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Heredity Jan 2022Linkage disequilibrium (LD) is the non-random association of alleles at different loci. Squared LD coefficients r (for phased genotypes) and [Formula: see text] (for...
Linkage disequilibrium (LD) is the non-random association of alleles at different loci. Squared LD coefficients r (for phased genotypes) and [Formula: see text] (for unphased genotypes) will converge to constants that are determined by the sample size, the recombination frequency, the effective population size and the mating system. LD can therefore be used for gene mapping and the estimation of effective population size. However, current methods work only with diploids. To resolve this problem, we here extend the linkage disequilibrium measures to include polysomic inheritance. We derive the values of r and [Formula: see text] at equilibrium state for various mating systems and different ploidy levels. For unlinked loci, [Formula: see text] for monoecious and dioecious (with random pairing) mating systems or [Formula: see text] for dioecious mating systems (with lifetime pairing), where f is the number of females in a half-sib family and η is a constant related to the ploidy level. We simulate the application of estimating N using unphased genotypes. We find that estimating N in polyploids requires similar sample sizes and numbers of loci as in diploids, with the main source of bias due to using 0.5 as the recombination frequency.
Topics: Genetics, Population; Genotype; Linkage Disequilibrium; Models, Genetic; Population Density
PubMed: 34983965
DOI: 10.1038/s41437-021-00482-1 -
American Journal of Primatology Dec 2013Density-dependence is hypothesized as the major mechanism of population regulation. However, the lack of long-term demographic data has hampered the use of...
Density-dependence is hypothesized as the major mechanism of population regulation. However, the lack of long-term demographic data has hampered the use of density-dependent models in nonhuman primates. In this study, we make use of the long-term demographic data from Cayo Santiago's rhesus macaques to parameterize and analyze both a density-independent and a density-dependent population matrix model, and compare their projections with the observed population changes. We also employ a retrospective analysis to determine how variance in vital rates, and covariance among them, contributed to the observed variation in long-term fitness across different levels of population density. The population exhibited negative density-dependence in fertility and the model incorporating this relationship accounted for 98% of the observed population dynamics. Variation in survival and fertility of sexually active individuals contributed the most to the variation in long-term fitness, while vital rates displaying high temporal variability exhibited lower sensitivities. Our findings are novel in describing density-dependent dynamics in a provisioned primate population, and in suggesting that selection is acting to lower the variance in the population growth rate by minimizing the variation in adult survival at high density. Because density-dependent mechanisms may become stronger in wild primate populations due to increasing habitat loss and food scarcity, our study demonstrates that it is important to incorporate variation in population size, as well as demographic variability into population viability analyses for a better understanding of the mechanisms regulating the growth of primate populations.
Topics: Animals; Fertility; Macaca mulatta; Population Density; Population Dynamics; Puerto Rico
PubMed: 23847126
DOI: 10.1002/ajp.22177 -
Microbiology Spectrum Dec 2016Fungal plant pathogens are ubiquitous and highly diverse. Key to their success is high host density, which notably is the case in agroecosystems. Several hypotheses... (Review)
Review
Fungal plant pathogens are ubiquitous and highly diverse. Key to their success is high host density, which notably is the case in agroecosystems. Several hypotheses related to the effects of plant pathogens on plant diversity (the Janzen-Connell hypothesis, the dilution effect hypothesis) and the phenomenon of higher biomass in plant mixtures (i.e., overyielding) can all be explained by the quantitative interplay between host and pathogen density. In many agroecosystems, fungal plant pathogens cause great losses, since in monocultures diseased plants cannot be replaced by healthy plants. On the other hand, in natural ecosystems fungal plant pathogens shape the succession of vegetation and enhance the biodiversity of forests and grasslands. When pathogens are introduced into areas outside their natural range, they may behave differently, causing severe damage. Once introduced, changes may occur such as hybridization with other closely related pathogens or host shifts, host jumps, or horizontal gene transfer. Such changes can be hazardous for both agricultural and natural ecosystems.
Topics: Ecosystem; Fungi; Plant Diseases; Population Density
PubMed: 28087933
DOI: 10.1128/microbiolspec.FUNK-0013-2016 -
Biological Reviews of the Cambridge... Apr 2022Dispersal is a key demographic process involving three stages: emigration, transience and settlement; each of which is influenced by individual, social and environmental... (Review)
Review
Dispersal is a key demographic process involving three stages: emigration, transience and settlement; each of which is influenced by individual, social and environmental determinants. An integrated understanding of species dispersal is essential for demographic modelling and conservation planning. Here, we review the dispersal patterns and determinants documented in the scientific literature for the grey wolf (Canis lupus) across its distribution range. We showed a surprisingly high variability within and among study areas on all dispersal parameters - dispersal rate, direction, distance, duration and success. We found that such large variability is due to multiple individual, social and environmental determinants, but also due to previously overlooked methodological research issues. We revealed a potential non-linear relationship between dispersal rate and population density, with dispersal rate higher at both ends of the gradient of population density. We found that human-caused mortality reduces distance, duration and success of dispersal events. Furthermore, dispersers avoid interaction with humans, and highly exposed areas like agricultural lands hamper population connectivity in many cases. We identified numerous methodological research problems that make it difficult to obtain robust estimates of dispersal parameters and robust inferences on dispersal patterns and their determinants. In particular, analyses where confounding factors were not accounted for led to substantial knowledge gaps on all aspects of dispersal in an otherwise much-studied species. Our understanding of wolf biology and management would significantly benefit if wolf dispersal studies reported the results and possible factors affecting wolf dispersal more transparently.
Topics: Animals; Population Density; Wolves
PubMed: 34664396
DOI: 10.1111/brv.12807 -
International Journal of Environmental... Feb 2022Over the last three decades, researchers have investigated population density and health outcomes at differing scale. There has not been a systematic review conducted in... (Review)
Review
Over the last three decades, researchers have investigated population density and health outcomes at differing scale. There has not been a systematic review conducted in order to synthesise this evidence. Following the Preferred Reporting Items for Systematic Reviews (PRISMA) guidelines, we systematically reviewed quantitative evidence published since 1990 on population density and non-communicable disease (NCD) within Westernised countries. Fifty-four studies met the inclusion criteria and were evaluated utilising a quality assessment tool for ecological studies. High population density appears to be associated with higher mortality rates of a range of cancers, cardiovascular disease and COPD, and a higher incidence of a range of cancers, asthma and club foot. In contrast, diabetes incidence was found to be associated with low population density. High and low population density are therefore risk markers for a range of NCDs, indicating that there are unidentified factors and mechanisms underlying aetiology. On closer examination, our synthesis revealed important and complex relationships between population density, the built environment, the nature of greenspace and man-made exposures. In light of increasing rates of morbidity and mortality, future research is required to investigate these associations in order to establish causative agents for each NCD.
Topics: Cardiovascular Diseases; Developed Countries; Humans; Neoplasms; Noncommunicable Diseases; Population Density
PubMed: 35270337
DOI: 10.3390/ijerph19052638 -
Trends in Ecology & Evolution Oct 2023Our ability to assess the threat posed by the genetic load to small and declining populations has been greatly improved by advances in genome sequencing and... (Review)
Review
Our ability to assess the threat posed by the genetic load to small and declining populations has been greatly improved by advances in genome sequencing and computational approaches. Yet, considerable confusion remains around the definitions of the genetic load and its dynamics, and how they impact individual fitness and population viability. We illustrate how both selective purging and drift affect the distribution of deleterious mutations during population size decline and recovery. We show how this impacts the composition of the genetic load, and how this affects the extinction risk and recovery potential of populations. We propose a framework to examine load dynamics and advocate for the introduction of load estimates in the management of endangered populations.
Topics: Genetics, Population; Genetic Load; Population Density; Inbreeding; Genetic Variation
PubMed: 37344276
DOI: 10.1016/j.tree.2023.05.008 -
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 -
Ecology Letters Apr 2019We address two fundamental ecological questions: what are the limits to animal population density and what determines those limits? We develop simple alternative models...
We address two fundamental ecological questions: what are the limits to animal population density and what determines those limits? We develop simple alternative models to predict population limits in relation to body mass. A model assuming that within-species area use increases with the square of daily travel distance broadly predicts the scaling of empirical extremes of minimum density across birds and mammals. Consistent with model predictions, the estimated density range for a given mass, 'population scope', is greater for birds than for mammals. However, unlike mammals and carnivorous birds, expected broad relationships between body mass and density extremes are not supported by data on herbivorous and omnivorous birds. Our results suggest that simple constraints on mobility and energy use/supply are major determinants of the scaling of density limits, but further understanding of interactions between dietary constraints and density limits are needed to predict future wildlife population responses to anthropogenic threats.
Topics: Animals; Birds; Carnivora; Mammals; Models, Biological; Population Density
PubMed: 30724435
DOI: 10.1111/ele.13227 -
British Medical Journal Sep 1972
Topics: Humans; Population Density; United Kingdom
PubMed: 5071708
DOI: 10.1136/bmj.3.5827.643-c -
Systematic Biology Aug 2022Balance indices that quantify the symmetry of branching events and the compactness of trees are widely used to compare evolutionary processes or tree-generating...
Balance indices that quantify the symmetry of branching events and the compactness of trees are widely used to compare evolutionary processes or tree-generating algorithms. Yet, existing indices are not defined for all rooted trees, are unreliable for comparing trees with different numbers of leaves, and are sensitive to the presence or absence of rare types. The contributions of this article are twofold. First, we define a new class of robust, universal tree balance indices. These indices take a form similar to Colless' index but can account for population sizes, are defined for trees with any degree distribution, and enable meaningful comparison of trees with different numbers of leaves. Second, we show that for bifurcating and all other full m-ary cladograms (in which every internal node has the same out-degree), one such Colless-like index is equivalent to the normalized reciprocal of Sackin's index. Hence, we both unify and generalize the two most popular existing tree balance indices. Our indices are intrinsically normalized and can be computed in linear time. We conclude that these more widely applicable indices have the potential to supersede those in current use. [Cancer; clone tree; Colless index; Sackin index; species tree; tree balance.].
Topics: Algorithms; Biological Evolution; Phylogeny; Population Density
PubMed: 35412638
DOI: 10.1093/sysbio/syac027