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Conservation Biology : the Journal of... Apr 2022Community-level resource management efforts are cornerstones in ensuring sustainable use of natural resources. Yet, understanding how community characteristics influence...
Community-level resource management efforts are cornerstones in ensuring sustainable use of natural resources. Yet, understanding how community characteristics influence management practices remains contested. With a sample size of ≥725 communities, we assessed the effects of key community (i.e., socioeconomic) characteristics (human population size and density, market integration, and modernization) on the probability of occurrence of fisheries management practices, including gear, species, and spatial restrictions. The study was based in Solomon Islands, a Pacific Island country with a population that is highly dependent on coastal fisheries. People primarily dwell in small communities adjacent to the coastline dispersed across 6 island provinces and numerous smaller islands. We used nationally collected data in binomial logistic regression models to examine the likelihood of management occurrence, given socioeconomic context of communities. In contrast to prevailing views, we identified a positive and statistically significant association between both human population size and market integration and all 3 management practices. Human population density, however, had a statistically significant negative association and modernization a varied and limited association with occurrence of all management practices. Our method offers a way to remotely predict the occurrence of resource management practices based on key socioeconomic characteristics. It could be used to improve understanding of why some communities conduct natural resource management activities when statistical patterns suggest they are not likely to and thus improve understanding of how some communities of people beat the odds despite limited market access and high population density.
Topics: Conservation of Natural Resources; Fisheries; Humans; Population Density; Sample Size; Socioeconomic Factors
PubMed: 34160100
DOI: 10.1111/cobi.13800 -
Plant, Cell & Environment Apr 2021Plant population density is an important variable in agronomy and forestry and offers an experimental way to better understand plant-plant competition. We made a... (Review)
Review
Plant population density is an important variable in agronomy and forestry and offers an experimental way to better understand plant-plant competition. We made a meta-analysis of responses of even-aged mono-specific stands to population density by quantifying for 3 stand and 33 individual plant variables in 334 experiments how much both plant biomass and phenotypic traits change with a doubling in density. Increasing density increases standing crop per area, but decreases the mean size of its individuals, mostly through reduced tillering and branching. Among the phenotypic traits, stem diameter is negatively affected, but plant height remains remarkably similar, partly due to an increased stem length-to-mass ratio and partly by increased allocation to stems. The reduction in biomass is caused by a lower photosynthetic rate, mainly due to shading of part of the foliage. Total seed mass per plant is also strongly reduced, marginally by lower mass per seed, but mainly because of lower seed numbers. Plants generally have fewer shoot-born roots, but their overall rooting depth seems hardly affected. The phenotypic plasticity responses to high densities correlate strongly with those to low light, and less with those to low nutrients, suggesting that at high density, shading affects plants more than nutrient depletion.
Topics: Biomass; Plant Development; Plant Physiological Phenomena; Plants; Population Density
PubMed: 33280135
DOI: 10.1111/pce.13968 -
Scientific Data Oct 2022Population and water withdrawal data sets are currently faced with difficulties in collecting, processing and verifying multi-source time series, and the spatial...
Population and water withdrawal data sets are currently faced with difficulties in collecting, processing and verifying multi-source time series, and the spatial distribution characteristics of long series are also relatively lacking. Time series is the basic guarantee for the accuracy of data sets, and the production of long series spatial distribution is a realistic requirement to expand the application scope of data sets. Through the time-consuming and laborious basic processing work, this research focuses on the population and water intake time series, and interpolates and extends them to specific land uses to ensure the accuracy of the time series and the demand of spatially distributed data sets. This research provides a set of population density and water intensity products from 1960 to 2020 distributed to the administrative units or the corresponding regions. The data set fills the gaps in the multi-year data set for the accuracy of population density and the intensity of water withdrawal.
Topics: Water Resources; Humans; Population Dynamics; Population Density
PubMed: 36271026
DOI: 10.1038/s41597-022-01760-1 -
Revista Brasileira de Psiquiatria (Sao... 2020
Topics: Adult; Brazil; Depression; Humans; Multilevel Analysis; Population Density; Risk Factors; Suicidal Ideation
PubMed: 32022164
DOI: 10.1590/1516-4446-2019-0541 -
Genes Dec 2022Dabieshan cattle (DBSC) are a valuable genetic resource for indigenous cattle breeds in China. It is a small to medium-sized breed with slower growth, but with good meat...
Dabieshan cattle (DBSC) are a valuable genetic resource for indigenous cattle breeds in China. It is a small to medium-sized breed with slower growth, but with good meat quality and fat deposition. Genetic markers could be used for the estimation of population genetic structure and genetic parameters. In this work, we genotyped the DBSC breeding population ( = 235) with the GeneSeek Genomic Profiler (GGP) 100 k density genomic chip. Genotype data of 222 individuals and 81,579 SNPs were retained after quality control. The average minor allele frequency (MAF) was 0.20 and the average linkage disequilibrium (LD) level (r) was 0.67 at a distance of 0-50 Kb. The estimated relationship coefficient and effective population size (Ne) were 0.023 and 86 for the current generation. In addition, we used genotype data to estimate the genetic parameters of the population's phenotypic traits. Among them, height at hip cross (HHC) and shin circumference (SC) were rather high heritability traits, with heritability of 0.41 and 0.54, respectively. The results reflected the current cattle population's extent of inbreeding and history. Through the principal breeding parameters, genomic breeding would significantly improve the genetic progress of breeding.
Topics: Animals; Cattle; Population Density; Linkage Disequilibrium; Genotype; Genome; Phenotype
PubMed: 36672850
DOI: 10.3390/genes14010107 -
Heredity Jun 2021Inferring the demographic history of species is one of the greatest challenges in populations genetics. This history is often represented as a history of size changes,...
Inferring the demographic history of species is one of the greatest challenges in populations genetics. This history is often represented as a history of size changes, ignoring population structure. Alternatively, when structure is assumed, it is defined a priori as a population tree and not inferred. Here we propose a framework based on the IICR (Inverse Instantaneous Coalescence Rate). The IICR can be estimated for a single diploid individual using the PSMC method of Li and Durbin (2011). For an isolated panmictic population, the IICR matches the population size history, and this is how the PSMC outputs are generally interpreted. However, it is increasingly acknowledged that the IICR is a function of the demographic model and sampling scheme with limited connection to population size changes. Our method fits observed IICR curves of diploid individuals with IICR curves obtained under piecewise stationary symmetrical island models. In our models we assume a fixed number of time periods during which gene flow is constant, but gene flow is allowed to change between time periods. We infer the number of islands, their sizes, the periods at which connectivity changes and the corresponding rates of connectivity. Validation with simulated data showed that the method can accurately recover most of the scenario parameters. Our application to a set of five human PSMCs yielded demographic histories that are in agreement with previous studies using similar methods and with recent research suggesting ancient human structure. They are in contrast with the view of human evolution consisting of one ancestral population branching into three large continental and panmictic populations with varying degrees of connectivity and no population structure within each continent.
Topics: Diploidy; Gene Flow; Genetics, Population; Humans; Population Density
PubMed: 33846579
DOI: 10.1038/s41437-021-00426-9 -
Influenza and Other Respiratory Viruses Nov 2022Better understanding of risk factors for influenza could help improve seasonal and pandemic planning. There is a dearth of literature on area-level risk factors such as...
BACKGROUND
Better understanding of risk factors for influenza could help improve seasonal and pandemic planning. There is a dearth of literature on area-level risk factors such as population density and rural/urban living.
METHODS
We used data from Flusurvey, an online community-based cohort that records influenza events. The study outcome was symptoms of influenza-like illness (ILI). Multivariable Poisson regression analysis was used to explore associations of both population density and rural/urban status with rate of ILI symptoms and whether these effects differed by vaccination status.
RESULTS
Of the 6177 study participants, the median age was 45 (IQR 32-57), 65.73% were female, and 66% reported at least one episode of ILI symptoms between 2011 and 2016. We found no evidence to suggest that the rate of ILI symptoms was higher in the medium [RR 1.02 (95% CI 0.95-1.09)] or high [RR 1.02 (95% CI 0.96-1.09)] population density group versus the low population density group. This was the same for the effect of urban living [RR 0.96 (95% CI 0.90-1.03)] versus rural living on symptom rate. There was weak evidence to suggest that the ILI symptom rate was lower in urban areas compared with rural areas among unvaccinated individuals only [RR 0.90 (95% CI 0.83-0.99)], whereas no difference was seen among vaccinated individuals [1.04 (95% CI 0.94-1.16)].
CONCLUSIONS
Although neither population density nor rural/urban status was associated with ILI symptom rate in this community cohort, future research that incorporates activity and contact patterns will help to elucidate this relationship further.
Topics: England; Female; Humans; Influenza, Human; Male; Middle Aged; Population Density; Virus Diseases; Wales
PubMed: 35922884
DOI: 10.1111/irv.13032 -
Philosophical Transactions of the Royal... Jan 2021As is the case today, both climate variability and population density influenced human behavioural change in the past. The mechanisms underpinning later Pleistocene...
As is the case today, both climate variability and population density influenced human behavioural change in the past. The mechanisms underpinning later Pleistocene human behavioural evolution, however, remain contested. Many complex behaviours evolved in Africa, but early evidence for these behaviours varies both spatially and temporally. Scientists have not been able to explain this flickering pattern, which is present even in sites and regions clearly occupied by . To explore this pattern, here the presence and frequency of evidence for backed stone artefact production are modelled against climate-driven, time-series population density estimates (Timmermann and Friedrich. 2016 , 92. (doi:10.1038/nature19365)), in all known African Late Pleistocene archaeological sites ( = 116 sites, = 409 assemblages, = 893 dates). In addition, a moving-window, site density population estimate is included at the scale of southern Africa. Backed stone artefacts are argued in many archaeological contexts to have functioned in elaborate technologies like composite weapons and, in the African Pleistocene, are accepted proxies for cultural complexity. They show a broad but sporadic distribution in Africa, prior to their association with dispersing into Europe 45-40 ka. Two independent population estimates explain this pattern and potentially implicate the interaction of climate change and demography in the expression of cultural complexity in African Pleistocene . This article is part of the theme issue 'Cross-disciplinary approaches to prehistoric demography'.
Topics: Africa; Archaeology; Cultural Evolution; Demography; History, Ancient; History, Medieval; Humans; Population Density; Technology
PubMed: 33250028
DOI: 10.1098/rstb.2019.0716 -
Genome Research Nov 2021Coalescent methods are proven and powerful tools for population genetics, phylogenetics, epidemiology, and other fields. A promising avenue for the analysis of large...
Coalescent methods are proven and powerful tools for population genetics, phylogenetics, epidemiology, and other fields. A promising avenue for the analysis of large genomic alignments, which are increasingly common, is coalescent hidden Markov model (coalHMM) methods, but these methods have lacked general usability and flexibility. We introduce a novel method for automatically learning a coalHMM and inferring the posterior distributions of evolutionary parameters using black-box variational inference, with the transition rates between local genealogies derived empirically by simulation. This derivation enables our method to work directly with three or four taxa and through a divide-and-conquer approach with more taxa. Using a simulated data set resembling a human-chimp-gorilla scenario, we show that our method has comparable or better accuracy to previous coalHMM methods. Both species divergence times and population sizes were accurately inferred. The method also infers local genealogies, and we report on their accuracy. Furthermore, we discuss a potential direction for scaling the method to larger data sets through a divide-and-conquer approach. This accuracy means our method is useful now, and by deriving transition rates by simulation, it is flexible enough to enable future implementations of various population models.
Topics: Animals; Computer Simulation; Genetics, Population; Humans; Models, Genetic; Population Density; Recombination, Genetic
PubMed: 34426513
DOI: 10.1101/gr.273631.120 -
Proceedings. Biological Sciences Jun 2022Background selection (BGS), the effect that purifying selection exerts on sites linked to deleterious alleles, is expected to be ubiquitous across eukaryotic genomes....
Background selection (BGS), the effect that purifying selection exerts on sites linked to deleterious alleles, is expected to be ubiquitous across eukaryotic genomes. The effects of BGS reflect the interplay of the rates and fitness effects of deleterious mutations with recombination. A fundamental assumption of BGS models is that recombination rates are invariant over time. However, in some lineages, recombination rates evolve rapidly, violating this central assumption. Here, we investigate how recombination rate evolution affects genetic variation under BGS. We show that recombination rate evolution modifies the effects of BGS in a manner similar to a localized change in the effective population size, potentially leading to underestimation or overestimation of the genome-wide effects of selection. Furthermore, we find evidence that recombination rate evolution in the ancestors of modern house mice may have impacted inferences of the genome-wide effects of selection in that species.
Topics: Alleles; Animals; Evolution, Molecular; Genetic Variation; Mice; Population Density; Recombination, Genetic; Selection, Genetic
PubMed: 35730151
DOI: 10.1098/rspb.2022.0782