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In population genetics, fixation is the change in a gene pool from a situation where there exists at least two variants of a particular gene (allele) in a given population to a situation where only one of the alleles remains. That is, the allele becomes fixed.
In the absence of mutation or heterozygote advantage, any allele must eventually be lost completely from the population or fixed (permanently established at 100% frequency in the population) | https://huggingface.co/datasets/fmars/wiki_stem |
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 | https://huggingface.co/datasets/fmars/wiki_stem |
In population genetics, a fixed allele is an allele that is the only variant that exists for that gene in a population. A fixed allele is homozygous for all members of the population.
The process by which alleles become fixed is called fixation | https://huggingface.co/datasets/fmars/wiki_stem |
In population genetics, the founder effect is the loss of genetic variation that occurs when a new population is established by a very small number of individuals from a larger population. It was first fully outlined by Ernst Mayr in 1942, using existing theoretical work by those such as Sewall Wright. As a result of the loss of genetic variation, the new population may be distinctively different, both genotypically and phenotypically, from the parent population from which it is derived | https://huggingface.co/datasets/fmars/wiki_stem |
A gene family is a set of several similar genes, formed by duplication of a single original gene, and generally with similar biochemical functions. One such family are the genes for human hemoglobin subunits; the ten genes are in two clusters on different chromosomes, called the α-globin and β-globin loci. These two gene clusters are thought to have arisen as a result of a precursor gene being duplicated approximately 500 million years ago | https://huggingface.co/datasets/fmars/wiki_stem |
In population genetics, gene flow (also known as migration and allele flow) is the transfer of genetic material from one population to another. If the rate of gene flow is high enough, then two populations will have equivalent allele frequencies and therefore can be considered a single effective population. It has been shown that it takes only "one migrant per generation" to prevent populations from diverging due to drift | https://huggingface.co/datasets/fmars/wiki_stem |
The gene pool is the set of all genes, or genetic information, in any population, usually of a particular species.
Description
A large gene pool indicates extensive genetic diversity, which is associated with robust populations that can survive bouts of intense selection. Meanwhile, low genetic diversity (see inbreeding and population bottlenecks) can cause reduced biological fitness and an increased chance of extinction, although as explained by genetic drift new genetic variants, that may cause an increase in the fitness of organisms, are more likely to fix in the population if it is rather small | https://huggingface.co/datasets/fmars/wiki_stem |
Genetic admixture occurs when previously diverged or isolated genetic lineages mix. Admixture results in the introduction of new genetic lineages into a population.
Examples
Climatic cycles facilitate genetic admixture in cold periods and genetic diversification in warm periods | https://huggingface.co/datasets/fmars/wiki_stem |
In mathematical genetics, a genetic algebra is a (possibly non-associative) algebra used to model inheritance in genetics. Some variations of these algebras are called train algebras, special train algebras, gametic algebras, Bernstein algebras, copular algebras, zygotic algebras, and baric algebras (also called weighted algebra). The study of these algebras was started by Ivor Etherington (1939) | https://huggingface.co/datasets/fmars/wiki_stem |
Genetic divergence is the process in which two or more populations of an ancestral species accumulate independent genetic changes (mutations) through time, often leading to reproductive isolation and continued mutation even after the populations have become reproductively isolated for some period of time, as there isn’t genetic exchange anymore. In some cases, subpopulations cover living in ecologically distinct peripheral environments can exhibit genetic divergence from the remainder of a population, especially where the range of a population is very large (see parapatric speciation). The genetic differences among divergent populations can involve silent mutations (that have no effect on the phenotype) or give rise to significant morphological and/or physiological changes | https://huggingface.co/datasets/fmars/wiki_stem |
Genetic diversity is the total number of genetic characteristics in the genetic makeup of a species, it ranges widely from the number of species to differences within species and can be attributed to the span of survival for a species. It is distinguished from genetic variability, which describes the tendency of genetic characteristics to vary.
Genetic diversity serves as a way for populations to adapt to changing environments | https://huggingface.co/datasets/fmars/wiki_stem |
Genetic drift, also known as random genetic drift, allelic drift or the Wright effect, is the change in the frequency of an existing gene variant (allele) in a population due to random chance. Genetic drift may cause gene variants to disappear completely and thereby reduce genetic variation. It can also cause initially rare alleles to become much more frequent and even fixed | https://huggingface.co/datasets/fmars/wiki_stem |
Genetic equilibrium is the condition of an allele or genotype in a gene pool (such as a population) where the frequency does not change from generation to generation. Genetic equilibrium describes a theoretical state that is the basis for determining whether and in what ways populations may deviate from it. Hardy–Weinberg equilibrium is one theoretical framework for studying genetic equilibrium | https://huggingface.co/datasets/fmars/wiki_stem |
Genetic erosion (also known as genetic depletion) is a process where the limited gene pool of an endangered species diminishes even more when reproductive individuals die off before reproducing with others in their endangered low population. The term is sometimes used in a narrow sense, such as when describing the loss of particular alleles or genes, as well as being used more broadly, as when referring to the loss of a phenotype or whole species.
Genetic erosion occurs because each individual organism has many unique genes which get lost when it dies without getting a chance to breed | https://huggingface.co/datasets/fmars/wiki_stem |
Genetic hitchhiking, also called genetic draft or the hitchhiking effect, is when an allele changes frequency not because it itself is under natural selection, but because it is near another gene that is undergoing a selective sweep and that is on the same DNA chain. When one gene goes through a selective sweep, any other nearby polymorphisms that are in linkage disequilibrium will tend to change their allele frequencies too. Selective sweeps happen when newly appeared (and hence still rare) mutations are advantageous and increase in frequency | https://huggingface.co/datasets/fmars/wiki_stem |
Genetic linkage is the tendency of DNA sequences that are close together on a chromosome to be inherited together during the meiosis phase of sexual reproduction. Two genetic markers that are physically near to each other are unlikely to be separated onto different chromatids during chromosomal crossover, and are therefore said to be more linked than markers that are far apart. In other words, the nearer two genes are on a chromosome, the lower the chance of recombination between them, and the more likely they are to be inherited together | https://huggingface.co/datasets/fmars/wiki_stem |
Genetic load is the difference between the fitness of an average genotype in a population and the fitness of some reference genotype, which may be either the best present in a population, or may be the theoretically optimal genotype. The average individual taken from a population with a low genetic load will generally, when grown in the same conditions, have more surviving offspring than the average individual from a population with a high genetic load. Genetic load can also be seen as reduced fitness at the population level compared to what the population would have if all individuals had the reference high-fitness genotype | https://huggingface.co/datasets/fmars/wiki_stem |
Genetic monitoring is the use of molecular markers to (i) identify individuals, species or populations, or (ii) to quantify changes in population genetic metrics (such as effective population size, genetic diversity and population size) over time. Genetic monitoring can thus be used to detect changes in species abundance and/or diversity, and has become an important tool in both conservation and livestock management. The types of molecular markers used to monitor populations are most commonly mitochondrial, microsatellites or single-nucleotide polymorphisms (SNPs), while earlier studies also used allozyme data | https://huggingface.co/datasets/fmars/wiki_stem |
Genetic variability is either the presence of, or the generation of, genetic differences.
It is defined as "the formation of individuals differing in genotype, or the presence of genotypically different individuals, in contrast to environmentally induced differences which, as a rule, cause only temporary, nonheritable changes of the phenotype". Genetic variability in a population is important for biodiversity | https://huggingface.co/datasets/fmars/wiki_stem |
Genetic variation is the difference in DNA among individuals or the differences between populations among the same species. The multiple sources of genetic variation include mutation and genetic recombination. Mutations are the ultimate sources of genetic variation, but other mechanisms, such as genetic drift, contribute to it, as well | https://huggingface.co/datasets/fmars/wiki_stem |
Genetic variation in populations can be analyzed and quantified by the frequency of alleles. Two fundamental calculations are central to population genetics: allele frequencies and genotype frequencies. Genotype frequency in a population is the number of individuals with a given genotype divided by the total number of individuals in the population | https://huggingface.co/datasets/fmars/wiki_stem |
Group selection is a proposed mechanism of evolution in which natural selection acts at the level of the group, instead of at the level of the individual or gene.
Early authors such as V. C | https://huggingface.co/datasets/fmars/wiki_stem |
Haldane's dilemma, also known as "the waiting time problem", is a limit on the speed of beneficial evolution, calculated by J. B. S | https://huggingface.co/datasets/fmars/wiki_stem |
A haplotype (haploid genotype) is a group of alleles in an organism that are inherited together from a single parent. Many organisms contain genetic material (DNA) which is inherited from two parents. Normally these organisms have their DNA organized in two sets of pairwise similar chromosomes | https://huggingface.co/datasets/fmars/wiki_stem |
Heritability is a statistic used in the fields of breeding and genetics that estimates the degree of variation in a phenotypic trait in a population that is due to genetic variation between individuals in that population. The concept of heritability can be expressed in the form of the following question: "What is the proportion of the variation in a given trait within a population that is not explained by the environment or random chance?"Other causes of measured variation in a trait are characterized as environmental factors, including observational error. In human studies of heritability these are often apportioned into factors from "shared environment" and "non-shared environment" based on whether they tend to result in persons brought up in the same household being more or less similar to persons who were not | https://huggingface.co/datasets/fmars/wiki_stem |
A heterozygote advantage describes the case in which the heterozygous genotype has a higher relative fitness than either the homozygous dominant or homozygous recessive genotype. Loci exhibiting heterozygote advantage are a small minority of loci. The specific case of heterozygote advantage due to a single locus is known as overdominance | https://huggingface.co/datasets/fmars/wiki_stem |
In biology, a hybrid is the offspring resulting from combining the qualities of two organisms of different varieties, species or genera through sexual reproduction. Generally, it means that each cell has genetic material from two different organisms, whereas an individual where some cells are derived from a different organism is called a chimera. Hybrids are not always intermediates between their parents (such as in blending inheritance), but can show hybrid vigor, sometimes growing larger or taller than either parent | https://huggingface.co/datasets/fmars/wiki_stem |
The hybrid iguana is a first-generation hybrid, the result of intergeneric breeding between a male marine iguana (Amblyrhynchus cristatus) and a female Galapagos land iguana (Conolophus subcristatus) on South Plaza Island in the Galápagos Islands, where the territories of the two species overlap.
Hybrid iguanas are dark with light speckles or bands of mottling near the head and a banded body. By contrast, marine iguanas are a solid blackish color, while land iguanas are reddish-yellow; neither are banded | https://huggingface.co/datasets/fmars/wiki_stem |
A hybrid swarm is a population of hybrids that has survived beyond the initial hybrid generation, with interbreeding between hybrid individuals and backcrossing with its parent types. Such population are highly variable, with the genetic and phenotypic characteristics of individuals ranging widely between the two parent types. Hybrid swarms thus blur the boundary between the parent taxa | https://huggingface.co/datasets/fmars/wiki_stem |
A hybrid zone exists where the ranges of two interbreeding species or diverged intraspecific lineages meet and cross-fertilize. Hybrid zones can form in situ due to the evolution of a new lineage but generally they result from secondary contact of the parental forms after a period of geographic isolation, which allowed their differentiation (or speciation). Hybrid zones are useful in studying the genetics of speciation as they can provide natural examples of differentiation and (sometimes) gene flow between populations that are at some point between representing a single species and representing multiple species in reproductive isolation | https://huggingface.co/datasets/fmars/wiki_stem |
In population genetics an idealised population is one that can be described using a number of simplifying assumptions. Models of idealised populations are either used to make a general point, or they are fit to data on real populations for which the assumptions may not hold true. For example, coalescent theory is used to fit data to models of idealised populations | https://huggingface.co/datasets/fmars/wiki_stem |
A DNA segment is identical by state (IBS) in two or more individuals if they have identical nucleotide sequences in this segment. An IBS segment is identical by descent (IBD) in two or more individuals if they have inherited it from a common ancestor without recombination, that is, the segment has the same ancestral origin in these individuals. DNA segments that are IBD are IBS per definition, but segments that are not IBD can still be IBS due to the same mutations in different individuals or recombinations that do not alter the segment | https://huggingface.co/datasets/fmars/wiki_stem |
Inbred strains (also called inbred lines, or rarely for animals linear animals) are individuals of a particular species which are nearly identical to each other in genotype due to long inbreeding. A strain is inbred when it has undergone at least 20 generations of brother x sister or offspring x parent mating, at which point at least 98. 6% of the loci in an individual of the strain will be homozygous, and each individual can be treated effectively as clones | https://huggingface.co/datasets/fmars/wiki_stem |
Inbreeding is the production of offspring from the mating or breeding of individuals or organisms that are closely related genetically. By analogy, the term is used in human reproduction, but more commonly refers to the genetic disorders and other consequences that may arise from expression of deleterious recessive traits resulting from incestuous sexual relationships and consanguinity. Animals avoid incest only rarely | https://huggingface.co/datasets/fmars/wiki_stem |
Inbreeding avoidance, or the inbreeding avoidance hypothesis, is a concept in evolutionary biology that refers to the prevention of the deleterious effects of inbreeding. Animals only rarely exhibit inbreeding avoidance. The inbreeding avoidance hypothesis posits that certain mechanisms develop within a species, or within a given population of a species, as a result of assortative mating and natural and sexual selection, in order to prevent breeding among related individuals | https://huggingface.co/datasets/fmars/wiki_stem |
== Exposure ==
Exposure of zebrafish to a chemical environmental agent, analogous to that caused by anthropogenic pollution, amplified the effects of inbreeding on key reproductive traits. Embryo viability was significantly reduced in inbred exposed fish and there was a tendency for inbred males to sire fewer offspring.
Effects
The effect of inbreeding on reproductive behavior was studied in the poeciliid fish Heterandria formosa | https://huggingface.co/datasets/fmars/wiki_stem |
Incomplete lineage sorting, also termed hemiplasy, deep coalescence, retention of ancestral polymorphism, or trans-species polymorphism, describes a phenomenon in population genetics when ancestral gene copies fail to coalesce (looking backwards in time) into a common ancestral copy until deeper than previous speciation events. It is caused by lineage sorting of genetic polymorphisms that were retained across successive nodes in the species tree. In other words, the tree produced by a single gene differs from the population or species level tree, producing a discordant tree | https://huggingface.co/datasets/fmars/wiki_stem |
The Infinite sites model (ISM) is a mathematical model of molecular evolution first proposed by Motoo Kimura in 1969. Like other mutation models, the ISM provides a basis for understanding how mutation develops new alleles in DNA sequences. Using allele frequencies, it allows for the calculation of heterozygosity, or genetic diversity, in a finite population and for the estimation of genetic distances between populations of interest | https://huggingface.co/datasets/fmars/wiki_stem |
In zoology, intergradation is the way in which two distinct subspecies are connected via areas where populations are found that have the characteristics of both. There are two types of intergradation: primary and secondary intergradation.
Primary intergradation
This occurs in cases where two subspecies are connected via one or more intermediate populations, each of which is in turn intermediate to its adjacent populations and exhibits more or less the same amount of variability as any other population within the species | https://huggingface.co/datasets/fmars/wiki_stem |
International migration occurs when people cross state boundaries and stay in the host state for some minimum length of the time. Migration occurs for many reasons. Many people leave their home countries in order to look for economic opportunities in another country | https://huggingface.co/datasets/fmars/wiki_stem |
Isolation by distance (IBD) is a term used to refer to the accrual of local genetic variation under geographically limited dispersal. The IBD model is useful for determining the distribution of gene frequencies over a geographic region. Both dispersal variance and migration probabilities are variables in this model and both contribute to local genetic differentiation | https://huggingface.co/datasets/fmars/wiki_stem |
The Khazar hypothesis of Ashkenazi ancestry, often called the Khazar myth by its critics, is a largely abandoned historical hypothesis that postulated that Ashkenazi Jews were primarily, or to a large extent, descended from Khazars, a multi-ethnic conglomerate of mostly Turkic peoples who formed a semi-nomadic khanate in and around the northern and central Caucasus and the Pontic–Caspian steppe. The hypothesis also postulated that after collapse of the Khazar empire, the Khazars fled to Eastern Europe and made up a large part of the Jews there. The hypothesis draws on medieval sources such as the Khazar Correspondence, according to which at some point in the 8th–9th centuries, a small number of Khazars were said by Judah Halevi and Abraham ibn Daud to have converted to Rabbinic Judaism | https://huggingface.co/datasets/fmars/wiki_stem |
In biology, a klepton (abbr. kl. ) and synklepton (abbr sk | https://huggingface.co/datasets/fmars/wiki_stem |
Lactase persistence is the continued activity of the lactase enzyme in adulthood, allowing the digestion of lactose in milk. In most mammals, the activity of the enzyme is dramatically reduced after weaning. In some human populations, though, lactase persistence has recently evolved as an adaptation to the consumption of nonhuman milk and dairy products beyond infancy | https://huggingface.co/datasets/fmars/wiki_stem |
Landscape genetics is the scientific discipline that combines population genetics and landscape ecology. It broadly encompasses any study that analyses plant or animal population genetic data in conjunction with data on the landscape features and matrix quality where the sampled population lives. This allows for the analysis of microevolutionary processes affecting the species in light of landscape spatial patterns, providing a more realistic view of how populations interact with their environments | https://huggingface.co/datasets/fmars/wiki_stem |
Landscape genomics is one of many strategies used to identify relationships between environmental factors and the genetic adaptation of organisms in response to these factors. Landscape genomics combines aspects of landscape ecology, population genetics and landscape genetics. The latter addresses how landscape features influence the population structure and gene flow of organisms across time and space | https://huggingface.co/datasets/fmars/wiki_stem |
In population genetics, linkage disequilibrium (LD) is the non-random association of alleles at different loci in a given population. Loci are said to be in linkage disequilibrium when the frequency of association of their different alleles is higher or lower than expected if the loci were independent and associated randomly. Linkage disequilibrium is influenced by many factors, including selection, the rate of genetic recombination, mutation rate, genetic drift, the system of mating, population structure, and genetic linkage | https://huggingface.co/datasets/fmars/wiki_stem |
The match/mismatch hypothesis (MMH) was first described by David Cushing (1969). The MMH "seeks to explain recruitment variation in a population by means of the relation between its phenology—the timing of seasonal activities such as flowering or breeding - and that of species at the immediate lower level", see Durant et al. (2007) | https://huggingface.co/datasets/fmars/wiki_stem |
Microevolution is the change in allele frequencies that occurs over time within a population. This change is due to four different processes: mutation, selection (natural and artificial), gene flow and genetic drift. This change happens over a relatively short (in evolutionary terms) amount of time compared to the changes termed macroevolution | https://huggingface.co/datasets/fmars/wiki_stem |
Microfluidic whole genome haplotyping is a technique for the physical separation of individual chromosomes from a metaphase cell followed by direct resolution of the haplotype for each allele.
Background
Whole genome haplotyping
Whole genome haplotyping is the process of resolving personal haplotypes on a whole genome basis. Current methods of next generation sequencing are capable of identifying heterozygous loci, but they are not well suited to identify which polymorphisms exist on the same (in cis) or allelic (in trans) strand of DNA | https://huggingface.co/datasets/fmars/wiki_stem |
In evolutionary genetics, Muller's ratchet (named after Hermann Joseph Muller, by analogy with a ratchet effect) is a process which, in the absence of recombination (especially in an asexual population), results in an accumulation of irreversible deleterious mutations. This happens because in the absence of recombination, and assuming reverse mutations are rare, offspring bear at least as much mutational load as their parents. Muller proposed this mechanism as one reason why sexual reproduction may be favored over asexual reproduction, as sexual organisms benefit from recombination and consequent elimination of deleterious mutations | https://huggingface.co/datasets/fmars/wiki_stem |
Multispecies Coalescent Process is a stochastic process model that describes the genealogical relationships for a sample of DNA sequences taken from several species. It represents the application of coalescent theory to the case of multiple species. The multispecies coalescent results in cases where the relationships among species for an individual gene (the gene tree) can differ from the broader history of the species (the species tree) | https://huggingface.co/datasets/fmars/wiki_stem |
In evolutionary genetics, mutational meltdown is a sub class of extinction vortex in which the environment and genetic predisposition mutually reinforce each other. Mutational meltdown (not to be confused with the concept of an error catastrophe) is the accumulation of harmful mutations in a small population, which leads to loss of fitness and decline of the population size, which may lead to further accumulation of deleterious mutations due to fixation by genetic drift.
A population experiencing mutational meltdown is trapped in a downward spiral and will go extinct if the phenomenon lasts for some time | https://huggingface.co/datasets/fmars/wiki_stem |
The nearly neutral theory of molecular evolution is a modification of the neutral theory of molecular evolution that accounts for the fact that not all mutations are either so deleterious such that they can be ignored, or else neutral. Slightly deleterious mutations are reliably purged only when their selection coefficient are greater than one divided by the effective population size. In larger populations, a higher proportion of mutations exceed this threshold for which genetic drift cannot overpower selection, leading to fewer fixation events and so slower molecular evolution | https://huggingface.co/datasets/fmars/wiki_stem |
In natural selection, negative selection or purifying selection is the selective removal of alleles that are deleterious. This can result in stabilising selection through the purging of deleterious genetic polymorphisms that arise through random mutations. Purging of deleterious alleles can be achieved on the population genetics level, with as little as a single point mutation being the unit of selection | https://huggingface.co/datasets/fmars/wiki_stem |
The neutral theory of molecular evolution holds that most evolutionary changes occur at the molecular level, and most of the variation within and between species are due to random genetic drift of mutant alleles that are selectively neutral. The theory applies only for evolution at the molecular level, and is compatible with phenotypic evolution being shaped by natural selection as postulated by Charles Darwin. The neutral theory allows for the possibility that most mutations are deleterious, but holds that because these are rapidly removed by natural selection, they do not make significant contributions to variation within and between species at the molecular level | https://huggingface.co/datasets/fmars/wiki_stem |
Niche microdifferentiation is the process a species undergoes to reach genetic diversity within that species; it is the process by which an ecotype is created. This process is regulated by various environmental influences whether they be morphological, spatial, and/or temporal. This means that a trait of one organism in one area is not advantageous for the same species in a different location: "the trait that alters the environment in a manner that is favorable to growth tends to be reinforced and this positive feedback can further, to a certain extent, modify the selection pressure on itself" | https://huggingface.co/datasets/fmars/wiki_stem |
Non-obese diabetic or NOD mice, like biobreeding rats, are used as an animal model for type 1 diabetes. Diabetes develops in NOD mice as a result of insulitis, a leukocytic infiltrate of the pancreatic islets. The onset of diabetes is associated with a moderate glycosuria and a non-fasting hyperglycemia | https://huggingface.co/datasets/fmars/wiki_stem |
Notch homolog 2 N-terminal-like is a family of proteins that in humans consists of 3 proteins (NOTCH2NLA, NOTCH2NLB, and NOTCH2NLC) and is encoded by NOTCH2NL gene. It appears to play a key role in the development of the prefrontal cortex, a part of the brain. NOTCH2NL increases the number of cortical stem cells, which while delaying the generation of neurons ultimately leads to a greater number of neurons and larger brains | https://huggingface.co/datasets/fmars/wiki_stem |
Orcas or killer whales have a cosmopolitan distribution and several distinct populations or types have been documented or suggested. Three to five types of orcas may be distinct enough to be considered different races, subspecies, or possibly even species (see Species problem). The IUCN reported in 2008, "The taxonomy of this genus is clearly in need of review, and it is likely that O | https://huggingface.co/datasets/fmars/wiki_stem |
In biology, outbreeding depression happens when crosses between two genetically distant groups or populations result in a reduction of fitness. The concept is in contrast to inbreeding depression, although the two effects can occur simultaneously. Outbreeding depression is a risk that sometimes limits the potential for genetic rescue or augmentations | https://huggingface.co/datasets/fmars/wiki_stem |
In population genetics overlapping generations refers to mating systems where more than one breeding generation is present at any one time. In systems where this is not the case there are non-overlapping generations (or discrete generations) in which every breeding generation lasts just one breeding season. If the adults reproduce over multiple breeding seasons the species is considered to have overlapping generations | https://huggingface.co/datasets/fmars/wiki_stem |
Panmixia (or panmixis) means random mating. A panmictic population is one where all individuals are potential partners. This assumes that there are no mating restrictions, neither genetic nor behavioural, upon the population and that therefore all recombination is possible | https://huggingface.co/datasets/fmars/wiki_stem |
A parahaplogroup is a term used in genetics to identify a paraphyletic haplogroup.
They are normally described with the name of their parent haplogroup plus an asterisk (for instance: F*, U2*), meaning that it includes all derivates from the parent haplogroup (F or U2 in the examples) except those mentioned elsewhere. Sometimes it is specified which other subclades are excluded and then the parent name is followed by the sign "x" and the list of those excluded haplogroups, separated by commas | https://huggingface.co/datasets/fmars/wiki_stem |
The popular sire effect (or popular stud/sire syndrome) occurs when an animal with desirable attributes is bred repeatedly. In dog breeding, a male dog that wins respected competitions becomes highly sought after, as breeders believe the sire possesses the genes necessary to produce champions. However, the popular sire effect is not just down to wanting to produce a champion | https://huggingface.co/datasets/fmars/wiki_stem |
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 | https://huggingface.co/datasets/fmars/wiki_stem |
Population genetics is a subfield of genetics that deals with genetic differences within and among populations, and is a part of evolutionary biology. Studies in this branch of biology examine such phenomena as adaptation, speciation, and population structure. Population genetics was a vital ingredient in the emergence of the modern evolutionary synthesis | https://huggingface.co/datasets/fmars/wiki_stem |
Population genomics is the large-scale comparison of DNA sequences of populations. Population genomics is a neologism that is associated with population genetics. Population genomics studies genome-wide effects to improve our understanding of microevolution so that we may learn the phylogenetic history and demography of a population | https://huggingface.co/datasets/fmars/wiki_stem |
In population genetics and population ecology, population size (usually denoted N) is a countable quantity representing the number of individual organisms in a population. Population size is directly associated with amount of genetic drift, and is the underlying cause of effects like population bottlenecks and the founder effect. Genetic drift is the major source of decrease of genetic diversity within populations which drives fixation and can potentially lead to speciation events | https://huggingface.co/datasets/fmars/wiki_stem |
Population structure (also called genetic structure and population stratification) is the presence of a systematic difference in allele frequencies between subpopulations. In a randomly mating (or panmictic) population, allele frequencies are expected to be roughly similar between groups. However, mating tends to be non-random to some degree, causing structure to arise | https://huggingface.co/datasets/fmars/wiki_stem |
In the theory of evolution and natural selection, the Price equation (also known as Price's equation or Price's theorem) describes how a trait or allele changes in frequency over time. The equation uses a covariance between a trait and fitness, to give a mathematical description of evolution and natural selection. It provides a way to understand the effects that gene transmission and natural selection have on the frequency of alleles within each new generation of a population | https://huggingface.co/datasets/fmars/wiki_stem |
In numerical mathematics, artificial precision is a source of error that occurs when a numerical value or semantic is expressed with more precision than was initially provided from measurement or user input.
For example, a person enters their birthday as the date 1984-01-01 but it is stored in a database as 1984-01-01T00:00:00Z which introduces the artificial precision of the hour, minute, and second they were born, and may even affect the date, depending on the user's actual place of birth. This is also an example of false precision, which is artificial precision specifically of numerical quantities or measures | https://huggingface.co/datasets/fmars/wiki_stem |
ArviZ ( AR-vees) is a Python package for exploratory analysis of Bayesian models. When working with Bayesian models there are a series of related tasks that need to be addressed besides inference itself:
Diagnoses of the quality of the inference, this is needed when using numerical methods such as Markov chain Monte Carlo techniques
Model criticism, including evaluations of both model assumptions and model predictions
Comparison of models, including model selection or model averaging
Preparation of the results for a particular audienceAll these tasks are part of the Exploratory analysis of Bayesian models approach, and successfully performing them is central to the iterative and interactive modeling process. These tasks require both numerical and visual summaries | https://huggingface.co/datasets/fmars/wiki_stem |
The auxiliary particle filter is a particle filtering algorithm introduced by Pitt and Shephard in 1999 to improve some deficiencies of the sequential importance resampling (SIR) algorithm when dealing with tailed observation densities.
Motivation
Particle filters approximate continuous random variable by
M
{\displaystyle M}
particles with discrete probability mass
π
t
{\displaystyle \pi _{t}}
, say
1
/
M
{\displaystyle 1/M}
for uniform distribution. The random sampled particles can be used to approximate the probability density function of the continuous random variable if the value
M
→
∞
{\displaystyle M\rightarrow \infty }
| https://huggingface.co/datasets/fmars/wiki_stem |
Bayesian inference using Gibbs sampling (BUGS) is a statistical software for performing Bayesian inference using Markov chain Monte Carlo (MCMC) methods. It was developed by David Spiegelhalter at the Medical Research Council Biostatistics Unit in Cambridge in 1989 and released as free software in 1991. The BUGS project has evolved through four main versions: ClassicBUGS, WinBUGS, OpenBUGS and MultiBUGS | https://huggingface.co/datasets/fmars/wiki_stem |
In statistics, the bootstrap error-adjusted single-sample technique (BEST or the BEAST) is a non-parametric method that is intended to allow an assessment to be made of the validity of a single sample. It is based on estimating a probability distribution representing what can be expected from valid samples. This is done use a statistical method called bootstrapping, applied to previous samples that are known to be valid | https://huggingface.co/datasets/fmars/wiki_stem |
Bootstrapping is any test or metric that uses random sampling with replacement (e. g. mimicking the sampling process), and falls under the broader class of resampling methods | https://huggingface.co/datasets/fmars/wiki_stem |
Bootstrapping populations in statistics and mathematics starts with a sample
{
x
1
,
…
,
x
m
}
{\displaystyle \{x_{1},\ldots ,x_{m}\}}
observed from a random variable.
When X has a given distribution law with a set of non fixed parameters, we denote with a vector
θ
{\displaystyle {\boldsymbol {\theta }}}
, a parametric inference problem consists of computing suitable values – call them estimates – of these parameters precisely on the basis of the sample. An estimate is suitable if replacing it with the unknown parameter does not cause major damage in next computations | https://huggingface.co/datasets/fmars/wiki_stem |
Conformal prediction (CP) is a statistical technique for producing prediction sets without assumptions on the predictive algorithm (often a machine learning system) and only assuming exchangeability of the data. CP works by computing a nonconformity measure, often called a score function, on previously labeled data, and using these to create prediction sets on a new (unlabeled) test data point. A version of CP was first proposed in 1998 by Gammerman, Vovk, and Vapnik, and since, several variants of conformal prediction have been developed with different computational complexities, formal guarantees, and practical applications | https://huggingface.co/datasets/fmars/wiki_stem |
In probability theory, a continuity correction is an adjustment that is made when a discrete distribution is approximated by a continuous distribution.
Examples
Binomial
If a random variable X has a binomial distribution with parameters n and p, i. e | https://huggingface.co/datasets/fmars/wiki_stem |
The control variates method is a variance reduction technique used in Monte Carlo methods. It exploits information about the errors in estimates of known quantities to reduce the error of an estimate of an unknown quantity.
Underlying principle
Let the unknown parameter of interest be
μ
{\displaystyle \mu }
, and assume we have a statistic
m
{\displaystyle m}
such that the expected value of m is μ:
E
[
m
]
=
μ
{\displaystyle \mathbb {E} \left[m\right]=\mu }
, i | https://huggingface.co/datasets/fmars/wiki_stem |
FastICA is an efficient and popular algorithm for independent component analysis invented by Aapo Hyvärinen at Helsinki University of Technology. Like most ICA algorithms, FastICA seeks an orthogonal rotation of prewhitened data, through a fixed-point iteration scheme, that maximizes a measure of non-Gaussianity of the rotated components. Non-gaussianity serves as a proxy for statistical independence, which is a very strong condition and requires infinite data to verify | https://huggingface.co/datasets/fmars/wiki_stem |
In statistics and machine learning, Gaussian process approximation is a computational method that accelerates inference tasks in the context of a Gaussian process model, most commonly likelihood evaluation and prediction. Like approximations of other models, they can often be expressed as additional assumptions imposed on the model, which do not correspond to any actual feature, but which retain its key properties while simplifying calculations. Many of these approximation methods can be expressed in purely linear algebraic or functional analytic terms as matrix or function approximations | https://huggingface.co/datasets/fmars/wiki_stem |
Group method of data handling (GMDH) is a family of inductive algorithms for computer-based mathematical modeling of multi-parametric datasets that features fully automatic structural and parametric optimization of models.
GMDH is used in such fields as data mining, knowledge discovery, prediction, complex systems modeling, optimization and pattern recognition. GMDH algorithms are characterized by inductive procedure that performs sorting-out of gradually complicated polynomial models and selecting the best solution by means of the external criterion | https://huggingface.co/datasets/fmars/wiki_stem |
In mathematical modeling, a guess value is more commonly called a starting value or initial value. These are necessary for most optimization problems which use search algorithms, because those algorithms are mainly deterministic and iterative, and they need to start somewhere. One common type of application is nonlinear regression | https://huggingface.co/datasets/fmars/wiki_stem |
Isomap is a nonlinear dimensionality reduction method. It is one of several widely used low-dimensional embedding methods. Isomap is used for computing a quasi-isometric, low-dimensional embedding of a set of high-dimensional data points | https://huggingface.co/datasets/fmars/wiki_stem |
In statistics, the jackknife (jackknife cross-validation) is a cross-validation technique and, therefore, a form of resampling.
It is especially useful for bias and variance estimation. The jackknife pre-dates other common resampling methods such as the bootstrap | https://huggingface.co/datasets/fmars/wiki_stem |
Joint Approximation Diagonalization of Eigen-matrices (JADE) is an algorithm for independent component analysis that separates observed mixed signals into latent source signals by exploiting fourth order moments. The fourth order moments are a measure of non-Gaussianity, which is used as a proxy for defining independence between the source signals. The motivation for this measure is that Gaussian distributions possess zero excess kurtosis, and with non-Gaussianity being a canonical assumption of ICA, JADE seeks an orthogonal rotation of the observed mixed vectors to estimate source vectors which possess high values of excess kurtosis | https://huggingface.co/datasets/fmars/wiki_stem |
Linear least squares (LLS) is the least squares approximation of linear functions to data.
It is a set of formulations for solving statistical problems involved in linear regression, including variants for ordinary (unweighted), weighted, and generalized (correlated) residuals.
Numerical methods for linear least squares include inverting the matrix of the normal equations and orthogonal decomposition methods | https://huggingface.co/datasets/fmars/wiki_stem |
Kernel density estimation is a nonparametric technique for density estimation i. e. , estimation of probability density functions, which is one of the fundamental questions in statistics | https://huggingface.co/datasets/fmars/wiki_stem |
Out-of-bag (OOB) error, also called out-of-bag estimate, is a method of measuring the prediction error of random forests, boosted decision trees, and other machine learning models utilizing bootstrap aggregating (bagging). Bagging uses subsampling with replacement to create training samples for the model to learn from. OOB error is the mean prediction error on each training sample xi, using only the trees that did not have xi in their bootstrap sample | https://huggingface.co/datasets/fmars/wiki_stem |
Particle filters, or sequential Monte Carlo methods, are a set of Monte Carlo algorithms used to find approximate solutions for filtering problems for nonlinear state-space systems, such as signal processing and Bayesian statistical inference. The filtering problem consists of estimating the internal states in dynamical systems when partial observations are made and random perturbations are present in the sensors as well as in the dynamical system. The objective is to compute the posterior distributions of the states of a Markov process, given the noisy and partial observations | https://huggingface.co/datasets/fmars/wiki_stem |
In statistics, resampling is the creation of new samples based on one observed sample.
Resampling methods are:
Permutation tests (also re-randomization tests)
Bootstrapping
Cross validation
Permutation tests
Permutation tests rely on resampling the original data assuming the null hypothesis. Based on the resampled data it can be concluded how likely the original data is to occur under the null hypothesis | https://huggingface.co/datasets/fmars/wiki_stem |
ProbLog is a probabilistic logic programming that extends Prolog with probabilities. It minimally extends Prolog by adding the notion of a probabilistic fact, which combines the idea of logic atoms and random variables. Similarly to Prolog, ProbLog can query an atom | https://huggingface.co/datasets/fmars/wiki_stem |
Projection filters are a set of algorithms based on stochastic analysis and information geometry, or the differential geometric approach to statistics, used to find approximate solutions for filtering problems for nonlinear state-space systems.
The filtering problem consists of estimating the unobserved signal of a random dynamical system from partial noisy observations of the signal. The objective is computing the probability distribution of the signal conditional on the history of the noise-perturbed observations | https://huggingface.co/datasets/fmars/wiki_stem |
PyMC (formerly known as PyMC3) is a Python package for Bayesian statistical modeling and probabilistic machine learning which focuses on advanced Markov chain Monte Carlo and variational fitting algorithms.
It is a rewrite from scratch of the previous version of the PyMC software.
Unlike PyMC2, which had used Fortran extensions for performing computations, PyMC relies on PyTensor, a Python library that allows defining, optimizing, and efficiently evaluating mathematical expressions involving multi-dimensional arrays | https://huggingface.co/datasets/fmars/wiki_stem |
In the field of mathematical modeling, a radial basis function network is an artificial neural network that uses radial basis functions as activation functions. The output of the network is a linear combination of radial basis functions of the inputs and neuron parameters. Radial basis function networks have many uses, including function approximation, time series prediction, classification, and system control | https://huggingface.co/datasets/fmars/wiki_stem |
Random forests or random decision forests is an ensemble learning method for classification, regression and other tasks that operates by constructing a multitude of decision trees at training time. For classification tasks, the output of the random forest is the class selected by most trees. For regression tasks, the mean or average prediction of the individual trees is returned | https://huggingface.co/datasets/fmars/wiki_stem |
Maximum Variance Unfolding (MVU), also known as Semidefinite Embedding (SDE), is an algorithm in computer science that uses semidefinite programming to perform non-linear dimensionality reduction of high-dimensional vectorial input data. It is motivated by the observation that kernel Principal Component Analysis (kPCA) does not reduce the data dimensionality, as it leverages the Kernel trick to non-linearly map the original data into an inner-product space.
Algorithm
MVU creates a mapping from the high dimensional input vectors to some low dimensional Euclidean vector space in the following steps:
A neighbourhood graph is created | https://huggingface.co/datasets/fmars/wiki_stem |
Spiking neural networks (SNNs) are artificial neural networks that more closely mimic natural neural networks. In addition to neuronal and synaptic state, SNNs incorporate the concept of time into their operating model. The idea is that neurons in the SNN do not transmit information at each propagation cycle (as it happens with typical multi-layer perceptron networks), but rather transmit information only when a membrane potential—an intrinsic quality of the neuron related to its membrane electrical charge—reaches a specific value, called the threshold | https://huggingface.co/datasets/fmars/wiki_stem |
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