Browse the glossary (Organised and compiled by E.Wlodarczyk)
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adaptation - 1. the process by which organisms undergo modifications so as to function more perfectly in a given environment 2. any developmental, behavioral, anatomical. or physiological characteristic of an organism that, in its environment, improves its chances for survival and of leaving descendants.

addition - a term used in reference to --> enhancement. A genuine addition of new stock (e.g. stocking artificial reefs) [in: Stocking and introduction of fish, edited by I.G. Cowx, 1998].

admixture - fish from genetically different population(s) which mingle with the local stock.

AFLP - amplified fragment length polymorphism. A technique which is a combination of RFLP and arbitrary primer PCR; does not require prior sequence knowledge.

alleles - different forms of a single --> gene -->locus. Different alleles have unigue nucleotide sequences. See --> null allele

allowable catch - the amount of biomass allowed to be removed from a given population of fish without disturbing its self-sustainability. In practice, the allowable catch is calculated from the --> VPA models, based on the concept of --> stock. Ant. fishing quota, catch quota.

allozymes - allelic forms of an enzyme that can be distinguished by gel electrophoresis. Allozyme analysis is used to observe genetic variation from the gene products.

augmentation - a term used in reference to --> enhancement. Compensation, through stock release, for loss of habitat [in: Stocking and introduction of fish, edited by I.G. Cowx, 1998].

autapomorphy - a derived character state unique to a particular taxon.

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bootstraping - a numerical resampling technique. It involves random resampling of subsets from the original data set to provide new samples of equivalent size as the original data set (sampling with replacement). This useful technique allows to estimate variance without collecting more original data.

bottleneck effect - a form of --> genetic drift that occurs when a population is drastically reduced in size. Some alleles may be lost from the -->gene pool as a result of random events.

broodstock - a number of fish kept in a hatchery for breeding purposes.

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catch quota - see --> allowable catch.

closed season - a period of time in which fishing/hunting for a given fish/animal species is forbidden by law (ant. open season).

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DGGE - denaturing gradient gel electrophoresis. It is used to separate DNA fragments of the same length but with different sequences. Separation is based on the decreased electrophoretic mobility of a partially melted double-stranded DNA molecule in polyacrylamide gel containing a linear gradient of DNA denaturants. See --> TGGE.

D-loop - displacement loop. A non-coding region of mtDNA, supposed to mutate at higher rate than the rest of the mitochondrial genome. Also, a region which in several species exhibits length mutations due to the presence of repetitive motifs.

domesticated fish - the offspring of wild fish kept in a hatchery for breeding purposes, often subjected to intensive selection for a particular trait, e.g. growth rate, age at sexual maturity, etc.

DSCP - double stranded conformational polimorphism.

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effective population size (Ne) - 1. number of individuals contributing directly to the gene pool 2. the size of an "ideal" population with the same rate of loss of heterozygosity as the actual population. The effective population size is usually lower than the census population size (i.e. the population size measured as number of individuals). Ne of a particular population is determined by several parameters describing deviations from "ideal" conditions such as sex ratio and the variance of family size. Long-term Ne is estimated by the harmonic mean of Ne over generations. At least three different effective population sizes have been identified in literature: the inbreeding effective size, the variance effective size, and the effective size for random loss of alleles (L.Laikre & N.Ryman, Effects of intraspecific biodiversity from harvesting and enhancing natural populations, AMBIO 25(8), 1996).

 

ESU - evolutionarily significant unit. It is a population (or group of populations) that: 1) is substantially reproductively isolated from other conspecific population units, and 2) represents an important component in the evolutionary legacy of the species (R. Waples, Pacific salmon, Oncorhynchus spp., and the definition of "species" under the Endangered Species Act, Mar. Fish. Rev. 53(3), 1991).

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FCA - factor correlation analysis

fixed for allele - a term used when no polymorphism has been observed for a given allele in a population.

fishing quota - see --> allowable catch

founder effect - a form of --> genetic drift that occurs when a small breeding unit has formed by--> migration of a small number of individuals from a large population. The genetic composition of the founders may not be representative of the composition of the source population, and small --> effective population size during the first generations following the founder event further leads to strong genetic drift. This results in genetic divergence of the founded population relative to the source population. See --> bottleneck.

Fst statistic - a calculated proportion of total genetic variability attributable to the genetic differences between population. It's a relative measure, therefore its value isn't expected to be affected by the type of genetic marker used. See--> Wright's island model.

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gene - a nucleotide sequence determining a characteristic of an organism. Genes are subject to mutational alterations.

gene flow - 1. the proportion of alleles in a population each generation that is of migrant origin, 2. the transfer of genetic material between populations resulting from movements of individuals or their gametes. Usually expressed as a migration rate 'm'.

gene diversity - a common measure which summarizes genetic variation. Within a population it represents the probability that two randomly chosen genes are different (Nei, Molecular Evolutionary Genetics, Columbia University Press, 1987). In diploid species it is equivalent to the expected--> heterozygosity in a randomly mating population.

genetic drift - the amount of random change in gene frequencies. It depends on the --> effective population size.

gene pool - the total number of genes in a breeding population existing at a given time.

genotype - the genetic makeup of an organism. The frequencies or percentages of different genotypes found within a--> population are the result of the population's evolution and may be different among cospecific populations.

GIS - geographical information system

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H --> see heterozygosity

Hardy-Weinberg equilibrium - a state attained by a population which displays constant gene and genotype frequencies from generation to generation. In the case of a locus with two alleles, A and B, occuring at frequencies p and q, respectively, the frequency of genotype AA is p2, the frequency of AB is 2pq and the frequency of BB is q2. The population in H-W equilibrium has to be large, random-mating with no selection, mutation, or migration.

heritability - proportion of trait variance attributable to genetic factors

hatchery - a facility in which stocking material is raised from wild or -->domesticated -->broodstock.

hatchery strain - stocking material produced by a given hatchery. See -->broodstock.

heteroduplex analysis - a type of -->DSCP. A method of distinguishing mutations in double-stranded DNA. Any base mismatches in dsDNA will produce conformational changes (bends and loops) in such heteroduplex molecules which migrate with different velocity in polyacrylamide gel.

heteroplasmy - the presence of more than one type of mtDNA in an individual. It has been ocassionally found in most major groups of organisms (in fish: Alosa sapidissima, Acipenser spp., Amia calva).

heterozygosity - presence of more than one allele type in an individual.

homoplasy - it occurs when the same change of character state is produced through different mutational events.

hybridization - production of offspring from genetically different organisms.

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ICES - International Council for the Exploration of the Sea/Conseil International pour l'Exploration de la Mer

inbreeding depression - the decrease in growth, survival and fertility often observed following matings among relatives or self-fertilization (plants). The same outcomes may be caused by matings among genetically very distant conspecific organisms, resulting in outbreeding depression.

introductions - species or races that are intentionally or accidentally transported and released by man into an environment outside their natural range [in: Stocking and introduction of fish, edited by I.G. Cowx, 1998].

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jackknifing - a numerical resampling technique. It eliminates one observation from the original data set at the time, and thus the number of new data sets is equal to the number of observations in the original data set. This techniques allows for calculating variance within data set. See -->bootstrapping.

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landlocked population - entirely freshwater resident populations of trout where access from the sea has been cut off. They have to be distinguished from freshwater resident individuals in localities accessible from the sea.

linkage disequilibrium - a departure from -->Hardy-Weinberg equilibrium due to the fact that sorted alleles are linked, therefore, they don't sort independently.

locus/loci - physical location(s) of genes on the chromosome

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MapInfo - software application employing--> GIS

MHC - major histocompatibility complex. In mammals, a cluster of closely linked loci (approx. 1500-2500 kb) involved in a variety of immunological processes. The gene products of MHC are cell membrane glycoproteins which demonstrate a high degree of polymorphism.

migration - the physical movement of individuals

molecular clock - the postulation that the amino acid substitutions (protein clock) or nucleotide substitutions (DNA clock) occur at a constant rate for a given family of genes. Hence, the degree of genetic divergence between two species can be used to estimate the elapsed time since their divergence from a common ancestor.

mtDNA - mitochondrial DNA. The mtDNA molecule is effectively a single locus, with the composite genotypes equivalent to alleles. Maternally inherited (but see --> heteroplasmy).

MU - management unit

mutation - any detectable and heritable change in the genetic material not caused by genetic recombination (see -->SMM model)

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Neighbor - Joining method - a clustering method which allows for unequal rates of mutation among branches of an evolutionary tree. See --.> UPGMA.

NOR - necleolar organizer region

null allele - an allele which does not amplify during the PCR due to the primer-template mismatch. Indirect evidence of null alleles comes from the departure from the -->Hardy-Weinberg equlibrium. Direct detection od alleles is possible through typing of parents and offspring.

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OCU - operative conservation unit.

OMPG rule - "One-Migrant Per Generation" rule. A common rule suggesting a desirable minimum of migrants per generation to diminish genetic effects of isolation by habitat fragmentation (Mills & Allendorf, Conservation Biology 10:1509-1518, 1996)

open season - see -->closed season

outbreeding depression - see -->inbreeding depression.

outcompeted bands - a term used in reference to RAPD. When the template DNA for a particular band is present in the PCR mix in a very low amount, such band gets outcompeted in number by other amplified bands, and therefore doesn't get detected. Outcompeted bands can be a source of bias in data nalysis.

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parr - a young salmonid before -->smoltification, still having dark coloration. See also --> precocious male.

PCR - polymerase chain reaction. A method used to amplify a DNA sequence by replicating it selectively and repeatedly from a DNA mixture.

phenotype - the observable properties of an organism, produced by the -->genotype in conjuction with the environment.

population - group of interbreeding individuals that share a --> gene pool and are isolated from other similar groups.

precocious male - (syn. mature parr) Sexually mature salmonid in the parr stage.

private allele - an allele specific only for one population

pseudogene - a gene which transcribes a non-functional peptide due to mutation(s). For example, a nuclear pseudogene of mtDNA is a copy of non-functional mtDNA gene incorpotated in the nuclear genome - a possible source of bias when mtDNA analysis is based on PCR with total genomic DNA as a template.

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QTL - quantitative trait loci

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ranching - identifiable stock released with the intention of being harvested by the releasing agency. Implies a cost-benefit analysis based on comparing the harvested value with the cost of production, release and harvesting [in: Stocking and introduction of fish, edited by I.G. Cowx, 1998].

RAPD - random amplified polymorphic DNA. Oligonucleotide primers of arbitrary sequence are used to PCR-amplify the undefined regions of template DNA. Many fragments are generated from a single reaction to be later separated by agarose or polyacrylamide gel electrophoresis.

recruitment - number (or biomass) of fish which comes to a given -->year-class or length-class during a specified period of time.

redd - a characteristic hollow in the bottom of the river or lake where salmonids lay their eggs

reproductive isolation - lack of interbreeding between the individulas of the same species due to different time or pattern of reproduction (examples: Lough Melvin trout, Balsfjord herring)

restocking - compensation for depletion of a natural resource. It's a form of --> enhancement. Also see --> augmentation, addition, ranching [in: Stocking and introduction of fish, edited by I.G. Cowx, 1998].

RFLP - restriction fragment length polymorphisms.

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selective fishing - fishing as a selective agent which has a potential to change populations. See a review paper by Peter Smith, FAO Fisheries Technical Paper 344, 1994, Genetic diversity of marine fisheries resources.

sibling species - species which don't cross-reproduce

silent substitution - it occurs when there is no amino acid substitution accompanying a mutation.

SMM - stepwise mutation model. The model which describes mutation of VNTR alleles by the loss or gain of a single tandem repeat in such a way that alleles mutate possibly towards allelic states already present in the population.

SSB - spawning stock biomass.

smolt - a young silvery salmonid migrating to the sea

smoltification - a change of color to silvery in young salmonids before they begin their migration to the sea

SSCP - single strand conformational polymorphism

stepping stone model - a theoretical model of population structure and gene flow. A species is assumed to be subdivided into populations (demes or islands) of equal size N, of which only adjacent demes exchange alleles. See --> Wright's island model.

stock - for an excellent review of many possible definitions of this term see [G.R. Carvalho & L. Hauser, Molecular genetics and the stock concept in fisheries, Rev. Fish Biol. Fisheries, 4, 326-350, 1994]. Examples:

1. biological stock - "a stock is an intraspecific group of randomly mating individuals with temporal and spatial integrity" 2. harvest stock - "locally accessible fish resources in which --> fishing pressure on one resource has no effect on the abundance of fish in another contigous resource" 3. genetic stock - "a reproductively isolated unit which is genetically different from other stocks".

stocking - repeated injection of fish into an ecosystem in which a population of that species already exists from one external to it, i.e. a stocked species may be either already native to the recipient water body or exotic to it but previously introduced [in: Stocking and introduction of fish, edited by I.G. Cowx, 1998]. See --> restocking

sustainable fishery - a fishery in which -->catch is balanced by -->recruitment, therefore, no disruption of complicated trophic relationships due to fishing occurs (syn. Utopia).

symplesiomorphy - an ancestral character state shared by two or more taxa.

synapomorhy - a derived character state shared by two or more taxa.

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TGGE - temperature gradient gel electrophoresis. It is used to separate DNA fragments of the same length but with different sequences. Separation is based on the decreased electrophoretic mobility of a partially melted double-stranded DNA molecule in polyacrylamide gel containing a linear temperature gradient. See --> DGGE.

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UPGMA - unweighted pair group method with arithmetic averages. A clustering procedure which uses a genetic distance matrix to draw an evolutionary dendrogram. The major assumption of UPGMA method is the equal rate of mutation along all dendrogram branches. See --> Neighbor - Joining method.

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V

VNTR - variable number of tandem repeats.

VPA - virtual population analysis.

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Wahlund effect - a deficyt of heterozygotes. When individuals from the populations of different gene frequencies mix (not interbreed!) then the calculated expected gene frequencies for the mixed population depart from the -->Hardy-Wienberg equilibrium. A significant deficyt of heterozygotes in a given sample indicates that the sample is a mixture of 2 or more populations with different gene frequencies.

Wright's island model - a theoretical model of population structure and gene flow. A species is assumed to be subdivided into populations (demes or islands) of equal size N, all of which exchange alleles with equal probabilities. See --> stepping stone model.

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year-class - fish born in the same year, e.g., 2+ year-class stands for the fish 2 years old and older.

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50/500 rule - a practical, however, oversimplified rule used in conservation genetics. When the population size drops down to 50 individuals then the inbreeding depression sets in; 500 is a secure number of individuals to prevent long-term erosion of variability due to genetic drift.


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