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- P
- proline.
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- palindromic sequence
- A DNA or RNA sequence that reads the same on the complementary strand (e.g., AATGCATT). A DNA or RNA sequence that shows symmetry about a central axis point.
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- PAML
- Phylogenetic Analysis using Maximum Likelihood.
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- parallel substitutions
- The independent occurrence of the same mutation at the same nucleotide site in two or more lineages.
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- paralogy
- Sequence similarity between the descendants of a duplicated ancestral gene.
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- pararetrovirus
- A virus that contains a gene for reverse transcriptase but cannot insert itself into the host chromosome.
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- parsimony
- Literally, the use of a minimum number of means to achieve an end. (see maximum parsimony)
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- pattern of substitution (substitution scheme)
- The relative frequency with which a nucleotide or an amino acid changes into another during evolution.
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- PAUP*
- Phyogenetic Analysis Using Parsimony, *and other methods (pronounced pop star).
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- PCR (see polymerase chain reaction)
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- phase-0 intron
- An intron that lies between two codons.
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- phase-1 intron
- An intron that lies between the first and second nucleotides of a codon.
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- phase-2 intron
- An intron that lies between the second and third nucleotides of a codon.
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- phenogram
- A graphic representation that portrays or attempts to portray the taxonomic relationships among a number of individuals, species, or higher taxa on the basis of overall similarities between them.
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- phenotype
- The observable characteristics of a genetically controlled trait.
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- PHYLIP
- PHYLogenetic Inference Package (pronounced fy-lip).
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- phylogenetic tree
- A graphic representation of the phylogeny of a group of taxa or genes.
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- phylogenetics
- The reconstruction of the evolutionary history of a group of taxa or genes.
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- phylogeny
- The evolutionary history of a group of taxa or genes and their ancestors.
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- plasmid
- An autonomous, self-replicating extrachromosomal circular DNA.
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- plesiomorphy
- A shared ancestral character state.
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- point mutation
- A mutation affecting only one nucleotide site. Usually, in reference to a nucleotide substitution.
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- polarity
- The property of nucleic acids to be read one way from 5' to 3' and differently in the opposite direction.
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- polyadenylation signal
- A box on most eukaryotic mRNA molecules that specifies the location of the polyadenylation site.
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- polyadenylation site (poly(A)-addition site)
- The 3' end of most mRNA molecules in eukaryotes. The site at which a poly-A tail is added.
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- Polygamy
- A mating system in which a male mates with more than one female (polygyny) or a female mates with more than one male (polyandry)
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- polymorphism (genetic polymorphism)
- The coexistence of two or more alleles at a locus.
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- polypeptide
- A molecule made of amino acids covalently linked to each other by peptide bonds. Often, a term used to denote the amino acid chain of a protein before it assumes a functional three-dimensional configuration.
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- polyphyletic
- Descended from different ancestors.
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- polyploidy (genome doubling, genome duplication)
- The presence in a cell or an individual of more than two haploid sets of chromosomes (e.g., tetraploidy, hexaploidy)
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- population
- A group of individuals in a species that share a common gene pool.
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- population size (census population size)
- The number of individuals in a population.
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- positive selection
- Selection for an advantageous mutant allele.
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- posterior probability
- The probability of a parameter value inferred from an analysis.
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- pre-messenger RNA (pre-mRNA)
- The primary transcript of a protein-coding gene before maturation.
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- preproprotein
- The primary product of translation before any posttranslational changes have been made.
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- pretermination codon
- A codon that requires only one mutation to become a termination codon.
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- primary amino acid
- One of the 20 amino acids specified by the universal genetic code.
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- primary structure
- The sequence of amino acids in a polypeptide chain. The sequence of nucleotides in a DNA or RNA molecule.
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- prior probability
- The probability of a parameter value at the start of an analysis.
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- processed gene (see retrogene)
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- progressive alignment
- A heuristic method for multiple sequence alignment wherein pairwise alignments are made of progressively less closely related sequences. These methods use a guide tree from an clustering method, such as neighbor-joining, as a starting point for pairwise comparison.
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- proproiein
- A product of translation after the signal pepticle has been removed and before additional posttranslational modifications have been made.
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- prosthetic group
- A nonprotein molecule attached to an apoprotein that is required for functionality (e.g., heme in hemoglobin).
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- protein
- A molecule composed of one or more polypepticle chains. May or may not contain prosthetic groups.
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- protein-coding gene
- A gene that contains a reading frame, the mRNA of which is translated.
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- provirus
- A viral genome integrated into the genome of the host cell.
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- pseudogene
- A functionless segment of DNA exhibiting sequence homology to a functional gene. A nonfunctional member of a gene family.
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- purifying selection (negative selection)
- A selection regime resulting in the removal of an allele from the population.
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- purine
- A type of nitrogen base present in nucleotides and composed of two joined ring structures, one five-membered and one six-membered. The purine bases in DNA and RNA are adenine and guanine.
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- pyrimidine
- A type of nitrogen base present in nucleotides and composed of a single six-membered ring. The pyrimidine bases in DNA are cytosine and thymine. The pyrimidine bases in RNA are cytosine and uracil.
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