On the bias of recombination fractions, Kosambi's and Haldane's distances based on frequencies of gametes

Genome ◽  
2011 ◽  
Vol 54 (3) ◽  
pp. 196-201 ◽  
Author(s):  
Manfred Huehn
Keyword(s):  
Genetic Mapping ◽  
Recombination Fraction ◽  
Positive Bias ◽  
Linkage Maps ◽  
Sample Sizes ◽  
Mapping Functions ◽  
Crucial Step ◽  
Additive Map ◽  
Wide Range ◽  
Binomial Function

The estimation of recombination frequencies is a crucial step in genetic mapping. For the construction of linkage maps, nonadditive recombination fractions must be transformed into additive map distances. Two of the most commonly used transformations are Kosambi’s and Haldane’s mapping functions. This paper reports on the calculation of the bias associated with estimation of recombination fractions, Kosambi’s distances, and Haldane’s distances. I calculated absolute and relative biases numerically for a wide range of recombination fractions and sample sizes. I assumed that the ratio of recombinant gametes to the total number of gametes can be adequately represented by a binomial function. I found that the bias in recombination fraction estimates is negative, i.e., the estimator is an underestimate. However, significant values were only obtained when recombination fractions were large and sample sizes were small. The relevant estimates of recombination fractions were, therefore, nearly unbiased. Haldane’s and Kosambi’s distances were found to be strongly biased, with positive bias for the most interesting values of recombination fractions and sample sizes. The bias of Kosambi’s distance was considerably smaller than the bias of Haldane’s distance.

scholarly journals Combatting Vitamin A deficiency

2017 ◽  
Vol 8 (2) ◽  
pp. 151 ◽  
Author(s):  
Ted H Greiner
Keyword(s):  
Vitamin A ◽  
Vitamin A Deficiency ◽  
Economic Benefits ◽  
Point Of View ◽  
Preschool Age ◽  
High Dose ◽  
Sample Sizes ◽  
Sweet Potatoes ◽  
Target Groups ◽  
Wide Range

Food-based approaches to combat vitamin A deficiency (VAD) continue to be largely ignored by governments and donor agencies. This review deals with common misperceptions as well as constraints that may lay behind this reality. First, high-dose vitamin A capsules provided to preschool age children are no solution for VAD. Second, researchers may assume that it is not possible to standardize foods adequately to study their efficacy in controlled trials. This review summarizes the results of 57 such trials, providing an overview that may assist researchers in making decisions on target groups to study, types of food supplements to provide, quantities, supplementation periods, impacts that are realistic to expect, and sample sizes. Even more complex is to design efficacy trials or impact evaluations of interventions. Again, the paper reviews 40 such trials, providing summary information on approaches, target groups, sample sizes, periods of intervention, and impacts measured using a variety of indicators. There are a number of barriers or constraints that must be planned for and overcome if food-based approaches are to work. This paper reviews several of the most important ones, briefly touching on many of the most effective ways that have been found to overcome them. Food-based approaches can reach all members of the community, are safe for pregnant women, tend to be at least partially sustainable, and confer a wide range of nutritional and other benefits in addition to improving vitamin A status. Food-based approaches are sometimes described as expensive, but this is based on a narrow view. For example, biofortification and dissemination of sweet potatoes cost $9 to $30 per disability-life-year (DALY) gained, while that from VAS was estimated at the estimated cost effectiveness of VAS is $73 per DALY gained. From the community point of view, the economic benefits of food based approaches are likely to subsidize or outweigh their costs.

scholarly journals DYNAMICS OF THE LINKAGE DISEQUILIBRIUM FUNCTION UNDER MODELS OF GENE-FREQUENCY HITCHHIKING

Genetics ◽  
1981 ◽  
Vol 99 (2) ◽  
pp. 337-356
Author(s):  
Marjorie A Asmussen ◽  
Michael T Clegg
Keyword(s):  
Linkage Disequilibrium ◽  
Gene Frequency ◽  
Initial Conditions ◽  
Recombination Fraction ◽  
Qualitative Description ◽  
Selection Intensity ◽  
Gene Frequencies ◽  
Dependent Behavior ◽  
Wide Range ◽  
Over Time

ABSTRACT The dynamic behavior of the linkage disequilibrium (D) between a neutral and a selected locus is analyzed for a variety of deterministic selection models. The time-dependent behavior of D is governed by the gene frequency at the selected locus (p) and by the selection (s) and recombination (r) parameters. Thomson (1977) showed numerically that D may increase under certain initial conditions. We give exact conditions for D to increase in time, which require that the selection intensity exceed the recombination fraction (s > r) and that p be near zero or one. We conclude from this result that gene frequency hitchhiking is most likely to be important when a new favorable mutant enters a population. We also show that, for what can be a wide range of gene frequencies, D will decay at a faster rate than the neutral rate. Consequently, the hitchhiking effect may quickly diminish as the selected gene becomes more common.—The method of analysis allows a complete qualitative description of the dynamics of D as a function of s and r. Two major findings concern the range of gene frequencies at the selected locus for which D either increases over time or decays at a faster rate than under neutrality. For all models considered, the region where D increases (i) first enlarges then shrinks as selection intensifies, and (ii) steadily shrinks as r increases. In contrast, the region of accelerated decay constantly enlarges as the selection intensity increases. This region will either shrink or enlarge as r increases, depending upon the form of selection in force.

scholarly journals SSR Markers for Analysing South American Nothofagus Species

2004 ◽  
Vol 53 (1-6) ◽  
pp. 240-243 ◽  
Author(s):  
M. M. Azpilicueta ◽  
H. Caron ◽  
C. Bodénès ◽  
L. A. Gallo
Keyword(s):  
Gene Flow ◽  
Genetic Mapping ◽  
Microsatellite Markers ◽  
Ssr Markers ◽  
Natural Populations ◽  
South American ◽  
Sample Sizes ◽  
Polymorphic Ssrs ◽  
The Cross ◽  
Qualitative Confirmation

Summary11 newly discovered microsatellites were used to identify SSR markers for characterising South American Nothofagus species. This was carried out in six species. The sample sizes used were between four and six individuals per species. The cross-genera transferability of 34 Quercus SSRs was also essayed. Out of the 11 new microsatellite markers, three proved to be polymorphic (NnBIO 11, NgBIO 13 and NgBIO 14). The qualitative confirmation of the inheritance of these markers could also be verified. Polymorphism was also observed in five of the cross-genera transferred SSRs (QrBIO7, quru-GA-0A01, quru-GA-0C11, quru-GA-0I01, quru-GA-0M07). The number of alleles per locus found range between 1 and 6 per species. The eight polymorphic SSRs identified in this study will constitute a valuable tool in the gene flow studies that are currently being carried out in natural populations of South American Nothofagus species. The confirmation of crossspecies and cross-genera transferability opens the way for the use of SSRs as bridge markers in genetic mapping.

scholarly journals Analytical guidelines to increase the value of citizen science data: using eBird data to estimate species occurrence

2019 ◽  
Author(s):  
A Johnston ◽  
WM Hochachka ◽  
ME Strimas-Mackey ◽  
V Ruiz Gutierrez ◽  
OJ Robinson ◽  
...  
Keyword(s):  
Data Processing ◽  
Citizen Science ◽  
Model Performance ◽  
Species Distributions ◽  
Ecological Knowledge ◽  
Sample Sizes ◽  
Science Data ◽  
Science Projects ◽  
Wide Range ◽  
The Impact

AbstractCitizen science data are valuable for addressing a wide range of ecological research questions, and there has been a rapid increase in the scope and volume of data available. However, data from large-scale citizen science projects typically present a number of challenges that can inhibit robust ecological inferences. These challenges include: species bias, spatial bias, and variation in effort.To demonstrate addressing key challenges in analysing citizen science data, we use the example of estimating species distributions with data from eBird, a large semi-structured citizen science project. We estimate two widely applied metrics of species distributions: encounter rate and occupancy probability. For each metric, we assess the impact of data processing steps that either degrade or refine the data used in the analyses. We also test whether differences in model performance are maintained at different sample sizes.Model performance improved when data processing and analytical methods addressed the challenges arising from citizen science data. The largest gains in model performance were achieved with: 1) the use of complete checklists (where observers report all the species they detect and identify); and 2) the use of covariates describing variation in effort and detectability for each checklist. Occupancy models were more robust to a lack of complete checklists and effort variables. Improvements in model performance with data refinement were more evident with larger sample sizes.Here, we describe processes to refine semi-structured citizen science data to estimate species distributions. We demonstrate the value of complete checklists, which can inform the design and adaptation of citizen science projects. We also demonstrate the value of information on effort. The methods we have outlined are also likely to improve other forms of inference, and will enable researchers to conduct robust analyses and harness the vast ecological knowledge that exists within citizen science data.

scholarly journals A MATHEMATICALLY TRACTABLE FAMILY OF GENETIC MAPPING FUNCTIONS WITH DIFFERENT AMOUNTS OF INTERFERENCE

Genetics ◽  
1979 ◽  
Vol 91 (4) ◽  
pp. 769-775
Author(s):  
Joseph Felsenstein
Keyword(s):  
Genetic Mapping ◽  
Simple Rule ◽  
Negative Interference ◽  
Mapping Functions ◽  
Special Cases ◽  
The Family

ABSTRACT By extension of the argument of KOSAMBI (1944), a family of mapping functions can be derived, which has a parameter regulating the intensity of interference. Different values of this parameter yield the HALDANE (1919) and KOSAMBI mapping functions as special cases. The parameter is the coincidence coefficient for nearby small intervals. The family includes mapping functions for negative interference. A simple rule for combining recombination fractions in adjacent intervals is also obtained.

scholarly journals Comparative evaluation of goodness of fit tests for normal distribution using simulation and empirical data

2020 ◽  
Vol 57 (2) ◽  
pp. 237-251
Author(s):  
Achilleas Anastasiou ◽  
Alex Karagrigoriou ◽  
Anastasios Katsileros
Keyword(s):  
Sample Size ◽  
Normal Distribution ◽  
Empirical Data ◽  
Goodness Of Fit ◽  
Small Sample Size ◽  
Small Sample ◽  
Type I ◽  
Sample Sizes ◽  
Omnibus Test ◽  
Wide Range

SummaryThe normal distribution is considered to be one of the most important distributions, with numerous applications in various fields, including the field of agricultural sciences. The purpose of this study is to evaluate the most popular normality tests, comparing the performance in terms of the size (type I error) and the power against a large spectrum of distributions with simulations for various sample sizes and significance levels, as well as through empirical data from agricultural experiments. The simulation results show that the power of all normality tests is low for small sample size, but as the sample size increases, the power increases as well. Also, the results show that the Shapiro–Wilk test is powerful over a wide range of alternative distributions and sample sizes and especially in asymmetric distributions. Moreover the D’Agostino–Pearson Omnibus test is powerful for small sample sizes against symmetric alternative distributions, while the same is true for the Kurtosis test for moderate and large sample sizes.

scholarly journals Tests for a Single Upper Outlier in a Johnson SB Sample with Unknown Parameters

2021 ◽  
Vol 9 (1) ◽  
pp. 1-3
Author(s):  
Tanuja Sriwastava ◽  
Mukti Kant Sukla
Keyword(s):  
Outlier Detection ◽  
Critical Points ◽  
Sample Sizes ◽  
Test Statistic ◽  
Unknown Parameters ◽  
Numerical Example ◽  
Wide Range ◽  
Challenging Tasks ◽  
Level Of Significance

Outliers are unexpected observations, which deviate from the majority of observations. Outlier detection and prediction are challenging tasks, because outliers are rare by definition. A test statistic for single upper outlier is proposed and applied to Johnson SB sample with unknown parameters. The Johnson SB distribution have four parameters and is extremely flexible, which means that it can fit a wide range of distribution shapes. Because of its distributional shapes it has a variety of applications in many fields. The test statistic proposed for the case when parameters are known (Sriwastava, T., 2018) used here for developing the test statistic when parameters are unknown. Critical points were calculated for different sample sizes and for different level of significance. The performance of the test in the presence of a single upper outlier is investigated. One numerical example was given for highlighting the result.

Analysis of Repeated Measures Under Second-Stage Sphericity: An Empirical Bayes Approach

1997 ◽  
Vol 22 (2) ◽  
pp. 155-192 ◽  
Author(s):  
Robert J. Boik
Keyword(s):  
Multivariate Analysis ◽  
Sample Size ◽  
Covariance Matrix ◽  
Repeated Measures ◽  
Empirical Bayes ◽  
Univariate Analysis ◽  
Sample Sizes ◽  
Multivariate Test ◽  
Orthogonal Contrasts ◽  
Wide Range

The conventional multivariate analysis of repeated measures is applicable in a wide variety of circumstances, in part, because assumptions regarding the pattern of covariances among the repeated measures are not required. If sample sizes are small, however, then the estimators of the covariance parameters lack precision and, as a result, the power of the multivariate analysis is low. If the covariance matrix associated with estimators of orthogonal contrasts is spherical, then the conventional univariate analysis of repeated measures is applicable and has greater power than the multivariate analysis. If sphericity is not satisfied, an adjusted univariate analysis can be conducted, and this adjusted analysis may still be more powerful than the multivariate analysis. As sample size increases, the power advantage of the adjusted univariate test decreases, and, for moderate sample sizes, the multivariate test can be more powerful. This article proposes a hybrid analysis that takes advantage of the strengths of each of the two procedures. The proposed analysis employs an empirical Bayes estimator of the covariance matrix. Existing software for conventional multivariate analyses can, with minor modifications, be used to perform the proposed analysis. The new analysis behaves like the univariate analysis when samples size is small or sphericity is nearly satisfied. When sample size is large or sphericity is strongly violated, then the proposed analysis behaves like the multivariate analysis. Simulation results suggest that the proposed analysis controls test size adequately and can be more powerful than either of the other two analyses under a wide range of non-null conditions.

scholarly journals Linkage mapping of sex-specific differences

2002 ◽  
Vol 79 (1) ◽  
pp. 85-96 ◽  
Author(s):  
RONGLING WU ◽  
CHANG-XING MA ◽  
S. S. WU ◽  
ZHAO-BANG ZENG
Keyword(s):  
Molecular Markers ◽  
Numerical Analysis ◽  
Gene Mapping ◽  
Meiotic Recombination ◽  
Linkage Mapping ◽  
Recombination Fraction ◽  
Linkage Maps ◽  
Information Functions ◽  
Marker Loci ◽  
Asymptotic Variances

Most current linkage analyses assume identical fractions of meiotic recombination between homologous marker loci of the two sexes. This assumption is not realistic, because considerable sex-related differences have been observed in recombination fraction. In this paper, a general EM-based algorithm is presented to estimate sex-specific recombination fractions for a mixed set of molecular markers segregating differently in a full-sib family derived from two heterozygous parents. The asymptotic variances of the estimates of linkage specifically for each of the parents are evaluated using a numerical analysis based on information functions. This approach will have important implications for precise gene mapping based on sex-specific linkage maps.

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