USFWS
Genetic Monitoring for Managers
Alaska

 

Glossary

The following glossary was obtained with permission from the following resource: Allendorf, F.W., and G. Luikart. 2007. Conservation and the Genetics of Populations. Blackwell Publishing. 642 pp.

A B C D E F G H I J K L M N O P Q R S T U V W X Y Z

ABC: See approximate Bayesian computation.

acrocentric: Chromosomes and chromatids with a centromere near one end.

addition rule: See sum rule.

additive genetic variation: The portion of total genetic variation that is the average effect of substituting one allele, responsible for a phenotypic trait, for another. The proportion of genetic variation that responds to natural selection.

admixture: The formation of novel genetic combinations through hybridization of genetically distinct groups.

AFLP: See amplified fragment length polymorphism.

agamospermy: The asexual formation of seeds without fertilization in which mitotic division is sometimes stimulated by male gametes.

alien species: A non-native or nonindigenous species.

allele: Alternative form of a gene.

allelic diversity: A measure of genetic diversity based on the average number of alleles per locus present in a population.

allelic richness: A measure of the number of alleles per locus; allows comparison between samples of different sizes by using various statistical techniques (e.g., rarefaction).

allopatric: Species or populations that occur in geographically separate areas.

allopolyploid: A polyploid originating through the addition of unlike chromosome sets, often in conjunction with hybridization between two species.

allozygous: An individual whose alleles at a locus are descended from different ancestral alleles in the base population. Allozygotes may be either homozygous or heterozygous in state at this locus.

allozyme: An allelic enzyme detected through protein electrophoresis used in many genetic applications such as hybrid identification and estimation of genetic variation.

AMOVA: See analysis of molecular variation.

amplified fragment length polymorphism (AFLP): A technique that uses PCR to amplify genomic DNA, cleaved by restriction enzymes, in order to generate DNA fingerprints; it is a combination of RFLP and arbitrary primer PCR. It does not require prior sequence knowledge.

amplify: To use PCR to make many copies of a segment of DNA.

anagenesis: Evolutionary changes that occur within a single lineage through time. See cladogenesis.

analysis of molecular variation (AMOVA): A statistical approach to partition the total genetic variation in a species into components within and among populations or groups at different levels of hierarchical subdivision. Analogous to ANOVA in statistics.

aneuploid: A chromosomal condition resulting from either an excess or deficit of a chromosome or chromosomes so that the chromosome number is not an exact multiple of the typical haploid set in the species.

anneal: The joining of single strands of DNA because of the pairing of complementary bases. In PCR, primers anneal to complementary target DNA sequences during cooling of the DNA (after DNA is made single stranded by heating).

ANOVA: Analysis of variance.

apomixis: Seed development without fertilization and meiosis. An apomict or apomictic plant produces seeds that are genetically identical to the parent plant.

approximate Bayesian computation(ABC): A statistical framework using simulation modeling to approximate the Bayesian posterior distribution of parameters of interest (e.g., Ne, Nm) often by using multiple summary statistics (He, number of alleles, FST). It is far faster computationally than fully Bayesian approaches but generally slightly less accurate and precise.

artificial selection: Anthropogenic selection of phenotypes, with a heritable genetic basis, to elicit a desired phenotypic change in succeeding generations.

ascertainment bias: Selection of loci for marker development(e.g., SNPs or microsatellites) from an unrepresentative sample of individuals, or using a particular method, which yields loci that are not representative of the spectrum of allele frequencies in a population. For example, the choice of loci with high heterozygosity may bias assessments of allele frequency distributions in future studies using the loci such that alleles at low frequency (rare alleles) are underrepresented.

assignment tests: A statistical method using multilocus genotypes to assign individuals to the population from which they most likely originated (i.e., in which their expected multilocus genotype frequency is highest).

associative overdominance: An increase in fitness of heterozygotes at a neutral locus because it is in gametic disequilibrium at a locus that is under selection. Also known as pseudo-overdominance. Compare with hitchhiking.

assortative mating: Preferential mating between individualswith a similar (or a different) phenotype is referred to positive (or negative) assortative mating. See also disassortative mating.

autogamy: Self-fertilization in a hermaphroditic specieswhere the two gametes fused in fertilization come from the same individual.

autosomal: A locus that is located on an autosome (i.e., not on a sex chromosome).

autosomes: Chromosomes that do not differ between sexes.

autozygosity: A measure of the expected homozygosity where alleles are identical by descent.

autozygous: Individuals whose alleles at a locus are identical by descent from the same ancestral allele.

B chromosome: See Supernumerary chromosome.

balancing selection: Diversifying selection that maintains polymorphism resulting from such mechanisms as frequency-dependent selection, spatially heterogeneous selection, or heterozygous advantage.

Barr bodies: Inactivated X chromosomes in female mammals that condense to form a darkly colored structure in the nuclei of somatic cells.

Bayesian inference: A procedure of statistical inference in which observed data are interpreted not as frequencies or proportions, but rather are used to compute the probability that a hypothesis is true, given what was observed. Bayesian inference also allows for the incorporation of prior data or information. Bayes’ theorem is named after the Reverend Thomas Bayes.

binomial proportion: A population will be in binomial proportions when it conforms to the binomial distribution so that the occurrence of a given event X, ri times with a probability (pi) of success, in a population of n total events, is not significantly different than that which would be expected based on random chance alone.

biogeography: The study of the geographic distribution of species and the principles and factors influencing these distributions.

biological species concept (BSC): Groups of naturally occurringinterbreeding populations that are reproductively isolated from other such groups or species.

BLAST: Basic Local Alignment Search Tool. Software program to search a DNA sequence data base for sequence similar to the one in hand.

Bonferroni correction: A correction used when several statistical tests are being performed simultaneously (since while a given á-value may be appropriate for each individual comparison, it is not for the set of all comparisons). In order to avoid a lot of spurious positives, the á-value needs to be adjusted to account for the number of comparisons being performed. Suppose we are testing for Hardy–Weinberg proportions at 20 loci. Instead of using the traditional 0.05 alpha-level, we would test at alpha of 0.05/20 = 0.0025 level. This insures that the overall chance of making a Type I error is still less than 0.05.

bootstrap analysis: A nonparametric statistical analysis for computing confidence intervals for a phylogeny or a point estimate (e.g., of FST). Re-sampling with replacement to estimate the proportion of times an event (such as the positioning of a node on a phylogenetic tree) appears during multiple re-sampling of a data set.

bottleneck: A special case of strong genetic drift where a population experiences a loss of genetic variation by temporarily going through a marked reduction in effective population size. In demography, a severe transient reduction in population size.

branch length: Length of branches on a phylogenetic tree. Often proportional to the amount of genetic divergence between species or groups.

broad sense heritability (HB): The proportion of phenotypic variation within a population that is due to genetic differences among individuals.

BSC: See biological species concept.

cDNA: Complementary DNA.

candidate gene: A gene, located in a chromosome region suspected of being involved in the expression of a trait such as a disease, whose protein product suggests that it could be the gene in question. A candidate gene can also be identified by association with the phenotype and by linkage analysis to a region of the genome.

census population size: The number of individuals in a population.

centromere: An constricted region of a chromosome containing spindle microtubules responsible for chromosomal movement during mitosis and meiosis.

chi-square test: A test of statistical significance based on the chi-squared statistic, which determines how closely experimental observed values fit theoretical expected values.

chloroplast DNA (cpDNA): A circular DNA molecule located in chloroplasts. Forty to 80 copies occur per organelle and replication occurs throughout the cell cycle.

chromosome: A molecule of DNA in association with proteins (histones and non-histones) constituting a linear array of genes. In prokaryotes, the circular DNA molecule contains the set of instructions necessary for the cell.

CITES: See Convention on International Trade in Endangered Species of Wild Fauna and Flora.

clade: A species, or group of species that has originated and includes all the descendents from a common ancestor. A monophyletic group.

cladistics: The classification of organisms based on phylogeny.

cladogenesis: The splitting of a single evolutionary lineage into multiple lineages.

cladogram: A diagram illustrating the relationship between taxa that is built using synapomorphies. Also called a phylogeny.

cline: A gradual directional change in a character across a geographic or environmental gradient. It usually refers to increased differences among populations in the frequency of an allele or trait with increased geographic distance.

coalescent: Relating to the mathematical and statistical properties of genealogies. A modelling framework in which two DNA sequence lineages converge in a common ancestral sequence, going backwards in time.

codon: A three nucleotide sequence on a strand of mRNA that gets translated into a specific amino acid forming a protein.

comparative anchor-tag sequences (CATS): Exon sequences that are conserved across taxa allowing the design of primers that amplify in divergent species (for example, across mammal orders).CATS-like primers speed the discovery of SNPs (in exons or introns) and comparative genome mapping across taxa.

conservation breeding: Efforts to manage plant and animal species breeding that do not necessarily involve captivity.

conservation collections: Living collections of rare or endangered organisms established for the purpose of contributing to the survival and recovery of a species.

conspecific: A member of the same species.

continuous characters: Phenotypic traits that are distributed continuously throughout the population (e.g., height or weight).

continuous distribution model of migration: Individuals are continuously distributed across the landscape; neighborhoods of individuals exist that are areas within which panmixia occurs, and across which genetic differentiation occurs due to isolation by distance.

Convention on International Trade in Endangered Species of Wild Fauna and Flora (CITES):
An agreement among 145 countries that bans commercial international trade in an agreed-upon list of endangered species, and that regulates and monitors trade in others that might become endangered.

converged: The point where a MCMC simulation has become independent of starting parameter biases, or has been “burnt in”. Typically, thousands of simulation steps are required (and discarded) before the MCMC simulation is used to estimate a parameter (e.g., Ne, Nm, etc.)

countergradient variation: Occurs when genetic effects on a trait oppose or compensate for environmental effects so that phenotypic differences across an environmental gradient among populations are minimized.

cpDNA: See chloroplast DNA.

CU: Conservation unit.

cultivars: A human-cultivated plant that was derived through athropogenenic selection.

cytogenetics: A discipline of science combining cytology, the study of cells (their structure, function, and life history), and genetics.

cytoplasmic genes: Genes located in cellular organelles such as mitochondria and chloroplasts.

degrees of freedom: The total number of items in a data set that are free to vary independently of each other. In testing for Hardy–Weinberg proportions this is the number of possible genotypes minus the number of alleles because the frequency of homozygous genotypes are determined by the frequency of heterozygous genotypes.

deme: A local conspecific group of individuals that mate at random.

demographic: Topics relating to the structure and dynamics of populations, such as birth, death, and migration rates.

demographic stochasticity:
Differences in the dynamics of a population that are the effects of random events on individuals in the population.

dendrogram: A tree diagram that serves as a visual representation of the relationships between populations within a species.

derived: A derived character is one found only in a particular lineage within a larger group. For example, feathers are derived characters that distinguish birds from their reptile ancestors.

deterministic: Events that have no random or probabilistic aspects but rather occur in a completely predictable fashion.

diagnostic locus: A locus that is fixed, or nearly fixed for different alleles allowing differentiation between parental species, populations, or their hybrids.

dioecious: Varieties or species of plants that have separate male and female reproductive organs on unisexual individuals.

diploid: The condition in which a cell or individual has two copies of every chromosome.

directional selection: The selective increase in the frequency of an advantageous allele, gene, or phenotypic trait in a population.

disassortative mating: Preferential mating of individuals with different phenotypes.

discrete generations: Generations that can be defined by whole integers and in which all individuals will breed only with individuals in their generation (e.g., pink salmon or annual flowers without a seed bank).

dispersal: In ecological literature dispersal is the movement of individuals from one genetic population (or birth place) into another. Dispersal is also known as migration in genetics literature.

distinct population segment (DPS): A level of classification under the ESA that allows for legal protection of populations that are distinct, relatively reproductively isolated, and represent a significant evolutionary lineage to the species.

DNA: Deoxyribonucleic acid.

DNA barcoding: The use of a short gene sequence from a standardized region of the genome that can be used to help discover, characterize, and distinguish species, and to assign unidentified individuals to species.

DNA fingerprinting: Individual identification through the use of multilocus genotyping.

Dobzhansky–Muller incompatibilities: Genic interactions between alleles at multiple loc in which alleles that enhance fitness within their parental genetic backgrounds may reduce fitness in the novel genetic background produced by hybridization.

dominance genetic variation: The proportion of total genetic variation that can be attributed to the interactions of alleles at a locus in heterozygotes.

dominant: An allele (A) whose phenotypic effect is expressed in both homozygotes (AA) and heterozygotes (Aa).

DPS: See distinct population segment.

ecosystem: A community of organisms and its environment.

ecosystem services: The products and services humans receive from functioning ecosystems.

ecotone: The region that encompasses the shift between two biological communities.

effective number of alleles: The number of equally frequent alleles that would create the same heterozygosity as observed in the population.

effective population size (Ne): The size of the ideal, panmictic population that would experience the same loss of genetic variation, through genetic drift, as the observed population. Or, roughly the number of breeding individuals that produce offspring that live toreproductive age. It influences the rate of loss of genetic variation, the efficiency of natural selection, and the accumulation of beneficial and deleterious mutations. It is frequently much smaller than the number of individuals in a population.

electrophoresis: The movement of molecules through a medium across an electric field. Electrophoresis is used to separate allelic enzymes (allozymes) and DNA molecules of differing charge, size, or shape.

Endangered Species Act of the United States: ESA.

endonuclease: An enzyme that cleaves either a single, or both, strands of a DNA molecule. Bacterial endonucleases are used to split genomic DNA at specific sites for analysis. See restriction enzyme.

Environmental Protection Agency of the United States: EPA.

environmental stochasticity: Random variation in environmental factors that influence population parameters affecting all individuals in that population.

epidemiology: The study of the spread and control of a disease in a population.

epistatic genetic variation: The proportion of total genetic variation that can be attributed to the interaction between loci producing a combined effect different from the sum of the effects of the individual loci.

ESPA: Endangered Species Protection Act of Australia.

evolutionary significant unit (ESU): A classification of populations that have substantial reproductive isolation which has led to adaptative differences so that the population represents a significant evolutionary component of the species. Evolutionary significant units have also been classified as populations that exhibit reciprocal monophyly and no recent gene flow. The original term used was “evolutionarily” rather than “evolutionary” (Ryder 1986). However, both terms are currently used in the literature.

ex situ conservation: The conservation of important evolutionary lineages of species outside the species natural habitat.

exact tests: An approach to compute the exact P-value for an observed result rather than use an approximation, such as the chi-square distribution.

exon: A coding portion of a gene that produces a functional gene product (e.g., a peptide).

exon-primed intron-crossing PCR (EPIC-PCR): EPIC primers are designed in conserved exons and amplify intron sequences that are generally more polymorphic
than exons, which are therefore useful for the development of SNP or RFLP markers.

expectation maximization algorithm (EM): A computational tool in statistics for finding maximum likelihood estimates of parameters in probabilistic models, where the model depends on unobserved variables. It can provide an estimate of the most likely allele frequencies assuming the sample is in Hardy–Weinberg proportions. Bayesians also use the EM algorithm to optimize the a posteriori distribution to compute the maximum a posteriori (MAP) estimate of an unknown parameter.

expressed sequence tags (ESTs). Short DNA sequences (several hundred base pairs) that are produced by reverse transcription of mRNA into DNA. ESTs are cDNAs that consist of exons and the sequences that flank exons. The sequencing of ESTs allows rapid identification (‘tagging’) of genes and can expedite DNA marker (SNP) development in coding genes.

extant: Currently living; not extinct.

extinction: The disappearance of a species or other taxon so that it no longer exists anywhere.

extirpation: The loss of a species or subspecies from a particular area, but not from its entire range.

FCA: Frequency correspondence analysis.

Fst: The most widely used index of genetic divergence between populations. A standardized measure of the distribution of genetic variation between populations on a scale between 0 (identical allele frequencies in populations) and 1 (populations
fixed for different alleles).

fecundity: The potential reproductive capacity of an individual or population (e.g., the number of eggs or young produced by an individual per unit time).

fertility: The ability to conceive and have offspring. Sometimes used for fecundity.

Fisher–Wright model: See Wright–Fisher model.

fitness: The ability of an individual, or genotype to survive and produce viable offspring. Quantified as the number of offspring contributed to the next generation, or as proportion of the individual’s genes in all the genes contributed to the next generation.

fitness rebound: Following an episode of inbreeding depression, successive generations of breeding may result in a rebound in fitness due to the selective decrease in frequency of deleterious alleles (purging). If inbreeding depression is due to deleterious recessive alleles (with negative fitness effects in a homozygous state) then successive generations of inbreeding may result in a rebound in fitness due to the selective decrease in frequency of deleterious alleles.

fixation index: The proportional increase of homozygosity through population subdivision. FST is sometimes referred to as the fixation index.

fluctuating asymmetry (FA): Asymmetry in which deviations from symmetry are randomly distributed about a mean of zero. FA provides a simple measure of developmental precision or stability.

forensics: The use of scientific methods and techniques, such as genetic fingerprinting, to solve crimes.

founder effect: A loss of genetic variation in a population that was established by a small number of individuals that carry only a fraction of the original genetic diversity from a larger population. A special case of genetic drift.

frequency-dependent selection: Natural selection in which fitness varies as a function of the frequency of a phenotype.

gametic disequilibrium: Nonrandom association of alleles at different loci within a population. Also known as linkage disequilibrium.

gametic equilibrium: Random association of alleles at different loci within a population. Also known as linkage equilibrium.

gametogenesis: The creation of gametes through meiosis.

gene: A segment of DNA whose nucleotide sequence codes for protein or RNA, or regulates other genes.

gene drop: Simulation of the transmission of alleles in a pedigree. Each founder is assigned two unique alleles, and the alleles are then passed on from parent to offspring, with each offspring receiving one allele chosen at random from each parent (modeling Mendelian segregation), until all individuals in the pedigree have an assigned genotype.

gene flow: Exchange of genetic information between demes through migration.

gene genealogies: The tracing of the inherited history of the genes in an individual. Gene genealogies are most easily constructed using nonrecombining DNA such as mtDNA or the mammalian Y chromosome.

genet: A genetically unique individual.

genetic assimilation: A process in which phenotypically plastic characters that were originally “acquired” become converted into inherited characters by natural selection. This term also has been applied to the situation in which hybrids are fertile and displace one or both parental taxa through the production of hybrid swarms (i.e., genomic extinction).

genetic distance matrix: A pairwise matrix composed of differentiation between population (or individual) pairs that is calculated using a measure of genetic divergence such as FST.

genetic divergence: The evolutionary change in allele frequencies between reproductively isolation populations.

genetic draft: A stochastic process in which selective substitutions at one locus will reduce genetic diversity at neutral linked loci through hitchhiking.

genetic drift: Random changes in allele frequencies in populations between generations due to binomial sampling of genes during meiosis. Genetic drift is more pronounced in small populations.

genetic engineering: A process in which an organism’s genes are selectively modified, often through splicing DNA fragments from different chromosomes or species, to achieve a desired result.

genetic exchange: See gene flow.

genetic load: The decrease in the average fitness of individuals in a population due to deleterious genes or heterozygous advantage.

genetic marker: A gene or DNA sequence with a known location on a chromosome that can be used to identify cells, individual or species. It can be described as a variation, which may arise due to mutation or alteration in the genomic loci, that can be observed. A genetic marker may be a short DNA sequence, such as a microsatellite or a sequence surrounding a single base-pair change (single nucleotide polymorphism, SNP), or a long one, like minisatellites.

genetic rescue: The recovery in the average fitness of individuals through increased gene flow into small populations, typically following a fitness reduction due to inbreeding depression.

genetic stochasticity: Random changes in the genetic characteristics of populations through genetic drift and binomial sampling of alleles during Mendelian segregation.

genetic swamping: The loss of locally adapted alleles or genotypes caused by constant immigration and gene flow.

genetics: The study of how genes are transmitted from one generation to the next and how those genes affect the phenotypes of the progeny.

genome: the entirety of an organism's hereditary information. It is encoded either in DNA or, for many types of virus, in RNA. The genome includes both the genes and the non-coding sequences of the DNA.

genome typing: The simultaneous genotyping of hundreds of loci from across the
genome,which ideally include smapped loci and different classes of loci such as allozymes, microsatellites and AFLPs, or synonymous (non-coding) and non-synonymous nucleotide polymorphisms.

genomic extinction: The situation in which hybrids are fertile and displace one or both parental taxa through the production of hybrid swarms so that the parentals no longer exist even though the parental alleles are still present.

genomic ratchet: A process where hybridization producing fertile offspring will result in a hybrid swarm over time, even in the presence of outbreeding depression and with relatively few hybrids per generation.

genomics: The study of the structure or function of large numbers of genes in a genome.

genotype: An organism’s genetic composition.

gynodioecy: The occurrence of female and hermaphroditic individuals in a population of plants.

haploid: The condition in which a cell or individual has one copy of every chromosome.

haplotype: The combination of alleles at loci that are found on a single chromosome or DNA molecule.

haplotype blocks: Long stretches (tens of megabases) along a chromosome that have low recombination rates (and relatively few haplotypes).Adjacent blocks are
separated by recombination hot spots (short regions with high recombination rates).

Hardy–Weinberg principle: The principle that allele and genotype frequencies will reach equilibrium, defined by the binomial distribution, in one generation and remain constant in large random mating populations that experience no migration, selection, mutation, or nonrandom mating.

Hardy–Weinberg proportion: A state in which a population’s genotypic proportions equal those expected with the binomial distribution.

hemizygous: A term used to denote the presence of only one copy of an allele due a locus being in a haploid genome, on a sex chromosome, or only one copy of the locus being present in an aneuploid organism.

heritability: The proportion of total phenotypic variation within a population that is due to individual genetic variation (HB; broad sense heritability). Heritability is more commonly referred to as the proportion of phenotypic variation within a population that is due to additive genetic variation (HN; narrow sense heritability).

hermaphrodite: An individual that produces both female and male gametes.

heterochromatin: Highly folded chromosomal regions that contain few functional genes. When these traits are characteristic of an entire chromosome, it is a heterochromosome or supernumerary chromosome.

heterogametic: The sex that is determined with different sex chromosomes (e.g., the male in mammals (XY) and female in birds (ZW) ).

heteroplasmy T: he presence of more than one mitochondrial DNA haplotype in a cell.

heterosis: A case when hybrid progeny have higher fitness than either of the parental organisms. Also called hybrid vigor.

heterozygosity: A measure of genetic variation that accounts for either the observed, or expected proportion of individuals in a population that are heterozygotes.

heterozygote: An organism that has different alleles at a locus (e.g., Aa).

heterozygous advantage: A situation where heterozygous genotypes are more fit than homozygous genotypes. This fitness advantage can create a stable polymorphism. Also called overdominance.

heterozygous disadvantage: A situation where heterozygous genotypes are less fit than homozygous genotypes. Also called underdominance.

HFC: Heterozygosity–fitness correlation.

Hill–Robertson effect: An effect where selection at one locus will reduce the effective population size of linked loci; increasing the chance of genetic drift forming negative genetic associations that reduce the ability of associating loci to respond to selection. See also genetic draft.

hitchhiking: The increase in frequency of a selectively neutral allele through gametic disequilibrium with a beneficial allele that selection increases in frequency in a population.

homogametic: The sex that possesses the same sex chromosomes (e.g., the female in mammals (XX) and male in birds (ZZ)).

homoplasmy: The presence of a single mitochondrial DNA haplotype within a cell.

homoplasy: Independent evolution or origin of similar traits, or gene sequences. At a locus, homoplasy can result from back mutation or mutation to an existing allelic state.

homozygosity: A measure of the proportion of individuals in a population that are homozygous; it is the reciprocal of heterozygosity.

homozygote: An organism that has two or more copies of the same alleles at a locus (e.g., AA).

homozygosity excess: A higher Hardy–Weinberg equilibrium homozygosity than
that which is expected in a population at mutation–drift equilibrium with the same
observed number of alleles. This is not an excess of homozygotes (deviation from
Hardy–Weinberg proportions).

hybrid sink: The situation where immigration of locally unfit genotypes produces hybrids with low fitness that reduces local density and thereby increases the immigration rate.

hybrid swarm: A population of individuals that are all hybrids by varying numbers of generations of backcrossing with parental types and matings among hybrids.

hybrid vigor: See heterosis.

hybrid zone: An area of sympatry between two genetically distinct populations where hybridization occurs without forming a hybrid swarm in either parental population beyond the area of co-occurrence.

hybridization: Mating between individuals of two genetically distinct populations.

identical by descent: Alleles that are identical copies of the same allele from a common ancestor.

inbreeding: The mating between related individuals that results in an increase of homozygosity in the progeny because they possess alleles that are identical by descent.

inbreeding coefficient: A measure of the level of inbreeding in a population that determines the probability that an individual possesses two alleles at a locus that are identical by decent. It can also be used to describe the proportion of loci in an individual that are homozygous.

inbreeding depression: The reduction in fitness of progeny from matings between related individuals compared to progeny from unrelated individuals.

inbreeding effect: Inbreeding eventually will occur in panmictic small populations due to the individuals becoming increasingly related through time.

inbreeding effective number (NeI): The size of the ideal panmictic population that loses heterozygosity at the same rate as the observed population.

introduction: The placement, or escape, of a species or individual into a novel habitat. Often introductions are used in conservation to aid genetic rescue of isolated populations.

introgression: The incorporation of genes from one population to another through hybridization that results in fertile offspring that further hybridize and backcross to parental populations.

intron: A portion of a gene that produces a nonfunctional RNA strand that is cleaved prior to translation; a noncoding region between the exons.

invasive species: An introduced alien species that is likely to cause harm to the natural ecosystem, the economy, or human health.

island model of migration: A model of migration in which a population is subdivided into a series of demes, of size N, that randomly exchange migrants at a given rate, m.

isolation by distance: The case where genetic differentiation is greater the further individuals (or populations) are from each other because gene flow decreases as geographic distance increases. Originally individuals used in the case where individuals are distributed continuously across large landscapes (e.g., coniferous tree species across boreal forests) and are not subdivided by sharp barriers to gene flow.

ISSR: Intersimple sequence repeat markers that use similar PCR methods as PINE fragments, but have primers based on simple sequence repeats of microsatellites.

IUCN: World Conservation Union (formerly International Union for Conservation of Nature).

karyotype: The composition of the chromosomal complement of a cell, individual, or species.

landscape genetics: The study of the interaction between landscape or environmental features and population genetics, such as gene flow.

LE: See lethal equivalent.

lek: A specific area where the males of a population that exhibits female sexual will congregate and display for females.

lethal equivalent: The number of deleterious alleles in an individual whose cumulative effect is the same as that of a single lethal allele. For example, four alleles each of which would be lethal 25% of the time (or to 25% of their bearers), are equivalent to one lethal allele.

library: Collection of DNA fragments from a given organism “stored” in a virus or bacteria.

likelihood statistics: An approach for parameter estimation and hypothesis testing that involves building a model (i.e., a likelihood function) and the use of the raw data (not a summary statistic), which often provides more precision and accuracy than frequentist statistic approaches (method of moments). The parameter of interest is estimated as the member of the parameter space that maximizes the probability of obtaining your observed data. Likelihood approaches facilitate comparisons between different models (e.g., via likelihood ratio tests) and thus the testing of alternate hypotheses (e.g., stable versus declining population size).

lineage sorting: A process where different gene lineageswithin an ancestral taxon are lost by drift or replaced by unique lineages evolving in different derived taxa.

linkage disequilibrium: The nonrandom association of alleles between linked loci. Also called gametic disequilibrium.

linkage equilibrium: Random association of alleles between liked loci. Also called gametic equilibrium.

local: Greater fitness of individuals in their local habitats due to natural selection.

local scale: The spatial scale at which individuals routinely interact with their environment.

locus: The position on a chromosome of a gene or other marker.

log of odds ratio (LOD): The odds ratio is the odds of an event occurring in one group to the odds of it occurring in another group. For example, if 80% of the individuals in a population are Aa and 20% are AA, then the odds of Aa over AA is four; there are four (4.0) times as many Aa as AA genotypes. The natural log of this ratio is often computed because it is convenient to work with statistically.

management unit (MU): A local population that is managed as a unit due to its demographic independence.

marginal overdominance: Greater fitness of heterozygous genotypes, which are not the most fit in any single environment, due to an organism’s interactions with multiple environments that each favor different alleles.

marker: a gene or DNA sequence with a known location on a chromosome that can be used to identify cells, individuals, or species. It can be described as a variation (which may arise due to mutation or alteration in the genomic loci) that can be observed. A genetic marker may be a short DNA sequence, such as a sequence surrounding a single base-pair change (single nucleotide polymorphism, SNP), or a long one, like minisatellites.

match probability (MP): The probability of sampling an individual with an identical multilocus genotype to the one already sampled (“in hand”).

maternal effects: The influence of the genotype or phenotype of the mother on the phenotype of the offspring. Because it has no genetic basis, maternal effects are not heritable.

maximum likelihood: A statistical method of determining which of two or more competing alternative hypotheses (such as alternative phylogenetic trees) yields the best fit to the data.

maximum likelihood estimate (MLE): A method of parameter estimation that obtains the parameter value that maximizes the likelihood of the observed data.

MCMC: Markov chain Monte Carlo. A tool or algorithm for sampling from probability distributions based on constructing a Markov chain. The state of the chain after many steps is then used as a sample from the desired distribution. Sometimes called a random walk Monte Carlo method.

MDS: Multidimensional scaling. A statistical graphing technique used to represent genetic distances between samples in two or three dimensions, and thereby visualizing similarities and differences between different groups or samples.

Mendelian segregation: The random separation of paired alleles (or chromosomes) into different gametes.

meristic character: A trait of an organism that can be counted using integers (e.g., fin rays or ribs).

metacentric: A chromosome in which the centromere is centrally located.

metapopulation: A collection of spatially divided subpopulations that experience a certain degree of gene flow among them.

metapopulation scale: The spatial scale at which individuals migrate between local subpopulations, often across habitat that is unsuitable for colonization.

MHC: (Major Histocompatibility Complex) a large genomic region or gene family found in most vertebrates that encodes MHC molecules. MHC molecules play an important role in the immune system and autoimmunity. The MHC gene is the most polymorphic in the human genome, yet with regions that are highly conserved. It is often the case that an allele from a particular HLA (human leukocyte antigens) gene is more closely related to an allele found in chimpanzees than it is to another human allele from the same gene.

microchromosomes: Small chromosomes found in many bird species which, unlike heterochromosomes, carry functional genes.

microevolution: Evolutionary processes or changes over relatively short time periods, such as change in allele frequencies, genotypic composition or gene expression, within or between populations.

microsatellite: Tandemly repeated DNA consisting of short sequences of one to six nucleotides repeated between approximately five and 100 times. Also known as VNTRs, SSRs, or STRs.

migration: The movement of individuals from one generically distinct population to another resulting in gene flow.

minimum viable population (MVP): The minimum population size at which a population is likely to persist over some defined period of time.

minisatellite: A tandemly repeated sequence of approximately 10–100 nucleotides that are 500 to 30,000 base pairs in length.

mitochondrial DNA (mtDNA): A small, circular, haploid DNA molecule found in the mitochondria cellular organelle of eukaryotes.

molecular adaptation: Genetic change (for example, allele frequency shift or amino-acid substitution) in response to natural selection.

molecular clock: The observation that mutations sometimes accumulate at relatively constant rates, thereby allowing researchers to estimate the time since two species diverged (TMRCA).

molecular genetics: The branch of genetics that studies the molecular structure and function of genes, or that (more generally) uses molecular markers to test hypotheses.

molecular mutations: Changes to the genetic material of a cell, including single nucleotide changes, deletions, and insertions of nucleotides as well as recombinations and inversions of DNA sequences.

monoecious: A plant in which male and female organs are found on the same plant but in different flowers (for example maize).

monomorphic: The presence of only one allele at a locus, or the presence of common allele at a high frequency (>95% or 99%) in a population.

monophyletic: A group of taxa that include all species, ancestral and derived, from a common ancestor.

monophyly: The presence of a monophyletic group.

monotypic: A taxonomic group that encompasses only one taxonomic representative. The reptile family that contains tuatara (Sphenodontia) is currently monotypic.

morphology: The study of the physical structures of an organism, including the evolution and development of these structures.

morphotypes: Distinctive phenotypes. Organisms that are classified together on the basis of similar physical features without knowledge of their genetic relationships.

MRCA: Most recent common ancestor. In cladistics, the organism at the base of a clade, from which that clade arose.

mRNA: Messenger ribonucleic acid.

MSD: Multiple factor sex determination.

mtDNA: See mitochondrial DNA.

MU: See management unit.

mutagenesis: The natural or intentional formation of mutations in a genome.

mutation: An error in the replication, or transmission, of DNA that cause a structural change in a gene. See also molecular mutations.

mutational meltdown: The process by which a small population accumulates deleterious mutations, which leads to loss of fitness and decline of the population size, which leads to further accumulation of deleterious mutations. A population experiencing mutational meltdown is trapped in a downward spiral and will eventually go extinct.

MVP: See minimum viable population.

narrow sense heritability (HN): The amount of individual phenotypic variation that is due to additive genetic variation.

native species: A species that was not introduced and historically, or currently, occurs in a given ecosystem.

natural catastrophes: Natural events causing great damage to populations and that increase their probability of extinction.

natural selection: Differential contribution of genotypes to the next generation due to differences in survival and reproduction.

NCA: Nested clade analysis. A statistical approach to describe how genetic variation is distributed spatially within a species’ geographic range. This method uses a haplotype tree to define a nested series of branches (clades), thereby allowing a nested analysis of the spatial distribution of genetic variation, often with the goal of resolving between past fragmentation, colonization, or range expansion events.

nearly exact test: A method of using a nearly exact P-value to test if the observed test statistic deviates from the expected value under the hypothesis, For example, a test of whether populations are in Hardy–Weinberg proportions by comparing the observed chi-squared value to the chi-squared values of random computer permutations of genotypes from the population’s allele frequencies.

neighborhood: The area in a continuously distributed population that call be considered panmictic.

neutral allele: An allele that is not under selection because it does not affect fitness.

neutral loci: Loci that are not evolving directly in response to selection, the dynamics of which are controlled mainly by genetic drift and migration. These loci
can, however, be influenced by selection on nearby (linked) loci.

NMFS: National Marine Fisheries Service.

NOAA: National Oceanic Atmospheric Administration.

node: A branching point or end point on a phylogenic tree that represents either an ancestral taxon (internal node) or an extant taxon (external node).

nonindigenous species: Species present in a given ecosystem that were introduced and did not historically occur in that ecosystem.

nuclear DNA (nDNA): DNA that forms chromosomes in the cell nucleus of eukaryotes.

nuclear gene: A gene located on a chromosome in the nucleus of a eukaryotic cell.

nucleotides: The building blocks of DNA and RNA made up of a nitrogen-containing purine or pyrimidine base linked to a sugar (ribose or deoxyribose) and a phosphate group.

null allele: An allele that is not detectable either dueto a failure to produce a functional product or a mutation in a primer site that precludes amplification during PCR analysis.

Ocham’s razor: The principle that the least complicated explanation (most parsimonious hypothesis) generally should be accepted to explain the data at hand.

offsite conservation: See ex situ conservation.

outbreeding depression: The relative reduction in the fitness of hybrids compared to parental types.

outlier loci: Loci that may be under selection (or linked to loci under selection) that are detected because they fall outside the range of expected variation for a given summary statistic (e.g., extremely high or low Fst compared to most “neutral” loci in a sample).

overdominance: See heterozygous advantage.

overlapping generations: A breeding system where sexual maturity does not occur at a specific age, or where individuals breed more than once, causing individuals from different brood years to interbreed in a given year.

panmictic: A population that is randomly mating.

paracentric inversion: A chromosomal inversion that does not include the centromere because both breaks were on the same chromosomal arm.

paraphyletic: A clade that does not include all of the descendants from the most recent common ancestor taxon. For examples, reptiles are paraphyletic because they do not include birds.

parentage analysis: The assessment of the maternity and/or paternity of a given individual.

parsimony: The principle that the preferred phylogeny of an organism is the one that requires the fewest evolutionary changes; the simplest explanation.

PAW: Partnership for Action against Wildlife Crime.

PCA: Principal component analysis.

PCoA: Principle coordinates analysis.

PCR: See polymerase chain reaction.

pdf: Probability density function.

PE: Paternity exclusion (probability of ).

pericentric inversion: A chromosomal inversion that includes the centromere because the breaks were on opposite chromosomal arms.

phenetics: Taxonomic classification solely based on overall similarity (usually of phenotypic traits), regardless of genealogy.

phenogram: A branching diagram or tree that is based on estimates of overall similarity between taxa derived from a suite of characters.

phenotype: The observable characteristics of an organism that are the product of the organism’s genotype and environment.

phenotypic: Relating to an aspect of an individual’s phenotype.

phenotypic plasticity: Variation in the phenotype of individuals with similar genotypes due to differences in environmental factors during development. For example, cod in areas with red algae develop a reddish color.

philopatry: A characteristic of reproduction of organisms where individuals faithfully home to natal sites. Individuals exhibiting philopatry are philopatric.

phylogenetic: Evolutionary relationships between taxa or gene lineages. These relationships are often expressed visually in phylogenetic trees with nodes representing taxa or lineages (ancestral or derived), and branch lengths often corresponding to the amount of divergence between groups.

phylogenetic species concept (PSC): States that a species is a discrete lineage or recognizable monophyletic group.

phylogeny: See cladogram.

phylogeography: The assessment of the geographic distributions of the taxa of a phylogeny to understand the evolutionary history (e.g., origin and spread) of a given taxon.

PINEs: Paired interspersed nuclear elements. Use of PCR primes that bind one end of a transposable element (along with a few adjacent single-copy nucleotides), to generate DNA markers for studies in population genetics (e.g., hybridization or admixture).

pleiotropy: The case where one gene affects more than one phenotypic trait.

Poisson distribution: A probability distribution, with identical mean and variance, that characterizes discrete events occurring independently of one another in time, when the mean probability of that event on any one trial is very small. Earthquake hazards, radioactive decay, and mutation events follow a Poisson distribution. The Poisson is a good approximation to the binomial distribution when the probability is small and the number of trials is large.

polygenic: Affected by more than one gene.

polymerase: A molecule that catalyzes the synthesis of DNA or RNA from a single-stranded template and free deoxynucleotides (e.g., during PCR).

polymerase chain reaction (PCR): A technique to replicate a desired segment of DNA. PCR starts with primers that flank the desired target fragment of DNA. The DNA strands are first separated with heat, and then cooled allowing the primers bind to their target sites. Polymerase then makes each single strand into a double strand, starting from the primer. This cycle is repeated multiple times creating a 106 increase in the gene product after 20 cycles and a 109 increase over 30 cycles.

polymorphic: The presence of more than one allele at a locus. Generally defined as having the most common allele at a frequency less than 95% or 99%.

polymorphism: The presence of more than one allele at a locus. Polymorphism is also used as a measure of the proportion of loci in a population that are genetically variable or polymorphic (P).

polyphyletic: A group of taxa classified together that have descended from different ancestor taxa (i.e., taxa that do not all share the same recent common ancestor).

polyploid: Individuals whose genome consists of more than two sets of chromosomes (e.g., tetraploids).

population viability: The probability that enough individuals in a population will survive to reproductive age to prevent extirpation of the population.

population viability analysis (PVA): The general term for the application of models that account for multiple threats facing the persistence of a population to access the likelihood of the population’s persistence over a given period of time. PVA helps identify the threats faced by a species, plan research and data collection, prioritize management options, and predict the likely response of species to management actions (e.g., reintroduction, captive breeding, or prescribed burning).

primer: A small oligonucleotide (typically 18 –22 base pairs long) that anneals to a specific singlestranded DNA sequence to serve as a starting point for DNA replication (e.g., extension by polymerase during PCR).

private allele: An allele present in only one of many populations sampled.

probability: The certainty of an event occurring. The observed probability of an event, r, will approach the true probability as the number of trials, n, approaches infinity.

probability of identity (PI): The probability that two unrelated (randomly sampled) individuals would have an identical genotype. This probability becomes very small if many highly polymorphic loci are considered.

product rule: A statistical rule that states that the probability of ni independent events occurring is equal to the product of the probability of each n independent event.

propagule: A dispersal vector. Any disnative unit or part of an organism capable of independent growth (e.g., a seed, spore, mycelial fragment, sclerotium bud, tuber, root, or shoot).

propagule pressure: A measure of the introduction of nonindigenous individuals that includes the number of individuals (or propagules) introduced and the number of introductions.

proportion of admixture: The proportion of alleles in a hybrid swarm that come from each of the parental taxa.

protein: A polypeptide molecule.

PSC: See phylogenetic species concept.

pseudo-overdominance: See associative overdominance.

purging: The removal of deleterious recessive alleles from a population through inbreeding which increases homozygosity which in turn increases the ability of selection to act on recessive alleles.

PVA: See population viability analysis.

QTLs: See quantitative trait loci.

quantitative trait loci (QTLs): Genetic loci that affect phenotypic variation (and potentially fitness), which are identified by a statistically significant association between genetic markers and measurable phenotypes. Quantitative traits are often influenced by multiple loci as well as environmental factors.

RAPD: Randomly amplified polymorphic DNA. A method of analysis where PCR amplification using two copies of an arbitrary oligonucleotide primer is used to create a multilocus fingerprint (i.e., band profile).

reciprocal monophyly: A genetic lineage is reciprocally monophyletic when all members of the lineage share a more recent common ancestor with each other than with any other lineage on a phylogenetic tree.

recombination: The process that generates a haploid product of meiosis with a genotype differing from both the haploid genotypes that originally combined to form the diploid zygote.

reintroduction: The introduction of a species or population into a historical habitat from which it had previously been extirpated.

relative fitness: A measure of fitness that is the ratio of a given genotype’s absolute fitness to the genotype with the greatest absolute fitness. Relative fitness is used to model genetic change by natural selection.

rescue effect: When immigration into an isolated deme (either genetically or demographically) reduces the probability of the extinction of that deme.

restriction enzyme: An enzyme (see endonuclease), isolated from bacteria, that cleaves DNA at a specific four or six nucleotide sequence. Over 400 such enzymes exist that recognize and cut over 100 different DNA sequences; used in RFLP, AFLP, and RAPD analysis and to construct recombinant DNA (in genetic engineering).

restriction fragment length polymorphism (RFLP): A method of genetic analysis that examines polymorphisms based on differences in the number of fragments produced by the digestion of DNA with specific endonucleases. The variation in the number of fragments is created by mutations within restriction sites for a given endonuclease.

Retrospective monitoring: monitoring changes from historical conditions by examining DNA extracted from previously archived samples.

reverse mutation rate: Back mutation rate. The rate at which a gene’s ability to produce a functional product is restored. This rate is much lower than the forward mutation rate because there are many more ways to remove the function of a gene than restore it. Also used to describe mutation at microsatellite loci where (under the stepwise mutation model, for example) a back mutation yields an allele of length that already exists (i.e., homoplasy) in the population.

ribonucleic acid (RNA): A polynucleotide similar to DNA that contains ribose in place of deoxyribose and uracil in place of thymine. RNA is involved in the transfer of information from DNA, programming protein synthesis, and maintaining ribosome structure.

Robertsonian fission: An event where a metacentric chromosome breaks near the centromere to form two acrocentric chromosomes.

Robertsonian fusion: An event where two acrocentric chromosomes fuse to form one metacentric chromosome.

Robertsonian translocation: A special type of translocation where the break occurs near the centromere or telomere and involves the whole chromosomal arm so balanced gametes are usually produced.

SARA: See Species at Risk Act of Canada.

selection coefficient: The reduction in relative fitness, and therefore genetic contribution to future generations, of one genotype compared to another.

selection differential: The difference the mean value of a quantitative trait found in a population as a whole compared to the mean value of the trait in the breeding population.

selective sweep: The rapid increase in frequency by natural selection of an initially rare allele that also fixes (or nearly fixes) alleles at closely linked loci thus reduces the genetic variation in a region of a chromosome. Leads to a local excess of rare alleles as new unique mutations accumulate.

sensitivity testing: A method used in population viability analyses where the effects ofs on the persistence of populations are determined by testing a range of possible values for each parameter.

sequential Bonferroni correction:
A method, similar to the Bonferroni correction, that is used to reduce the probability of a Type I statistical error when conducting multiple simultaneous tests.

sex chromosomes: Chromosomes that pair during meiosis but differ in the hererogametic sex.

sex-linked locus: A locus that is located on a sex chromosome.

sexual selection: Selection due to differential mating success either through competition for mates or mate choice.

shadow effect: A case usually caused by low marker polymorphism in mark–recapture studies in which a novel capture is labeled as a recapture due to identical genotypes at the loci studied.

SINEs: Short interspersed nuclear elements.

single nucleotide polymorphism (SNP): A nucleotide site (base pair) in a DNA sequence that is polymorphic in a population either due to transitions or transversions and can be used as a marker to assess genetic variation within and among populations. Usually only two alleles exist for a SNP in a population.

SMM: See stepwise mutation model.

SNP: See single nucleotide polymorphism.

species: A group of organisms with a high degree of physical and genetic similarity, that naturally interbreed among themselves and can be differentiated from members of related groups of organisms.

Species at Risk Act of Canada (SARA): Legislation (passed in 2002) to prevent wildlife species from becoming extinct and secure the necessary actions for their recovery. It provides for the legal protection of wildlife species and the conservation of critical habitat.

species concepts: The ideas of what constitutes a species, such as reproductive isolation (BSC), or monophyly of a lineage (PSC).

species scale: The spatial scale encompassing an entire species’ distribution.

SSRs: Simple sequence repeats. See microsatellite.

stable polymorphism: A polymorphism that is maintained at a locus through natural selection.

stabilizing selection: Selection for a phenotype with a more intermediate state.

stepping stone model of migration: A model of migration in which the probability of migration between nearby or adjacent populations is higher than the probability of migration between distant populations.

stepwise mutation model (SMM): A model of mutation in which the microsatellite allele length has an equal probability of either increasing or decreasing (usually by a single repeat unit, as in the strict one-step SMM).

stochastic: The presence of a random variable in determining the outcome of an event.

stock: A term generally used in fisheries management that refers to a population that is demographically independent and often represents a subunit (e.g., MU) of an ESU.

STR: Short tandem repeat. See microsatellite.

subpopulations: Groups within a population delineated by reduced levels of gene flow with other groups.

subspecies: A taxonomically defined subdivision within a species that is physically or genetically distinct, and often geographically separated.

sum rule: A statistical rule that states that the probability of ni mutually exclusive, independent events occurring is equal to the sum of the probabilities of each n event.

supergene: Allelic combinations found at closely linked loci that affect related traits and are inherited together. An example of a supergene is the major histocompatibility complex (MHC), which in humans contains more than 200 genes adjacently located over several megabases of sequence on chromosome 6.

supernumerary chromosome: A chromosome, often present in varying numbers, that is not needed for normal development, lacks functional genes, and does not segregate during meiosis. These small chromosomes, which are also called B chromosomes, are present in addition to the normal complement of functional chromosomes in an organism.

supportive breeding: The practice of removing a subset of individuals from a wild population for captive breeding and releasing the captive-born offspring back into their native habitat to intermix with wild-born individuals and increase population size or persistence.

sympatric: Populations or species that occupy the same geographic area.

synapomorphy: A shared derived trait between evolutionary lineages. A homology that evolved in an ancestor common to all species on one branch of a phylogeny, but not common to species on other branches.

Taq: The bacterium Thermus aquaticus from which a heat stable DNA polymerase used in PCR was isolated.

telomere: A tandemly repeated segment of a short DNA sequences, one strand of which is G-rich and the other strand is C-rich, that form the ends of linear eukaryotic chromosomes.

threshold: The point at which environmental (or genetic) changes produce large phenotypic changes in an organism (or population). For example, there could be a threshold effect of inbreeding on fitness such that after a certain level of inbreeding is reached, individual fitness declines increasingly rapidly.

threshold character: A phenotypic character that contains a few discrete states that are controlled by many genes underlying continuous variation, which affects a character phenotypically only when a certain physiological threshold is exceeded.

TMRCA: Time since the most recent common ancestor.

TRAFFIC: A wildlife trade monitoring network sponsored by the WWF and IUCN.

transgressive segregation: Hybridization events that produce progeny that express phenotypic values outside the range of either parental phenotypic value. These differences are usually due to the disruption of polygenic traits.

transition: The more common single nucleotide mutation (or polymorphism) that results from a point mutation in which a purine is substituted with a purine (G?A) or a pyrimidine is substituted with a pyrimidine (C?T).

translocation: (1) The movement of individuals from one population (or location) to another that is usually intended to achieve either genetic or demographic rescue of an isolated population. (2) A rearrangement occurring when a piece of one chromosome is broken off and joined to another chromosome.

transposable element: Any genetic unit that can insert into a chromosome, exit, and relocate; includes insertion sequences, transposons, some bacteriophages, and controlling element. A region of the genome, flanked by inverted repeats, a copy of which can be inserted at another place; also called a transposon or a jumping gene.

transposon: A mobile element of DNA that jumps to new genomic locations through a DNA intermediate and which usually carries genes other than those that encode for transposase proteins used to catalyze movement.

transversion: The replacement of a purine with a pyrimidine (A or G to C or T) or vice versa (C or T to A or G). Less common than a transition.

Type I statistical error: The probability of rejecting a true null hypothesis. Usually chosen, by convention, to be 0.05 or 0.01.

Type II statistical error: The probability of accepting a false null hypothesis.

underdominance: See heterozygous disadvantage.

UNEP: United Nations Environmental Program.

UPGMA: Unweighted pair group method with arithmetic averages.

USFWS: United States Fish and Wildlife Service.

variance effective number (NeV): The size of the ideal population that experiences changes in allele frequency at the same rate as the observed population.

viability: The probability of the survival of a given genotype to reproductive maturity (or of a population to persist through a certain time interval).

VNTRs: Variable number of tandem repeats. See microsatellite.

Wahlund principle: The deficit of heterozygotes in subdivided populations, compared to expected Hardy–Weinberg proportions, due to subdivision into small panmictic (random mating) demes within the large population.

Wright–Fisher model: A random mating population model with complete random union of gametes (including the possibility of selfing).

WWF: World Wide Fund For Nature (formerly known as the World Wildlife Fund).