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"Population (statistical)"
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The uncounted
\"What we count matters, and in a world where policies and decisions are underpinned by numbers, statistics and data, if you're not counted, you don't count. In this book, Alex Cobham argues that systematic gaps in economic and demographic data not only lead us to understate a wide range of damaging inequalities, but also to actively exacerbate them\"-- Provided by publisher.
Book
Estimating Mountain Lion Abundance in Arizona Using Statistical Population Reconstruction
Directly monitoring abundance of cryptic species, such as mountain lions (Puma concolor), over large areas is a challenge for wildlife managers because traditional population estimation techniques may be impractical and expensive. We generated annual estimates of mountain lion abundance in Arizona, USA, for 2004–2018 by employing statistical population reconstruction methods, which use available age-at-harvest data and auxiliary information such as estimated survival rates, harvest probabilities, and hunter effort. Using PopRecon 2.0 software, we estimated that the statewide abundance of all mountain lions including kittens ranged from 1,848 (95% CI = 650–3,046) to 4,661 (95% CI = 393–9,030) during 2004–2018. Abundance for subadults and adults was more stable and precisely estimated, ranging from 1,166 (95% CI = 622–1,709) to 1,715 (95% CI = 872–2,558). Our results suggest a stable statewide mountain lion population. This approach provides a practical and cost-effective option for monitoring Arizona’s mountain lion population, and will improve the ability of managers to monitor the population annually to respond to changes in abundance and to evaluate factors that influence mountain lion abundance.
Journal Article
Insights into the genetic variability and evolutionary dynamics of tomato spotted wilt orthotospovirus in China
Background
Viral diseases are posing threat to annual production and quality of tobacco in China. Recently, tomato spotted wilt orthotospovirus (TSWV) has been reported to infect three major crops including tobacco. Current study was aimed to investigate the population dynamics and molecular diversity of the TSWV. In the current study, to assess and identify the prevalence and evolutionary history of TSWV in tobacco crops in China, full-length genome sequences of TSWV isolates from tobacco, were identified and analyzed.
Methods
After trimming and validation, sequences of new isolates were submitted to GenBank. We identified the full-length genomes of ten TSWV isolates, infecting tobacco plants from various regions of China. Besides these, six isolates were partially sequenced. Phylogenetic analysis was performed to assess the relativeness of newly identified sequences and corresponding sequences from GenBank. Recombination and population dynamics analysis was performed using RDP4, RAT, and statistical estimation. Reassortment analysis was performed using MegaX software.
Results
Phylogenetic analysis of 41 newly identified sequences, depicted that the majority of the Chinese isolates have separate placement in the tree. RDP4 software predicted that RNA M of newly reported isolate YNKM-2 had a recombinant region spanning from 3111 to 3811 bp. The indication of parental sequences (YNKMXD and YNHHKY) from newly identified isolates, revealed the conservation of local TSWV population. Genetic diversity and population dynamics analysis also support the same trend. RNA M was highlighted to be more capable of mutating or evolving as revealed by data obtained from RDP4, RAT, population dynamics, and phylogenetic analyses. Reassortment analysis revealed that it might have happened in L segment of TSWV isolate YNKMXD (reported herein).
Conclusion
Taken together, this is the first detailed study revealing the pattern of TWSV genetic diversity, and population dynamics helping to better understand the ability of this pathogen to drastically reduce the tobacco production in China. Also, this is a valuable addition to the existing worldwide profile of TSWV, especially in China, where a few studies related to TSWV have been reported including only one complete genome of this virus isolated from tobacco plants.
Journal Article
Exploring the U.S. census : your guide to America's data
\"The United States census provides researchers, students, and the public with some of the richest and broadest information available about the American people. Exploring the U.S. Census by Frank Donnelly gives social science students and researchers alike the tools to understand, extract, process, and analyze data from the decennial census, the American Community Survey, and other data collected by the U.S. Census Bureau. More than just a data collection exercise performed every ten years, the census is a series of datasets updated on an ongoing basis. With all that data comes opportunities and challenges: opportunities to teach students the value of census data for studying communities and answering research questions, and the challenges of navigating and comprehending such a massive data source and transforming it into usable information that students and researchers can analyze with basic skills and software. Just as important as showing what the census can tell social researchers is showing how to ask good questions of census data. Exploring the U.S. Census provides a thorough background on the data collection methods, structures, and potential pitfalls of the census for unfamiliar researchers, collecting information previously available only in widely disparate sources into one handy guide. Hands-on, applied exercises at the end of the chapters help readers dive into the data\"-- Provided by publisher.
Book
Inferring Population Structure and Admixture Proportions in Low-Depth NGS Data
Meisner and Albrechtsen present two methods for inferring population structure and admixture proportions in low depth next-generation sequencing (NGS). NGS methods provide large amounts of genetic data but are associated with statistical uncertainty, especially for low-depth... We here present two methods for inferring population structure and admixture proportions in low-depth next-generation sequencing (NGS) data. Inference of population structure is essential in both population genetics and association studies, and is often performed using principal component analysis (PCA) or clustering-based approaches. NGS methods provide large amounts of genetic data but are associated with statistical uncertainty, especially for low-depth sequencing data. Models can account for this uncertainty by working directly on genotype likelihoods of the unobserved genotypes. We propose a method for inferring population structure through PCA in an iterative heuristic approach of estimating individual allele frequencies, where we demonstrate improved accuracy in samples with low and variable sequencing depth for both simulated and real datasets. We also use the estimated individual allele frequencies in a fast non-negative matrix factorization method to estimate admixture proportions. Both methods have been implemented in the PCAngsd framework available at http://www.popgen.dk/software/.
Journal Article
The sum of the people : how the census has shaped nations, from the ancient world to the modern age
Provides a 3,000-year history of the census, chronicling the practices of the ancient world through the Supreme Court rulings of today, examining how censuses have been used as tools of democracy, exclusion and mass surveillance.
Book
Utility of Radio-Telemetry Data for Improving Statistical Population Reconstruction
Statistical population reconstruction using age-at-harvest and catch-effort data has recently emerged as a robust and versatile approach to estimating the demographic dynamics of harvested populations of wildlife. Although there are clear benefits to incorporating radio-telemetry data into reconstruction efforts, these data are costly and time-consuming to collect. Managers that consider collecting these data alongside existing efforts could benefit from a comprehensive examination of how such benefits are influenced by the amount of radio-telemetry data collected. Using a harvested population of American marten (Martes americana) in northeastern Minnesota, USA as a case study, we investigated the performance of population reconstruction using information on natural, harvest, or combined mortality derived from radio-telemetry data collected over different numbers of years and with different numbers of animals collared each year. We simulated populations under a range of conditions and determined that incorporating radio-telemetry data on natural and harvest mortality significantly improved model precision, and that each additional animal collared per year yielded a 0.50 ± 0.14% (SE) improvement in precision, whereas every additional year of radio-telemetry data resulted in a 2.42 ± 0.70% improvement. Thus, including another year of radio-telemetry resulted in similar gains in precision as including approximately 5 additional animals collared per year. In our applied marten example, incorporating radio-telemetry data resulted in a significantly higher estimate of trapping vulnerability (0.20 vs. 0.058) and an overall smaller population size than reconstruction based solely on age-at-harvest and trapper effort data. These results illustrate the benefits of performing auxiliary studies, caution against relying on the results of population reconstruction based solely on age-at-harvest and hunter-effort data, and demonstrate that improvements from incorporating radio-telemetry data become evident even after as few as 2 years of data collection.
Journal Article
Prospective longevity : a new vision of population aging
\"The study of aging is not fundamentally about how old people are. It is about people's capabilities and their disabilities. In the field of population aging, measurements have generally been made with instruments devised many decades ago. Those measurements systems did not take the changing characteristics of older people into account. Using them 65-year-olds with a remaining life expectancy of 5 years could not be distinguished from 65-year-olds with a remaining life expectancy of 25 years. Although, in the past, those instruments did help us see better, it is now clear that there is a great deal that they did not allow us to see. Prospective Longevity provide a new view of who is old, how healthy people are in old age, the gender gap in survival at older ages, differences in patterns of survival across Russian regions and United States, the effects on the pace of population aging of medical breakthroughs that allow people to live much longer lives, and how an intergenerationally equitable pension age should change as life expectancy increases\"-- Provided by publisher.
Book
Utility of Particle Swarm Optimization in Statistical Population Reconstruction
Statistical population reconstruction models based on maximum likelihood and minimum chi-square objective functions provide a robust and versatile approach to estimating the demographic dynamics of harvested populations of wildlife. These models employ numerical optimization techniques to determine which set of model parameters best describes observed age-at-harvest, catch-effort, and other auxiliary field data. Although numerous optimization methods have been used in the past, the benefits of using particle swarm optimization (PSO) have yet to be explored. Using a harvested population of North American river otter (Lontra canadensis) in Indiana as a case study, we investigated the performance of population reconstruction using particle swarm optimization, spectral projected gradient (SPG), Nelder–Mead, and Broyden–Fletcher–Goldfarb–Shanno (BFGS) methods. We used Monte Carlo studies to simulate populations under a wide range of conditions to compare the relative performance of population reconstruction models using each of the four optimization methods. We found that using particle swarm optimization consistently and significantly improved model stability and precision when compared with other numerical optimization methods that may be used in statistical population reconstruction. Given that these models are frequently used to guide management decisions and set harvest limits, we encourage management agencies to adopt this more precise method of estimating model parameters and corresponding population abundance. These results illustrate the benefits of using particle swarm optimization, caution against relying on the results of population reconstruction based on optimization methods that are highly dependent on initial conditions, and reinforce the need to ensure model convergence to a global rather than a local maximum.
Journal Article