Autumn
2012

FISH/BIOL 340 - Genetics and Molecular Ecology

Glossary of Terms

(modified from Carvalho G.R., (ed.) Advances in Molecular Ecology, IOS Press, Ohmsha, pp. 305-312). See also a glossary from Ridley M (2003) Evolution, 3rd edition. Another excellent resource is Wikipedia, with an evolutionary and a genetics glossary. If there are any terms you can't find, let me know and I'll add them here.

Alignment: The juxtaposition of amino acids or nucleotides in homologous molecules to maximise similarity or minimise the number of inferred changes among the sequences. Alignment is used to infer positional homology prior to or in parallel with phylogenetic analysis.
Allele: One or more alternative forms of a gene or a locus, each possessing a unique nucleotide sequence. In diploid cells, a maximum of two alleles will be present, each in the same relative position or locus on homologous chromosomes of the chromosome set.
Allozymes: Enzymes differing in electrophoretic mobility as a result of allelic differences at a single gene (cf. Isozyme).; Amplify (in the molecular sense) To increase the number of copies of a nucleotide sequence using the polymerase chain reaction.
Ancient DNA (aDNA): DNA found in palaeontological, archaeological, museum, forensic, and clinical specimens. The unifying component is that preserved DNA is damaged over time by processes such as oxidation and hydrolysis, leaving only trace amounts of DNA containing cross-links and modified bases.
Anneal (in the molecular sense): To bring together individual strands of DNA that pair due to the sharing of some complementary base pairs.
Apomorphy: A derived character state.
Autapomorphy: A derived character state unique to a particular taxon.
Autoradiograph: Image on an X-ray film created by radioactive or chemiluminescent labelled DNA fragments.
Bacteriophage (= phage ): A virus that infects bacteria.
Band-sharing coefficient: A pairwise measure of similarity which is often used to estimate relatedness using multibanded DNA fingerprints. It is calculated simply as twice the number of bands in common divided by the total number of bands scored.
Base composition: The relative proportions of the four respective nucleotides in a given sequence of DNA or RNA.
Base pairs (bp): The bases adenine (A) and thymine (T), or cytosine (C) and guanine (G), linked by hydrogen bonds (A = T; C = G) binding complementary strands of DNA.
Bifurcation: A node in a tree that connects exactly three branches. If the tree is directed (rooted), then one of the branches represents an ancestral lineage and the other two branches represent descendant lineages.
Biparental inheritance: Genes and genetic elements in sexual organisms which are inherited from both parents.
Chromatin: The substance of chromosomes, which includes DNA, chromosomal proteins and chromosomal RNA.

Cloning of gene sequence: Involves the replication of an isolated gene sequence by incorporating it into a bacterial or viral host (or more rarely into a eukaryotic cell) and growing up that host. Most frequently, such cloning involves the insertion of the sequence into a plasmid vector.
Coalescence: The evolutionary process viewed backward through time, so that allelic diversity is traced back through mutations to ancestral alleles. Coalescent theory can be used to make predictions about effective population sizes, ages and frequencies of alleles, selection, rates of mutation, or time to common ancestry of a set of alleles.
Codon: A sequence of three nucleotide bases along a DNA or RNA chain which represents the code of a single amino acid.
cDNA (= complementary DNA): DNA reverse transcribed from an RNA template.
Complementary sequence: A sequence of nucleotides related by the base-pairing rules. For example in DNA, a sequence A-G-T in one strand is complementary to T-C-A in the other. A given sequence defines the complementary sequence.
Concerted evolution: The generation and maintenance of homogeneity among members of a family of DNA repeats within a species or population.
Congruence: Agreement among data or data sets.
CpDNA: Chloroplast DNA.
Denature: To break the hydrogen bonds between two complementary strands of DNA, separating them into two single-stranded molecules.
Directional selection: Selection which acts on individuals showing a phenotypic distribution in such a way that those individuals towards, or at the end of, the distribution are favoured.
Disruptive (= diversifying) selection: Where individuals with an intermediate phenotype are as a selective disadvantage and extreme phenotypes are favoured.
D-loop: A non-coding region of (vertebrate) mitochondrial DNA (mtDNA) that serves as the initiator of mtDNA replication and is often more variable than the coding regions of mtDNA.
DNA fingerprinting: In original usage, the use of multilocus probes to reveal hypervariability (see Hypervariable sequence) at many loci in the human genome. More generally used to refer to the characterisation of an individual's genome by developing a DNA fragment band (allele) pattern. If a sufficient number of different-sized fragments are revealed, these banding patterns, which resemble a bar-code profile, will usually be unique for each individual except identical twins.
DNA ligases: One of the enzymes involved in DNA replication in prokaryotes by catalysing nucleotide phosphodiester bond formation.
Effective population size (Ne): The effective size of a population is defined as the size of an idealised population (a random mating population of self-compatible hermaphrodites, with no selection, mutation or genetic migration occurring) which behaves in the same way as the real population under consideration. It is important to understand that effective population size does not mean something as simple as that fraction of the population able to reproduce (e.g. it does not mean total population minus juveniles and senescent adults), but incorporates information on mating patterns and the extent of population subdivision.
Electrophoresis: The separation of macromolecules (e.g. enzymes or DNA) in the presence of an electric current. In molecular genetics, differences in charge, size or shape (i.e. differences in electrophoretic mobility) of the macromolecules are used to estimate genetic differentiation.
Electromorph: Protein or microsatellite variant detected by its distinct electrophoretic mobility.
Endonuclease: See Restriction enzyme
Exon: That portion of a DNA strand within a gene that codes for a protein. Coding regions that are broken up into one or more segments within a gene, are separated by regions of non-coding DNA called introns.
Fishery stock: A group of individuals exploited in a particular area or by a specific method. The definition takes no account of the biological basis of stock identity or extent of stock integrity (cf. Genetic stock and Harvest stock). See also Stock.
Fixed: In population genetics, a gene is said to be fixed when it has a frequency of 100%.
FST: This was defined by Wright as the correlation between random gametes, drawn from the same subpopulation, relative to the total. For a two-allele locus, FST = VP /pq, where VP is the variance of one allele over subpopulations, and p is the average frequency of that allele in the total population. This was generalised by Nei for any number of alleles to GST = 1 - (HS/HT), where HS is the average Hardy-Weinberg expected heterozygosity per subpopulation, and HT is the Hardy-Weinberg heterozygosity of the total population. Effectively, GST and FST measure the same quantity. See GST.
Gel: A supporting matrix used for sample application during electrophoresis. Gels are most commonly composed of starch, cellulose acetate, polyacrylamide or agarose.
Gene: A hereditary unit consisting of a nucleotide sequence and occupying a specific position or locus within the genome.
Gene flow (= migration in population genetic terms): The movement of genes into or out of a population by interbreeding, or by migration (of individuals or their propagules) and interbreeding. It is important to distinguish migration in the genetic sense from animal movement, because the latter may not necessarily lead to gene flow due to death or failure of migrants to reproduce.
Gene pool: All the alleles (pool of eggs and sperm) in a population at a particular time. The extent to which individuals in a population share a common gene pool will determine the extent of genetic differentiation among taxa.
Gene tree: A branching diagram that depicts the known or (usually) inferred relationships among historically related groups of genes or other nucleotide or amino acid sequences.
Genetic distance: The quantitatively measured differences between taxa (between genes, individuals, populations, or species) in terms of their allele frequencies.
Genetic drift: Variation in allele frequency from one generation to another due to chance fluctuations. It is generally greater in populations with small effective population size and high inbreeding.
Genetic fingerprinting: See DNA fingerprinting.
Genetic management: The incorporation of information on the levels and distribution of genetic variability into management programmes, with the overall aim of conserving genetic resources (levels of allelic diversity and associated genotypic variance in ecologically significant traits).
Genetic marker (= molecular marker): A genetically inherited variant from which the genotype can be inferred from the phenotype as identified during genetic screening.
Genetic stock: A reproductively isolated unit* that is genetically different from other stocks. The degree of integrity here is high, since very few migrants are sufficient to prevent the development of genetic differentiation between monospecific stocks. *The reproductive isolation referred to above is not usually absolute and operative over evolutionary time, as in the case of interspecific stocks. Cf. Stock, Harvest stock and Fishery stock.
Genome: All the genetic material contained in an individual.
Genotype: The specific allelic composition of an organism, either of the entire genome or more commonly of a certain gene or a set of genes.
GST: The proportion of total genetic diversity attributable to subpopulation differentiation. See FST.
Gynogenesis: Unisexual reproduction in which the egg is stimulated to commence cleavage by the sperm but without fertilisation, and therefore no genetic contribution from the male. Gynogenetic offspring therefore are genetically identical to the mother.
Haplotype: Nucleotide sequence of an individual's mtDNA genes characterised by restriction fragment length polymorphisms (RFLPS) or direct sequencing. It is the multilocus analogue of an allele.
Hardy-Weinberg equilibrium: Ratio of genotype frequencies expected in a population when mating is random and neither selection nor drift is operating. For two alleles (A and a) with frequencies p and q there are three genotypes AA, Aa, and aa; and the expected Hardy-Weinberg ratio for the three is p2 AA, 2pq Aa, q2 aa. Genotypic frequencies obtained from molecular genetic analysis of natural populations can be compared with predicted frequencies calculated from allele frequencies to determine whether samples are drawn from large, randomly mating populations.
Harvest stock: Locally accessible fish resources in which fishing pressure on one resource has no effect on the abundance of fish in another contiguous resource. This definition does not imply any genetic, nor any phenotypic, differences between stocks, but describes a group of individuals whose abundance depends to a very much larger degree on recruitment and mortality, especially that caused by fishing, than on immigration and emigration. cf. Stock, Genetic stock and Fishery stock.
Heritability: In the 'narrow sense', the ratio of the additive genetic variance (differences that will be inherited consistently by the offspring) to the total phenotypic variance.
Heterologous: Homologous molecule from a species other than that which is being examined.
Heteroplasmy: The containment by one cell or individual of more than one type of a particular organellar DNA (e.g. cpDNA, mtDNA).
Heterozygosity: Proportion of individuals in a population that are heterozygous (see Heterozygote) at a given locus. Can be calculated: HL = 1 - sum. xi2, where xi is the frequency of the ith allele at a locus. The mean heterozygosity per locus, HL is the sum of HL over all loci (including loci with two identical alleles where HL = 0), divided by the total number of loci examined. An observed heterozygosity (Ho) can be determined from a direct count of the frequency of heterozygous genotypes in a sample. HL and Ho can be compared statistically to determine whether genotypic ratios are in accordance with Hardy-Weinberg expectations (see Hardy-Weinberg equilibrium).
Heterozygote: The presence of two dissimilar alleles at a given genetic locus.
Homology: Common ancestry of two or more genes or gene products (or portions thereof).
Homoplasy: Similarities in character states due to reasons other than inheritance from a common ancestor. These include convergence, parallelism or reversion. At the gene level, two alleles are homoplasic when they are identical in state, though not identical by descent.
Homozygote: Two identical alleles at a genetic locus.
Hotspot: Position on a gene where nucleotide substitutions are particularly common.
Hybridization (in the breeding sense): Crossing of inbred lines or individual organisms of differing genetic constitution or species.
Hybridization (in the molecular sense): To induce, experimentally, the pairing of complementary nucleic acid strands, often from different individuals or species, to form a DNA-DNA or RNA-DNA hybrid molecule.
Hybridogenesis: A form of unisexual reproduction where an ancestral genome from the maternal line is transmitted to the egg without recombination, whereas paternally-derived chromosomes are discarded premeiotically, only to be replaced each generation through fertilisation by sperm from a related sexual species.
Hypervariable sequence: A segment of a chromosome characterised by considerable variation in the number of tandem repeats at one or more loci. See Tandem array.; Iceman Name given by the mass-media to the Neolithic (5100-5300 BP) human body found on 19 September 1991 in an Alpine glacier.
Imperfect microsatellite: Microsatellite for which one of the motif(s) has mutated (e.g. AGAGACAGAGAG).
Indel: Insertion/deletion event.
Infinite allele model (IAM): Mutation model which assumes an infinite number of possible alleles at a given locus, so that any new allele arising by mutation is different from those previously present in the species.
Insertion: Mutation in which one or more nucleotides are inserted into DNA sequence.
Interrupted microsatellite: Microsatellite with an inserted base(s) separating motifs (e.g. AGAGAGTAGAGAG).
Introgression: The sexual transfer of genes between genetically differentiated populations.
Intron: The non-coding sequence in a gene between the exons. Because introns never code for a protein, they are expected to have few functional constraints, and tend therefore to evolve more rapidly (and are correspondingly more variable) than coding regions.
Isoloci: Two or more loci of a multilocus enzyme system that produce products of the same electrophoretic mobility.
Isozymes: Enzymes differing in electrophoretic mobility but which share the same substrate. Isozymes may arise from genetic (multiple loci or alleles) or epigenetic (post-translational) sources. It is therefore essential to exclude epigenetic variability if isozymes are to be used as genetic markers.
K-allele model (KAM): Mutation model which assumes that there are exactly K possible allelic states and that any allele has a constant probability [µ/(K-1)] of mutating towards any of the other K-1 allelic states.
Karyotype: The entire chromosome complement of an individual or cell, as seen during mitotic metaphase.
Linkage: A measure of the degree to which alleles of two genes do not assort independently at meiosis or in genetic crosses. Those loci on different chromosomes are non-linked, whereas those close together on the same chromosome are closely linked and are usually inherited together.
Linkage disequilibrium: Departure from the predicted frequencies of multiple locus gamete types assuming alleles are randomly associated. When there is no deviation, the population is said to be in linkage equilibrium.
Linkage map: A chromosome map showing the linear order of the genes associated with the chromosome.
Local adaptation: A process that increases the frequency of traits which enhance the survival or reproductive success of individuals in a particular environment.
Locus: A physical position of a gene on a chromosome.
Mapping: Determination of the position of genes (genetic map), or of physical features such as restriction endonuclease sites (restriction map, physical map).
Marker: Any diagnostic feature (e.g. allozyme, mtDNA haplotype, meristic, morphometric) of an individual, population or species. See genetic marker.
Maximum likelihood: A criterion to find parameter values by maximising the probability of observed data under an explicit model.
Metapopulation: A group of populations in a local geographic area.
Microsatellite: Tandem array of short (1-6 base pairs) repeated sequences, with a total degree of repetition of five to about one hundred at each locus, and usually scattered randomly throughout the genome. For example, the repeat unit can be simply CA, and might exist in a tandem array of, for instance, 50 repeats, denoted by (CA)50. The number of repeats in an array can be highly variable, giving rise to extensive polymorphism.
Migration rate: The rate at which subpopulations exchange migrants per generation. For genetic studies this is often synonymous with the rate of gene flow.
Minisatellite: Tandem array of from two to several hundred copies of a short (9- 100 base pairs) sequence of DNA, usually interspersed but often clustered in telomeric regions of the chromosome. Arrays generally have different numbers of copies on different chromosomes, which when cut by restriction enzymes produce DNA fragments of differing lengths, thereby potentially giving rise to a DNA fingerprint.
Mitochondrial DNA (mtDNA): DNA located in the mitochondrion. In animals it is generally a small circular molecule, 16 000 to 18 000 base pairs long, and is, with rare exceptions, solely maternally inherited.
Mixed stock analysis (MSA): The use of markers to determine the relative proportions of identifiable stocks in a mixed-stock fishery. MSA is widely employed in the management of Pacific salmon.
Molecular drive (= meiotic drive): Any one of a number of mechanisms that produce unequal numbers of the two gametic types formed by a heterozygote.
Monophyly (monophyletic group): Taxon derived from a single ancestor and only consisting of all its descendents
Multilocus probe: Used typically to refer to probes used in DNA fingerprinting (e.g. minisatellites) where many loci are visualised simultaneously, producing a banding pattern comprising many DNA fragments. In such cases it is usually not possible to identify loci or assess levels of heterozygosity.
Mutation rate: Number of mutations (alteration of a DNA sequence) arising in an individual per gene or per nucleotide site per unit time (for example per generation).
Mutational load: Genetic burden in a population resulting from the accumulation of recessive deleterious mutations. Such mutations are not expressed in heterozygous state and are thus not effectively removed by selection if they have a low frequency in the population.
Mutational meltdown: Positive feedback cycle, in which the accumulation of mutational load causes a decrease in population size, which causes an increase in inbreeding depression (that is, deleterious recessive alleles are expressed in homozygous state after mating of related individuals), which causes a further decrease in population size and so on. Computer models suggest that such a mutational meltdown can lead to population extinction.
ND genes: Sequences of DNA in the mitochondrial genome that code for enzymes in the NADH dehydrogenase complex.
nDNA: Nuclear DNA, the DNA contained in the chromosomes within the nucleus of eukaryotic cells, and inherited from both maternal and paternal parents.
Neutrality: The state of being free from the effects of selection.
Non-synonymous substitution: A nucleotide substitution that results in an amino acid replacement.
Normalizing (= balancing) selection: The situation in which individuals with an intermediate phenotype are at a selective advantage.
Nucleotide: One of the monomeric units from which DNA molecules are constructed, consisting of a purine (adenine and guanine) or pyrimidine (thymine and cytosine) base, a pentose sugar, and a phosphoric acid group.
Null alleles at microsatellite loci: Alleles that give no PCR product due to mutations (base substitution or deletion) occurring at one or both primer site(s).
Oligonucleotide: Short DNA fragment typically of 10-20 nucleotides. Generally refers to single-stranded, synthetic DNA molecules used as a probe or primer.
Parallel substitution(s): Independent occurrence of the same mutation in two or more evolutionary lineages.
Paraphyly (paraphyletic group): A group in which all members share a common ancestor but which does not include all the descendants of that ancestor.
Perfect microsatellite: Microsatellite with a stretch of tandem repeats having no interruption in the run of repeats (e.g. AGAGAGAGAGAGAGAG).

Phylogeny: The historical relationships among lineages of organisms or their parts (e.g. genes).
Phylogeography: The principles and processes governing geographical distributions of genealogical lineages, especially at the intraspecific level.
Plasmid: A self-replicating extrachromosomal circular DNA.
Plesimorphy: An ancestral character state.
Polymerase: An enzyme that assembles the subunits of macromolecules. DNA polymerases have the ability to synthesise the complementary strand of single-stranded DNA template. Synthesis only extends from existing double-stranded sequences across a single-stranded template.
Polymerase chain reaction (PCR): The amplification of particular regions of DNA using primers (which flank the region of DNA to be amplified) and the DNA polymerase of the thermophilic bacterium Thermophilus aquaticus. PCR involves a cycle of denaturation to single strands (around 94oC, primer annealing (37-60 oC), and primer extension (around 72oC). Thirty or more cycles are typically carried out to create a large number of copies of the target DNA sequence.
Polymorphism: Existence at the same time of two or more different classes of a morph within a population, that is, individuals with discrete phenotype differences. In the molecular sense, polymorphism may be detected as alternative forms of a gene (e.g. allozymes or nucleotide sequence), and is sometimes defined as variants with a frequency of > 1% or 5% in the population. The latter criterion is employed more often to exclude the incidence of rare mutations.
Polyphyly (polyphyletic group): Artificial taxon derived from several distinct ancestors
Population size: Number of individuals in a population (census population size).
Primer: A short single-stranded sequence of DNA which binds to a complementary sequence and initiates the extension of adjacent DNA regions (DNA strand synthesis, e.g. in PCR) using DNA polymerase. Primers can be designed so that they will bind to a very specific region of the DNA, and will thus initiate synthesis of a targeted sequence (as in PCR or DNA sequencing).
Probe: A length of RNA or single-stranded DNA radioactively (or otherwise) labelled and used to locate complementary sequences by base-pairing in a heterogeneous collection of sequences. The probe therefore hybridises with the target sequence (one or many repeat copies) making it visible to the naked eye (e.g. through autoradiography), so allowing the degree of variability to be assayed.
Random amplified polymorphic DNA (RAPD): A technique allowing detection of DNA polymorphisms by randomly amplifying multiple regions of the genome by PCR using single arbitrary primers. The primers are generally between 10 and 20 base pairs long, of an arbitrary but known sequence.
rDNA Ribosomal DNA.: Repetitive DNA Nucleotide sequences occurring repeatedly in chromosomal DNA. Repetitive DNA can belong to the highly repetitive (sequences of several nucleotides repeated millions of times) or middle repetitive (sequences of 1-500 base pairs in length, repeated 100 to 10000 times each) categories.
Restriction enzyme (= endonuclease): An enzyme that cleaves double-stranded DNA. Type I are not sequence specific; type II (the type used routinely in molecular genetic analyses) cleave DNA at a specific sequence of nucleotides known as restriction or recognition sites. The enzymes are named by an acronym that indicates the bacterial species from which they were isolated, followed by a roman numeral that gives the chronological order of discovery when more than one enzyme came from the same source. Most restriction enzymes currently employed in molecular ecology recognize sequences of either four, five or six bases.
Restriction fragment length polymorphism (RFLP): Variations occurring within a species in the length of DNA fragments generated by a specific restriction enzyme. Such variation is generated either by base substitutions that cause a gain or loss of sites, or by insertion/deletion mutations that change the length of fragments independent of restriction site changes.
Restriction site (= recognition site): A specific sequence of nucleotide bases which is recognised by a restriction enzyme. The enzyme will cleave both DNA strands at a specific location within that sequence. Variation in the presence and absence of restriction sites among individuals generates restriction fragment length polymorphisms (RFLPs).
Reticulate evolution: The fusing of previously separated branches on an evolutionary tree.
Reversion: Mutation resulting in a come back to the ancestral state.
rRNA: Ribosomal RNA.
Satellite DNA: DNA from a eukaryote that separates on gradient centrifugation as a distinct fraction. The separation results from differences in the base composition of the distinct fraction and main band of genomic DNA (i.e. the A + T or G + C content is higher in the satellite than in the main band). Many satellites consist of highly repetitive DNA, usually millions of tandem repeats of a relatively short sequence (tandem array).; scnDNA (single copy nuclear DNA) Sequences that occur once, or very few times, in a genome.
Silent mutation: A change in the DNA structure that has no effect on the phenotype of the cell.
Single-locus probe (SLP): A probe consisting of short repeat sequences (e.g. minisatellites) that identify allelic products at a single locus, thus producing banding patterns typically consisting of either one (homozygote) or two (heterozygote) DNA fragments. (cf. Multilocus probe).
Size homoplasy: Identity of microsatellite alleles by state not by descent. Microsatellite variation is essentially revealed through electrophoresis of PCR products and allelic classes differ by the length (in bp) of the amplified fragments. Two PCR products of the same length may not be a copy of the same ancestral sequence without mutation, introducing the possibility of size homoplasy.
Southern blot: A membrane (e.g. nitrocellulose or nylon) onto which DNA has been transferred directly from an electrophoretic gel. The transfer is facilitated by simple diffusion of salts across the membrane, or by using automated vacuum blotters. The membrane can then be exposed to a labelled probe that will bind to the specific fragments of interest, allowing their visualisation independent of thousands of other fragments from the gel.
Stepwise mutation model (SMM): Mutation model which assumes that alleles are represented by integer values and that a mutation either increases or decreases the allele value by one. For variable number tandem repeats loci (VNTR), the allele value is generally taken as the number of tandem repeats in the DNA sequence.
Stock: Unit of an exploited species that is employed in stock assessment. Definition depends on management aims and time scale of interest (seeFishery stock, Genetic stock and Harvest stock).
Stock assessment: The use of various statistical and mathematical calculations to make quantitative predictions about the reactions of exploited populations to alternative management options
Substitution: Mutation in which one nucleotide is substituted for another.
Symplesimorphy: A shared ancestral character state.
Synapomorphy: A shared derived character state that is indicative of a phylogenetic relationship among two or more operational taxonomic units (OTU).
Synonymous substitution: Nucleotide substitution which does not alter the amino acid composition of a gene because of the redundancy of the genetic code.
Tandem array: Multiple copies of a sequence of DNA that are arranged one after another in series. Repeat units can be short nucleotide sequences or entire sets of genes.
Taphonomy: Grecian neologism created in the 1940s by the Russian palaeontologist, Efremov, meaning literally "the law of the tomb". Taphonomy is usually described as a subdiscipline of palaeontology, but its methods and data are often applied to more recent, that is, archaeological, contexts.; Template The use of a nucleic acid strand to carry the information required for the synthesis of a new (complementary) strand.
Transposon: A segment of DNA flanked by transposable elements that is capable of moving its location in the genome.; Transition A nucleotide substitution from one purine to another purine (e.g. adenine (A) to guanine (G)), or from one pyrimidine to another pyrimidine (e.g. thymine (T) to cytosine (C)).
Transversion: A nucleotide substitution from a purine to pyrimidine (e.g. adenine (A) to cytosine (C)), or vice versa.; Two-phase model (TPM) Mutation model in which mutations introduce a gain/loss of X repeats. With probability p, X is equal to one (this corresponds to the SMM) and with probability, 1-p, X follows a geometric distribution defined as Proba(X=k) = Zak, in which a specified variance V(X)=a/(1-a)2 or expectation E(X)=1/(1-a) determines the value of a and of the normalisation constant Z=(1-a)/a.
Vector: A self-replicating DNA molecule capable of transferring foreign DNA into a cell. For example, the human insulin gene can be cloned into the plasmid vector pBR 322 which in turn will replicate in Escherichia coli cultures.
Vicariance: The fragmentation or fusion of a species range as a consequence of processes such as plate tectonic or glacial movements.
VNTR loci (variable number of tandem repeats): The variable number of repeat core base pair sequences at specific loci in the genome. Variation in the length of the alleles formed from the repeats provides the basis for the detected polymorphism.
Wahlund effect: Deficiency of heterozygotes in a mixture of populations, which each are in Hardy-Weinberg equilibrium.
Wright-Fisher population model: An idealised population with a fixed number, N, of individuals living only one generation without migration and selection. Each individual produces a large number gametes, and all reproduce at the same time. In the gamete pool of a diploid species, : 2N gametes are drawn randomly, and random pairs form N diploid individuals in the next generation. In the gamete pool of haploid species, N gametes are drawn randomly and form N individuals in the next generation. There are many extensions of this basic model to include additional population parameters.