton functioning in urban water reservoires (based on the example of Basivkut Reservoir, Ukraine)

The study states fundamental patterns of development for species and taxonomic composition, structure and seasonal population dynamics, biomass and informational diversity of phytoplankton in Basivkut Reservoir. During the research (June–October, 2022) it has been identified 121 algae species represented with 125 intraspecific taxa that belong to 84 genera, 43 families, 29 orders, 12 classes and 8 divisions. Floristic aspect of plankton algae is presented with Chlorophyta (40.1% of the total species number), Bacillariophyta (26.4%), Euglenozoa (13.2%) and Cyanobacteria (12.4%). The population of phytoplankton in Basivkut water storage was ranging from 4654 thous. cells/dm3 to 14212 thous. cells/dm3 (August), and the population of biomass was changing from 0.8732 mg/dm3 (July) to 9.4828 mg/dm3 (October). Shannon index has changed within 0.62–5.07 bit/mg according to biomass, 2.13–4.50 bit/sp. according to the population. The average values of the saprobic index have ranged from 1.74 to 2.14 that correspond to the third class of water quality (poorly polluted). The author highlights the increasing of Cyanobacteria development whose population and biomass reached 86.1% and 33.2% that caused intensive algal blooms in all summer months and is the impact of algal groups on the anthropogenic factors effect and climate changes. Aphanizomenon flos-aquae (10.5–32.2% and 10.6–12.4%) and Cuspidothrix issatschenkoi (11.6–31.2% and 10.2–14.5%) have dominated according to their population and biomass. Bacillariophyta impacted on population (39.5–74.0%) and biomass (88.7–98.4%) in autumn. Small cell type Stephanodiscus hantzschii has been characterized with significant population (16.9–65.4%) and biomass (51.1–92.9%) that focuses on increasing degree of trophic level in the Basivkut water storage.

The optimal momentum of population growth and decline

About 50 years ago, Keyfitz (1971) asked how much further a growing human population would increase if its fertility rate were immediately to be reduced to replacement level and remain there forever. The reason for demographic momentum is an age–structure inertia due to relatively many potential parents because of past high fertility. Although nobody expects such a miraculous reduction in reproductive behavior, a gradual decline in fertility in rapidly growing populations seems inevitable. As any delay in fertility decline to a stationary level leads to an increase in the momentum, it makes sense to think about the timing and the quantum of the reduction in reproduction. More specifically, we consider an intertemporal trade-off between costly pro- and anti-natalistic measures and the demographic momentum at the end of the planning period. This paper uses the McKendrick–von Foerster partial differential equation of age–structured population dynamics to study a sketched problem in a distributed parameter control framework. Among the results obtained by applying an appropriate extension of Pontryagin’s Maximum Principle are the following: (i) monotony of adaptation efforts to net reproduction rate and convex decrease/concave increase (if initial net reproduction rate exceeds 1/is below 1); and (ii) oscillating efforts and reproduction rate if, additionally, the size of the total population does not deviate from a fixed level.

A Bayesian stock assessment of the eastern Pacific gray whale using abundance and harvest data from 1967-1996

Abundance and harvest data since 1966/67 were used to assess the eastern Pacific stock of gray whales. A Bayesian statistical method was used to estimate probability distributions for the parameters of both a simple and an age and sex structured population dynamics model, as well as output quantities of interest. Model comparisons using the Bayes Factor provided conclusive evidence that an additional parameter should be used to account for unexplained variation in the abundance time series. Incorporating the additional variance parameter decreased the precision of the estimates of the other parameters. Point estimates of carrying capacity ranged from 24,640-31,840 for the different models, but the posterior distributions from the selected models were very broad and excluded few values. The current depletion level (population size as a fraction of carrying capacity) was estimated to be about 0.75, with a lower 2.5th percentile of 0.36. The probability that the population was still below one-half of its carrying capacity was estimated to be 0.21, with a corresponding probability of 0.28 that the population was still below its maximum sustainable yield level. Quantities from which catch limits could potentially be calculated were estimated, including current replacement yield, maximum sustainable yield and the quantity Q1 (described in Wade and Givens, 1997).

Correction To "Null controllability of a nonlinear age, space and two-sex structured population dynamics model"

Correction To "Null controllability of a nonlinear age, space and two-sex structured population dynamics model"

Null controllability of a nonlinear age, space and two-sex structured population dynamics model

&lt;p style='text-indent:20px;'&gt;In this paper, we study the null controllability of a nonlinear age, space and two-sex structured population dynamics model. This model is such that the nonlinearity and the couplage are at birth level. We consider a population with males and females and we are dealing with two cases of null controllability problems.&lt;/p&gt;&lt;p style='text-indent:20px;'&gt;The first problem is related to the total extinction, which means that, we estimate a time &lt;inline-formula&gt;&lt;tex-math id="M1"&gt;\begin{document}$ T $\end{document}&lt;/tex-math&gt;&lt;/inline-formula&gt; to bring the male and female subpopulation density to zero. The second case concerns null controllability of male or female subpopulation. Since the absence of males or females in the population stops births; so, if we have the total extinction of the females at time &lt;inline-formula&gt;&lt;tex-math id="M2"&gt;\begin{document}$ T, $\end{document}&lt;/tex-math&gt;&lt;/inline-formula&gt; and if &lt;inline-formula&gt;&lt;tex-math id="M3"&gt;\begin{document}$ A $\end{document}&lt;/tex-math&gt;&lt;/inline-formula&gt; is the life span of the individuals, at time &lt;inline-formula&gt;&lt;tex-math id="M4"&gt;\begin{document}$ T+A $\end{document}&lt;/tex-math&gt;&lt;/inline-formula&gt; one will get certainly the total extinction of the population. Our method uses first an observability inequality related to the adjoint of an auxiliary system, a null controllability of the linear auxiliary system, and after the Schauder's fixed point theorem.&lt;/p&gt;

Mathematical Models of the Generation of Radiation-induced DNA Double-strand Breaks and Misrepair Cells by Direct and Indirect Action

Free radical carries an unpaired electron in the outer shell which is very reactive and becomes toxic to DNA. The direct action hits cell directly, while indirect action is the interaction between ionizing radiation and water molecule which later produces free radical. Hydrated electron (e), hydroxyl radical (OH), hydrogen radical (OH), ionized water, hydroperoxyl radical and hydrogen peroxide are examples of free radical products. Among of these three free radicals, DNA damage dominantly caused by hydroxyl radical (OH) because it is found to be highly reactive compared to others. This paper aimed to develop a model by using structured population dynamics approach to study the effects of ionizing radiation by direct and indirect actions. The effects of ionizing radiation are mathematically described in a model using Ordinary Differential Equations (ODEs). The simulation results are fitted to the Linear Quadratic (LQ) formulation to give the ratio for alpha/beta . Next, the parameter estimation of the model is carried out using experimental data of human colon carcinoma cell by the aid of the MATLAB programming. The estimated parameter values can explain the biological meaning, which can support the result of the experimental design. The result showed that the sum-squared error (SSE) between simulation data and experimental data obtained is 0.0019 which indicates an excellent t to the experimental data. Thus, the model developed is in line with the experimental result. The model is able to explain the dynamics process of the direct and indirect effect of ionizing radiation on the cell population.

Mining hourly population dynamics by activity type based on decomposition of sequential snapshot data

ABSTRACT The dynamic population distributions by activity type (e.g. working, shopping or in-home) are vital for resource allocation, urban planning and epidemic containment. Although studies have incorporated individual-level human mobility data to map population distribution by activity type, access to such data is hindered due to privacy issues and they rely on auxiliary data to provide priori activity knowledge. This paper presents a method for generating the population dynamics by activity type. We first introduce more readily available sequential snapshot data to construct the population mixture model, then decompose the population mixture, and finally estimate the dynamic population size for each activity. We test the method in the central districts of Guangzhou city, China, based on real-time Tencent user density data. Correlation analysis and accuracy assessment prove that our method can accurately estimate hourly distributions for populations engaging in working, stay-at-home, and socializing activities. The temporal distribution of the working population reproduces the regular work scenarios and socializing population displays complex spatial patterns. We also find that there is an underlying relationship between a region’s function and its dynamic population structure. The presented method has great potential for application and could provide new insight for studying urban dynamic functions.

Laws of Spatially Structured Population Dynamics on a Lattice

We consider spatial population dynamics on a lattice, following a type of a contact (birth–death) stochastic process. We show that simple mathematical approximations for the density of cells can be obtained in a variety of scenarios. In the case of a homogeneous cell population, we derive the cellular density for a two-dimensional (2D) spatial lattice with an arbitrary number of neighbors, including the von Neumann, Moore, and hexagonal lattice. We then turn our attention to evolutionary dynamics, where mutant cells of different properties can be generated. For disadvantageous mutants, we derive an approximation for the equilibrium density representing the selection–mutation balance. For neutral and advantageous mutants, we show that simple scaling (power) laws for the numbers of mutants in expanding populations hold in 2D and 3D, under both flat (planar) and range population expansion. These models have relevance for studies in ecology and evolutionary biology, as well as biomedical applications including the dynamics of drug-resistant mutants in cancer and bacterial biofilms.

Multimorph Eco-Evolutionary Dynamics in Structured Populations.

AbstractOur understanding of the evolution of quantitative traits in nature is still limited by the challenge of including realistic trait distributions in the context of frequency-dependent selection and ecological feedbacks. We extend to class-structured populations a recently introduced "oligomorphic approximation," which bridges the gap between adaptive dynamics and quantitative genetics approaches and allows for the joint description of the dynamics of ecological variables and of the moments of multimodal trait distributions. Our theoretical framework allows us to analyze the dynamics of populations composed of several morphs and structured into distinct classes (e.g., age, size, habitats, infection status, and species). We also introduce a new approximation to simplify the eco-evolutionary dynamics using reproductive values. We illustrate the effectiveness of this approach by applying it to the important conceptual case of two-habitat migration-selection models. In particular, we show that our approach allows us to predict both the long-term evolutionary end points and the short-term transient dynamics of the eco-evolutionary process, including fast evolution regimes. We discuss the theoretical and practical implications of our results and sketch perspectives for future work.

Survival of Indian market attractiveness amid dynamic youth population structure

Changes in the population structure is an inevitable phenomenon that every country has to face. The youth population structure plays pivotal role in shaping the future of a country’s prosperity. It becomes extremely crucial to understand and be ready to face the challenges that may arise out of the dynamic youth population structure. This paper aims to review the youth population in India, analyze the future projections and preempt the future market attractiveness. The study reveals that the Indian population is aging and the median age of the country is on a rise. A shift of focus from India to African countries is likely after a couple of decades and alternative developmental plans would be a necessity to keep India on the track and be among the top few frontiers of market attractiveness.

Detection, genotyping and virulence characterization of Fusarium wilt race 4 (VCG0114) causing cotton wilt in three Texas fields

AbstractFusarium wilt of cotton, caused by the soilborne fungus Fusarium oxysporum f.sp. vasinfectum race 4 (Fov4, VCG0114), is a serious disease that has adversely affected cotton production in California since 2001 and in the Upper Rio Grande Region near El Paso in the border areas between Texas and New Mexico since 2017. Fov4 was isolated from cotton stem samples collected from wilted or asymptomatic plants adjacent to the wilting plants from the El Paso area. The MT genotype was the only Fov4 genotype found in two fields in the Lower Valley of El Paso and the T genotype was the only Fov4 genotype found in one field in the Upper Valley Region of El Paso. No N, MiT or mixed genotypes of Fov4 were detected in any of these fields. Furthermore, the F. oxysporum f.sp. vasinfectum isolates were exclusively Fov4. The results support the observation that the MT genotype of Fov4 is mainly distributed in the Lower Valley of El Paso and the T genotype of Fov4 is mainly distributed in the Upper Valley Region of El Paso. Virulence of the MT genotype of Fov4 was higher than that of the T genotype. PCR methods previously developed for Fov4 specific PCR detection and multiplex Fov4 genotyping were validated by VCG analyses of the newly obtained isolates. These PCR methods were adapted for the in planta detection of Fov4, but Fov4 genotyping was limited to the detection of T, MT and MiT genotypes. It is important to continue to monitor dynamic population structure of Fov4 genotypes to prevent the spread of Fov4 and optimize disease control.

Robust uniform persistence for structured models of delay differential equations

&lt;p style='text-indent:20px;'&gt;We consider a general class of delay differential equations systems, typically used to model the dynamics of structured biological populations, and establish necessary conditions for the part of the attractor contained in the boundary of the state space to repel the complementary dynamics contained in the interior of the state space. The conditions are formulated in terms of Lyapunov exponents and invariant probability measures and we use them to prove a robust uniform persistence result.&lt;/p&gt;

Dynamic maximum entropy provides accurate approximation of structured population dynamics.

Realistic models of biological processes typically involve interacting components on multiple scales, driven by changing environment and inherent stochasticity. Such models are often analytically and numerically intractable. We revisit a dynamic maximum entropy method that combines a static maximum entropy with a quasi-stationary approximation. This allows us to reduce stochastic non-equilibrium dynamics expressed by the Fokker-Planck equation to a simpler low-dimensional deterministic dynamics, without the need to track microscopic details. Although the method has been previously applied to a few (rather complicated) applications in population genetics, our main goal here is to explain and to better understand how the method works. We demonstrate the usefulness of the method for two widely studied stochastic problems, highlighting its accuracy in capturing important macroscopic quantities even in rapidly changing non-stationary conditions. For the Ornstein-Uhlenbeck process, the method recovers the exact dynamics whilst for a stochastic island model with migration from other habitats, the approximation retains high macroscopic accuracy under a wide range of scenarios in a dynamic environment.

Modelling the potential consequences of adaptive closure management in a penaeid trawl fishery

Spatial management of fishing effort can be used to avoid catching undesirable size classes for target species, and improve yield-per-recruit for the exploited stock. Adaptive closure management has been proposed as a means to more effectively utilise spatial management, however these management provisions often lack quantitative evaluation which constrains the information available to inform decisions. We demonstrate the use of a spatially and size structured population dynamics model to evaluate the potential impact of spatial management on a multijurisdictional fishery for a highly migratory species (eastern king prawn, Penaeus [Melicertus] plebejus). Under current conditions in the fishery, the overall effect of closures on harvest was estimated to be comparatively minor, regardless of assumptions about how effort or fisher behavior are affected by spatial management. Alternative assumptions about the movement patterns of eastern king prawn had little influence on the impact of closures on overall harvest. However, when effort was increased to historic levels similar to those observed when the closures were implemented, a much greater impact on overall harvest was observed. The approach taken and simulation outcomes are discussed in the context of spatial management for both eastern king prawn, and penaeid fisheries more broadly.

First assessment of genetic diversity, population structure and historical population dynamics ofMyocastor coypus(Rodentia: Echimyidae) in the centre of its native range

AbstractMyocastor coypus is a rodent native to South America that is strongly linked to river systems. Past studies on the coypu in its native distribution range were aimed mainly at its ecology and parasitology and genetic studies are very limited. Here, we used sequences of the mitochondrial D-loop control region to study the genetic diversity, population genetic structure and some aspects of historical population dynamics of coypu at the centre of its native range. Our results showed moderate to high levels of genetic diversity and an absence of genetic structure in the study area. Bayesian analysis of population structure (BAPS) showed the existence of two haplogroups distributed in most sampling sites. These results suggest that movement of coypu is independent of the structure of current known river networks and its dispersal patterns are related to flooding events and the presence of lagoons connecting river basins. The demographic expansion patterns in these populations and those of other South American mammals during the Late Pleistocene support the hypothesis that demographic changes in wild populations are related to fluctuations in climate and ecology. The mitochondrial data obtained in this study constitute the first record of these types of sequences in the native range of M. coypus.Myocastor coypus es un roedor nativo de Sudamérica fuertemente ligado a los sistemas fluviales. En su área de distribución nativa, los estudios llevados a cabo en la especie estuvieron dirigidos principalmente a estudiar su ecología y zoonosis, sin embargo, los estudios genéticos son muy limitados. En el presente trabajo, utilizamos secuencias del d-loop de la Región Control del ADN mitocondrial para estudiar la diversidad genética, la estructura genética de la población y algunos aspectos de la dinámica poblacional histórica del coipo en el centro de su área de distribución. Nuestros resultados develaron niveles moderados y altos de diversidad genética, y ausencia de estructuración genética en el área de estudio. El BAPS exhibió la existencia de dos haplogrupos distribuidos en la mayoría de los sitios de muestreo. Estos resultados sugieren que el movimiento de los coipos sería independiente de la estructura de las redes fluviales actuales conocidas y que sus patrones de dispersión estarían relacionados con eventos de inundación y con la presencia de lagunas que conectan las cuencas fluviales. Los patrones de expansión demográfica observados en esta población de coipos y en otras poblaciones de mamíferos sudamericanos durante el Pleistoceno tardío, apoyan la hipótesis de que las fluctuaciones climáticas y los cambios ecológicos están relacionados con cambios demográficos en las poblaciones silvestres. Los datos mitocondriales obtenidos en este estudio constituyen el primer registro de este tipo de secuencias en el área de distribución nativa de esta especie.

A structured seabird population model reveals how alternative forage fish control rules benefit seabirds and fisheries.

Fisheries for forage fish may affect the survival and reproduction of piscivorous predators, especially seabirds. However, seabirds have evolved life history strategies to cope with natural fluctuations in prey and it is difficult to separate effects of fishing on seabirds from impacts of natural variability. To date, potential impacts of forage fisheries on seabirds have mainly been explored using ecosystem models that simplify seabird-forage-fish dynamics. We sought to explore how different forage fish harvest policies affect seabirds, accounting for structured population dynamics, life history specifics, and variation in forage fish dependencies across life stages; and how impacts vary across seabird and forage fish life histories. To explore these impacts, we developed an age-stage structured seabird model that incorporates seabird diet specialization, foraging behavior, and reproductive strategy, as well as different functional responses between prey availability and adult survival, juvenile survival, reproductive success, and breeder propensity. We parameterized this model for two contrasting seabird life histories: (1) a low fecundity, limited foraging range, diet specialist ("restricted"); and (2) a high fecundity, wide ranging, diet generalist ("flexible"). Each was paired with two different forage fish prey archetypes that were fished under various control rules. The restricted seabird population was expectedly less robust to constant fishing pressure than the flexible seabird, and this sensitivity was mainly due to functional response parameterization, rather than other life history parameters. Particularly, the restricted seabird was highly sensitive to the relationship between prey availability and adult survival but was not sensitive to the relationship between prey and reproductive success. An adaptive biomass-limit harvest rule for forage fish resulted in substantially higher seabird abundance compared to constant fishing across all scenarios, with minimal trade-offs to the fishery (depending on fishery management objectives). However, mechanisms governing the impact of the forage fish fishery on the seabird varied by forage fish type. Therefore, tailoring forage fish management strategies to forage fish life history can lead to mutually acceptable outcomes for fisheries and seabirds. If data or time are limited, an adaptive control rule is likely a safe bet for meeting seabird conservation objectives with limited impacts to fisheries.

Bioinformatics tools used for whole-genome sequencing analysis of Neisseria gonorrhoeae: a literature review.

Whole-genome sequencing (WGS) data are well established for the investigation of gonococcal transmission, antimicrobial resistance prediction, population structure determination and population dynamics. A variety of bioinformatics tools, repositories, services and platforms have been applied to manage and analyze Neisseria gonorrhoeae WGS datasets. This review provides an overview of the various bioinformatics approaches and resources used in 105 published studies (as of 30 April 2021). The challenges in the analysis of N. gonorrhoeae WGS datasets, as well as future bioinformatics requirements, are also discussed.

Inferring Population Histories for Ancient Genomes Using Genome-Wide Genealogies.

Ancient genomes anchor genealogies in directly observed historical genetic variation and contextualize ancestral lineages with archaeological insights into their geography and cultural associations. However, the majority of ancient genomes are of lower coverage and cannot be directly built into genealogies. Here, we present a fast and scalable method, Colate, the first approach for inferring ancestral relationships through time between low-coverage genomes without requiring phasing or imputation. Our approach leverages sharing patterns of mutations dated using a genealogy to infer coalescence rates. For deeply sequenced ancient genomes, we additionally introduce an extension of the Relate algorithm for joint inference of genealogies incorporating such genomes. Application to 278 present-day and 430 ancient DNA samples of >0.5x mean coverage allows us to identify dynamic population structure and directional gene flow between early farmer and European hunter-gatherer groups. We further show that the previously reported, but still unexplained, increase in the TCC/TTC mutation rate, which is strongest in West Eurasia today, was already present at similar strength and widespread in the Late Glacial Period ~10k−15k years ago, but is not observed in samples >30k years old. It is strongest in Neolithic farmers, and highly correlated with recent coalescence rates between other genomes and a 10,000-year-old Anatolian hunter-gatherer. This suggests gene-flow among ancient peoples postdating the last glacial maximum as widespread and localizes the driver of this mutational signal in both time and geography in that region. Our approach should be widely applicable in future for addressing other evolutionary questions, and in other species.