Variance additivity of genetic populational parameter estimates obtained through bootstrapping

Studying the genetic structure of natural populations is very important for conservation and use of the genetic variability available in nature. This research is related to genetic population structure analysis using real and simulated molecular data. To obtain variance estimates of pertinent parameters, the bootstrap resampling procedure was applied over different sampling units, namely: individuals within populations (I), populations (P), and individuals and populations simultaneously (I, P). The considered parameters were: the total fixation index (F or F IT), the fixation index within populations (f or F IS) and the divergence among populations or intrapopulation coancestry (theta or F ST). The aim of this research was to verify if the variance estimates of <IMG SRC="/img/fbpe/sa/v60n1/14549x09.gif">, <IMG SRC="/img/fbpe/sa/v60n1/14549x10.gif">and <IMG SRC="/img/fbpe/sa/v60n1/14549x11.gif">, found through the resampling over individuals and populations simultaneously (I, P), correspond to the sum of the respective variance estimates obtained from separated resampling over individuals and populations (I+P). This equivalence was verified in all cases, showing that the total variance estimate of <IMG SRC="/img/fbpe/sa/v60n1/14549x09.gif">, <IMG SRC="/img/fbpe/sa/v60n1/14549x10.gif">and <IMG SRC="/img/fbpe/sa/v60n1/14549x11.gif">can be obtained summing up the variances estimated for each source of variation separately. Results also showed that this facilitates the use of the bootstrap method on data with hierarchical structure and opens the possibility of obtaining the relative contribution of each source of variation to the total variation of estimated parameters.

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Population Genetic Diversity and Structure of an Endangered Salicaceae Species in Northeast China: Chosenia arbutifolia (Pall.) A. Skv.

Forests ◽

10.3390/f12091282 ◽

2021 ◽

Vol 12 (9) ◽

pp. 1282

Author(s):

Yu Wang ◽

Zhongyi Jiao ◽

Jiwei Zheng ◽

Jie Zhou ◽

Baosong Wang ◽

...

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Management Strategies ◽

Natural Populations ◽

Snp Markers ◽

Fixation Index ◽

Landscape Genomics ◽

Population Structure Analysis ◽

Genetic Diversity And Structure ◽

Chosenia Arbutifolia

Chosenia arbutifolia (Pall.) A. Skv. is a unique and endangered species belonging to the Salicaceae family. It has great potential for ornamental and industrial use. However, human interference has led to a decrease in and fragmentation of its natural populations in the past two decades. To effectively evaluate, utilize, and conserve available resources, the genetic diversity and population structure of C. arbutifolia were analyzed in this study. A total of 142 individuals from ten provenances were sampled and sequenced. Moderate diversity was detected among these, with a mean expected heterozygosity and Shannon’s Wiener index of 0.3505 and 0.5258, respectively. The inbreeding coefficient was negative, indicating a significant excess of heterozygotes. The fixation index varied from 0.0068 to 0.3063, showing a varied genetic differentiation between populations. Analysis of molecular variance demonstrated that differentiation accounted for 82.23% of the total variation among individuals, while the remaining 17.77% variation was between populations. Furthermore, the results of population structure analysis indicated that the 142 individuals originated from three primitive groups. To provide genetic information and help design conservation and management strategies, landscape genomics analysis was performed by investigating loci associated with environmental variables. Eighteen SNP markers were associated with altitude and annual average temperature, of which five were ascribed with specific functions. In conclusion, the current study furthers the understanding of C. arbutifolia genetic architecture and provides insights for germplasm protection.

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Evaluation of Inter-Observer Reliability of Animal Welfare Indicators: Which Is the Best Index to Use?

Animals ◽

10.3390/ani11051445 ◽

2021 ◽

Vol 11 (5) ◽

pp. 1445

Author(s):

Mauro Giammarino ◽

Silvana Mattiello ◽

Monica Battini ◽

Piero Quatto ◽

Luca Maria Battaglini ◽

...

Keyword(s):

Animal Welfare ◽

Confidence Intervals ◽

Bootstrap Method ◽

Dairy Goat ◽

Microsoft Excel ◽

Bootstrap Methods ◽

Welfare Indicators ◽

Observer Reliability ◽

High Concordance ◽

Variance Estimates

This study focuses on the problem of assessing inter-observer reliability (IOR) in the case of dichotomous categorical animal-based welfare indicators and the presence of two observers. Based on observations obtained from Animal Welfare Indicators (AWIN) project surveys conducted on nine dairy goat farms, and using udder asymmetry as an indicator, we compared the performance of the most popular agreement indexes available in the literature: Scott’s π, Cohen’s k, kPABAK, Holsti’s H, Krippendorff’s α, Hubert’s Γ, Janson and Vegelius’ J, Bangdiwala’s B, Andrés and Marzo’s ∆, and Gwet’s γ(AC1). Confidence intervals were calculated using closed formulas of variance estimates for π, k, kPABAK, H, α, Γ, J, ∆, and γ(AC1), while the bootstrap and exact bootstrap methods were used for all the indexes. All the indexes and closed formulas of variance estimates were calculated using Microsoft Excel. The bootstrap method was performed with R software, while the exact bootstrap method was performed with SAS software. k, π, and α exhibited a paradoxical behavior, showing unacceptably low values even in the presence of very high concordance rates. B and γ(AC1) showed values very close to the concordance rate, independently of its value. Both bootstrap and exact bootstrap methods turned out to be simpler compared to the implementation of closed variance formulas and provided effective confidence intervals for all the considered indexes. The best approach for measuring IOR in these cases is the use of B or γ(AC1), with bootstrap or exact bootstrap methods for confidence interval calculation.

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Wolbachia and Cytoplasmic Incompatibility in the CaliforniaCulex pipiensMosquito Species Complex: Parameter Estimates and Infection Dynamics in Natural Populations

Genetics ◽

10.1093/genetics/165.4.2029 ◽

2003 ◽

Vol 165 (4) ◽

pp. 2029-2038 ◽

Cited By ~ 3

Author(s):

Jason L Rasgon ◽

Thomas W Scott

Keyword(s):

Species Complex ◽

Cytoplasmic Incompatibility ◽

Natural Populations ◽

Wolbachia Infection ◽

Field Conditions ◽

Parameter Estimates ◽

Infection Prevalence ◽

Infection Frequency ◽

Specific Pcr ◽

Vector Borne

AbstractBefore maternally inherited bacterial symbionts like Wolbachia, which cause cytoplasmic incompatibility (CI; reduced hatch rate) when infected males mate with uninfected females, can be used in a program to control vector-borne diseases it is essential to understand their dynamics of infection in natural arthropod vector populations. Our study had four goals: (1) quantify the number of Wolbachia strains circulating in the California Culex pipiens species complex, (2) investigate Wolbachia infection frequencies and distribution in natural California populations, (3) estimate the parameters that govern Wolbachia spread among Cx. pipiens under laboratory and field conditions, and (4) use these values to estimate equilibrium levels and compare predicted infection prevalence levels to those observed in nature. Strain-specific PCR, wsp gene sequencing, and crossing experiments indicated that a single Wolbachia strain infects Californian Cx. pipiens. Infection frequency was near or at fixation in all populations sampled for 2 years along a >1000-km north-south transect. The combined statewide infection frequency was 99.4%. Incompatible crosses were 100% sterile under laboratory and field conditions. Sterility decreased negligibly with male age in the laboratory. Infection had no significant effect on female fecundity under laboratory or field conditions. Vertical transmission was >99% in the laboratory and ∼98.6% in the field. Using field data, models predicted that Wolbachia will spread to fixation if infection exceeds an unstable equilibrium point above 1.4%. Our estimates accurately predicted infection frequencies in natural populations. If certain technical hurdles can be overcome, our data indicate that Wolbachia can invade vector populations as part of an applied transgenic strategy for vector-borne disease reduction.

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Comparison of complex networks and tree-based methods of phylogenetic analysis and proposal of a bootstrap method

PeerJ ◽

10.7717/peerj.4349 ◽

2018 ◽

Vol 6 ◽

pp. e4349 ◽

Cited By ~ 3

Author(s):

Aristóteles Góes-Neto ◽

Marcelo V.C. Diniz ◽

Daniel S. Carvalho ◽

Gilberto C. Bomfim ◽

Angelo A. Duarte ◽

...

Keyword(s):

Biological Sciences ◽

Phylogenetic Analysis ◽

Complex Networks ◽

Complex Network ◽

Bootstrap Method ◽

Molecular Data ◽

Data Sets ◽

Fungal Cell ◽

Taxonomic Groups ◽

Inference Methods

Complex networks have been successfully applied to the characterization and modeling of complex systems in several distinct areas of Biological Sciences. Nevertheless, their utilization in phylogenetic analysis still needs to be widely tested, using different molecular data sets and taxonomic groups, and, also, by comparing complex networks approach to current methods in phylogenetic analysis. In this work, we compare all the four main methods of phylogenetic analysis (distance, maximum parsimony, maximum likelihood, and Bayesian) with a complex networks method that has been used to provide a phylogenetic classification based on a large number of protein sequences as those related to the chitin metabolic pathway and ATP-synthase subunits. In order to perform a close comparison to these methods, we selected Basidiomycota fungi as the taxonomic group and used a high-quality, manually curated and characterized database of chitin synthase sequences. This enzymatic protein plays a key role in the synthesis of one of the exclusive features of the fungal cell wall: the presence of chitin. The communities (modules) detected by the complex network method corresponded exactly to the groups retrieved by the phylogenetic inference methods. Additionally, we propose a bootstrap method for the complex network approach. The statistical results we have obtained with this method were also close to those obtained using traditional bootstrap methods.

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Models for Expected Returns with Statistical Factors

Journal of Risk and Financial Management ◽

10.3390/jrfm13120314 ◽

2020 ◽

Vol 13 (12) ◽

pp. 314

Author(s):

José Manuel Cueto ◽

Aurea Grané ◽

Ignacio Cascos

Keyword(s):

Time Series ◽

Coefficient Of Variation ◽

Stock Prices ◽

Bootstrap Method ◽

Block Bootstrap ◽

Time Series Regression ◽

Cross Sectional ◽

Multifactor Models ◽

Two Factors ◽

Resampling Procedure

In this paper, we propose multifactor models for the pan-European Equity Market using a block-bootstrap method and compare the results with those of traditional inferential techniques. The new factors are built from statistical measurements on stock prices—in particular, coefficient of variation, skewness, and kurtosis. Data come from Reuters, correspond to nearly 2000 EU companies, and span from January 2008 to February 2018. Regarding methodology, we propose a non-parametric resampling procedure that accounts for time dependency in order to test the validity of the model and the significance of the parameters involved. We compare our bootstrap-based inferential results with classical proposals (based on F-statistics). Methods under assessment are time-series regression, cross-sectional regression, and the Fama–MacBeth procedure. The main findings indicate that the two factors that better improve the Capital Asset Pricing Model with regard to the adjusted R2 in the time-series regressions are the skewness and the coefficient of variation. For this reason, a model including those two factors together with the market is thoroughly studied. We also observe that our block-bootstrap methodology seems to be more conservative with the null of the GRS test than classical procedures.

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A quantitative genetic analysis of fitness and its components in Drosophila melanogaster

Genetics Research ◽

10.1017/s0016672300024526 ◽

1986 ◽

Vol 47 (1) ◽

pp. 59-70 ◽

Cited By ~ 50

Author(s):

Trudy F. C. Mackay

Keyword(s):

Drosophila Melanogaster ◽

Natural Populations ◽

Strongly Correlated ◽

Wild Type ◽

Relative Contribution ◽

Quantitative Characters ◽

Quantitative Genetic ◽

Bristle Number ◽

Metric Traits ◽

Average Fitness

SummaryForty-one third chromosomes extracted from a natural population of Drosophila melanogaster were assessed for net fitness and for the quantitative characters viability, net fertility, female productivity, male weight, abdominal bristle number, and sternopleural bristle number. Net homozygous and heterozygous fitness of the third chromosomes was estimated by competition against a marked balancer third chromosome. Average fitness of the homozygous lines relative to wild-type heterozygotes was 0·13, indicating substantial inbreeding depression for net fitness. All significant correlations of quantitative characters with fitness and with each other were high and positive. Homozygous fitness is strongly correlated with net fertility, viability, and female productivity, moderately associated with male weight, and not significantly associated with bristle traits. The combination of metric traits which best predicts homozygous fitness is the simple multiple of viability and female productivity. Heterozygous fitness is not correlated with homozygous fitness; furthermore, the relative contribution of metric traits to fitness in a heterozygous population is likely to be different from that deduced from homozygous lines. These observations are consistent with a model of genetic variation for fitness in natural populations caused by segregation of rare deleterious recessive alleles.

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Influence of Swiss needle cast on foliage age-class structure and vertical foliage distribution in Douglas-fir plantations in north coastal Oregon

Canadian Journal of Forest Research ◽

10.1139/x06-044 ◽

2006 ◽

Vol 36 (6) ◽

pp. 1497-1508 ◽

Cited By ~ 17

Author(s):

Aaron R Weiskittel ◽

Douglas A Maguire ◽

Sean M Garber ◽

Alan Kanaskie

Keyword(s):

Vertical Distribution ◽

Douglas Fir ◽

Parameter Estimates ◽

Class Structure ◽

Needle Cast ◽

Age Class ◽

Relative Contribution ◽

Crown Structure ◽

Growth Decline ◽

Swiss Needle Cast

Swiss needle cast (SNC) causes premature loss of foliage and subsequent growth decline in Douglas-fir (Pseudotsuga menziesii (Mirb.) Franco). Although the mechanisms leading to this growth decline include loss of photosynthetic surface area and physiological disruption of surviving foliage, estimating the relative contribution of these two primary sources requires precise quantification of SNC effects on total foliage mass, foliage age-class structure, and vertical foliage distribution. The effect of SNC severity on these crown structural attributes was tested across a range of stand densities and site qualities in 10- to 60-year-old plantations in north coastal Oregon. Foliage mass in each age-class was sampled at the branch level, and the resulting equations were applied to all live branches on intensively measured sample trees. Vertical distribution of each foliage age-class was described by a beta distribution fitted to each sample tree, and sources of variation in vertical distribution were tested by regressing beta parameter estimates on SNC intensity and other covariates representing tree, stand, and site attributes. Distribution of foliage mass by age-class and by relative height in the crown was significantly affected by SNC severity, in addition to other covariates such as crown size and tree social position. SNC caused a reduction in the amount of foliage in each age-class and greater relative representation of younger needles. SNC also shifted the mode of relative vertical distribution toward the top of the tree for the three youngest foliage age-classes, but toward the base of the crown for 4- and 5-year-old foliage. Quantification of foliage age-class structure and vertical distribution across a range of SNC severity has helped to establish diagnostic criteria for assessing changes in crown structure that precede declines in growth and vigor. The induced changes in crown structure will also help to identify the relative contribution of several mechanisms causing growth losses in diseased trees.

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Microsatellite analysis to rationalize grape germplasm in India and development of a molecular database

Plant Genetic Resources ◽

10.1017/s1479262113000117 ◽

2013 ◽

Vol 11 (3) ◽

pp. 225-233 ◽

Cited By ~ 2

Author(s):

Anuradha Upadhyay ◽

Lalitkumar B. Aher ◽

Manisha P. Shinde ◽

Kavita Y. Mundankar ◽

Anuj Datre ◽

...

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Molecular Data ◽

Computer Application ◽

Parental Genotype ◽

Application Software ◽

Microsatellite Data ◽

Population Structure Analysis ◽

Varietal Improvement ◽

User Friendly

Three hundred and seventeen grape accessions from the National Active Grape Germplasm Site in India were analysed with 25 microsatellite markers. A total of 411 alleles were detected, of which 42% were rare alleles. Unique alleles for 56 genotypes were also identified. The analysis of microsatellite data identified 63 duplicate accessions and only 254 accessions were unique genotypes. Several cases of misnomers, synonymy and homonymy were identified. Parental genotype for a few clonal selections was ascertained. Population structure analysis grouped 254 unique genotypes into four major clusters. The analysis also revealed the presence of admixtures with only 79% of pure ancestry. A core collection comprising 80 genotypes was identified, which represented all the alleles and genetic diversity. A user-friendly and interactive computer application software was developed for storage and the retrieval of molecular data. A molecular database for the 254 genotypes was created. This analysis will help in the rationalization and better management of germplasm. Information on genetic diversity and population structure will form the basis for varietal improvement programmes.

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