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PloS One 2024Population structure and genetic diversity are the key parameters to study the breeding history of animals. This research aimed to provide a characterization of the...
Population structure and genetic diversity are the key parameters to study the breeding history of animals. This research aimed to provide a characterization of the population structure and to compare the effective population size (Ne), LD decay, genetic diversity, and genomic inbreeding in Iranian native Caspian (n = 38), Turkmen (n = 24) and Kurdish (n = 29) breeds and some other exotic horses consisting of Arabian (n = 24), Fell pony (n = 21) and Akhal-Teke (n = 20). A variety of statistical population analysis techniques, such as principal component analysis (PCA), discriminant analysis of principal component (DAPC) and model-based method (STRUCTURE) were employed. The results of the population analysis clearly demonstrated a distinct separation of native and exotic horse breeds and clarified the relationships between studied breeds. The effective population size (Ne) for the last six generations was estimated 54, 49, 37, 35, 27 and 26 for the Caspian, Kurdish, Arabian, Turkmen, Akhal-Teke and Fell pony breeds, respectively. The Caspian breed showed the lowest LD with an average r2 value of 0.079, while the highest was observed in Fell pony (0.148). The highest and lowest average observed heterozygosity were found in the Kurdish breeds (0.346) and Fell pony (0.290) breeds, respectively. The lowest genomic inbreeding coefficient based on run of homozygosity (FROH) and excess of homozygosity (FHOM) was in the Caspian and Kurdish breeds, respectively, while based on genomic relationship matrix) FGRM) and correlation between uniting gametes) FUNI) the lowest genomic inbreeding coefficient was found in the Kurdish breed. The estimation of genomic inbreeding rates in the six breeds revealed that FROH yielded lower estimates compared to the other three methods. Additionally, the Iranian breeds displayed lower levels of inbreeding compared to the exotic breeds. Overall, the findings of this study provide valuable insights for the development of effective breeding management strategies aimed at preserving these horse breeds.
Topics: Horses; Animals; Humans; Inbreeding; Population Density; Iran; Genomics; Discriminant Analysis
PubMed: 38442089
DOI: 10.1371/journal.pone.0299109 -
Sensors (Basel, Switzerland) Sep 2023Crowd counting, as a basic computer vision task, plays an important role in many fields such as video surveillance, accident prediction, public security, and intelligent...
Crowd counting, as a basic computer vision task, plays an important role in many fields such as video surveillance, accident prediction, public security, and intelligent transportation. At present, crowd counting tasks face various challenges. Firstly, due to the diversity of crowd distribution and increasing population density, there is a phenomenon of large-scale crowd aggregation in public places, sports stadiums, and stations, resulting in very serious occlusion. Secondly, when annotating large-scale datasets, positioning errors can also easily affect training results. In addition, the size of human head targets in dense images is not consistent, making it difficult to identify both near and far targets using only one network simultaneously. The existing crowd counting methods mainly use density plot regression methods. However, this framework does not distinguish the features between distant and near targets and cannot adaptively respond to scale changes. Therefore, the detection performance in areas with sparse population distribution is not good. To solve such problems, we propose an adaptive multi-scale far and near distance network based on the convolutional neural network (CNN) framework for counting dense populations and achieving a good balance between accuracy, inference speed, and performance. However, on the feature level, in order to enable the model to distinguish the differences between near and far features, we use stacked convolution layers to deepen the depth of the network, allocate different receptive fields according to the distance between the target and the camera, and fuse the features between nearby targets to enhance the feature extraction ability of pedestrians under nearby targets. Secondly, depth information is used to distinguish distant and near targets of different scales and the original image is cut into four different patches to perform pixel-level adaptive modeling on the population. In addition, we add density normalized average precision (nAP) indicators to analyze the accuracy of our method in spatial positioning. This paper validates the effectiveness of NF-Net on three challenging benchmarks in Shanghai Tech Part A and B, UCF_ CC_50, and UCF-QNRF datasets. Compared with SOTA, it has more significant performance in various scenarios. In the UCF-QNRF dataset, it is further validated that our method effectively solves the interference of complex backgrounds.
PubMed: 37765861
DOI: 10.3390/s23187805 -
Communications Biology Sep 2023Sex-specific differences in habitat selection and space use are common in ungulates. Yet, it is largely unknown how this behavioral dimorphism, ultimately leading to...
Sex-specific differences in habitat selection and space use are common in ungulates. Yet, it is largely unknown how this behavioral dimorphism, ultimately leading to sexual segregation, translates to population-level patterns and density gradients across landscapes. Alpine chamois (Rupicapra rupicapra r.) predominantly occupy habitat above tree line, yet especially males may also take advantage of forested habitats. To estimate male and female chamois density and determinants thereof, we applied Bayesian spatial capture-recapture (SCR) models in two contrasting study areas in the Alps, Germany, during autumn. We fitted SCR models to non-invasive individual encounter data derived from genotyped feces. Sex-specific densities were modeled as a function of terrain ruggedness, forest canopy cover, proportion of barren ground, and site severity. We detected pronounced differences in male and female density patterns, driven primarily by terrain ruggedness, rather than by sex-specific effects of canopy cover. The positive effect of ruggedness on density was weaker for males which translated into a higher proportion of males occupying less variable terrain, frequently located in forests, compared to females. By estimating sex-specific variation in both detection probabilities and density, we were able to quantify and map how individual behavioral differences scale up and shape spatial patterns in population density.
Topics: Animals; Male; Female; Rupicapra; Bayes Theorem; Genotype; Sex Characteristics; Germany
PubMed: 37749272
DOI: 10.1038/s42003-023-05313-z -
Sensors (Basel, Switzerland) Sep 2023Farm tractors have become a key part of daily routine agriculture, converting complex and time-consuming tasks into tasks that are easier to perform and less dependent...
Farm tractors have become a key part of daily routine agriculture, converting complex and time-consuming tasks into tasks that are easier to perform and less dependent on human labor, contributing directly to increasing the economic value generated by this activity sector, either by increasing the productivity or by making certain agricultural crops viable, which otherwise would not be sustainable. However, despite all the advantages, accidents with this type of equipment are common, often with critical and sometimes fatal consequences. The evolution of safety requirements of these machines has occurred at a good level; however, a significant part of the agricultural tractors in use are older models that do not have such solutions. Even in the new models, which contain such solutions, these are not always correctly used, and it is even common that they are turned off or simply not used at all. It is therefore natural that accidents continue to occur, a situation that is aggravated by other factors. Lack of situational awareness of the operators, which can result from advanced age, inadequate training, reduced sensitivity/respect for safety rules, or working on irregular terrain like mountainous areas, contribute to high-risk contexts that end in the loss of human life. The consequences of such accidents are clearly aggravated by the time it takes to assist the victims-either because accidents are simply not identified/reported immediately, or by the time it takes to locate and provide help to the victims. This is a scenario that is more common in mountainous regions and regions with low population density. The current paper, using NB-IoT, a set of sensors, and a web application, presents a conceptual toolset conceived to prevent accidents and minimize consequences (human and material) that can be applied to old and new farm tractors. The development was carried out taking the characterization of the farmers and the land in the region in which the authors' research institution is located into account, which has the highest rate of fatal accidents with agricultural tractors in the country; it is a region of mountainous with a very low population density.
Topics: Humans; Farms; Population Density; Accidents; Agriculture; Awareness
PubMed: 37765868
DOI: 10.3390/s23187811 -
The Lancet. Planetary Health Dec 2023Cities are becoming increasingly important habitats for mosquito vectors of disease. The pronounced heterogeneity of urban landscapes challenges our understanding of the...
BACKGROUND
Cities are becoming increasingly important habitats for mosquito vectors of disease. The pronounced heterogeneity of urban landscapes challenges our understanding of the effects of climate and socioeconomic factors on mosquito-borne disease dynamics at different spatiotemporal scales. Here, we quantify the impact of climatic and socioeconomic factors on urban malaria risk, using an extensive dataset in both space and time for reported Plasmodium falciparum cases in the city of Surat, northwest India.
METHODS
We analysed 10 years of monthly P falciparum cases resolved at three nested spatial resolutions (seven zones, 32 units, and 478 worker units) with a Bayesian hierarchical mixed model that incorporates the effects of population density, poverty, relative humidity, and temperature, in addition to random effects (structured and unstructured). To reduce dimensionality and avoid correlation of covariates, socioeconomic variables from survey data were summarised into main axes of variation using principal component analysis. With model selection, we identified the main drivers of spatiotemporal variation in malaria incidence rates at each of the three spatial resolutions. We also compared observations to model-fitted cases by quantifying the percentage of predictions within five discrete levels of malaria risk.
FINDINGS
The spatial variation of urban malaria cases was stationary over time, whereby locations with high and low yearly cases remained largely consistent across years. Local socioeconomic variation could be summarised with three principal components accounting for approximately 80% of the variance. The model that incorporated local temperature and relative humidity together with two of these principal components, largely representing population density and poverty, best explained monthly malaria patterns in models formulated at the three different spatial scales. As model resolution increased, the effect size of humidity decreased, whereas those of temperature and the principal component associated with population density increased. Model predictions accurately captured aggregated total monthly cases for the city; in space-time, they more closely matched observations at the intermediate scale, with around 57% of units estimated to fall in the observed category on average across years. The mean absolute error was lower at the intermediate level, showing that this is the best aggregation level to predict the space-time dynamics of malaria incidence rates across the city with the selected model.
INTERPRETATION
This statistical modelling framework provides a basis for development of a climate-driven early warning system for urban malaria for the units of Surat, including spatially explicit prediction of malaria risk several weeks to months in advance. Results indicate environmental and socioeconomic covariates for which further measurement at high resolution should lead to model improvement. Advanced warning combined with local surveillance and knowledge of disease hotspots within the city could inform targeted intervention as part of urban malaria elimination efforts.
FUNDING
US National Institutes of Health.
Topics: Animals; Bayes Theorem; Models, Statistical; Malaria; Socioeconomic Factors; India
PubMed: 38056969
DOI: 10.1016/S2542-5196(23)00249-8 -
PloS One 2023Many gibbon species are threatened with extinction, including the endangered northern yellow-cheeked crested gibbon, Nomascus annamensis. Assessing gibbon populations...
Density and population size estimates of the endangered northern yellow-cheeked crested gibbon Nomascus annamensis in selectively logged Veun Sai-Siem Pang National Park in Cambodia using acoustic spatial capture-recapture methods.
Many gibbon species are threatened with extinction, including the endangered northern yellow-cheeked crested gibbon, Nomascus annamensis. Assessing gibbon populations and understanding how human disturbances and environmental factors impact these populations is vital for effective conservation planning. In 2010, auditory surveys revealed that Veun Sai-Siem Pang National Park (VSSP) in Cambodia contains one of the largest known N. annamensis populations in the world, with an estimated 456 (95% CI 421-490) gibbon groups. Illegal selective logging is common in the park, but the impact of continued logging on the gibbon population has not been investigated. To determine any change in the N. annamensis population since 2010, between January and April 2019 we conducted auditory surveys at 13 sites that were at least 4 km apart. We surveyed each site for three days, each day recording the gibbon calls heard over 3.25 hours from three listening posts located 500 m apart. At the same sites, we assessed the logging intensity using transects and ecological plots. Gibbon densities can be influenced by various environmental factors such as canopy height and forest type. Therefore, in addition to investigating the relationship between the density of N. annamensis groups and logging, we included five additional environmental variables in our acoustic spatial capture-recapture models. Our best fit model with the lowest AIC value included canopy height, forest type, distance to villages, and logging. We estimate that there are 389 (95% CI 284-542) N. annamensis groups currently in VSSP. Selective logging is widespread in the park, primarily targeting four tree species. The estimated felling time of these logged trees, together with previous reports, indicate that the species most targeted in VSSP varies over time. To conserve the N. annamensis population in VSSP, it is crucial that action is taken to reduce illegal logging.
Topics: Animals; Humans; Hylobates; Population Density; Cambodia; Parks, Recreational; Conservation of Natural Resources; Trees
PubMed: 38011169
DOI: 10.1371/journal.pone.0292386 -
Scientific Reports Nov 2023Risk assessment of properties and associated population was conducted for the state of Nebraska, leveraging only open-source datasets. The flood risk framework consisted...
Risk assessment of properties and associated population was conducted for the state of Nebraska, leveraging only open-source datasets. The flood risk framework consisted of interactions among drivers, i.e. hazard, exposure, vulnerability, and response, to assess the risks related to properties and associated populations. To quantify hazard on a county scale, we considered properties at risk of flooding based on a flood score (a higher score represents a greater chance of flooding). Exposure was quantified by considering population density at the county level. We quantified vulnerability under four categories: social, ecological, economic, and health. Response, a relatively newer component in flood risk assessment, was also quantified under three distinct categories: structural, non-structural, and emergency. Overall, we found that counties in eastern Nebraska (Sarpy, Dakota, Wayne, and Adams) have a higher risk of flooding consequences due to more exposure to vulnerable assets such as population and property. The assessment also observed that counties in eastern Nebraska are in the process of improving their flood control measures with dams, levees, and higher insurance coverage that can subdue the risks associated with flooding. The results from this study are anticipated to guide water managers and policymakers in making more effective and locally relevant policies and measures to mitigate flood risks and consequences.
Topics: Floods; Nebraska; Risk Assessment; Probability; Insurance Coverage
PubMed: 37952065
DOI: 10.1038/s41598-023-45827-4 -
Current Research in Insect Science 2024Population density and structure are critical to nature conservation and pest management. Traditional sampling methods such as capture-mark-recapture and catch-effort... (Review)
Review
Population density and structure are critical to nature conservation and pest management. Traditional sampling methods such as capture-mark-recapture and catch-effort can't be used in situations where catching, marking, or removing individuals are not feasible. N-mixture models use repeated count data to estimate population abundance based on detection probability. They are widely adopted in wildlife surveys in recent years to account for imperfect detection. However, its application in entomology is relatively new. In this paper, we describe the general procedures of N-mixture models in population studies from data collection to model fitting and evaluation. Using egg mass survey data at 28 plots in seven sites from the field, we found that detection probability () was negatively correlated with tree diameter at breast height (DBH), ranged from 0.516 [95 % CI: 0.470-0.561] to 0.614 [95 % CI: 0.566-0.660] between the 1st and the 3rd sample period. Furthermore, egg mass abundance (λ) was positively associated with basal area (BA) for the sample unit (single tree), with more egg masses on tree of heaven (TOH) trees. More egg masses were also expected on trees of other species in TOH plots. Predicted egg mass density (masses/100 m) ranged from 5.0 (95 % CI: 3.0-16.0) (Gordon) to 276.9 (95 % CI: 255.0-303.0) (Susquehannock) for TOH plots, and 11.0 (95 % CI: 9.00-15.33) (Gordon) to 228.3 (95 % CI: 209.7-248.3) (Burlington) for nonTOH plots. Site-specific abundance estimates from N-mixture models were generally higher compared to observed maximum counts. N-mixture models could have great potential in insect population surveys in agriculture and forestry in the future.
PubMed: 38576775
DOI: 10.1016/j.cris.2024.100078 -
PloS One 2023The present study aimed to assess the population density, structure, and population change of nine wild prey species in the semi-arid landscape of Saurashtra, Gujarat,...
The present study aimed to assess the population density, structure, and population change of nine wild prey species in the semi-arid landscape of Saurashtra, Gujarat, India. A total of eight sites, representing a gradient from highly protected woodlands and grasslands to unreserved grasslands, were selected for sampling. We employed the road transect methodology under a distance sampling framework to achieve our objectives. We evaluated the realized growth rate of the Gir ungulate population through linear regression analysis. Our findings revealed that deer species exhibited higher density and biomass in woodlands compared to grasslands and coastal forests. On the other hand, antelopes showed higher density and biomass in grasslands and coastal forests compared to woodlands. The density gradient of wild prey species was influenced by various factors, including habitat structure, social organization, grouping tendencies, and topography. Over the last four decades, the population of wild prey species in Gir showed minimal changes. Our study provides a comprehensive understanding of wild prey species' density and biomass patterns at the landscape level. The inclusion of findings from ecologically significant and unique areas, such as coastal forests, further enhances the importance of this study. The implications of this study extend beyond the conservation of wild prey species alone; they also contribute to the conservation of the large carnivore guild in the Saurashtra landscape.
Topics: Animals; Ecosystem; Biomass; Lions; Population Density; Conservation of Natural Resources; Deer; Forests; Carnivora
PubMed: 37768920
DOI: 10.1371/journal.pone.0292048 -
PeerJ 2023The harvest of the edible sea urchin is intensively practiced in some regions of the Western Mediterranean Sea. The removal of the largest individuals can determine an...
The harvest of the edible sea urchin is intensively practiced in some regions of the Western Mediterranean Sea. The removal of the largest individuals can determine an overall reduction in population size and a size class truncation that can lead to a drastic drop the self-sustenance. The aim of this study is to evaluate the variability of the population reproductive potential across 5 years in one of the main harvest hotspots of Sardinia (Western Mediterranean Sea). The breeding stock consists of commercial and under-commercial size individuals which were sampled on a monthly basis to estimate their GonadoSomatic Index (GSI) and the Individual Gamete Output (IGO). In addition, the reproductive potential of the population-Total Gamete Output (TGO)-was calculated across the 5-year period in relation with the variation of the density of the breeding stock. During the last year, the reproductive potential was also estimated in a well-conserved population of a nearby Marine Protected Area. No significant variability in GSI and IGO was found over the 5 years nor when compared with the ones of protected population in the last year. However, the intensive harvest drastically rescaled the population body-size: although density of the commercial size class remained low, density of the under-commercial size-class halved from the beginning to the end of the study. Accordingly, the proportional decrease of their gamete output contribution led to a 40% loss of the reproductive potential of the whole population in the 5-year period. Interestingly, despite the loss of reproductive potential due to the decrease of the breeding stock density, the average values of IGO slightly increased across the years leading to the highest Annual Gamete Output (AGO) during the fourth year of sampling. This positive pattern could suggest a mechanism of reproductive investments of the survivors in terms of gonad production rate or increase in spawning intensity. This work provides evidence of the direct effect of size-selective harvesting on the rapid loss of population self-sustenance. Furthermore, it lays new prospective for future research of the indirect effects of the rescaling population body-size in functional traits of the sea urchin and that could become important for both, sustainable exploitation and ecosystem conservation management.
Topics: Animals; Ecosystem; Italy; Paracentrotus; Population Density; Prospective Studies
PubMed: 38025682
DOI: 10.7717/peerj.16220