Glossary

This listing includes the full Glossary from the book and additional terms from the online chapters.

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absolute fitness: See fitness.

acritarch: An organic-walled microfossil, found in ancient rocks, that is interpreted as the reproductive cyst of a eukaryote.

acrocentric: A chromosome with the centromere close to one end.

adaptation: A trait that functions to increase fitness and that evolved for that function.

adaptationist program: An approach to understanding evolution that assumes that traits are adaptations.

adaptive dynamics: A method for finding which phenotypes will invade a population; related to game theory. Alleles that differ slightly from the resident alleles are introduced into a population, and may invade it; if they do, they will either displace the allele, or may coexist with it, in a balanced polymorphism.

adaptive landscape: See fitness landscape.

adaptive peak: A local maximum in the fitness landscape.

adaptive radiation: Diversification of a single lineage into species that exploit diverse ecological niches.

additive genetic variance: The total variance, V_A, contributed by the additive effects of each gene (in other words, the variance of breeding values). The response to selection on a quantitative trait is proportional to V_A.

additive genetic variance in fitness: The additive genetic variance, V_W, of fitness. Fisher’s Fundamental Theorem states that the increase in mean fitness is proportional to this quantity.

additive model: A model in which a quantitative trait is the sum of effects of all the genes involved and of a random environment.

additive tree: A phylogenetic tree in which the branch lengths are proportional to the evolutionary distance between nodes; also known as a phylogram.

ADH: The enzyme alcohol dehydrogenase.

aging: A decrease in survival or reproduction with age. It is equivalent to senescence.

algorithm: A logical process by which a problem can be solved.

align, aligned, alignment: To line up different DNA, RNA, or protein sequences. In most cases alignments include gaps where one molecule has an insertion or deletion relative to others. For phylogenetic analysis, each position (i.e., column) in the alignment should include homologous residues (bases or amino acids) from the different molecules.

allele: A particular form of a gene.

allele frequency: The frequency of a particular allele in a population.

allelic: Two variants are allelic if they are alleles at the same genetic locus.

allometry: Change in proportions with body size. For example, the size of a stag’s antlers relative to its body size increases with body size.

allopatric speciation: The formation of reproductively isolated species due to the divergence of populations that are geographically isolated from each other.

allopatry: The complete separation of populations by geographic barriers.

allopolyploid: A polyploid in which the multiple genomes are derived from different populations or species.

allosteric interaction: See allostery.

allostery: A change in the shape of a protein or ribozyme due to binding of a molecule at one site, which then changes activity at a distant site.

allozyme: One of several variant forms of an enzyme coded by alternative alleles at a single genetic locus.

α-helix: Common structural motif of proteins in which a linear sequence of amino acids folds into a right-hand helix stabilized by internal hydrogen bonding between backbone atoms.

α-proteobacteria: A major class of bacteria that includes many photosynthetic species, many pathogens (e.g., Rickettsias), and many mutualistic symbionts, including the ancestors of mitochondria.

alternative splicing: The process by which the initial RNA made from a single gene can be spliced into different mature messenger RNAs, which in turn produce different proteins.

altruistic: A gene, trait, or behavior that reduces the fitness of its bearer but increases the fitness of other individuals.

alveolate: Member of Alveolata, one of the major kingdoms of eukaryotes. It includes apicomplexans, dinoflagellates, and ciliates.

amelioration: The process in which DNA that has been acquired by lateral gene transfer changes in composition (e.g., G + C content and codon usage) to resemble the genome in which it resides.

AMH: See anatomically modern human.

amniocentesis: Removal of amniotic fluid that surrounds the embryo. The fluid contains fetal cells that can be used for prenatal diagnosis.

amoeba: A single-celled eukaryote that has no fixed shape. This phenotype is found in many eukaryotic lineages.

Amoebozoa: One of the major kingdoms of eukaryotes. Most species are heterotrophic. It includes some species that do not have mitochondria.

amphipathic: A molecule that has both hydrophobic and hydrophilic components (e.g., the phospholipids that make up membranes).

analogy: Similarity that is not due to homology (i.e., common ancestry).

analysis of variance: The separation of the variance into a sum of components, a widely used statistical technique that is the basis for quantitative genetics.

anatomically modern human (AMH): A member of the human lineage that is recognized by anthropologists as having essentially the same anatomy as present-day Homo sapiens.

ancestral characteristic: A trait found in both an organism being studied and the common ancestor of a group to which the study organism belongs.

aneuploid: A cell or organism having an abnormal set of chromosomes.

angiosperm: Flowering plant.

anisogamy: Differentiation of gametes into two (or more) sizes.

annelids: Member of Annelida, a phylum within the Lophotrochozoa. This group of segmented worms includes earthworms, leeches, and bristle worms.

antagonistic pleiotropy: Describes alleles that increase one fitness component but decrease another. It is also a term for theories of aging that involve such alleles.

anther: The male reproductive organ where pollen is produced in a flowering plant.

antibody: A protein that binds to a specific antigen.

antigen: A chemical that triggers an immune response by binding to a specific antibody.

antimutator: An allele or genotype that reduces mutation rates.

antisense oligonucleotide: A short synthetic nucleic acid sequence that is complementary to an mRNA sequence. Through a variety of mechanisms, antisense oligonucleotides can be used to inactivate gene function by interfering with the ability of an mRNA to produce its corresponding protein product.

apicomplexan: Member of Apicomplexa, a phylum of eukaryotes, in the alveolate kingdom. Many species in this phylum are parasites (e.g., Plasmodium falciparum, the causative agent of malaria).

apicoplast: An organelle found in apicomplexan species that is involved in metabolic processes. It is derived from photosynthetic chloroplasts even though it is not now involved in photosynthesis.

archaea: One of the three domains of life. These are species that do not have nuclei and thus were originally grouped with bacteria into the “ prokaryotes.” They were identified as a separate domain by analysis of rRNA sequences.

archaic human: A hominin that does not have the modern anatomy of Homo sapiens. Contrast with anatomically modern human.

argument from design: The argument that the order seen in the living world implies that it was created by a divine power.

arthropod: Member of Arthropoda, a major phylum within the ecdysozoa. This group, which is characterized by jointed legs, includes the insects, centipedes, millipedes, spiders, and crustaceans.

association study: A survey of associations between genetic markers and quantitative traits (including human disease) that aims to locate the QTLs that cause trait variation.

ATP: Adenosine triphosphate.

autocatalytic network: A chemical system that outputs a chemical that is a catalyst for the original reaction or that leads to other reactions that eventually output a catalyst for the original reaction.

autoinducer: A chemical used in quorum sensing that is secreted by cells and then used to quantify cell density.

autoinduction: The induction of a regulatory cascade in quorum sensing. It is triggered in response to the crossing of a threshold concentration of autoinducer in the environment.

automatic selection: The increase in frequency of an allele that increases the rate of selfing. It is closely related to the twofold cost of genome dilution.

autopolyploid: A polyploid that carries multiple genomes derived from within the same population.

autosome: A chromosome that is inherited in the usual Mendelian way, in contrast to sex chromosomes and mtDNA.

average effect: The effect of an allele on a quantitative trait as estimated by regression. For a random-mating population that is in linkage equilibrium, this is equivalent to the average excess.

average excess: The difference between the average trait value of individuals who carry a particular allele and the average of the population. For a random-mating population that is in linkage equilibrium, this is equivalent to the average effect.

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B chromosome: An extra chromosome that is not required for normal function in either sex and is present in only some individuals.

backcross: A cross between a hybrid individual and one of the parental genotypes.

background selection: The reduction in genetic diversity caused by selection against deleterious alleles at linked loci.

bacteria: One of the three domains of life. These are species that do not have nuclei and thus were originally grouped with archaea into the “ prokaryotes.”

bacteriocin: A toxin produced by a bacterium that kills its competitors.

bacteriophage: A virus that infects bacteria. The term is commonly used to refer to viruses that infect archaea as well.

balanced polymorphism: A stable polymorphism maintained by balancing selection.

balancer chromosome: A Drosophila chromosome that carries multiple inversions, recessive lethals, and dominant markers. Such chromosomes cannot recombine and cannot become homozygous and so can be used to keep individual wild-type chromosomes intact.

balance view: The view that genetic variation is mostly maintained by balancing selection. This contrasts with the classical view that most variation is due to deleterious mutations.

balancing selection: Selection that maintains polymorphism.

Batesian mimicry: A palatable mimic evolves to resemble a distasteful model species and thereby suffers less predation.

benthic: Living at the bottom of a body of water.

β: See selection gradient.

β-sheet: Common structural motif of proteins in which linear amino acid sequences (“strands”) located in different regions of the polypeptide chain align adjacent to each other and are stabilized by hydrogen bonding between backbone atoms located in different strands.

bilaterian: Member of the group that includes the majority of animal phyla and includes all animals with bilateral (left/right) symmetry.

binomial distribution: If n genes are sampled from a population in which the P allele has frequency p, then the chance of finding j P alleles is

binomial nomenclature: Naming scheme for species in which there is a genus name and a species name.

biological species concept (BSC): Definition of species as groups of individuals that can successfully interbreed with each other in nature but that are reproductively isolated from other such groups.

biometry: The application of statistical methods to biology.

body plan: An organism’s overall morphology that is created by the reproducible spatial positioning of differentiated cell types.

bootstrap: A statistical method for measuring consistency in datasets in which new simulated datasets are generated by sampling with replacement. In phylogenetic inference, bootstrap values represent the percentage of times that a particular clade is seen in trees generated with different simulated datasets.

bottleneck: See population bottleneck.

brachiopod: Member of the phylum Brachiopoda within the lophotrochozoa, composed of a group of marine animals that superficially resemble clams but are only distantly related to the mollusks.

branch: Portion of an evolutionary tree diagram connecting two nodes.

branching process: A process in which individuals produce a random number of offspring, independently of each other.

branch length: The length of a particular branch in an evolutionary tree. In certain types of evolutionary trees, the branch length is used to represent the amount of evolutionary change or time. A scale bar is used to represent the units of measurement.

breeding value: The sum of the average effect of each gene. If an individual is mated at random to others in the population, its offspring will deviate from the population average by one-half the breeding value.

broad-sense heritability (H²): See heritability.

bryozoan: Member of a phylum (Ectoprocta or Bryozoa) of sessile colonial animals, commonly referred to as sea mats or moss animals, that are superficially similar to corals but are instead members of the Lophotrochozoa.

BSC: See biological species concept.

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C-value: See genome size.

canalization: The buffering of development such that the same form is produced despite genetic and environmental perturbations.

candidate gene: A gene that is thought likely to influence the trait of interest, usually because major mutations at the gene affect the trait.

canonical code: The genetic code that is used almost universally.

capsid: A protein casing that makes up the outside of a virus particle.

case-control study: A form of association study in which “case” individuals with, for example, a disease are compared with “control” individuals without it.

catalysis: The facilitation of a chemical reaction by a molecule that is not itself altered by the reaction.

cDNA: See complementary DNA.

centiMorgan (cM): A distance on the genetic map that corresponds to a 1% recombination rate. See Morgan.

Central Dogma: Information can pass from nucleic acid to protein but not in the opposite direction.

Central Limit Theorem: A theorem that states that the sum of a large number of independent variables tends toward a normal distribution.

centromere: The region of chromosome that attaches to the spindle at mitosis and meiosis.

chaetognath: Any worm of the phylum Chaetognatha, commonly called an arrowworm. This is a transparent marine worm with horizontal lateral and caudal fins and a row of movable curved spines at each side of the mouth.

chaperone: A protein that assists other proteins in achieving a properly folded state.

character state: The particular form that a character trait takes (e.g., a three-chambered vs. four-chambered heart, or an A vs. a T at a particular position in homologous gene sequences).

character state reconstruction: A method used to infer ancestral and derived character states and traits.

character trait: Particular parts or properties of an organism. Used in phylogenetic analysis and to study the evolution of traits over time. Character traits include both discrete (e.g., presence of a heart or globin molecules, type of globins found) and quantitative traits (e.g., four-chambered heart, number of different types of globins).

chemical evolution: Chemical reactions that could have generated complex compounds from simple ones prior to the origin of life.

chemostat: A device that allows populations of microorganisms to be maintained in a steady state.

chert: Very fine grained silica (SiO₂) that forms layers or nodules in sequences of sedimentary rocks.

chiasma: The cross-like structure formed by crossing over during meiosis.

chi-square distribution: The distribution of the sum of squares of a number n of normally distributed variables; written as .

chlorophyte: Member of a phylum of eukaryotes that are all single-celled green algae and closely related to green plants.

chloroplast: A photosynthetic organelle found in many plants, algae, and other microbial eukaryotes. All chloroplasts are evolutionarily derived from cyanobacteria.

choanoflagellate: Member of a phylum of eukaryotes including single-celled flagellated species. This is the sister phylum to animals.

chordate: Member of a major phylum (Chordata) within the deuterostomes, which includes the vertebrates and closely allied invertebrates such as tunicates and amphioxus. All chordates contain a solid rod, called a notochord, along the length of the body during embryogenesis and a dorsal nerve cord and pharyngeal pouches.

chromatid: One of the two copies of a chromosome after it has been replicated.

chromatin: A compact structure of DNA and protein found in eukaryotic nuclei.

chromosomal fusion: See fusion, chromosomal.

chromosomal inversion: See inversion, chromosomal.

ciliate: Member of a phylum of eukaryotes including single-celled species. Most are coated on the outside with cilia, which are used for movement and cellular functions. They are in the kingdom Alveolata.

cis-regulation: Refers to the regulation of when and where a gene is transcribed by DNA sequences that lie to either side (5′ or 3′) of the gene or within the introns of the gene.

clade: A group of species or genes that includes all descendants of an ancestral species or gene. See monophyletic.

cladistics: A method of classification that is based on the order of branching in a phylogenetic tree rather than on phenotypic similarity.

cladogram: A phylogenetic tree in which the only information given is about the relationships among taxa (i.e., the length of the branches is not meaningful).

classical view: The view that genetic variation is mostly due to deleterious mutations. This contrasts with the balance view that most variation is maintained by balancing selection.

cline: A smooth change from place to place across a spatially continuous habitat. The term refers to a spatial gradient in any measurable characteristic—for example, allele frequency or the mean of a quantitative trait.

clonal interference: In an asexual population, different clones, each favored by selection, compete with each other so that only one can succeed.

clone: A set of genetically identical individuals. In genetic engineering, a line of microbes that carry a particular sequence from another species.

cM: See centiMorgan.

CMS: See cytoplasmic male sterility.

cnidarian: Member of a major animal phylum (Cnidaria) that includes corals, sea anemones, hydra, and jellyfish. The group is characterized by the presence of stinging cells called nematocysts.

coalescence: The merging of two genetic lineages into a single common ancestor.

coalescence time: The time back to when two genes share a common ancestor.

coalescent process: A model in which as one moves back in time, each pair of lineages coalesces at a rate 1/2N_e.

coancestry: A measure of the relatedness of two individuals. It is the chance that two randomly chosen genes, one from each individual, are identical by descent.

codon: Three bases that code for a single amino acid.

codon usage: The frequency with which each of the alternative codons that code for an amino acid is used.

codon usage bias: A bias toward use of one of several alternative codons that code for the same amino acid.

coefficient of kinship: See coancestry.

coevolution: The joint evolution of two species, with each responding to selection imposed by the other.

colloid: A substance that contains components in different phases (e.g., minute solid particles within a liquid).

compartmentalization: Subdivision of molecules, cells, or genetic functions into discrete spatial or temporal units. For example, this can refer to the grouping together of a protein into distinct parts of the cell or of networks of genetic interactions into distinct functional units.

competence: The uptake of DNA directly from the environment.

competitive exclusion: Species that use exactly the same resources cannot coexist in a stable equilibrium.

complementary DNA (cDNA): DNA that is complementary to messenger RNA. By producing cDNA using reverse transcription from mRNA, actively expressed genes can be identified.

complementation test: A test for determining whether two mutations are in the same gene (they do not complement) or different genes (they complement).

component of fitness: See fitness component.

component of variance: See variance component.

concerted evolution: The evolution of repeated sequences, which tend to remain homogeneous because of processes such as unequal crossing over and gene conversion.

confidence interval: The range of parameter values that do not deviate significantly from a null hypothesis.

congruency: A measure of how similar are different phylogenetic trees containing the same operational taxonomic units (OTUs).

conjugation: The transfer through a pilus of DNA from one bacterium or archaeon to another.

conservative DNA transposons: A DNA-based transposable element that moves itself to a new place in the genome but does not leave a copy in the original location.

consistency: A measure of whether, given sufficient data, a method will generate a correct answer.

consistency index: A measure of how well the character states for a specific character trait map on a phylogenetic tree. It is calculated as the ratio of the minimum number of evolutionary state changes (aka steps) that could be seen from all possible trees divided by the actual number of changes on the tree being examined.

constitutive: Referes to a gene that is always expressed.

contingency loci: Loci made up of microsatellite repeats (e.g., ATATATAT) in which, when the number of copies of the repeat changes, the phenotype of the cell changes drastically. These are common in the genomes of some bacterial pathogens.

convergence (also convergent evolution): The process by which features with no common ancestry become similar as a result of selection.

correlation coefficient: The most commonly used measure of correlation between two variables (x, y). It was devised by Karl Pearson and is defined as the ratio between the covariance and the square roots of the variances:

correlation, genetic: See genetic correlation.

cosexual: Producing both male and female gametes. It is equivalent to hermaphrodite.

cost of genome dilution: The disadvantage to a female who reproduces sexually and therefore devotes resources to propagating her mate’s genes.

cost of meiosis: See cost of genome dilution.

cost of natural selection: See substitution load.

covariance: A measure of association between two variables (x, y). It is defined as the expected product of their deviations from the mean:

Note that cov(x, x) = var(x).

covariance matrix: An n × n matrix giving the covariances between a set of n variables. The diagonal gives the covariances of each variable with itself (i.e., the variances).

covirus: One of a pair of viruses that have complementary functions and that must coinfect a cell for successful viral transmission.

cristae: Infolded internal membranes, such as those seen in mitochondria and plastids.

crossover: A recombination event within a chromosome at meiosis.

crown group: That part of a clade of living and fossil organisms that includes the last common ancestor of all the living forms and all of its descendants. See stem group.

ctenophore: Member of a major animal phylum of solitary gelatinous marine animals commonly called comb jellies or sea gooseberries (phylum Ctenophora). Members of this group have rows of small combs composed of cilia that are used for locomotion.

cultural evolution: Change in culture (i.e., information passed on by learning and imitation rather than by biological inheritance).

culturing: The growth of a particular microorganism in the laboratory in isolation from other organisms.

cumulative distribution: The probability that a random variable will be less than a given value is called its cumulative distribution.

cyanobacteria: One of the major phyla of bacteria. Most species are photosynthetic, and chloroplasts are derived from this group.

cytology: Study of cells.

cytoplasmic male sterility (CMS): Loss of male function due to a cytoplasmically inherited factor in flowering plants.

cytoskeleton: The system of protein filaments in the cytoplasm of eukaryotic cells that gives the cell its shape and its capacity for directed movement and that participates in the directed transport of molecules within a cell.

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D: This symbol is used in several ways. See genetic distance and linkage disequilibrium. D_n and D_s are also used as alternative notations for K_a and K_s.

Darwin (d): A unit for the rate of change of morphology. It was introduced by J.B.S. Haldane and is equal to a change by a factor e = 2.718... per million years or 1 part per million per year.

Darwinian Demon: A hypothetical organism with indefinitely high survival and fertility. This is an idea used to emphasize that all real organisms must face constraints on their fitness.

Darwinian medicine: The application of evolutionary principles to medicine.

defective interfering virus (DIV): A virus that has lost some function and that depends on coinfection with intact virus for transmission.

deism: The view that God works through fixed laws of nature; that is, that events occur without supernatural intervention.

deme: A discrete local population.

dendrogram: A phylogenetic tree in which the branch lengths are constrained to all be equidistant from the root; also known as an ultrameric tree.

density-dependent selection: Selection that occurs when relative fitness depends on population density.

derived characteristic: A trait found in an organism that was not present in the common ancestor of a group of organisms being studied.

descent with modification: Darwin’s term for evolution.

deuterostome: Member of one of the two large groups of bilaterian animals including the echinoderms, hemichordates, and chordates. In this group, the initial embryonic opening becomes the anus. See protostome.

developmental constraints: Limits on what kinds of organism can develop.

diapause: A resting stage that allows organisms to survive harsh conditions.

differential equation: An equation that gives the rate of change of a system as a function of its present state.

differentiation: The process by which a cell becomes more and more specialized in its function and morphology through the regulation of gene expression and biochemical activities.

diffusion: Spreading due to the cumulative effect of small random movements.

diffusion approximation: A mathematical approximation that describes diffusion using a differential equation. It describes the spread of chemical concentration or allele frequency through physical space and also the spread of a probability distribution through the space of allele or genotype frequencies.

diffusion equation: An equation that describes how a probability distribution spreads out with time; it applies when random fluctuations are small.

dimer: Two molecules that are bound together. Similarly, trimers and tetramers are clusters of three and four molecules, respectively.

dinoflagellate: Member of a phylum of eukaryotes in the Alveolate kingdom. All are single-celled organisms and many are photosynthetic.

diploid: Carrying two copies of each chromosome.

direct selection: See selection, direct.

directional selection: Selection favoring one allele over another or favoring increased values of a quantitative trait. It is equivalent to positive selection.

discicristate: A kingdom of eukaryotes. It includes the kinetoplastids (e.g., trypanosomes) and euglenoids.

disruptive selection: Selection favoring extreme values of a trait.

distance matrix: A table showing the evolutionary distance between sets of operational taxonomic units (e.g., species or genes).

distyly: A polymorphism with two different arrangements of anther and stigma that promotes outcrossing.

DIV: See defective interfering virus.

divergence: The acquisition of differences after evolutionary separation (e.g., of species).

dizygotic twins: Twins formed from separate zygotes and therefore related in the same way as siblings.

DNA ligation: Chemical connection of two DNA strands. It is used in DNA repair, replication, and other molecular processes.

Dobzhansky–Muller model: A simple model for the evolution of reproductive isolation in which two populations accumulate different alleles. These alleles cause no loss of fitness within the genetic background in which they arose, but derived alleles from different populations are incompatible with each other.

domain of attraction: The domain of attraction of a stable equilibrium is the set of states from which a system will evolve toward that equilibrium.

dominance: If the heterozygote is precisely intermediate between the two homozygotes, there is no dominance. Any deviation from this additive model is described as dominance.

dominance deviation: The difference between the trait value of a genotype and the value expected with no dominance.

dominance theory: An explanation for Haldane’s rule, which assumes that F₁ sterility or inviability is caused by recessive alleles.

dominance variance (V_D): The variance in a quantitative trait that is caused by dominance. It is defined as the variance of dominance deviations.

dominant: An allele is completely dominant with respect to a certain phenotype if it produces that phenotype when present in either one or two copies.

dominant lethal: See lethal.

dosage compensation: A mechanism that ensures that sex-linked genes are expressed at the appropriate level in both males and females.

drift: See random genetic drift.

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ecdysozoan: Member of a major subdivision within the protostomes that includes the arthropods, nematodes, and several smaller phyla. Members of this group possess an external covering called a cuticle that molts as the animal grows.

echinoderm: Member of a major phylum within the deuterostomes that includes sea urchins, starfish, crinoids, and sea cucumbers. Although they possess bilateral symmetry initially, adults usually show a fivefold radial symmetry.

ecotype: A genotype adapted to a particular environment.

ectoderm: One of three cell layers found in bilaterian embryos (the other two being the endoderm and mesoderm). The ectoderm goes on to form structures such as the external skin, mouth, and the nervous system.

ectopic recombination: Recombination between repetitive DNA elements found in different regions of the genome (e.g., between transposable elements at different sites). This can lead to chromosome rearrangements and deletions.

EEA: See environment of evolutionary adaptation.

effectively neutral: An allele that alters fitness by less than approximately 1/N_e. Its probability of fixation is approximately the same as if it were absolutely neutral.

effective population size (N_e): The size of the ideal Wright–Fisher population that would give the same rate of random drift as the actual population in question.

efficiency: A measure of the speed at which a method performs.

electrophoresis: A technique in which molecules are pulled through a porous medium by an electric field and so are separated according to their charge and mobility.

endocytosis: The engulfment of material found outside a cell by surrounding it with the cell membrane.

endoderm: One of three cell layers found in bilaterian embryos (the other two being the ectoderm and mesoderm). The endoderm goes on to form structures such as the lining of the digestive system and portions of organs such as the liver, lung, and pancreas.

endomembrane system: Series of intracellular membrane compartments found in eukaryotic cells.

endomitosis: Mitosis with no cell division, which leads to a doubling of ploidy.

endoplasmic reticulum: Eukaryotic membrane compartment involved in translation, folding, and transport of proteins.

endosymbiosis: A symbiosis in which one organism lives within cells of another.

entropy: A quantitative measure of disorder. The Second Law of Thermodynamics states that the entropy of a closed system can never decrease.

environmental deviation: The difference E between the expected trait value of a given genotype and its actual value.

environmental genomics: See metagenomics.

environmental variance (V_E): The variance of the environmental deviation, var(E) = V_E.

environmental variation: Variation between genetically identical individuals.

environment of evolutionary adaptation (EEA): In evolutionary psychology, the Pleistocene environment in which adaptive human traits evolved.

epigenesis: The development of an organism from a zygote through cell differentiation and formation of morphology. The term also refers to the theory that organisms develop in this way rather than by preformation.

epistasis: Interaction between alleles in their effect on a trait. If a quantitative trait is given by adding up contributions from different loci, then we say that there is no epistasis.

ESS: See evolutionarily stable strategy.

euchromatin: The part of the eukaryote genome that is not condensed and that contains most active genes. It contrasts with heterochromatin.

eugenics: Improvement of the human gene pool through selective breeding.

euglenoid: Member of a class of eukaryotic microorganisms bearing flagella. Most members live in freshwater and many possess chloroplasts.

eukaryote: One of the three domains of life. Its species are characterized by the presence of a nucleus.

eusocial: Fully social organisms in which only one or a few individuals in a colony reproduce.

eutherian mammal: A mammal having a placenta. This includes all mammals except monotremes and marsupials.

evolutionarily stable strategy (ESS): A strategy that cannot be displaced by any alternative. Individuals that play the ESS must be at least as fit as any feasible alternative when the rest of the population is playing the ESS.

evolutionary character state reconstruction: See character state reconstruction.

evolutionary computation: Using evolutionary processes—especially natural selection—to solve computational problems. See genetic programming, genetic algorithm.

evolutionary ecology: Study of the evolutionary consequences of interactions between species and between a species and its environment.

evolutionary game: An interaction between individuals in which the payoff depends on the strategy played by each of them.

evolutionary psychology: A field that applies evolutionary principles to understand universal human traits. It is usually assumed that humans are adapted to their past “ environment of evolutionary adaptation.”

Evolutionary Synthesis: The synthesis during the 1930s and 1940s of population genetics with other fields of biology (e.g., paleontology, systematics, and botany).

evolvability: Ability to generate heritable variation that can be exploited by selection.

excavate: Member of a kingdom of eukaryotes. All are single-celled species and none are known to have mitochondria.

exon: A protein-coding region of a protein-coding gene.

exon shuffling: Recombination events that mix exons from two different genes.

expectation: The average value of a function g(x) of a random variable x is called its expectation,

where f(x) is the probability density of x.

expected heterozygosity: See gene diversity.

exploratory system: Systems that shape initially random variation so as to produce a well-coordinated functional outcome.

exponential: Growing at a constant rate r, so that numbers increase with e^rt.

exponential distribution: A continuous distribution with density λ exp(λx). The distribution of times between events that occur at a consant rate is exponential.

extended phenotype: The phenotype of all the individuals affected by a gene.

extremophile: An organism that thrives in environments that are at the extremes of conditions where life is normally found.

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falsifiability: A measure of whether the results of a method allow one to determine if assumptions used have been violated.

fitness: The number of offspring left by an individual after one generation. The fitness of an allele is the average fitness of individuals that carry that allele.

fitness component: Traits, such as survival, mating success, and reproduction, that combine to determine fitness.

fitness landscape: Either a graph of fitness as a function of individual genotype or phenotype or of population mean fitness as a function of allele frequencies or trait means.

fitness, mean: The average fitness of a population.

fitness, relative: The fitness divided by the mean fitness or by the fitness of a reference genotype.

fixation probability: See probability of fixation.

fixed (also fix): When all copies of a gene carry the same allele, that allele is said to be fixed.

fluctuation test: An experimental method for measuring mutation rates and for determining whether mutations arise prior to or in response to selection.

founder effect: The loss of genetic variation and the consequent change in genotype frequencies that occurs when a small number of individuals found a new population. It is equivalent to a burst of random genetic drift.

frameshift mutation: An insertion or a deletion mutation that leads to a change in the reading frame in a protein-coding gene.

frequency-dependent selection: Selection that occurs when relative fitness depends on genotype frequencies.

frequency spectrum: The distribution of allele frequencies.

F_ST: A measure of the genetic diversity between subpopulations relative to the total:

It was devised by Sewall Wright.

Fundamental Theorem (of Natural Selection): The increase in mean fitness due to selection on allele frequencies is equal to the additive genetic variance in fitness divided by the mean fitness:

fusion, chromosomal: A mutation in which two chromosomes are connected at their ends. The product is a metacentric chromosome.

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galls: Structures induced in a plant by a parasite (e.g., a bacterium or an insect) that nurture that parasite.

game: See evolutionary game.

game theory: See evolutionary game.

gametophyte: In plants, the haploid structure that produces gametes. It contrasts with sporophyte.

γ: See selection gradient, quadratic.

Gamma distribution: The sum of a number of independent, exponentially distributed variables (e.g., the time taken for a number of independent events to occur) follows a Gamma distribution.

gas hydrate: Frozen deposits rich in hydrocarbons that occur in the deep ocean basins.

Gaussian distribution: See normal distribution.

gene: A stretch of DNA (or, in some viruses, RNA) sequence that codes for a protein or RNA molecule, together with associated regulatory elements.

genealogical species: A group of individuals for whom the genealogies at all loci in the genome are reciprocally monophyletic. See Web Notes.

genealogy: The tree-like ancestral relationship that connects a set of genes at a single genetic locus.

gene conversion: A meiotic process in which nonreciprocal exchange of genetic information occurs as a result of heteroduplex formation between non-sister chromatids. Thus, heterozygous sites are converted to sites homozygous for one or the other allele.

gene diversity (H): The probability that two randomly chosen genes will carry different alleles. It is equal to the heterozygosity for a randomly mating diploid population with no selection.

gene dosage: The number of copies of a gene within an individual.

gene flow: The movement of genes from place to place. The term usually refers to movement in space but can also refer to movement between microhabitats or to introgression between distinct populations or species.

gene therapy: A treatment in which functional genes are introduced into the patient.

genetic algorithm: An algorithm that applies selection, mutation, and recombination to a population of computer programs in order to solve computational problems.

genetic assimilation: The process in which a phenotype, normally expressed only in a specific environment, through selection shows increased expression in that environment, which may cause the phenotype to be expressed under normal conditions as well.

genetic background: The set of genes with which a gene of interest is associated. Recombination moves genes from one genetic background to another.

genetic code: The code that translates 64 possible triplet codons into amino acids and translation stop signals.

genetic correlation: A correlation between the breeding values for different traits. This may be due to linkage disequilibrium between genes affecting the different traits or to pleiotropy, in which alleles affect both traits.

genetic distance: A measure of the difference in allele frequencies between populations. The most widely used measure of genetic distance is Nei’s D.

genetic drift: See random genetic drift.

genetic engineering: The manipulation of organisms by the artificial introduction of DNA sequence in order to change their characteristics.

genetic load: The loss of mean fitness relative to some ideal fitness:

It includes mutation, substitution, recombination, and segregation loads.

genetic locus: See locus.

genetic map: A map of the linear order of genes constructed by measuring the rates of recombination between them.

genetic marker: A polymorphic locus that is used to observe genetic variation but that is not itself of primary interest.

genetic programming: Generating computer programs by selection on a population of variant programs. It is similar to the use of genetic algorithms.

genetic recombination: See recombination.

genetic system: The system immediately responsible for transmission of genetic information.

genome size (C-value): The size of a single haploid genome. It is sometimes expressed as the mass of a single haploid genome measured in picograms (1 pg = 10^–12 g) and corresponding to approximately 1000 Mb of DNA.

genomic imprinting: See imprinting, genomic.

genotype: The set of alleles carried by an individual.

genotype frequency: The frequency of a particular genotype in the population.

genotypic value: The average trait value G of individuals with a particular genotype.

genotypic variance (V_G): The variance of the genotypic value: var(G)= V_G.

geometric mean: An average defined by the nth root of the product of n values:

germ line: In a multicellular organism, the lineage of cells that will generate gametes via meiosis. It contrasts with soma.

glaucocystophyte: Member of a phylum of eukaryotes that contains single-celled photosynthetic species.

good genes: Genes that increase fitness for reasons that are not due to sexual selection on a signal trait. Such components of fitness are most conveniently thought of as viability, but fertility and mating success could also be included.

gracile: Graceful, slender, and delicate. The term is used to describe the large rear teeth of certain Australopithecenes. It contrasts with robust.

Gram stain: A stain that specifically detects the type of cell wall and membrane structure found in some bacterial species. These are known as “gram-positive” species.

great plate count anomaly: A phenomenon in which the number of cells from natural environments that can be grown in culture is much less than what can be seen through a microscope. This was one of the first indications of the difficulties in culturing many of the microbes found in the environment.

green beard: An allele that causes a hypothetical trait (a “green beard”) will tend to increase if individuals with “green beards” tend to help others that carry the same trait. This thought experiment shows that kin selection need not depend on a family relationship.

group selection: Selection of traits that increase survival and proliferation of groups of individuals.

gynodioecious: A population that contains both females and hermaphrodites.

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H: See gene diversity.

H²: See heritability.

h²: See heritability.

Haldane’s rule: When in the offspring of two different animal taxa, one sex is absent, rare, or sterile, that sex is the sex with heterozygous sex chromosomes. Defined by J.B.S. Haldane in 1922.

halophilic: Describes an organism with a preference for growth in high-salt environments.

haltere: Sense organs found in Diptera on the second thoracic segment, evolutionarily derived by modification of the wings. They are used to help balance during flight.

Hamilton’s rule: An allele that increases the fitness of its neighbors by B but reduces the fitness of its carrier by C will increase if rB > C, where r is a measure of the genetic similarity of neighbors to the focal individual.

handicap: A trait that signals a male’s genetic quality. Its association with good genes is maintained because it is less costly to males of higher quality.

haplodiploid: A system of sex determination in which fertilized eggs develop as diploid females and unfertilized eggs develop as haploid males.

haploid: Carrying one copy of each chromosome.

haplotype: A particular combination of alleles in a haploid—that is, a haploid genotype.

hard selection: Selection where numbers produced by a patch are directly proportional to the relative survival of the individuals of that patch, see Web Notes.

Hardy–Weinberg proportions: The frequencies of diploid genotypes produced after random mating. In the simplest case of two alleles at frequencies q + p = 1, the three genotypes QQ, PQ, PP are at frequencies q ², 2pq, p ².

harmonic mean: An average defined by

It gives greatest weight to small values. The effective population size is the harmonic mean of the population sizes in each generation.

hemichordate: Member of a diverse phylum of marine animals including the acorn worms and pterobranchs (phylum Hemichordata).

hemimetabolous: Developing directly through a series of nymphal stages with a similar morphology to the adult (e.g., as in grasshoppers and bugs). It contrasts with holometabolous.

heritability: The fraction of phenotypic variance that is inherited. The broad-sense heritability refers to the total genotypic variance (H²= V_G/V_P), whereas the narrow-sense heritability refers to the additive genetic variance (h²= V_A/V_P).

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

heterochrony: The change in the relative timing or duration of events during development achieved by altering the relative onset or ending of particular developmental processes.

heterogametic: The sex that carries distinct sex chromosomes. For example, in mammals, males are the heterogametic sex.

heterokont: One of the kingdoms of eukaryotes. It includes a diverse collection of single-celled species including diatoms.

heterosis: The increase in fitness seen in a cross between different populations.

heterostyly: A polymorphism for distinct arrangements of anther and stigma.

heterozygosity: The proportion of heterozygotes in a population.

heterozygote: A diploid individual that carries two different alleles at a locus.

heterozygote advantage: See overdominance.

hierarchical classification: A system of classifying organisms in a nested series of levels—domain, kingdom, phylum, class, order, family, genus, species.

Hill–Robertson effect: The interference between selection at linked loci. It was first analyzed by Hill and Robertson in 1966.

hitchhiking: The increase in a neutral allele that happens to be associated with a selectively favorable allele at another locus. It is sometimes used more broadly to refer to any kind of indirect selection.

HIV: See human immunodeficiency virus.

HLA: Human leukocyte antigen. See major histocompatibility complex.

Holliday junction: The cross-like structure formed by crossing over between two DNA double helices.

holometabolous: Metamorphosis through a pupal stage (as in flies, butterflies, and beetles). It contrasts with hemimetabolous.

homeobox: A sequence, approximately 180 nucleotides long, that is translated into a DNA-binding domain called the homeodomain. This sequence is found in many transcription factors that play a role in pattern formation and cell differentiation.

homeodomain: A sequence, approximately 60 amino acids long, that is encoded by a homeobox DNA sequence. This protein motif forms a DNA-binding domain that is found in many transcription factors that play a role in pattern formation and cell differentiation.

homeotic: Describes a class of mutations that transforms one part of an organism into another part. For example, a particular homeotic mutation in Drosophila transforms the antennae into legs.

hominid: Member of the great apes (family Hominidae), which now include human, gorilla, orangutan, and chimpanzee.

hominin: All taxa closer to humans than to chimpanzee. Apart from ourselves, all these taxa are now extinct.

homologous recombination: The process by which two pieces of DNA, identical or nearly identical in sequence (e.g., two copies of a chromosome), align and exchange a portion of DNA.

homology: A similarity attributable to its derivation from the same ancestral feature. In genetic studies, it refers to genes that are present in the same locus in the genome. In phenotypic studies, it refers to character traits or states that are present in a set of species and their common ancestor.

homoplasy: A similarity of traits that is not due to homology but instead to convergence or parallel evolution.

homozygote: A diploid individual that carries the same allele at a genetic locus.

homunculus: A “little man” that was supposedly introduced into a fertilized egg by the sperm and that guided its development. See preformation.

horizontal transmission: Transmission of genetic information between different individuals other than from parent to offspring.

host races: Genetically distinct populations that specialize on different hosts.

hot spots, recombination: See recombination hot spots.

human immundeficiency virus (HIV): The virus responsible for AIDS.

hybrid rescue allele: An allele that alleviates hybrid sterility or inviability.

hybrid zone: A narrow region in which genetically distinct populations meet, mate, and hybridize.

hydrogenosome: An organelle of some eukaryotes that produces hydrogen gas and ATP. It is possibly derived from mitochondria.

hydrophilic: A molecule or portion of a molecule that readily dissolves in water via the formation of hydrogen bonds.

hydrophobic: A molecule or portion of a molecule that does not readily dissolve in water.

hydrophobic core: A portion of a protein that avoids dissolution in water and is composed of a set of hydrophobic amino acids.

hypercycle: Cooperation between a set of replicating molecules (A, B, ..., Z), in which A aids replication of B, B aids C, ..., and Z aids A. It was proposed as a way for early life to replicate genetic information despite high mutation rates.

hyperthermophile: An organism that thrives at temperatures above 80°C.

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IBD: See identity by descent.

identical twins: Twins formed from a single zygote and therefore genetically identical. See monozygotic twins.

identity by descent (IBD): Genes that are inherited from the same gene in an ancestral population are identical by descent.

immune memory: The increased response of the immune system to an antigen that had been encountered before. This is the basis of vaccination.

immunoglobulin: A family of proteins involved in the immune system. It includes antibodies.

immunological distance: A measurement of phylogenetic relationship based on differences in antibody– antigen binding affinity between species. The magnitude of the difference is used as a rough evolutionary clock.

imprinting, genomic: A phenomenon in which the phenotype of a heterozygote depends on which allele came from the father and which from the mother.

inbred: Produced by mating between relatives.

inbred line: A population produced by continued self-fertilization or mating between close relatives. After several generations of inbreeding, an inbred line becomes genetically homogeneous.

inbreeding: Mating between relatives.

inbreeding coefficient: The chance that two homologous genes in a diploid individual are identical by descent.

inbreeding depression: Reduced vigor of inbred individuals.

inclusive fitness: A measure of individual fitness that includes the effects of that individual on its neighbors’ fitness, weighed by their relatedness, and discounts the effects of neighbors on the individual’s own fitness.

incomplete dominance: A condition in which heterozygotes express a trait that is distinguishable from both homozygotes.

indel: An insertion or a deletion mutation involving a small number of bases.

indirect selection: Selection on a trait that arises from its association with other traits rather than because of its direct causal effect on fitness. The term may also refer to selection that arises from the effects of a gene in one individual on the fitness of other individuals.

induction: Increase in gene expression in response to a regulatory signal.

infinite-alleles model: A model that assumes that every mutation generates a new allele.

infinitesimal model: A model that assumes that quantitative trait variation is caused by a very large number of loci, with infinitesimally small additive effects. Selection alters the mean, but the genetic variance remains constant. It is equivalent to assuming that offspring are normally distributed around the mid-parental value, with constant variance.

infinite-sites model: A model that assumes a very large number of sites, each with a very low mutation rate, so that every mutation is unique.

informational genes: Genes involved in core “informational” processes including DNA replication and repair, transcription, and translation. They are thought to be less prone to lateral gene transfer than operational genes.

ingroup: A set of operational taxonomic units for which the phylogenetic relationships are being determined relative to an outgroup.

inheritance of acquired characteristics: Transmission of characteristics acquired during an organism’s lifetime to its offspri