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Ecology Feb 2023Open-population spatial capture-recapture (OPSCR) models use the spatial information contained in individual detections collected over multiple consecutive occasions to...
Open-population spatial capture-recapture (OPSCR) models use the spatial information contained in individual detections collected over multiple consecutive occasions to estimate not only occasion-specific density, but also demographic parameters. OPSCR models can also estimate spatial variation in vital rates, but such models are neither widely used nor thoroughly tested. We developed a Bayesian OPSCR model that not only accounts for spatial variation in survival using spatial covariates but also estimates local density-dependent effects on survival within a unified framework. Using simulations, we show that OPSCR models provide sound inferences on the effect of spatial covariates on survival, including multiple competing sources of mortality, each with potentially different spatial determinants. Estimation of local density-dependent survival was possible but required more data due to the greater complexity of the model. Not accounting for spatial heterogeneity in survival led to up to 10% positive bias in abundance estimates. We provide an empirical demonstration of the model by estimating the effect of country and density on cause-specific mortality of female wolverines (Gulo gulo) in central Sweden and Norway. The ability to make population-level inferences on spatial variation in survival is an essential step toward a fully spatially explicit OPSCR model capable of disentangling the role of multiple spatial drivers of population dynamics.
Topics: Female; Humans; Population Density; Bayes Theorem; Population Dynamics; Norway; Sweden
PubMed: 36458376
DOI: 10.1002/ecy.3934 -
Genome Biology and Evolution Jul 2022We discuss the genetic, demographic, and selective forces that are likely to be at play in restricting observed levels of DNA sequence variation in natural populations...
We discuss the genetic, demographic, and selective forces that are likely to be at play in restricting observed levels of DNA sequence variation in natural populations to a much smaller range of values than would be expected from the distribution of census population sizes alone-Lewontin's Paradox. While several processes that have previously been strongly emphasized must be involved, including the effects of direct selection and genetic hitchhiking, it seems unlikely that they are sufficient to explain this observation without contributions from other factors. We highlight a potentially important role for the less-appreciated contribution of population size change; specifically, the likelihood that many species and populations may be quite far from reaching the relatively high equilibrium diversity values that would be expected given their current census sizes.
Topics: Genetic Variation; Genetics, Population; Models, Genetic; Population Density; Selection, Genetic
PubMed: 35738021
DOI: 10.1093/gbe/evac096 -
Genetics May 2023Population bottlenecks are commonplace in experimental evolution, specifically in serial passaging experiments where microbial populations alternate between growth and...
Population bottlenecks are commonplace in experimental evolution, specifically in serial passaging experiments where microbial populations alternate between growth and dilution. Natural populations also experience such fluctuations caused by seasonality, resource limitation, or host-to-host transmission for pathogens. Yet, how unlimited growth with periodic bottlenecks influence the adaptation of populations is not fully understood. Here, we study theoretically the effects of bottlenecks on the accessibility of evolutionary paths and on the rate of evolution. We model an asexual population evolving on a minimal fitness landscape consisting of two types of beneficial mutations with the empirically supported trade-off between mutation rate and fitness advantage, in the regime where multiple beneficial mutations may segregate simultaneously. In the limit of large population sizes and small mutation rates, we show the existence of a unique most likely evolutionary scenario, determined by the size of the wild-type population at the beginning and at the end of each cycle. These two key demographic parameters determine which adaptive paths may be taken by the evolving population by controlling the supply of mutants during growth and the loss of mutants at the bottleneck. We do not only show that bottlenecks act as a deterministic control of evolutionary paths but also that each possible evolutionary scenario can be forced to occur by tuning demographic parameters. This work unveils the effects of demography on adaptation of periodically bottlenecked populations and can guide the design of evolution experiments.
Topics: Mutation Rate; Mutation; Adaptation, Physiological; Population Density
PubMed: 36728496
DOI: 10.1093/genetics/iyad001 -
Journal of Plant Research Jul 2023Changes in environmental factors, human impact, and interactions between them accelerate the extinction of woody species. Therefore, conservation programs are needed to...
Changes in environmental factors, human impact, and interactions between them accelerate the extinction of woody species. Therefore, conservation programs are needed to protect endangered taxa. However, the relationship between climate, habitat fragmentation, and anthropogenic activities and their consequences are still not well understood. In this work, we aimed to evaluate the impact of climate change and human population density on the Buxus hyrcana Pojark distribution range, as well as the phenomenon of habitat fragmentation. Based on species occurrence data throughout the Hyrcanian Forests (north of Iran), the MAXENT model was employed to estimate the potential distribution and suitability changes. Morphological-spatial analysis (MSPA) and CIRCUITSCAPE were used to assess habitat fragmentation and its connectivity. According to the main results obtained from future scenarios, the potential range will significantly decrease due to the lack of suitable climatic conditions. Meanwhile, B. hyrcana may not be able to shift in potentially suitable areas because of human influence and geographic barriers. Under RCP scenarios the extent of the core area would be reduced and the edge/core ratio significantly increased. Altogether, we found negative effects of the environmental change and the human population density on the continuity of habitats of B. hyrcana. The results of the presented work may improve our knowledge connected with in situ and ex situ protection strategies.
Topics: Humans; Buxus; Population Density; Ecosystem; Forests; Climate Change
PubMed: 37115338
DOI: 10.1007/s10265-023-01457-5 -
Molecular Ecology Resources Feb 2022In genomic-scale data sets, loci are closely packed within chromosomes and hence provide correlated information. Averaging across loci as if they were independent...
In genomic-scale data sets, loci are closely packed within chromosomes and hence provide correlated information. Averaging across loci as if they were independent creates pseudoreplication, which reduces the effective degrees of freedom (df') compared to the nominal degrees of freedom, df. This issue has been known for some time, but consequences have not been systematically quantified across the entire genome. Here, we measured pseudoreplication (quantified by the ratio df'/df) for a common metric of genetic differentiation (F ) and a common measure of linkage disequilibrium between pairs of loci (r ). Based on data simulated using models (SLiM and msprime) that allow efficient forward-in-time and coalescent simulations while precisely controlling population pedigrees, we estimated df' and df'/df by measuring the rate of decline in the variance of mean F and mean r as more loci were used. For both indices, df' increases with N and genome size, as expected. However, even for large N and large genomes, df' for mean r plateaus after a few thousand loci, and a variance components analysis indicates that the limiting factor is uncertainty associated with sampling individuals rather than genes. Pseudoreplication is less extreme for F , but df'/df ≤0.01 can occur in data sets using tens of thousands of loci. Commonly-used block-jackknife methods consistently overestimated var (F ), producing very conservative confidence intervals. Predicting df' based on our modelling results as a function of N , L, S, and genome size provides a robust way to quantify precision associated with genomic-scale data sets.
Topics: Genome Size; Genomics; Linkage Disequilibrium; Models, Genetic; Pedigree; Population Density
PubMed: 34351073
DOI: 10.1111/1755-0998.13482 -
PloS One 2023Large carnivores face numerous threats, including habitat loss and fragmentation, direct killing, and prey depletion, leading to significant global range and population...
Large carnivores face numerous threats, including habitat loss and fragmentation, direct killing, and prey depletion, leading to significant global range and population declines. Despite such threats, leopards (Panthera pardus) persist outside protected areas throughout most of their range, occupying diverse habitat types and land uses, including peri-urban and rural areas. Understanding of leopard population dynamics in mixed-use landscapes is limited, especially in South Africa, where the majority of leopard research has focused on protected areas. We use spatially explicit capture-recapture models to estimate leopard density across a mixed-use landscape of protected areas, farmland, and urban areas in the Overberg region of the Western Cape, South Africa. Data from 86 paired camera stations provided 221 independent captures of 25 leopards at 50 camera trap stations with a population density estimate of 0.64 leopards per 100 km2 (95% CI: 0.55-0.73). Elevation, terrain ruggedness, and vegetation productivity were important drivers of leopard density in the landscape, being highest on elevated remnants of natural land outside of protected areas. These results are similar to previous research findings in other parts of the Western Cape, where high-lying natural vegetation was shown to serve as both a refuge and a corridor for leopard movement in otherwise transformed landscapes. Given the low leopard density and the prevalence of transformed land intermixed with patches of more suitable leopard habitat, prioritising and preserving connectivity for leopards is vital in this shared landscape. Ecological corridors should be developed in partnership with private landowners through an inclusive and multifaceted conservation strategy which also incorporates monitoring of and rapid mitigation of emerging threats to leopards.
Topics: Animals; Panthera; South Africa; Anthropogenic Effects; Ecosystem; Population Density; Conservation of Natural Resources
PubMed: 37889916
DOI: 10.1371/journal.pone.0293445 -
Evolution; International Journal of... Feb 2022Even if a species' phenotype does not change over evolutionary time, the underlying mechanism may change, as distinct molecular pathways can realize identical...
Even if a species' phenotype does not change over evolutionary time, the underlying mechanism may change, as distinct molecular pathways can realize identical phenotypes. Here we use linear system theory to explore the consequences of this idea, describing how a gene network underlying a conserved phenotype evolves, as the genetic drift of small changes to these molecular pathways causes a population to explore the set of mechanisms with identical phenotypes. To do this, we model an organism's internal state as a linear system of differential equations for which the environment provides input and the phenotype is the output, in which context there exists an exact characterization of the set of all mechanisms that give the same input-output relationship. This characterization implies that selectively neutral directions in genotype space should be common and that the evolutionary exploration of these distinct but equivalent mechanisms can lead to the reproductive incompatibility of independently evolving populations. This evolutionary exploration, or system drift, is expected to proceed at a rate proportional to the amount of intrapopulation genetic variation divided by the effective population size ( ). At biologically reasonable parameter values this could lead to substantial interpopulation incompatibility, and thus speciation, on a time scale of generations. This model also naturally predicts Haldane's rule, thus providing a concrete explanation of why heterogametic hybrids tend to be disrupted more often than homogametes during the early stages of speciation.
Topics: Biological Evolution; Genetic Drift; Genetic Speciation; Genotype; Hybridization, Genetic; Models, Genetic; Population Density; Reproduction
PubMed: 34529267
DOI: 10.1111/evo.14356 -
PloS One 2023Since November 2019, most countries across the globe have suffered from the disastrous consequences of the Covid-19 pandemic which redefined every aspect of human life....
Since November 2019, most countries across the globe have suffered from the disastrous consequences of the Covid-19 pandemic which redefined every aspect of human life. Given the inevitable spread and transmission of the virus, it is critical to acknowledge the factors that catalyse transmission of the disease. This research investigates the relation of the external demographic parameters such as total population, population density and weighted population density on the spread of Covid-19 in Malaysia. Pearson correlation and simple linear regression were utilized to identify the relation between the population-related variables and the spread of Covid-19 in Malaysia using data from 15th March 2020 to 31st March 2021. As a result, a strong positive significant correlation between the total population and Covid-19 cases was found. However, a weak positive relationship was found between the density variable (population density and weighted population density) and the spread of Covid-19. Our findings suggest that the transmission of Covid-19 during lockdown (Movement Control Order, MCO) in Malaysia was more readily explained by the demographic variable population size, than population density or weighted population density. Thus, this study could be helpful in intervention planning and managing future virus outbreaks in Malaysia.
Topics: Humans; COVID-19; Malaysia; Population Density; SARS-CoV-2; Pandemics; Communicable Disease Control
PubMed: 37104371
DOI: 10.1371/journal.pone.0284157 -
PeerJ 2023Density-dependent regulation is ubiquitous in population dynamics, and its potential interaction with environmental stochasticity complicates the characterization of the...
BACKGROUND
Density-dependent regulation is ubiquitous in population dynamics, and its potential interaction with environmental stochasticity complicates the characterization of the random component of population dynamics. Yet, this issue has not received attention commensurate with its relevance for descriptive and predictive modeling of population dynamics. Here we use a Bayesian modeling approach to investigate the contribution of density regulation to population variability in stochastic environments.
METHODS
We analytically derive a formula linking the stationary variance of population abundance/density under Gompertz regulation in a stochastic environment with constant variance to the environmental variance and the strength of density feedback, to investigate whether and how density regulation affects the stationary variance. We examine through simulations whether the relationship between stationary variance and density regulation inferred analytically under the Gompertz model carries over to the Ricker model, widely used in population dynamics modeling.
RESULTS
The analytical decomposition of the stationary variance under stochastic Gompertz dynamics implies higher variability for strongly regulated populations. Simulation results demonstrate that the pattern of increasing population variability with increasing density feedback found under the Gompertz model holds for the Ricker model as well, and is expected to be a general phenomenon with stochastic population models. We also analytically established and empirically validated that the square of the autoregressive parameter of the Gompertz model in AR(1) form represents the proportion of stationary variance due to density dependence.
DISCUSSION
Our results suggest that neither environmental stochasticity nor density regulation can alone explain the patterns of population variability in stochastic environments, as these two components of temporal variation interact, with a tendency for density regulation to amplify the magnitude of environmentally induced population fluctuations. This finding has far-reaching implications for population viability. It implies that intense intra-specific resource competition increases the risk of environment-driven population collapse at high density, making opportune harvesting a sensible practice for improving the resistance of managed populations such as fish stocks to environmental perturbations. The separation of density-dependent and density-independent processes will help improve population dynamics modeling, while providing a basis for evaluating the relative importance of these two categories of processes that remains a topic of long-standing controversy among ecologists.
Topics: Animals; Bayes Theorem; Population Dynamics; Population Density; Computer Simulation
PubMed: 36751641
DOI: 10.7717/peerj.14701 -
Journal of the Royal Society, Interface Apr 2024Describing the space-time evolution of urban population is a fundamental challenge in the science of cities, yet a complete theoretical treatment of the underlying...
Describing the space-time evolution of urban population is a fundamental challenge in the science of cities, yet a complete theoretical treatment of the underlying dynamics is still missing. Here, we first reconstruct the evolution of London (UK) over 180 years and show that urban growth consists of an initial phase of diffusion-limited growth, followed by the development of the railway transport network and a consequential shift from central to suburban living. Such dynamics-which are analogous to angiogenesis in biological systems-can be described by a minimalist reaction-diffusion model coupled with economic constraints and an adaptive transport network. We then test the generality of our approach by reproducing the evolution of Sydney, Australia, from 1851 to 2011. We show that the rail system coevolves with urban population, displaying hierarchical characteristics that remain constant over time unless large-scale interventions are put in place to alter the modes of transport. These results demonstrate that transport schemes are first-order controls of long-term urbanization patterns and efforts aimed at creating more sustainable and healthier cities require careful consideration of population-transport feedbacks.
Topics: Humans; Cities; Urbanization; Urban Population; Population Dynamics; Population Density
PubMed: 38565159
DOI: 10.1098/rsif.2023.0657