Allele in the context of Homeosis

A phenotypic trait, simply trait, or character state is a distinct variant of a phenotypic characteristic of an organism; it may be either inherited or determined environmentally, but typically occurs as a combination of the two. For example, having eye color is a character of an organism, while blue, brown and hazel versions of eye color are traits. The term trait is generally used in genetics, often to describe the phenotypic expression of different combinations of alleles in different individual organisms within a single population, such as the famous purple vs. white flower coloration in Gregor Mendel's pea plants. By contrast, in systematics, the term character state is employed to describe features that represent fixed diagnostic differences among taxa, such as the absence of tails in great apes, relative to other primate groups.

Alzheimer's disease (AD) is a neurodegenerative disease and is the most common form of dementia, accounting for around 60–70% of cases. The most common early symptom is difficulty in remembering recent events. As the disease advances, symptoms can include problems with language, disorientation (including easily getting lost), mood swings, loss of motivation, self-neglect, and behavioral issues. As a person's condition declines, they often withdraw from family and society. Gradually, bodily functions are lost, ultimately leading to death. Although the speed of progression can vary, the average life expectancy following diagnosis is three to twelve years.

The causes of Alzheimer's disease remain poorly understood. There are many environmental and genetic risk factors associated with its development. The strongest genetic risk factor is from an allele of apolipoprotein E. Other risk factors include a history of head injury, clinical depression, and high blood pressure. The progression of the disease is largely characterised by the accumulation of malformed protein deposits in the cerebral cortex, called amyloid plaques and neurofibrillary tangles. These misfolded protein aggregates interfere with normal cell function, and over time lead to irreversible degeneration of neurons and loss of synaptic connections in the brain. A probable diagnosis is based on the history of the illness and cognitive testing, with medical imaging and blood tests to rule out other possible causes. Initial symptoms are often mistaken for normal brain aging. Examination of brain tissue is needed for a definite diagnosis, but this can only take place after death.

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.

Fitness (often denoted ${\displaystyle w}$ or ω in population genetics models) is a quantitative representation of individual reproductive success. It is also equal to the average contribution to the gene pool of the next generation, made by the same individuals of the specified genotype or phenotype. Fitness can be defined either with respect to a genotype or to a phenotype in a given environment or time. The fitness of a genotype is manifested through its phenotype, which is also affected by the developmental environment. The fitness of a given phenotype can also be different in different selective environments.

With asexual reproduction, it is sufficient to assign fitnesses to genotypes. With sexual reproduction, recombination scrambles alleles into different genotypes every generation; in this case, fitness values can be assigned to alleles by averaging over possible genetic backgrounds. Natural selection tends to make alleles with higher fitness more common over time, resulting in Darwinian evolution.

Ploidy (/ˈplɔɪdi/) is the number of complete sets of chromosomes in a cell, and hence the number of possible alleles for autosomal and pseudoautosomal genes. Here sets of chromosomes refers to the number of maternal and paternal chromosome copies, respectively, in each homologous chromosome pair—the form in which chromosomes naturally exist. Somatic cells, tissues, and individual organisms can be described according to the number of sets of chromosomes present (the "ploidy level"): monoploid (1 set), diploid (2 sets), triploid (3 sets), tetraploid (4 sets), pentaploid (5 sets), hexaploid (6 sets), heptaploid or septaploid (7 sets), etc. The generic term polyploid is often used to describe cells with three or more sets of chromosomes.

Virtually all sexually reproducing organisms are made up of somatic cells that are diploid or greater, but ploidy level may vary widely between different organisms, between different tissues within the same organism, and at different stages in an organism's life cycle. Half of all known plant genera contain polyploid species, and about two-thirds of all grasses are polyploid. Many animals are uniformly diploid, though polyploidy is common in invertebrates, reptiles, and amphibians. In some species, ploidy varies between individuals of the same species (as in the social insects), and in others entire tissues and organ systems may be polyploid despite the rest of the body being diploid (as in the mammalian liver). For many organisms, especially plants and fungi, changes in ploidy level between generations are major drivers of speciation. In mammals and birds, ploidy changes are typically fatal. There is, however, evidence of polyploidy in organisms now considered to be diploid, suggesting that polyploidy has contributed to evolutionary diversification in plants and animals through successive rounds of polyploidization and rediploidization.

A gene product is the biochemical material, either RNA or protein, resulting from the expression of a gene. A measurement of the amount of gene product is sometimes used to infer how active a gene is. Abnormal amounts of gene product can be correlated with disease-causing alleles, such as the overactivity of oncogenes, which can cause cancer.A gene is defined as "a hereditary unit of DNA that is required to produce a functional product". Regulatory elements include:

• Promoter region
• TATA box
• Polyadenylation sequences
• Enhancers

These elements work in combination with the open reading frame to create a functional product. This product may be transcribed and be functional as RNA or is translated from mRNA to a protein to be functional in the cell.

The genotype of an organism is its complete set of genetic material. Genotype can also be used to refer to the alleles or variants an individual carries in a particular gene or genetic location. The number of alleles an individual can have in a specific gene depends on the number of copies of each chromosome found in that species, also referred to as ploidy. In diploid species like humans, two full sets of chromosomes are present, meaning each individual has two alleles for any given gene. If both alleles are the same, the genotype is referred to as homozygous. If the alleles are different, the genotype is referred to as heterozygous.

Genotype contributes to phenotype, the observable traits and characteristics in an individual or organism. The degree to which genotype affects phenotype depends on the trait. For example, the petal color in a pea plant is exclusively determined by genotype. The petals can be purple or white depending on the alleles present in the pea plant. However, other traits are only partially influenced by genotype. These traits are often called complex traits because they are influenced by additional factors, such as environmental and epigenetic factors. Not all individuals with the same genotype look or act the same way because appearance and behavior are modified by environmental and growing conditions. Likewise, not all organisms that look alike necessarily have the same genotype.

A nucleic acid sequence is a succession of bases within the nucleotides forming alleles within a DNA (using GACT) or RNA (GACU) molecule. This succession is denoted by a series of a set of five different letters that indicate the order of the nucleotides. By convention, sequences are usually presented from the 5' end to the 3' end. For DNA, with its double helix, there are two possible directions for the notated sequence; of these two, the sense strand is used. Because nucleic acids are normally linear (unbranched) polymers, specifying the sequence is equivalent to defining the covalent structure of the entire molecule. For this reason, the nucleic acid sequence is also termed the primary structure.

The sequence represents genetic information. Biological deoxyribonucleic acid represents the information which directs the functions of an organism.

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. Populations can diverge due to selection even when they are exchanging alleles, if the selection pressure is strong enough. Gene flow is an important mechanism for transferring genetic diversity among populations. Migrants change the distribution of genetic diversity among populations, by modifying allele frequencies (the proportion of members carrying a particular variant of a gene). High rates of gene flow can reduce the genetic differentiation between the two groups, increasing homogeneity. Gene flow has been thought to constrain speciation and prevent range expansion by combining the gene pools of the groups, thus preventing the development of differences in genetic variation that would have led to differentiation and adaptation for this reason. In some cases dispersal resulting in gene flow may also result in the addition of novel genetic variants under positive selection to the gene pool of a species or population (adaptive introgression.)

There are a number of factors that affect the rate of gene flow between different populations. Gene flow is expected to be lower in species that have low dispersal or mobility, that occur in fragmented habitats, where there are long distances between populations, and when there are small population sizes. Mobility plays an important role in dispersal rate, as highly mobile individuals tend to have greater movement prospects. Although animals are thought to be more mobile than plants, pollen and seeds may be carried great distances by animals, water or wind. When gene flow is impeded, there can be an increase in inbreeding, measured by the inbreeding coefficient (F) within a population. For example, many island populations have low rates of gene flow due to geographic isolation and small population sizes. The Black Footed Rock Wallaby has several inbred populations that live on various islands off the coast of Australia. The population is so strongly isolated that lack of gene flow has led to high rates of inbreeding.

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 either be lost completely from the population, or fixed, i.e. permanently established at 100% frequency in the population. Whether a gene will ultimately be lost or fixed is dependent on selection coefficients and chance fluctuations in allelic proportions. Fixation can refer to a gene in general or particular nucleotide position in the DNA chain (locus).

In the process of substitution, a previously non-existent allele arises by mutation and undergoes fixation by spreading through the population by random genetic drift or positive selection. Once the frequency of the allele is at 100%, i.e. being the only gene variant present in any member, it is said to be "fixed" in the population.

In genetics, dominance is the phenomenon of one variant (allele) of a gene on a chromosome masking or overriding the effect of a different variant of the same gene on the other copy of the chromosome. The first variant is termed dominant and the second is called recessive. This state of having two different variants of the same gene on each chromosome is originally caused by a mutation in one of the genes, either new (de novo) or inherited. The terms autosomal dominant or autosomal recessive are used to describe gene variants on non-sex chromosomes (autosomes) and their associated traits, while those on sex chromosomes (allosomes) are termed X-linked dominant, X-linked recessive or Y-linked; these have an inheritance and presentation pattern that depends on the sex of both the parent and the child (see Sex linkage). Since there is only one Y chromosome, Y-linked traits cannot be dominant or recessive. Additionally, there are other forms of dominance, such as incomplete dominance, in which a gene variant has a partial effect compared to when it is present on both chromosomes, and co-dominance, in which different variants on each chromosome both show their associated traits.

Dominance is a key concept in Mendelian inheritance and classical genetics. Letters and Punnett squares are used to demonstrate the principles of dominance in teaching, and the upper-case letters are used to denote dominant alleles and lower-case letters are used for recessive alleles. An often quoted example of dominance is the inheritance of seed shape in peas. Peas may be round, associated with allele R, or wrinkled, associated with allele r. In this case, three combinations of alleles (genotypes) are possible: RR, Rr, and rr. The RR (homozygous) individuals have round peas, and the rr (homozygous) individuals have wrinkled peas. In Rr (heterozygous) individuals, the R allele masks the presence of the r allele, so these individuals also have round peas. Thus, allele R is dominant over allele r, and allele r is recessive to allele R.

A blood type (also known as a blood group) is a classification of blood based on the presence and absence of antibodies and inherited antigenic substances on the surface of red blood cells (RBCs). These antigens may be proteins, carbohydrates, glycoproteins, or glycolipids, depending on the blood group system. Some of these antigens are also present on the surface of other types of cells of various tissues. Several of these red blood cell surface antigens can stem from one allele (or an alternative version of a gene) and collectively form a blood group system.

Blood types are inherited and represent contributions from both parents of an individual. As of June 2025, a total of 48 human blood group systems are recognized by the International Society of Blood Transfusion (ISBT). The two most important blood group systems are ABO and Rh; they determine someone's blood type (A, B, AB, and O, with + or − denoting RhD status) for suitability in blood transfusion.

The wild type (WT) is the phenotype of the typical form of a species as it occurs in nature. Originally, the wild type was conceptualized as a product of the standard "normal" allele at a locus, in contrast to that produced by a non-standard, "mutant" allele. "Mutant" alleles can vary to a great extent, and even become the wild type if a genetic shift occurs within the population. Continued advancements in genetic mapping technologies have created a better understanding of how mutations occur and interact with other genes to alter phenotype. It is now regarded that most or all gene loci exist in a variety of allelic forms, which vary in frequency throughout the geographic range of a species, and that a uniform wild type does not exist. In general, however, the most prevalent allele – i.e., the one with the highest gene frequency – is the one deemed wild type.

The concept of wild type is useful in some experimental organisms such as fruit flies Drosophila melanogaster, in which the standard phenotypes for features such as eye color or wing shape are altered by particular mutations that produce distinctive phenotypes, such as "white eyes" or "vestigial wings". Wild-type alleles are indicated with a "+" superscript, for example w and vg for red eyes and full-size wings, respectively. Manipulation of the genes behind these traits led to the current understanding of how organisms form and how traits mutate within a population. Research involving the manipulation of wild-type alleles has application in many fields, including fighting disease and commercial food production.

Genetic recombination (also known as genetic reshuffling) is the exchange of genetic material between different organisms which leads to production of offspring with combinations of traits that differ from those found in either parent. In eukaryotes, genetic recombination during meiosis can lead to a novel set of genetic information that can be further passed on from parents to offspring. Most recombination occurs naturally and can be classified into two types: (1) interchromosomal recombination, occurring through independent assortment of alleles whose loci are on different but homologous chromosomes (random orientation of pairs of homologous chromosomes in meiosis I); & (2) intrachromosomal recombination, occurring through crossing over.

During meiosis in eukaryotes, genetic recombination involves the pairing of homologous chromosomes. This may be followed by information transfer between the chromosomes. The information transfer may occur without physical exchange (a section of genetic material is copied from one chromosome to another, without the donating chromosome being changed) (see SDSA – Synthesis Dependent Strand Annealing pathway in Figure); or by the breaking and rejoining of DNA strands, which forms new molecules of DNA (see DHJ pathway in Figure).

Recurrent evolution also referred to as repeated or replicated evolution is the repeated evolution of a particular trait, character, or mutation. Most evolution is the result of drift, often interpreted as the random chance of some alleles being passed down to the next generation and others not. Recurrent evolution is said to occur when patterns emerge from this stochastic process when looking across multiple distinct populations. These patterns are of particular interest to evolutionary biologists, as they can demonstrate the underlying forces governing evolution.

Recurrent evolution is a broad term, but it is usually used to describe recurring regimes of selection within or across lineages. While most commonly used to describe recurring patterns of selection, it can also be used to describe recurring patterns of mutation; for example, transitions are more common than transversions. The concept encompasses both convergent evolution and parallel evolution; it can be used to describe the observation of similar repeating changes through directional selection as well as the observation of highly conserved phenotypes or genotypes across lineages through continuous purifying selection over large periods of evolutionary time.