Gene Conservation Laboratory
Glossary of Terms
To assist with understanding technical language, definitions of commonly used terms used in genetic analyses are listed here. See our glossary of terms for commonly used terms in salmon management.
- Allele Alternative form of a given gene or DNA sequence.
- Bootstrapping Pseudorandom resampling of data with replacement to estimate the error of estimates of parameters of interest.
- Credibility Interval In Bayesian statistics, a credibility interval is a posterior probability interval. Credibility intervals differ from the confidence intervals in frequentist statistics in that they do not assume an underlying distribution (e.g., normal distribution) and are direct statements of probability: i.e., a 90% credibility interval has a 90% chance of containing the true answer.
- Effective Population Size (Ne). The size of an ideal population that would be affected by genetic drift at the same rate as the actual population. This idealized population has discrete generations, an even sex ratio, constant size, random union of gametes and random survivorship of offspring (Kalinowski and Waples 2002).
- F-statistics (FIS, FST, FIT). Measures used to hierarchically partition genetic diversity within and among populations. Common measures include: 1) FIS, which is the average departure of genotype frequencies from Hardy-Weinberg expectations within a population; 2) FST, which is the proportion of the variation due to allele-frequency differences among populations; and 3) FIT, which is the departure of genotype frequencies from Hardy-Weinberg expectations relative to the entire collection of populations. In this common hierarchy, the subscripts refer to comparisons between levels in the hierarchy: IS refers to individuals within populations, ST to subpopulations within the total population, and IT to individuals within the total population. Hierarchies and subscript notation can be extended to any level to accommodate different study designs.
- Genetic Drift Chance changes in allele frequencies that result from the sampling of gametes from generation to generation in a finite population. The magnitude of these changes is inversely related to twice effective population size (2Ne), because each diploid fish carries two sets of genes.
- Genetic Marker (Marker) A known DNA sequence that can be identified by a simple assay. For the purpose of this document, a marker can be a single SNP or a combination of SNPs.
- Genotype The set of alleles at one or more loci for an individual.
- Hardy-Weinberg Expectations (HWE). Genotypic frequencies expected from given allele frequencies, assuming random mating, no mutation (the alleles do not change), no migration or emigration (no exchange of alleles between populations), infinitely large population size, and no selective pressure for or against any of the genotypes.
- Heterozygosity The proportion of individuals in a population that carry two different alleles at a particular marker. This statistics can be used as a measure of genetic variability in a population.
- Gametic Disequilibrium (or Linkage Disequilibrium) A state that exists in a population when alleles at different loci are not distributed independently of each other in a population’s gamete pool, often because the loci are physically linked on the same fragment of DNA.
- Locus (plural Loci). A fixed position or region on a chromosome that may contain more than one genetic marker.
- Mitochondrial DNA (mtDNA). Circular, maternally inherited DNA located outside the nucleus in organelles in a cell called mitochondria.
- Mixed Stock Analysis (MSA). Method using allele frequencies from populations and genotypes from mixture samples to estimate stock compositions.
- Microsatellites DNA sequences containing short (2–5 base pairs) tandem repeats of nucleotides (e.g., GTGTGTGT).
- Polymerase Chain Reaction (PCR). The enzymatic amplification a single or few copies of a DNA fragment several orders of magnitude, generating millions of copies.
- Population A randomly mating group of fish that are largely reproductively isolated from other populations.
- Reporting Group A group of populations in a genetic baseline to which portions of a mixture are allocated during mixed stock analyses. In this study, reporting groups were constructed based on stakeholder needs, on the extent of genetic distinction among populations, and on advice from the WASSIP Technical Committee and Advisory Panel.
- Single nucleotide polymorphism (SNP). DNA sequence variation occurring when a single nucleotide (A, T, C, or G) differs among individuals or within an individual between paired chromosomes.
Kalinowski, S. T., and R. S. Waples. 2002. Relationship of effective to census size in fluctuating populations. Conservation Biology 16(1):129–136.