-
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 -
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 -
Trends in Ecology & Evolution Jul 2017Additive genetic variance (V) reflects the potential for evolutionary shifts and can be low for some traits or populations. High V is critical for the conservation of... (Review)
Review
Additive genetic variance (V) reflects the potential for evolutionary shifts and can be low for some traits or populations. High V is critical for the conservation of threatened species under selection to facilitate adaptation. Theory predicts tight associations between population size and V, but data from some experimental models, and managed and natural populations do not always support this prediction. However, V comparisons often have low statistical power, are undertaken in highly controlled environments distinct from natural habitats, and focus on traits with limited ecological relevance. Moreover, investigations of V typically fail to consider rare alleles, genetic load, or linkage disequilibrium, resulting in deleterious effects associated with favored alleles in small populations. Large population size remains essential for ensuring adaptation.
Topics: Alleles; Biological Evolution; Genetic Variation; Population Density; Selection, Genetic
PubMed: 28476215
DOI: 10.1016/j.tree.2017.03.012 -
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 -
PLoS Computational Biology Apr 2022Population size has long been considered an important driver of cultural diversity and complexity. Results from population genetics, however, demonstrate that in...
Population size has long been considered an important driver of cultural diversity and complexity. Results from population genetics, however, demonstrate that in populations with complex demographic structure or mode of inheritance, it is not the census population size, N, but the effective size of a population, Ne, that determines important evolutionary parameters. Here, we examine the concept of effective population size for traits that evolve culturally, through processes of innovation and social learning. We use mathematical and computational modeling approaches to investigate how cultural Ne and levels of diversity depend on (1) the way traits are learned, (2) population connectedness, and (3) social network structure. We show that one-to-many and frequency-dependent transmission can temporally or permanently lower effective population size compared to census numbers. We caution that migration and cultural exchange can have counter-intuitive effects on Ne. Network density in random networks leaves Ne unchanged, scale-free networks tend to decrease and small-world networks tend to increase Ne compared to census numbers. For one-to-many transmission and different network structures, larger effective sizes are closely associated with higher cultural diversity. For connectedness, however, even small amounts of migration and cultural exchange result in high diversity independently of Ne. Extending previous work, our results highlight the importance of carefully defining effective population size for cultural systems and show that inferring Ne requires detailed knowledge about underlying cultural and demographic processes.
Topics: Biological Evolution; Computer Simulation; Genetics, Population; Phenotype; Population Density
PubMed: 35395004
DOI: 10.1371/journal.pcbi.1009430 -
Ecology Letters Jan 2018Rarity is a population characteristic that is usually associated with a high risk of extinction. We argue here, however, that chronically rare species (those with low...
Rarity is a population characteristic that is usually associated with a high risk of extinction. We argue here, however, that chronically rare species (those with low population densities over many generations across their entire ranges) may have individual-level traits that make populations more resistant to extinction. The major obstacle to persistence at low density is successful fertilisation (union between egg and sperm), and chronically rare species are more likely to survive when (1) fertilisation occurs inside or close to an adult, (2) mate choice involves long-distance signals, (3) adults or their surrogate gamete dispersers are highly mobile, or (4) the two sexes are combined in a single individual. In contrast, external fertilisation and wind- or water-driven passive dispersal of gametes, or sluggish or sedentary adult life habits in the absence of gamete vectors, appear to be incompatible with sustained rarity. We suggest that the documented increase in frequency of these traits among marine genera over geological time could explain observed secular decreases in rates of background extinction. Unanswered questions remain about how common chronic rarity actually is, which traits are consistently associated with chronic rarity, and how chronically rare species are distributed among taxa, and among the world's ecosystems and regions.
Topics: Animals; Ecosystem; Invertebrates; Population Density
PubMed: 29110416
DOI: 10.1111/ele.12872 -
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 -
Communications Biology Sep 2023Our brains continuously acquire and store memories through synaptic plasticity. However, spontaneous synaptic changes can also occur and pose a challenge for maintaining...
Our brains continuously acquire and store memories through synaptic plasticity. However, spontaneous synaptic changes can also occur and pose a challenge for maintaining stable memories. Despite fluctuations in synapse size, recent studies have shown that key population-level synaptic properties remain stable over time. This raises the question of how local synaptic plasticity affects the global population-level synaptic size distribution and whether individual synapses undergoing plasticity escape the stable distribution to encode specific memories. To address this question, we (i) studied spontaneously evolving spines and (ii) induced synaptic potentiation at selected sites while observing the spine distribution pre- and post-stimulation. We designed a stochastic model to describe how the current size of a synapse affects its future size under baseline and stimulation conditions and how these local effects give rise to population-level synaptic shifts. Our study offers insights into how seemingly spontaneous synaptic fluctuations and local plasticity both contribute to population-level synaptic dynamics.
Topics: Brain; Neuronal Plasticity; Population Density; Population Dynamics
PubMed: 37696988
DOI: 10.1038/s42003-023-05303-1 -
The Science of the Total Environment Mar 2022The world's population is shifting to the cities, and consequently, cities worldwide are growing in number and in size. Cities are complex systems, making it extremely...
The world's population is shifting to the cities, and consequently, cities worldwide are growing in number and in size. Cities are complex systems, making it extremely difficult to build and run cities in a way that all the elements of the system operate in harmony. Recently a concept of urbanome, the genome of the city was proposed to address this complexity. Here we first explore this concept and analogy, taking advantage of the potential of other 'omics, modern data collection techniques, Big Data analysis methods and a transdisciplinary approach. Then, we propose a theoretical approach to build the urbanome as a means of quantifying and qualifying population outcomes, being a function of the form of an urban area including the built environment, the physical and social services it provides, and the population density.
Topics: Cities; City Planning; Population Density
PubMed: 34914999
DOI: 10.1016/j.scitotenv.2021.152310 -
The Journal of Animal Ecology Aug 2019Numerous studies have demonstrated that dispersal is dependent on both disperser phenotype and the local environment. However, there is substantial variability in the...
Numerous studies have demonstrated that dispersal is dependent on both disperser phenotype and the local environment. However, there is substantial variability in the observed strength and direction of phenotype- and environment-dependent dispersal. This has been hypothesized to be the result of interactive effects among the multiple phenotypic and environmental factors that influence dispersal. Here, our goal was to test the hypothesis that these interactions are responsible for generating variation in dispersal behaviour. We achieved these goals by conducting a large, 2-year, mark-release-recapture study of the backswimmer Notonecta undulata in an array of 36 semi-natural ponds. We measured the effects of multiple phenotypic (sex and body size) and environmental (population density and sex ratio) factors, on both dispersal probability and dispersal distance. We found support for the hypothesis that interactive effects influence dispersal and produce variability in phenotype- and environment-dependent dispersal: dispersal probability was dependent on the three-way interaction between sex, body mass and population density. Small males displayed strong, positive density dependence in their dispersal behaviour, while large males and females overall did not respond strongly to density. Small notonectids, regardless of sex, were more likely to disperse, but this effect was strongest at high population densities. Finally, the distance dispersed by backswimmers was a negative function of population density, a pattern which we hypothesize could be related to: (a) individuals from high and low density patches having different dispersal strategies, or (b) the effect of density on dispersal capacity. These results suggest that phenotype-by-environment interactions strongly influence dispersal. Since phenotype- and environment-dependent dispersal has different consequences for ecological and evolutionary dynamics (e.g. metapopulation persistence and local adaptation) than random dispersal, interactive effects may have wide-reaching impacts on populations and communities. We therefore argue that more investment should be made into estimating the effects of multiple, interacting factors on dispersal and determining whether similar interactive effects are acting across systems.
Topics: Animals; Biological Evolution; Ecology; Female; Gene-Environment Interaction; Male; Phenotype; Population Density; Population Dynamics
PubMed: 31077361
DOI: 10.1111/1365-2656.13008