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Genetics and Genomics 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.



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.

PI
See
probability of identity.

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 disseminative 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.

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

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