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Allele Frequency Spectrum
In population genetics, the allele frequency spectrum, sometimes called the site frequency spectrum, is the distribution of the allele frequencies of a given set of loci (often SNPs) in a population or sample. Because an allele frequency spectrum is often a summary of or compared to sequenced samples of the whole population, it is a histogram with size depending on the number of sequenced individual chromosomes. Each entry in the frequency spectrum records the total number of loci with the corresponding derived allele frequency. Loci contributing to the frequency spectrum are assumed to be independently changing in frequency. Furthermore, loci are assumed to be biallelic (that is, with exactly two alleles present), although extensions for multiallelic frequency spectra exist. Many summary statistics of observed genetic variation are themselves summaries of the allele frequency spectrum, including estimates of \theta such as Watterson's \theta_W and Tajima's \theta_\pi , Ta ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Population Genetics
Population genetics is a subfield of genetics that deals with genetic differences within and between populations, and is a part of evolutionary biology. Studies in this branch of biology examine such phenomena as Adaptation (biology), adaptation, speciation, and population stratification, population structure. Population genetics was a vital ingredient in the emergence of the Modern synthesis (20th century), modern evolutionary synthesis. Its primary founders were Sewall Wright, J. B. S. Haldane and Ronald Fisher, who also laid the foundations for the related discipline of quantitative genetics. Traditionally a highly mathematical discipline, modern population genetics encompasses theoretical, laboratory, and field work. Population genetic models are used both for statistical inference from DNA sequence data and for proof/disproof of concept. What sets population genetics apart from newer, more phenotypic approaches to modelling evolution, such as evolutionary game theory and evo ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Fixation Index
The fixation index (FST) is a measure of population differentiation due to genetic structure. It is frequently estimated from genetic polymorphism data, such as single-nucleotide polymorphisms (SNP) or microsatellites. Developed as a special case of Wright's F-statistics, it is one of the most commonly used statistics in population genetics. Definition Two of the most commonly used definitions for FST at a given locus are based on 1) the variance of allele frequencies between populations, and on 2) the probability of Identity by descent. If \bar is the average frequency of an allele in the total population, \sigma^2_S is the variance in the frequency of the allele between different subpopulations, weighted by the sizes of the subpopulations, and \sigma^2_T is the variance of the allelic state in the total population, FST is defined as : F_ = \frac = \frac Wright's definition illustrates that FST measures the amount of genetic variance that can be explained by population stru ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Out Of Africa Hypothesis
In paleoanthropology, the recent African origin of modern humans, also called the "Out of Africa" theory (OOA), recent single-origin hypothesis (RSOH), replacement hypothesis, or recent African origin model (RAO), is the dominant model of the geographic origin and early migration of anatomically modern humans (''Homo sapiens''). It follows the early expansions of hominins out of Africa, accomplished by ''Homo erectus'' and then '' Homo neanderthalensis''. The model proposes a "single origin" of ''Homo sapiens'' in the taxonomic sense, precluding parallel evolution in other regions of traits considered anatomically modern, but not precluding multiple admixture between ''H. sapiens'' and archaic humans in Europe and Asia. ''H. sapiens'' most likely developed in the Horn of Africa between 300,000 and 200,000 years ago, although an alternative hypothesis argues that diverse morphological features of ''H. sapiens'' appeared locally in different parts of Africa and converged due ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Population Bottleneck
A population bottleneck or genetic bottleneck is a sharp reduction in the size of a population due to environmental events such as famines, earthquakes, floods, fires, disease, and droughts; or human activities such as specicide, widespread violence or intentional culling, and human population planning. Such events can reduce the variation in the gene pool of a population; thereafter, a smaller population, with a smaller genetic diversity, remains to pass on genes to future generations of offspring through sexual reproduction. Genetic diversity remains lower, increasing only when gene flow from another population occurs or very slowly increasing with time as random mutations occur. This results in a reduction in the robustness of the population and in its ability to adapt to and survive selecting environmental changes, such as climate change or a shift in available resources. Alternatively, if survivors of the bottleneck are the individuals with the greatest genetic fitness, the ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Maximum Likelihood
In statistics, maximum likelihood estimation (MLE) is a method of estimating the parameters of an assumed probability distribution, given some observed data. This is achieved by maximizing a likelihood function so that, under the assumed statistical model, the observed data is most probable. The point in the parameter space that maximizes the likelihood function is called the maximum likelihood estimate. The logic of maximum likelihood is both intuitive and flexible, and as such the method has become a dominant means of statistical inference. If the likelihood function is differentiable, the derivative test for finding maxima can be applied. In some cases, the first-order conditions of the likelihood function can be solved analytically; for instance, the ordinary least squares estimator for a linear regression model maximizes the likelihood when all observed outcomes are assumed to have Normal distributions with the same variance. From the perspective of Bayesian infere ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Goodness Of Fit
The goodness of fit of a statistical model describes how well it fits a set of observations. Measures of goodness of fit typically summarize the discrepancy between observed values and the values expected under the model in question. Such measures can be used in statistical hypothesis testing, e.g. to test for normality of residuals, to test whether two samples are drawn from identical distributions (see Kolmogorov–Smirnov test), or whether outcome frequencies follow a specified distribution (see Pearson's chi-square test). In the analysis of variance, one of the components into which the variance is partitioned may be a lack-of-fit sum of squares. Fit of distributions In assessing whether a given distribution is suited to a data-set, the following tests and their underlying measures of fit can be used: * Bayesian information criterion *Kolmogorov–Smirnov test *Cramér–von Mises criterion *Anderson–Darling test * Shapiro–Wilk test *Chi-squared test * Akaike informa ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Outgroup (cladistics)
In cladistics or phylogenetics, an outgroup is a more distantly related group of organisms that serves as a reference group when determining the evolutionary relationships of the ingroup, the set of organisms under study, and is distinct from sociological outgroups. The outgroup is used as a point of comparison for the ingroup and specifically allows for the phylogeny to be rooted. Because the polarity (direction) of character change can be determined only on a rooted phylogeny, the choice of outgroup is essential for understanding the evolution of traits along a phylogeny. History Although the concept of outgroups has been in use from the earliest days of cladistics, the term "outgroup" is thought to have been coined in the early 1970s at the American Museum of Natural History. Prior to the advent of the term, various other terms were used by evolutionary biologists, including "exgroup", "related group", and "outside groups". Choice of outgroup The chosen outgroup is hypothes ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Natural Selection
Natural selection is the differential survival and reproduction of individuals due to differences in phenotype. It is a key mechanism of evolution, the change in the heritable traits characteristic of a population over generations. Charles Darwin popularised the term "natural selection", contrasting it with artificial selection, which in his view is intentional, whereas natural selection is not. Variation exists within all populations of organisms. This occurs partly because random mutations arise in the genome of an individual organism, and their offspring can inherit such mutations. Throughout the lives of the individuals, their genomes interact with their environments to cause variations in traits. The environment of a genome includes the molecular biology in the cell, other cells, other individuals, populations, species, as well as the abiotic environment. Because individuals with certain variants of the trait tend to survive and reproduce more than individuals ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Itô Diffusion
In mathematics – specifically, in stochastic analysis – an Itô diffusion is a solution to a specific type of stochastic differential equation. That equation is similar to the Langevin equation used in physics to describe the Brownian motion of a particle subjected to a potential in a viscous fluid. Itô diffusions are named after the Japanese mathematician Kiyosi Itô. Overview A (time-homogeneous) Itô diffusion in ''n''-dimensional Euclidean space R''n'' is a process ''X'' : , +∞) × Ω → R''n'' defined on a probability space (Ω, Σ, P) and satisfying a stochastic differential equation of the form :\mathrm X_ = b(X_t) \, \mathrm t + \sigma (X_) \, \mathrm B_, where ''B'' is an ''m''-dimensional Brownian motion and ''b'' : R''n'' → R''n'' and σ : R''n'' → R''n''×''m'' satisfy the usual Lipschitz continuity condition :, b(x) - b(y) , + , \sigma (x) - \sigma (y) , \leq C , ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Coalescent Theory
Coalescent theory is a model of how alleles sampled from a population may have originated from a common ancestor. In the simplest case, coalescent theory assumes no recombination, no natural selection, and no gene flow or population structure, meaning that each variant is equally likely to have been passed from one generation to the next. The model looks backward in time, merging alleles into a single ancestral copy according to a random process in coalescence events. Under this model, the expected time between successive coalescence events increases almost exponentially back in time (with wide variance). Variance in the model comes from both the random passing of alleles from one generation to the next, and the random occurrence of mutations in these alleles. The mathematical theory of the coalescent was developed independently by several groups in the early 1980s as a natural extension of classical population genetics theory and models, but can be primarily attributed to John ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Fay And Wu's H
Fay and Wu's H is a statistical test created by and named after two researchers Justin Fay and Chung-I Wu. The purpose of the test is to distinguish between a DNA sequence evolving randomly ("neutrally") and one evolving under positive selection. This test is an advancement over Tajima's D, which is used to differentiate neutrally evolving sequences from those evolving non-randomly (through directional selection or balancing selection, demographic expansion or contraction or genetic hitchhiking). Fay and Wu's H is frequently used to identify sequences which have experienced selective sweeps in their evolutionary history. Concept Imagine a DNA sequence which has very few polymorphisms in its alleles across different populations. This could arise due to at least three causes: # The sequence is experiencing heavy negative selection, so any new mutation in the sequence is deleterious and is purged off immediately, or # The sequence just experienced a bout of selective sweep (an allele ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Frequency Distribution
In statistics, the frequency (or absolute frequency) of an event i is the number n_i of times the observation has occurred/recorded in an experiment or study. These frequencies are often depicted graphically or in tabular form. Types The cumulative frequency is the total of the absolute frequencies of all events at or below a certain point in an ordered list of events. The (or empirical probability) of an event is the absolute frequency normalized by the total number of events: : f_i = \frac = \frac. The values of f_i for all events i can be plotted to produce a frequency distribution. In the case when n_i = 0 for certain i, pseudocounts can be added. Depicting frequency distributions A frequency distribution shows us a summarized grouping of data divided into mutually exclusive classes and the number of occurrences in a class. It is a way of showing unorganized data notably to show results of an election, income of people for a certain region, sales of a product within ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
