|
Tajima's D
Tajima's D is a population genetic test statistic created by and named after the Japanese researcher Fumio Tajima. Tajima's D is computed as the difference between two measures of genetic diversity: the mean number of pairwise differences and the number of segregating sites, each scaled so that they are expected to be the same in a neutrally evolving population of constant size. The purpose of Tajima's D test is to distinguish between a DNA sequence evolving randomly ("neutrally") and one evolving under a non-random process, including directional selection or balancing selection, demographic expansion or contraction, genetic hitchhiking, or introgression. A randomly evolving DNA sequence contains mutations with no effect on the fitness and survival of an organism. The randomly evolving mutations are called "neutral", while mutations under selection are "non-neutral". For example, a mutation that causes prenatal death or severe disease would be expected to be under selection. In the ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Statistic
A statistic (singular) or sample statistic is any quantity computed from values in a sample which is considered for a statistical purpose. Statistical purposes include estimating a population parameter, describing a sample, or evaluating a hypothesis. The average (or mean) of sample values is a statistic. The term statistic is used both for the function (e.g., a calculation method of the average) and for the value of the function on a given sample (e.g., the result of the average calculation). When a statistic is being used for a specific purpose, it may be referred to by a name indicating its purpose. When a statistic is used for estimating a population parameter, the statistic is called an '' estimator''. A population parameter is any characteristic of a population under study, but when it is not feasible to directly measure the value of a population parameter, statistical methods are used to infer the likely value of the parameter on the basis of a statistic computed from a s ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Variance
In probability theory and statistics, variance is the expected value of the squared deviation from the mean of a random variable. The standard deviation (SD) is obtained as the square root of the variance. Variance is a measure of dispersion, meaning it is a measure of how far a set of numbers is spread out from their average value. It is the second central moment of a distribution, and the covariance of the random variable with itself, and it is often represented by \sigma^2, s^2, \operatorname(X), V(X), or \mathbb(X). An advantage of variance as a measure of dispersion is that it is more amenable to algebraic manipulation than other measures of dispersion such as the expected absolute deviation; for example, the variance of a sum of uncorrelated random variables is equal to the sum of their variances. A disadvantage of the variance for practical applications is that, unlike the standard deviation, its units differ from the random variable, which is why the standard devi ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
P-value
In null-hypothesis significance testing, the ''p''-value is the probability of obtaining test results at least as extreme as the result actually observed, under the assumption that the null hypothesis is correct. A very small ''p''-value means that such an extreme observed outcome would be very unlikely ''under the null hypothesis''. Even though reporting ''p''-values of statistical tests is common practice in academic publications of many quantitative fields, misinterpretation and misuse of p-values is widespread and has been a major topic in mathematics and metascience. In 2016, the American Statistical Association (ASA) made a formal statement that "''p''-values do not measure the probability that the studied hypothesis is true, or the probability that the data were produced by random chance alone" and that "a ''p''-value, or statistical significance, does not measure the size of an effect or the importance of a result" or "evidence regarding a model or hypothesis". That ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Selective Sweep
In genetics, a selective sweep is the process through which a new beneficial mutation that increases its frequency and becomes fixed (i.e., reaches a frequency of 1) in the population leads to the reduction or elimination of genetic variation among nucleotide sequences that are near the mutation. In selective sweep, positive selection causes the new mutation to reach fixation so quickly that linked alleles can "hitchhike" and also become fixed. Overview A selective sweep can occur when a rare or previously non-existing allele that increases the fitness of the carrier (relative to other members of the population) increases rapidly in frequency due to natural selection. As the prevalence of such a beneficial allele increases, genetic variants that happen to be present on the genomic background (the DNA neighborhood) of the beneficial allele will also become more prevalent. This is called ''genetic hitchhiking''. A selective sweep due to a strongly selected allele, which arose on ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Combination
In mathematics, a combination is a selection of items from a set that has distinct members, such that the order of selection does not matter (unlike permutations). For example, given three fruits, say an apple, an orange and a pear, there are three combinations of two that can be drawn from this set: an apple and a pear; an apple and an orange; or a pear and an orange. More formally, a ''k''-combination of a set ''S'' is a subset of ''k'' distinct elements of ''S''. So, two combinations are identical if and only if each combination has the same members. (The arrangement of the members in each set does not matter.) If the set has ''n'' elements, the number of ''k''-combinations, denoted by C(n,k) or C^n_k, is equal to the binomial coefficient \binom nk = \frac, which can be written using factorials as \textstyle\frac whenever k\leq n, and which is zero when k>n. This formula can be derived from the fact that each ''k''-combination of a set ''S'' of ''n'' members has k! permu ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Average
In colloquial, ordinary language, an average is a single number or value that best represents a set of data. The type of average taken as most typically representative of a list of numbers is the arithmetic mean the sum of the numbers divided by how many numbers are in the list. For example, the mean or average of the numbers 2, 3, 4, 7, and 9 (summing to 25) is 5. Depending on the context, the most representative statistics, statistic to be taken as the average might be another measure of central tendency, such as the mid-range, median, Mode (statistics), mode or geometric mean. For example, the average income, personal income is often given as the median the number below which are 50% of personal incomes and above which are 50% of personal incomes because the mean would be higher by including personal incomes from a few billionaires. General properties If all numbers in a list are the same number, then their average is also equal to this number. This property is shared by each o ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Expected Value
In probability theory, the expected value (also called expectation, expectancy, expectation operator, mathematical expectation, mean, expectation value, or first Moment (mathematics), moment) is a generalization of the weighted average. Informally, the expected value is the arithmetic mean, mean of the possible values a random variable can take, weighted by the probability of those outcomes. Since it is obtained through arithmetic, the expected value sometimes may not even be included in the sample data set; it is not the value you would expect to get in reality. The expected value of a random variable with a finite number of outcomes is a weighted average of all possible outcomes. In the case of a continuum of possible outcomes, the expectation is defined by Integral, integration. In the axiomatic foundation for probability provided by measure theory, the expectation is given by Lebesgue integration. The expected value of a random variable is often denoted by , , or , with a ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Effective Population Size
The effective population size (''N''''e'') is the size of an idealised population that would experience the same rate of genetic drift as the real population. Idealised populations are those following simple one- locus models that comply with assumptions of the neutral theory of molecular evolution. The effective population size is normally smaller than the census population size ''N'', partly because chance events prevent some individuals from breeding, and partly due to background selection and genetic hitchhiking. The same real population could have a different effective population size for different properties of interest, such as genetic drift (or more precisely, the speed of coalescence) over one generation vs. over many generations. Within a species, areas of the genome that have more genes and/or less genetic recombination tend to have lower effective population sizes, because of the effects of selection at linked sites. In a population with selection at many loci an ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Single Nucleotide Polymorphism
In genetics and bioinformatics, a single-nucleotide polymorphism (SNP ; plural SNPs ) is a germline substitution of a single nucleotide at a specific position in the genome. Although certain definitions require the substitution to be present in a sufficiently large fraction of the population (e.g. 1% or more), many publications do not apply such a frequency threshold. For example, a G nucleotide present at a specific location in a reference genome may be replaced by an A in a minority of individuals. The two possible nucleotide variations of this SNP – G or A – are called alleles. SNPs can help explain differences in susceptibility to a wide range of diseases across a population. For example, a common SNP in the CFH gene is associated with increased risk of age-related macular degeneration. Differences in the severity of an illness or response to treatments may also be manifestations of genetic variations caused by SNPs. For example, two common SNPs in the ''A ... [...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 genocide, speciocide, widespread violence or intentional culling. 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. 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 frequency of the fitter genes within the gen ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Neutral Mutation
Neutral mutations are changes in DNA sequence that are neither beneficial nor detrimental to the ability of an organism to survive and reproduce. In population genetics, mutations in which natural selection does not affect the spread of the mutation in a species are termed neutral mutations. Neutral mutations that are inheritable and not linked to any genes under selection will be lost or will replace all other alleles of the gene. That loss or fixation of the gene proceeds based on random sampling known as genetic drift. A neutral mutation that is in linkage disequilibrium with other alleles that are under selection may proceed to loss or fixation via genetic hitchhiking and/or background selection. While many mutations in a genome may decrease an organism’s ability to survive and reproduce, also known as fitness, those mutations are selected against and are not passed on to future generations. The most commonly-observed mutations that are detectable as variation in the genet ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Null Hypothesis
The null hypothesis (often denoted ''H''0) is the claim in scientific research that the effect being studied does not exist. The null hypothesis can also be described as the hypothesis in which no relationship exists between two sets of data or variables being analyzed. If the null hypothesis is true, any experimentally observed effect is due to chance alone, hence the term "null". In contrast with the null hypothesis, an alternative hypothesis (often denoted ''H''A or ''H''1) is developed, which claims that a relationship does exist between two variables. Basic definitions The null hypothesis and the ''alternative hypothesis'' are types of conjectures used in statistical tests to make statistical inferences, which are formal methods of reaching conclusions and separating scientific claims from statistical noise. The statement being tested in a test of statistical significance is called the null hypothesis. The test of significance is designed to assess the strength of the e ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
