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Trends in Ecology & Evolution Jun 2024Measuring and tracking biodiversity from local to global scales is challenging due to its multifaceted nature and the range of metrics used to describe spatial and... (Review)
Review
Measuring and tracking biodiversity from local to global scales is challenging due to its multifaceted nature and the range of metrics used to describe spatial and temporal patterns. Abundance can be used to describe how a population changes across space and time, but it can be measured in different ways, with consequences for the interpretation and communication of spatiotemporal patterns. We differentiate between relative and absolute abundance, and discuss the advantages and disadvantages of each for biodiversity monitoring, conservation, and ecological research. We highlight when absolute abundance can be advantageous and should be prioritized in biodiversity monitoring and research, and conclude by providing avenues for future research directions to better assess the necessity of absolute abundance in biodiversity monitoring.
Topics: Biodiversity; Conservation of Natural Resources; Population Density; Population Dynamics; Animals
PubMed: 38508923
DOI: 10.1016/j.tree.2024.01.012 -
Ecology and Evolution Oct 2023The conservation and management of wildlife populations, particularly for threatened and endangered species are greatly aided with abundance, growth rate, and density...
The conservation and management of wildlife populations, particularly for threatened and endangered species are greatly aided with abundance, growth rate, and density measures. Traditional methods of estimating abundance and related metrics represent trade-offs in effort and precision of estimates. Pedigree reconstruction is an emerging, attractive alternate approach because its use of one-time, noninvasive sampling of individuals to infer the existence of unsampled individuals. However, advances in pedigree reconstruction could improve its utility, including forming a measure of precision for the method, establishing required spatial sampling effort for accurate estimates, ascertaining the spatial extent of abundance estimates derived from pedigree reconstruction, and assessing how population density affects the estimator's performance. Using established relationships for a stochastic, spatially explicit simulated moose () population, pedigree reconstruction provided accurate estimates of the adult moose population size and trend. Novel bootstrapped confidence intervals performed as expected with intensive sampling but underperformed with moderate sampling efforts that could produce abundance estimates with low bias. Adult population estimates more closely reflected the total number of adults in the extant population, rather than number of adults inhabiting the area where sampling occurred. Increasing sampling effort, measured as the proportion of individuals sampled and as the proportion of a hypothetical study area, yielded similar asymptotic patterns over time. Simulations indicated a positive relationship between animal density and sampling effort required for unbiased estimates. These results indicate that pedigree reconstruction can produce accurate abundance estimates and may be particularly valuable for surveying smaller areas and low-density populations.
PubMed: 37869434
DOI: 10.1002/ece3.10650 -
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 -
Bulletin of Entomological Research Dec 2023The effect of climate factors (temperature, humidity, precipitation, and frost days) on the population changes, damage, and infestation area of the leopard moth, L.,...
The effect of climate factors (temperature, humidity, precipitation, and frost days) on the population changes, damage, and infestation area of the leopard moth, L., was studied during 2006-2018 in four parts of Iran including Saman, Arak, Najaf-abad, and Baft. For trend analysis, the Mann-Kendall test was run on time series data of both climate and pest population. According to the results, the annual mean (Kendall's statistics, = 0.64 and 0.48), annual minimum ( = 0.60 and 0.42), and January mean ( = 0.64 and 0.61, respectively) temperatures showed increasing trends in Saman and Najaf-abad. Moreover, the annual mean minimum and January temperatures ( = 0.41 and 0.45, respectively) in Arak and the annual mean maximum temperature ( = 0.79) in Baft showed increasing trends. The number of frost days/year (Kendall's statistics, = -0.63, -0.53, -0.32 and -0.37) and annual mean relative humidity ( = -0.43, -0.63, -0.64 and -0.42, respectively) showed decreasing trends in Saman, Arak, Baft, and Najaf-abad stations. Trend analysis indicated significant increases in the mean number of moths caught ( = 0.59, 0.76 and 0.90), the percentage of infested branches/tree ( = 0.66, 0.58, and 0.90), the number of active holes/tree ( = 0.79, 0.55, and 0.68) and the infested areas ( = 0.99, 0.73, and 0.98, respectively) in Saman, Arak and Najaf-abad stations. According to stepwise regression, the mean temperatures of January, autumn, and winter were the most effective variables for increasing damage and population, while relative humidity and the number of frost days played the major role in reducing it.
Topics: Animals; Moths; Juglans; Iran; Population Density; Climate; Temperature; Climate Change
PubMed: 37855138
DOI: 10.1017/S0007485323000470 -
Proceedings. Biological Sciences Nov 2023Following severe environmental change that reduces mean population fitness below replacement, populations must adapt to avoid eventual extinction, a process called...
Following severe environmental change that reduces mean population fitness below replacement, populations must adapt to avoid eventual extinction, a process called evolutionary rescue. Models of evolutionary rescue demonstrate that initial size, genetic variation and degree of maladaptation influence population fates. However, many models feature populations that grow without negative density dependence or with constant genetic diversity despite precipitous population decline, assumptions likely to be violated in conservation settings. We examined the simultaneous influences of density-dependent growth and erosion of genetic diversity on populations adapting to novel environmental change using stochastic, individual-based simulations. Density dependence decreased the probability of rescue and increased the probability of extinction, especially in large and initially well-adapted populations that previously have been predicted to be at low risk. Increased extinction occurred shortly following environmental change, as populations under density dependence experienced more rapid decline and reached smaller sizes. Populations that experienced evolutionary rescue lost genetic diversity through drift and adaptation, particularly under density dependence. Populations that declined to extinction entered an extinction vortex, where small size increased drift, loss of genetic diversity and the fixation of maladaptive alleles, hindered adaptation and kept populations at small densities where they were vulnerable to extinction via demographic stochasticity.
Topics: Animals; Biological Evolution; Population Dynamics; Population Density; Probability; Extinction, Biological
PubMed: 37989246
DOI: 10.1098/rspb.2023.1228 -
ArXiv Dec 2023We introduce a broad class of mechanistic spatial models to describe how spatially heterogeneous populations live, die, and reproduce. Individuals are represented by...
We introduce a broad class of mechanistic spatial models to describe how spatially heterogeneous populations live, die, and reproduce. Individuals are represented by points of a point measure, whose birth and death rates can depend both on spatial position and local population density, defined at a location to be the convolution of the point measure with a suitable non-negative integrable kernel centred on that location. We pass to three different scaling limits: an interacting superprocess, a nonlocal partial differential equation (PDE), and a classical PDE. The classical PDE is obtained both by a two-step convergence argument, in which we first scale time and population size and pass to the nonlocal PDE, and then scale the kernel that determines local population density; and in the important special case in which the limit is a reaction-diffusion equation, directly by simultaneously scaling the kernel width, timescale and population size in our individual based model. A novelty of our model is that we explicitly model a juvenile phase. The number of juveniles produced by an individual depends on local population density at the location of the parent; these juvenile offspring are thrown off in a (possibly heterogeneous, anisotropic) Gaussian distribution around the location of the parent; they then reach (instant) maturity with a probability that can depend on the local population density at the location at which they land. Although we only record mature individuals, a trace of this two-step description remains in our population models, resulting in novel limits in which the spatial dynamics are governed by a nonlinear diffusion. Using a lookdown representation, we are able to retain information about genealogies relating individuals in our population and, in the case of deterministic limiting models, we use this to deduce the backwards in time motion of the ancestral lineage of an individual sampled from the population. We observe that knowing the history of the population density is not enough to determine the motion of ancestral lineages in our model. We also investigate (and contrast) the behaviour of lineages for three different deterministic models of a population expanding its range as a travelling wave: the Fisher-KPP equation, the Allen-Cahn equation, and a porous medium equation with logistic growth.
PubMed: 37292478
DOI: No ID Found -
Mathematical Biosciences and... Jan 2024Epidemiologists have used the timing of the peak of an epidemic to guide public health interventions. By determining the expected peak time, they can allocate resources...
Epidemiologists have used the timing of the peak of an epidemic to guide public health interventions. By determining the expected peak time, they can allocate resources effectively and implement measures such as quarantine, vaccination, and treatment at the right time to mitigate the spread of the disease. The peak time also provides valuable information for those modeling the spread of the epidemic and making predictions about its future trajectory. In this study, we analyze the time needed for an epidemic to reach its peak by presenting a straightforward analytical expression. Utilizing two epidemiological models, the first is a generalized $ SEIR $ model with two classes of latent individuals, while the second incorporates a continuous age structure for latent infections. We confirm the conjecture that the peak occurs at approximately $ T\sim(\ln N)/\lambda $, where $ N $ is the population size and $ \lambda $ is the largest eigenvalue of the linearized system in the first model or the unique positive root of the characteristic equation in the second model. Our analytical results are compared to numerical solutions and shown to be in good agreement.
Topics: Humans; Epidemics; Quarantine; Public Health; Population Density
PubMed: 38454709
DOI: 10.3934/mbe.2024126 -
Ecology and Evolution May 2024Gamete traits can vary widely among species, populations and individuals, influencing fertilisation dynamics and overall reproductive fitness. Sexual selection can play...
Gamete traits can vary widely among species, populations and individuals, influencing fertilisation dynamics and overall reproductive fitness. Sexual selection can play an important role in determining the evolution of gamete traits with local environmental conditions determining the strength and direction of sexual selection. Here, we test for signatures of post-mating selection on gamete traits in relation to population density, and possible interactive effects of population density and sperm concentration on sperm motility and fertilisation rates among natural populations of mussels. Our study shows that males from high-density populations produce smaller sperm compared with males from low-density populations, but we detected no effect of population density on egg size. Our results also reveal that females from low-density populations tended to exhibit lower fertilisation rates across a range of sperm concentrations, although this became less important as sperm concentration increased. Variances in fertilisation success were higher for females than males and the effect of gamete compatibility between males and females increases as sperm concentrations increase. These results suggest that local population density can influence gamete traits and fertilisation dynamics but also highlight the importance of phenotypic plasticity in governing sperm-egg interactions in a highly dynamic selective environment.
PubMed: 38698926
DOI: 10.1002/ece3.11338 -
Genetics Jun 2024The rate at which recombination events occur in a population is an indicator of its effective population size and the organism's reproduction mode. It determines the...
The rate at which recombination events occur in a population is an indicator of its effective population size and the organism's reproduction mode. It determines the extent of linkage disequilibrium along the genome and, thereby, the efficacy of both purifying and positive selection. The population recombination rate can be inferred using models of genome evolution in populations. Classic methods based on the patterns of linkage disequilibrium provide the most accurate estimates, providing large sample sizes are used and the demography of the population is properly accounted for. Here, the capacity of approaches based on the sequentially Markov coalescent (SMC) to infer the genome-average recombination rate from as little as a single diploid genome is examined. SMC approaches provide highly accurate estimates even in the presence of changing population sizes, providing that (1) within genome heterogeneity is accounted for and (2) classic maximum-likelihood optimization algorithms are employed to fit the model. SMC-based estimates proved sensitive to gene conversion, leading to an overestimation of the recombination rate if conversion events are frequent. Conversely, methods based on the correlation of heterozygosity succeed in disentangling the rate of crossing over from that of gene conversion events, but only when the population size is constant and the recombination landscape homogeneous. These results call for a convergence of these two methods to obtain accurate and comparable estimates of recombination rates between populations.
Topics: Recombination, Genetic; Models, Genetic; Markov Chains; Linkage Disequilibrium; Genome; Algorithms; Genetics, Population; Gene Conversion; Animals; Humans; Population Density
PubMed: 38565705
DOI: 10.1093/genetics/iyae051 -
Genetics, Selection, Evolution : GSE Dec 2023Effective conservation and utilization of farm animals are fundamental for realizing sustainable increases in food production. In situ and ex situ conservation are the...
BACKGROUND
Effective conservation and utilization of farm animals are fundamental for realizing sustainable increases in food production. In situ and ex situ conservation are the two main strategies that are currently used to protect the genetic integrity of Chinese domestic chicken breeds. However, genomic diversity and population structure have not been compared in these conserved populations.
RESULTS
Three hundred and sixty-one individuals from three Chinese domestic chicken breeds were collected from populations conserved in situ and ex situ and genotyped using genotyping-by-sequencing (GBS). First, we used different parameters based on heterozygosity, genomic inbreeding, and linkage disequilibrium to estimate the genomic diversity of these populations, and applied principal component analysis (PCA), neighbor-joining tree, and ADMIXTURE to analyze population structure. We found that the small ex situ conserved populations, which have been maintained in controlled environments, retained less genetic diversity than the in situ conserved populations. In addition, genetic differentiation was detected between the in situ and ex situ conserved populations of the same breed. Next, we analyzed signatures of selection using three statistical methods (fixation index (F), nucleotide diversity (Pi), and cross-population extended haplotype homozygosity (XP-EHH) to study the genetic footprints that underlie the differentiation between in situ and ex situ conserved populations. We concluded that, in these small populations, differentiation might be caused by genetic drift or by mutations from the original populations. The differentiation observed in the population of Beijing You chicken probably reflects adaptation to environmental changes in temperature and humidity that the animals faced when they were moved from their place of origin to the new site for ex situ conservation.
CONCLUSIONS
Conservation programs of three Chinese domestic chicken breeds have maintained their genomic diversity to a sustainable degree. The small ex situ conserved populations, which are maintained in controlled environments, retain less genetic diversity than populations conserved in situ. In addition, the transfer of populations from their place of origin to another site for conservation purposes results in genetic differentiation, which may be caused by genetic drift or adaptation. This study provides a basis for further optimization of in situ and ex situ conservation programs for domestic chicken breeds in China.
Topics: Humans; Animals; Chickens; Genetic Variation; Population Density; Genomics; China; Polymorphism, Single Nucleotide
PubMed: 38097971
DOI: 10.1186/s12711-023-00866-3