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An allele is one of the alternative inherited states at a genetic locus, often distinguished by a difference in DNA sequence. A population can contain many alleles, although a two-copy diploid individual carries at most two at that genetic locus, one inherited from each parent. See NHGRI: allele.

Count copies, not just individuals, when computing allele frequency: in 100 individuals with genotype counts $49AA$, $42Aa$, $9aa$, there are $2(49)+42=140$ copies of $A$ among 200, so $p_A=0.70$. The heterozygotes contribute to both allele counts. This converts observed genotypes into the population quantity needed by the Hardy-Weinberg principle.

An allele fixes when all copies at the relevant locus in the population are that allele. Fixation can occur through selection or genetic drift. Spatial polymorphism means that fixation within an individual habitat need not imply fixation across a metapopulation.

The allele frequency is the proportion of gene copies at a specified genetic locus carrying an allele. Two unrelated copies can have the same observed allele without being identical by descent; under independent sampling their matching probability is the sum of squared allele frequencies. Pedigree autozygosity instead traces copies to the same ancestral copy.

Measurement of the relative expression of distinguishable alleles within the same sample. In an informative hybrid, the shared cellular environment helps test local regulatory differences, but mapping bias and parent-of-origin effects can complicate interpretation.

pleiotropy in which a change has benefits and costs in different traits, environments, sexes or life stages. Whether an allele spreads depends on its net contribution to genotype fitness, rather than the sign of any one effect.

A chromosome carries genes and other genetic material. A haplotype records the alleles carried on one chromosome at specified genetic loci.

In a typical eukaryotic cell nucleus, an unreplicated chromosome comprises one long double-stranded DNA molecule with associated proteins; a replicated chromosome comprises two associated sister chromatids. It need not be X-shaped: that familiar outline depicts a condensed, replicated state.^[ref]

For these ordinary centromere-bearing chromosomes, count by centromere units before separation: the paired sister centromere regions count together as one replicated chromosome. Once sister chromatids separate in anaphase of mitosis or meiosis II, each becomes a daughter chromosome. Thus the undivided anaphase biological cell in the $2n=6$ mitotic example transiently contains twelve daughter chromosomes, but each pole receives six and each completed daughter cell nucleus remains diploid. State the counting compartment and stage; summing both poles is not the ploidy of one daughter.

For a specified characteristic, complete dominance means that the heterozygote has the same phenotype as one of the two homozygotes. It does not mean that the dominant allele is more common, more advantageous, or transmitted more often. Penetrance specifies the conditional probability of an expressed phenotype given a genotype and is a separate modeling assumption.

Targeted alteration of a genome using a guide-directed CRISPR system. Independent targeting reagents, verification of the resulting alleles and functional rescue help distinguish an intended effect from unrelated damage.

Transfer of pollen between different individuals of the same species; compare self-pollination.^[ref]

A flower can contain both reproductive groups and still receive pollen from another individual. Conversely, transfer between two flowers on one plant does not by itself imply cross-pollination. Following the donor and recipient individuals makes pollination useful for studying genetics: organ position alone cannot identify whose alleles meet at fertilization.

Diploid biological cells have two sets of chromosomes. In the ordinary one-locus inheritance model, a diploid genotype therefore contains two allele copies at each genetic locus.

Two homologous chromosomes of a given type are distinct inherited members of the two sets; the two sister chromatids of one replicated chromosome are its copied members. In the stipulated $2n=6$ example, a diploid G2 phase cell nucleus has six replicated chromosomes, not twelve sets or twelve independently counted chromosomes.

A harmful interaction between alleles that evolved in separate lineages and are compatible with their own genetic backgrounds. For example, substitutions yielding $Ab$ and $aB$ can each be tolerated, while the combination $AB$ is harmful in a hybrid. This is a form of epistasis.

The relationship between the phenotype of a heterozygote and those of the two corresponding homozygotes at a genetic locus. Under complete dominance, one allele gives the same phenotype in the heterozygote as in its homozygote; the term describes expression rather than the frequency or evolutionary advantage of the allele.

Evolution is descent with inherited modification. Within a population, changes in allele frequencies provide a precise genetic description; over longer histories, branching descent connects populations through common descent. An individual growing larger is biological development, whereas an inherited variant becoming more frequent across generations is evolution. See UC Museum of Paleontology: the definition of evolution.

Mutation supplies new alleles, genetic recombination reshuffles inherited material, natural selection favors variants with greater reproductive contribution in a specified environment, and genetic drift changes frequencies through chance. Gene flow moves variants between populations. Consequently, an increasing allele frequency alone does not identify natural selection. See Clark, Douglas and Choi, Biology 2e: population genetics.

Evidence includes ordered fossils, shared inherited structures and similarities in DNA; phylogenetics uses such observations to infer relationships. A phylogenetic tree is an inferred historical account, with uncertainty about particular branches. See Clark, Douglas and Choi, Biology 2e: evidence of evolution. Evidence also comes from experiments: Blount, Borland and Lenski reported an Escherichia coli lineage able to use citrate with oxygen present by 31,500 generations, and tested historical dependence by replaying evolution from stored ancestors. See Blount, Borland and Lenski, 2008: original experimental report. Such observations constrain explanations; no single frequency equation captures every evolutionary process.

Experimental tractability is the practical ability to cultivate a system, manipulate the variables of interest, and obtain an interpretable readout with appropriate scientific controls. In Saccharomyces cerevisiae, inexpensive cultivation, accessible haploid and diploid states, and tools for introducing DNA make controlled changes of genotype feasible. A haploid biological strain exposes a changed allele without a second copy at that genetic locus, while crosses and meiosis permit tests of inheritance. ^[ref]

An accessible readout is not necessarily a direct measurement of the mechanism. Growth of a biological colony integrates many cellular functions. Failure to grow could reflect the intended gene deletion, unsuitable conditions, failed genetic transformation, or another mutation. Matching the genetic background and using scientific controls narrows these alternatives. Ease of doing an experiment and strength of its inference are distinct advantages.

The proposal that genetic recombination can accelerate adaptation by combining beneficial alleles that arise in different lineages. Recombination also produces other combinations, so the benefit depends on the inherited associations and ensuing natural selection.

The probability that an allele eventually occupies every copy at the specified genetic locus under a population model. For a rare favorable variant in a suitable large-population, small-effect branching approximation, $P_{\mathrm{fix}}\approx 2s$; inheritance, reproduction and competition assumptions matter.

A gene is an inherited functional unit of genetic material. In cellular organisms, a gene is a region of DNA whose information produces a functional RNA or contributes to a protein. This connects inheritance to cellular chemistry: a change in a gene can alter the amount or activity of a protein, and thereby a phenotype. See NHGRI: gene.

Alternative inherited versions at a genetic locus are alleles. The distinction matters: two parents can carry the same gene but different alleles, and a genetic locus can have variation outside a gene. Neither the word gene nor a change in DNA alone specifies the resulting phenotype.

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The genetic background is the rest of the genotype against which a focal allele or gene deletion is studied. Other genes can influence the resulting phenotype, so comparisons should specify which background is held fixed.

A genetic genetic carrier has one disease-associated recessive allele and one normal allele at a genetic locus, and is unaffected under a fully penetrant recessive model. Two genetic carriers have affected-offspring probability $1/4$ under Mendelian segregation; a genetic carrier and an individual with no disease allele have affected-offspring probability zero under that same mutation-free model.

Genetic drift is random variation of allele frequencies due to finite-population reproduction. In the neutral ancestry description, randomly sampled gene copies merge into common ancestors according to Kingman's coalescent.

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