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Glossary

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A B C D E F G H I J K L M N O P Q R S T U V W X Y Z

A

adaptation: A process of genetic change in a population whereby, as a result of natural selection, the average state of a character becomes improved with reference to a specific function, or whereby a population is thought to have become better suited to some feature of its environment. Also, an adaptation: a feature that has become prevalent in a population because of a selective advantage conveyed by that feature in the improvement in some function. A complex concept; see Chapter 11.
adaptive peak: That allele frequency, or combination of allele frequencies at two or more loci, at which the mean fitness of a population has a (local) maximum. Also, the mean phenotype (for one or more characters) that maximizes mean fitness. An adaptive valley is a set of allele frequencies at which mean fitness has a minimum.
adaptive radiation: Evolutionary divergence of members of a single phylogenetic lineage into a variety of different adaptive forms; usually the taxa differ in the use of resources or habitats, and have diverged over a relatively short interval of geological time. The term evolutionary radiation describes a pattern of rapid diversification without assuming that the differences are adaptive.
adaptive zone: A set of similar ecological niches occupied by a group of (usually) related species, often constituting a higher taxon.
additive effect: The magnitude of the effect of an allele on a character, measured as half the phenotypic difference between homozygotes for that allele compared with homozygotes for a different allele.
additive genetic variance: That component of the genetic variance in a character that is attributable to additive effects of alleles.
allele: One of several forms of the same gene, presumably differing by mutation of the DNA sequence. Alleles are usually recognized by their phenotypic effects; DNA sequence variants, which may differ at several or many sites, are usually called haplotypes.
allele frequency: The proportion of gene copies in a population that are a given allele; i.e., the probability of finding this allele when a gene is taken randomly from the population; also called gene frequency.
allometric growth: Growth of a feature during ontogeny at a rate different from that of another feature with which it is compared.
allopatric: Of a population or species, occupying a geographic region different from that of another population or species. Cf. parapatric, sympatric.
allopolyploid: A polyploid in which the several chromosome sets are derived from more than one species.
allozyme: One of several forms of an enzyme encoded by different alleles at a locus.
alternative splicing: Splicing of different sets of exons from mRNA to form mature transcripts that are translated into different proteins (thus allowing the same gene to encode different proteins).
altruism: Conferral of a benefit on other individuals at an apparent cost to the donor.
anagenesis: Evolution of a feature within a lineage over an arbitrary period of time.
aneuploid: Of a cell or organism, possessing too many or too few of one or more chromosomes.
antagonistic selection: A source of natural selection that opposes another source of selection on a trait.
apomixis: Parthenogenetic reproduction in which an individual develops from one or more mitotically produced cells that have not experienced recombination or syngamy.
apomorphic: Having a derived character or state, with reference to another character or state. See synapomorphy.
aposematic: Coloration or other features that advertise noxious properties; warning coloration.
artificial selection: Selection by humans of a deliberately chosen trait or combination of traits in a (usually captive) population; differing from natural selection in that the criterion for survival and reproduction is the trait chosen, rather than fitness as determined by the entire genotype.
asexual: Pertaining to reproduction that does not entail meiosis and syngamy.
assortative mating: Nonrandom mating on the basis of phenotype; usually refers to positive assortative mating, the propensity to mate with others of like phenotype.
autopolyploid: A polyploid in which the several chromosome sets are derived from the same species.
autosome: A chromosome other than a sex chromosome.

B

background extinction: A long-prevailing rate at which taxa become extinct, in contrast to the highly elevated rates that characterize mass extinction.
background selection: Elimination of deleterious mutations in a region of the genome; may explain low levels of neutral sequence variation.
balancing selection: A form of natural selection that maintains polymorphism at a locus within a population.
benthic: Inhabiting the bottom, or substrate, of a body of water. Cf. planktonic.
biogeography: The study of the geographic distribution of organisms.
biological species: A population or group of populations within which genes are actually or potentially exchanged by interbreeding, and which are reproductively isolated from other such groups.
bottleneck: A severe, temporary reduction in population size.

C

canalization: The evolution of internal factors during development that reduce the effect of perturbing environmental and genetic influences, thereby constraining variation and consistently producing a particular (usually wild-type) phenotype.
candidate gene: A gene thought to be involved in the evolution of a particular trait based on its mutant phenotype or the function of the protein it encodes.
carrying capacity: The population density that can be sustained by limiting resources.
category: In taxonomy, one of the ranks of classification (e.g., genus, family). Cf. taxon.
character: A feature, or trait. Cf. character state.
character displacement: Usually refers to a pattern of geographic variation in which a character differs more greatly between sympatric than between allopatric populations of two species; sometimes used for the evolutionary process of accentuation of differences between sympatric populations of two species as a result of the reproductive or ecological interactions between them.
character state: One of the variant conditions of a character (e.g., yellow versus brown as state of the character “color of snail shell”).
chronospecies: A segment of an evolving lineage preserved in the fossil record that differs enough from earlier or later members of the lineage to be given a different binomial (name). Not equivalent to biological species.
cis-regulatory element: A noncoding DNA sequence in or near a gene required for proper spatiotemporal expression of that gene, often containing binding sites for transcription factors. Often used interchangeably with enhancer.
clade: The set of species descended from a particular ancestral species.
cladistic: Pertaining to branching patterns; a cladistic classification classifies organisms on the basis of the historical sequences by which they have diverged from common ancestors.
cladogenesis: Branching of lineages during phylogeny.
cladogram: A branching diagram depicting relationships among taxa; i.e., an estimated history of the relative sequence in which they have evolved from common ancestors. Used by some authors to mean a branching diagram that displays the hierarchical distribution of derived character states among taxa.
cline: A gradual change in an allele frequency or in the mean of a character over a geographic transect.
clone: A lineage of individuals reproduced asexually, by mitotic division.
coadapted gene pool: A population or set of populations in which prevalent genotypes are composed of alleles at two or more loci that confer high fitness in combination with each other, but not with alleles that are prevalent in other such populations.
coalescence: Derivation of the gene copies in one or more populations from a single ancestral copy, viewed retrospectively (from the present back into the past).
coevolution: Strictly, the joint evolution of two (or more) ecologically interacting species, each of which evolves in response to selection imposed by the other. Sometimes used loosely to refer to evolution of one species caused by its interaction with another, or simply to a history of joint divergence of ecologically associated species.
commensalism: An ecological relationship between species in which one is benefited but the other is little affected.
common garden: A place in which (usually conspecific) organisms, perhaps from different geographic populations, are reared together, enabling the investigator to ascribe variation among them to genetic rather than environmental differences. Originally applied to plants, but now more generally used to describe any experiment of this design.
comparative method: A procedure for inferring the adaptive function of a character by correlating its states in various taxa with one or more variables, such as ecological factors hypothesized to affect its evolution.
compartment: A contiguous group of cells, descended from the same progenitor cell, that form a spatially discrete part of a developing organ or structure and often act as a discrete developmental unit. Cells from one compartment typically do not intermix with cells from other compartments.
competition: An interaction between individuals of the same species or different species whereby resources used by one are made unavailable to others.
competitive exclusion: Extinction of a population due to competition with another species.
concerted evolution: Maintenance of a homogeneous nucleotide sequence among the members of a gene family, which evolves over time.
conspecific: Belonging to the same species.
convergent evolution (convergence): Evolution of similar features independently in different evolutionary lineages, usually from different antecedent features or by different developmental pathways.
co-option: The evolution of a function for a gene, tissue, or structure other than the one it was originally adapted for. At the gene level, used interchangeably with recruitment and, occasionally, exaptation.
cost: A reduction in fitness caused by a correlated effect of a feature that provides an increment in fitness (i.e., a benefit).
correlation: A statistical relationship that quantifies the degree to which two variables are associated. For phenotypic correlation, genetic correlation, environmental correlation as applied to the relationship between two traits, see Chapter 13.
creationism: The doctrine that each species (or perhaps higher taxon) was created separately, essentially in its present form, by a supernatural Creator.
C-value paradox: The lack of correlation between the DNA content of eukaryotic genomes and a given organism’s phenotypic complexity (i.e., the genome of a less complex eukaryotic organism, such as a plant, may contain far more DNA than that of a more complex organism, such as a human being). The paradox is explained by the amount of noncoding repetitive DNA sequences in a genome.

D

deme: A local population; usually, a small, panmictic population.
demographic: Pertaining to processes that change the size of a population (i.e., birth, death, dispersal).
density-dependent: Affected by population density.
derived character (state): A character (or character state) that has evolved from an antecedent (ancestral) character or state.
deterministic: Causing a fixed outcome, given initial conditions. Cf. stochastic.
differential gene expression: Differences in the time, location, and/or quantitative level at which a gene expresses the protein it encodes. Differential gene expression involves differences between species, developmental stages, or physiological states in the specific cells, tissues, structures, or body segments that express a given gene; it is believed to be a significant agent of morphological change over evolutionary time.
diploid: Of a cell or organism, possessing two chromosome complements. See also haploid, polyploid.
direct development: A life history in which the intermediate larval stage is omitted and development proceeds directly from an embryonic form to an adult-like form. Cf. indirect development.
directional selection: Selection for a value of a character that is higher or lower than its current mean value.
dispersal: In population biology, movement of individual organisms to different localities; in biogeography, extension of the geographic range of a species by movement of individuals.
disruptive selection: Selection in favor of two or more modal phenotypes and against those intermediate between them; also called diversifying selection.
divergence: The evolution of increasing difference between lineages in one or more characters.
diversification: An evolutionary increase in the number of species in a clade, usually accompanied by divergence in phenotypic characters.
diversifying selection: See disruptive selection.
domain: A relatively small protein segment or module (100 amino acids or less) that can fold into a specific three-dimensional structure independently of other domains.
dominance: Of an allele, the extent to which it produces when heterozygous the same phenotype as when homozygous. Of a species, the extent to which it is numerically (or otherwise) predominant in a community.
duplication: The production of another copy of a locus (or other sequence) that is inherited as an addition to the genome.

E

ecological niche: The range of combinations of all relevant environmental variables under which a species or population can persist; often more loosely used to describe the “role” of a species, or the resources it utilizes.
ecological release: The expansion of a population’s niche (e.g., range of habitats or resources used) where competition with other species is alleviated.
ecotype: A genetically determined phenotype of a species that is found as a local variant associated with certain ecological conditions.
effective population size: The effective size of a real population is equal to the number of individuals in an ideal population (i.e., a population in which all individuals reproduce equally) that produces the rate of genetic drift seen in the real population.
enhancer: A DNA sequence that, when acted on by transcription factors controls transcription of an associated gene. Cf. cis-regulatory element, promoter.
endemic: Of a species, restricted to a specified region or locality.
environment: Usually, the complex of external physical, chemical, and biotic factors that may affect a population, an organism, or the expression of an organism’s genes; more generally, anything external to the object of interest (e.g., a gene, an organism, a population) that may influence its function or activity. Thus, other genes within an organism may be part of a gene’s environment, or other individuals in a population may be part of an organism’s environment.
environmental variance: Variation among individuals in a phenotypic trait that is caused by variation in the environment rather than by genetic differences.
epistasis: An effect of the interaction between two or more gene loci on the phenotype or fitness whereby their joint effect differs from the sum of the loci taken separately.
equilibrium: An unchanging condition, as of population size or genetic composition. Also, the value (e.g., of population size, allele frequency) at which this condition occurs. An equilibrium need not be stable. See stability, unstable equilibrium.
ESS: See evolutionarily stable strategy.
essentialism: The philosophical view that all members of a class of objects (such as a species) share certain invariant, unchanging properties that distinguish them from other classes.
evolution: In a broad sense, the origin of entities possessing different states of one or more characteristics and changes in the proportions of those entities over time. Organic evolution, or biological evolution, is a change over time in the proportions of individual organisms differing genetically in one or more traits. Such changes transpire by the origin and subsequent alteration of the frequencies of genotypes from generation to generation within populations, by alteration of the proportions of genetically differentiated populations within a species, or by changes in the numbers of species with different characteristics, thereby altering the frequency of one or more traits within a higher taxon.
evolutionarily stable strategy (ESS): A phenotype such that, if almost all individuals in a population have that phenotype, no alternative phenotype can invade the population or replace it.
evolutionary radiation: See adaptive radiation.
evolutionary reversal: The evolution of a character from a derived state back toward a condition that resembles an earlier state.
evolutionary synthesis: The reconciliation of Darwin’s theory with the findings of modern genetics, which gave rise to a theory that emphasized the coaction of random mutation, selection, genetic drift, and gene flow; also called the modern synthesis.
exaptation: The evolution of a function of a gene, tissue, or structure other than the one it was originally adapted for; can also refer to the adaptive use of a previously nonadaptive trait.
exon: That part of a gene that is translated into a polypeptide (protein). Cf. intron.
exon shuffling: The formation of new genes by assembly of exons from two or more preexisting genes. The classical model of exon shuffling generates new combinations of exons mediated via recombination of intervening introns; however, exon shuffling can also come about by retrotransposition of exons into pre-existing genes.

F

fecundity: The quantity of gametes (usually eggs) produced by an individual.
fitness: The success of an entity in reproducing; hence, the average contribution of an allele or genotype to the next generation or to succeeding generations. See also relative fitness.
fixation: Attainment of a frequency of 1 (i.e., 100 percent) by an allele in a population, which thereby becomes monomorphic for the allele.
founder effect: The principle that the founders of a new population carry only a fraction of the total genetic variation in the source population.
frameshift mutation: An insertion or deletion of base pairs in a translated DNA sequence that alters the reading frame, resulting in multiple downstream changes in the gene product.
frequency: In this book, usually used to mean proportion (e.g., the frequency of an allele is the proportion of gene copies having that allelic state).
frequency-dependent selection: A mode of natural selection in which the fitness of each genotype varies as a function of its frequency in the population.
function: The way in which a character contributes to the fitness of an organism.

G

gene: The functional unit of heredity. A complex concept.
gene complex: A group of two or more genes that are members of the same family and in most cases are located in close proximity to one another in the genome, often in tandem separated by various amounts of intergenic, noncoding DNA.
gene conversion: A process involving the unidirectional transfer of DNA information from one gene to another. In a typical conversion event, a gene or part of a gene acquires the same sequence as the other allele at that locus (intralocus or intra-allelic conversion), or the same sequences as a different, usually paralogous, locus (interlocus conversion). One consequence of gene conversion may be the homogenization of sequences among members of a gene family.
gene duplication: When new genes arise as copies of preexisting gene sequences. The result can be a gene family.
gene family: Two or more loci with similar nucleotide sequences that have been derived from a common ancestral sequence.
gene flow: The incorporation of genes into the gene pool of one population from one or more other populations.
gene frequency: See allele frequency.
gene pool: The totality of the genes of a given sexual population.
gene tree: A diagram representing the history by which gene copies have been derived from ancestral gene copies in previous generations.
genetic conflict: Antagonistic fitness relationships between alleles at different loci in a genome.
genetic correlation: Correlated differences among genotypes in two or more phenotypic characters, due to pleiotropy or linkage disequilibrium.
genetic distance: Any of several measures of the degree of genetic difference between populations, based on differences in allele frequencies.
genetic drift: Random changes in the frequencies of two or more alleles or genotypes within a population.
genetic load: Any reduction of the mean fitness of a population resulting from the existence of genotypes with a fitness lower than that of the most fit genotype.
genetic variance: Variation in a trait within a population, as measured by the variance that is due to genetic differences among individuals.
genic selection: A form of selection in which the single gene is the unit of selection, such that the outcome is determined by fitness values assigned to different alleles. See individual selection, kin selection, natural selection.
genome: The entire complement of DNA sequences in a cell or organism. A distinction may be made between the nuclear genome and organelle genomes, such as those of mitochondria and plastids.
genotype: The set of genes possessed by an individual organism; often, its genetic composition at a specific locus or set of loci singled out for discussion.
genotype × environment interaction: Phenotypic variation arising from the difference in the effect of the environment on the expression of different genotypes.
geographic variation: Differences among spatially distributed populations of a species.
grade: A group of species that have evolved the same state in one or more characters and typically constitute a paraphyletic group relative to other species that have evolved further in the same direction.
gradualism: The proposition that large differences in phenotypic characters have evolved through many slightly different intermediate states.
group selection: The differential rate of origination or extinction of whole populations (or species, if the term is used broadly) on the basis of differences among them in one or more characteristics. See also interdemic selection, species selection.

H

habitat selection: The capacity of an organism (usually an animal) to choose a habitat in which to perform its activities. Habitat selection is not a form of natural selection.
haploid: Of a cell or organism, possessing a single chromosome complement, hence a single gene copy at each locus.
haplotype: A DNA sequence that differs from homologous sequences at one or more base pair sites.
Hardy-Weinberg: Pertaining to the genotype frequencies expected at a locus under ideal equilibrium conditions in a randomly mating population.
heritability: The proportion of the variance in a trait among individuals that is attributable to differences in genotype. Heritability in the narrow sense is the ratio of additive genetic variance to phenotypic variance.
heterochrony: An evolutionary change in phenotype caused by an alteration of timing of developmental events.
heterokaryotype: A genome or individual that is heterozygous for a chromosomal rearrangement such as an inversion. Cf. homokaryotype.
heterozygosity: In a population, the proportion of loci at which a randomly chosen individual is heterozygous, on average.
heterozygote: An individual organism that possesses different alleles at a locus.
heterozygous advantage: The manifestation of higher fitness by heterozygotes than by homozygotes at a specific locus.
hitchhiking: Change in the frequency of an allele due to linkage with a selected allele at another locus.
homeobox genes: A large family of eukaryotic genes that contain a DNA sequence known as the homeobox. The homeobox sequence encodes a protein homeodomain about 60 amino acids in length that binds DNA. Most homeobox genes are transcriptional regulators. Cf. domain; Hox genes.
homeostasis: Maintenance of an equilibrium state by some self-regulating capacity of an individual.
homeotic mutation: A mutation that causes a transformation of one structure into another of the organism’s structures.
homokaryotype: A genome or individual that is homozygous for a chromosomal rearrangement such as an inversion. Cf. heterokaryotype.
homology: Possession by two or more species of a character state derived, with or without modification, from their common ancestor. Homologous chromosomes are those members of a chromosome complement that bear the same genes.
homonymous: Pertaining to biological structures that occur repeatedly within one segment of the organism, such as teeth or bristles.
homoplasy: Possession by two or more species of a similar or identical character state that has not been derived by both species from their common ancestor; embraces convergence, parallel evolution, and evolutionary reversal.
homozygote: An individual organism that has the same allele at each of its copies of a genetic locus.
horizontal transmission: Movement of genes or symbionts (such as parasites) between individual organisms other than by transmission from parents to their offspring (which is vertical transmission). Horizontal transmission of genes is also called lateral gene transfer.
Hox genes: A subfamily of homeobox genes, conserved in all metazoan animals, that controls anterior-posterior segment identity by regulating the transcription of many genes during development.
hybrid: An individual formed by mating between unlike forms, usually genetically differentiated populations or species.
hybrid zone: A region in which genetically distinct populations come into contact and produce at least some offspring of mixed ancestry.
hypermorphosis: An evolutionary increase in the duration of ontogenetic development, resulting in features that are exaggerated compared to those of the ancestor.

I

identical by descent: Of two or more gene copies, being derived from a single gene copy in a specified common ancestor of the organisms that carry the copies.
inbreeding: Mating between relatives that occurs more frequently than if mates were chosen at random from a population.
inbreeding depression: Reduction, in inbred individuals, of the mean value of a character (usually one correlated with fitness).
inclusive fitness: The fitness of a gene or genotype as measured by its effect on the survival or reproduction of both the organism bearing it and the genes, identical by descent, borne by the organism’s relatives.
indirect development: A life history consisting of a larval stage between embryo and adult stages. Cf. direct development.
individual selection: A form of natural selection consisting of nonrandom differences among different genotypes (or phenotypes) within a population in their contribution to subsequent generations. See also genic selection, natural selection.
inter-, intra-: Prefixes meaning, respectively, “between” and “within.” For example, “interspecific” differences are differences between species and “intraspecific” differences are differences among individuals within a species.
interaction: Strictly, the dependence of an outcome on a combination of causal factors, such that the outcome is not predictable from the average effects of the factors taken separately. More loosely, an interplay between entities that affects one or more of them (as in interactions between species). See also genotype × environment interaction.
interdemic selection: Group selection of populations within a species.
intrinsic rate of natural increase: The potential per capita rate of increase of a population with a stable age distribution whose growth is not depressed by the negative effects of density.
introgression: Movement of genes from one species or population into another by hybridization and backcrossing; carries the implication that some genes in a genome undergo such movement, but others do not.
intron: A part of a gene that is not translated into a polypeptide. Cf. exon.
inversion: A 180° reversal of the orientation of a part of a chromosome, relative to some standard chromosome.
isolating barrier, isolating mechanism: A genetically determined difference between populations that restricts or prevents gene flow between them. The term does not include spatial segregation by extrinsic geographic or topographic barriers.
iteroparous: Pertaining to a life history in which individuals reproduce more than once. Cf. semelparous.

K

karyotype: The chromosome complement of an individual.
key adaptation: An adaptation that provides the basis for using a new, substantially different habitat or resource.
kin selection: A form of selection whereby alleles differ in their rate of propagation by influencing the impact of their bearers on the reproductive success of individuals (kin) who carry the same alleles by common descent.

L

Lamarckism: The theory that evolution is caused by inheritance of character changes acquired during the life of an individual due to its behavior or to environmental influences.
lateral gene transfer: See horizontal transmission.
lethal allele: An allele (usually recessive) that causes virtually complete mortality, usually early in development.
lineage: A series of ancestral and descendant populations through time; usually refers to a single evolving species, but may include several species descended from a common ancestor.
lineage sorting: The process by which each of several descendant species, carrying several gene lineages inherited from a common ancestral species, acquires a single gene lineage; hence, the derivation of a monophyletic gene tree, in each species, from the paraphyletic gene tree inherited from their common ancestor.
linkage: Occurrence of two loci on the same chromosome: the loci are functionally linked only if they are so close together that they do not segregate independently in meiosis.
linkage disequilibrium: The association of two alleles at two or more loci more frequently (or less frequently) than predicted by their individual frequencies.
linkage equilibrium: The association of two alleles at two or more loci at the frequency predicted by their individual frequencies.
locus (plural: loci): A site on a chromosome occupied by a specific gene; more loosely, the gene itself, in all its allelic states.
logistic equation: An equation describing the idealized growth of a population subject to a density-dependent limiting factor. As density increases, the rate of growth gradually declines until population growth stops.

M

macroevolution: A vague term, usually meaning the evolution of substantial phenotypic changes, usually great enough to place the changed lineage and its descendants in a distinct genus or higher taxon. Cf. microevolution.
mass extinction: A highly elevated rate of extinction of species, extending over an interval that is relatively short on a geological time scale (although still very long on a human time scale).
maternal effect: A nongenetic effect of a mother on the phenotype of her offspring, stemming from factors such as cytoplasmic inheritance, transmission of symbionts from mother to offspring, or nutritional conditions.
maximum parsimony: See parsimony.
mean: Usually the arithmetic mean or average; the sum of n values, divided by n. The mean value of x, symbolized as x, equals (x₁ + x₂ + … + x_n)/n.
mean fitness: The arithmetic average fitness of all individuals in a population, usually relative to some standard.
meiotic drive: Used broadly to denote a preponderance (> 50 percent) of one allele among the gametes produced by a heterozygote; results in genic selection.
metapopulation: A set of local populations, among which there may be gene flow and patterns of extinction and recolonization.
microevolution: A vague term, usually referring to slight, short-term evolutionary changes within species. Cf. macroevolution.
microsatellite: A short, highly repeated, untranslated DNA sequence.
migration: Used in theoretical population genetics as a synonym for gene flow among populations; in other contexts, refers to directed large-scale movements of organisms that do not necessarily result in gene flow.
mimicry: Similarity of certain characters in two or more species due to convergent evolution when there is an advantage conferred by the resemblance. Common types include Batesian mimicry, in which a palatable mimic experiences lower predation because of its resemblance to an unpalatable model; and Müllerian mimicry, in which two or more unpalatable species enjoy reduced predation due to their similarity.
modern synthesis: See evolutionary synthesis.
modularity: The ability of individual parts of an organism, such as segments or organs, to develop or evolve independently from one another; the ability of developmental regulatory genes and pathways to be regulated independently in different tissues and developmental stages.
molecular clock: The concept of a steady rate of change in DNA sequences over time, providing a basis for dating the time of divergence of lineages if the rate of change can be estimated.
monomorphic: Having one form; refers to a population in which virtually all individuals have the same genotype at a locus. Cf. polymorphism.
monophyletic: Refers to a taxon, phylogenetic tree, or gene tree whose members are all derived from a common ancestral taxon. In cladistic taxonomy, the term describes a taxon consisting of all the known species descended from a single ancestral species. Cf. paraphyletic, polyphyletic.
mosaic evolution: Evolution of different characters within a lineage or clade at different rates, hence more or less independently of one another.
mutation: An error in the replication of a nucleotide sequence, or any other alteration of the genome that is not manifested as reciprocal recombination.
mutational variance: The increment in the genetic variance of a phenotypic character caused by new mutations in each generation.
mutualism: A symbiotic relation in which each of two species benefits by their interaction.

N

natural selection: The differential survival and/or reproduction of classes of entities that differ in one or more characteristics. To constitute natural selection, the difference in survival and/or reproduction cannot be due to chance, and it must have the potential consequence of altering the proportions of the different entities. Thus natural selection is also definable as a deterministic difference in the contribution of different classes of entities to subsequent generations. Usually the differences are inherited. The entities may be alleles, genotypes or subsets of genotypes, populations, or, in the broadest sense, species. A complex concept; see Chapter 11. See also genic selection, individual selection, kin selection, group selection.
neo-Darwinism: The modern belief that natural selection, acting on randomly generated genetic variation, is a major, but not the sole, cause of evolution.
neofunctionalization: Divergence of duplicate genes whereby one acquires a new function. Cf. subfunctionalization.
neoteny: Heterochronic evolution whereby development of some or all somatic features is retarded relative to sexual maturation, resulting in sexually mature individuals with juvenile features. See also paedomorphosis, progenesis.
neutral alleles: Alleles that do not differ measurably in their effect on fitness.
nonsynonymous substitution: A base pair substitution in DNA that results in an amino acid substitution in the protein product; also called replacement substitution. Cf. synonymous substitution.
norm of reaction: The set of phenotypic expressions of a genotype under different environmental conditions. See also phenotypic plasticity.
normal distribution: A bell-shaped frequency distribution of a variable; the expected distribution if many factors with independent, small effects determine the value of a variable; the basis for many statistical formulations.
nucleotide substitution: The complete replacement of one nucleotide base pair by another within a lineage over evolutionary time.

O

ontogeny: The development of an individual organism, from fertilized zygote until death.
organism: Usually used in this book to refer to an individual member of a species.
orthologous: Refers to corresponding (homologous) members of a gene family in two or more species. Cf. paralogous.
outcrossing: Mating with another genetic individual. Cf. selfing.
outgroup: A taxon that diverged from a group of other taxa before they diverged from one another.
overdominance: The expression by two alleles in heterozygous condition of a phenotypic value for some character that lies outside the range of the two corresponding homozygotes.

P

paedomorphosis: Possession in the adult stage of features typical of the juvenile stage of the organism’s ancestor.
panmixia: Random mating among members of a population.
parallel evolution (parallelism): The evolution of similar or identical features independently in related lineages, thought usually to be based on similar modifications of the same developmental pathways.
paralogous: Refers to the homologous relationship between two different members of a gene family, within a species or in a comparison of different species. Cf. orthologous.
parapatric: Of two species or populations, having contiguous but non-overlapping geographic distributions.
paraphyletic: Refers to a taxon, phylogenetic tree, or gene tree whose members are all derived from a single ancestor, but which does not include all the descendants of that ancestor. Cf. monophyletic.
parental investment: Parental activities or processes that enhance the survival of existing offspring but whose costs reduce the parent’s subsequent reproductive success.
parsimony: Economy in the use of means to an end (Webster’s New Collegiate Dictionary); the principle of accounting for observations by that hypothesis requiring the fewest or simplest assumptions that lack evidence; in systematics, the principle of invoking the minimal number of evolutionary changes to infer phylogenetic relationships.
parthenogenesis: Virgin birth; development from an egg to which there has been no paternal contribution of genes.
PCR (polymerase chain reaction): A laboratory technique by which the number of copies of a DNA sequence is increased by replication in vitro.
peak shift: Change in allele frequencies within a population from one to another local maximum of mean fitness by passage through states of lower mean fitness.
peripatric: Of a population, peripheral to most of the other populations of a species.
peripatric speciation: Speciation by evolution of reproductive isolation in peripatric populations as a consequence of a combination of genetic drift and natural selection.
phenetic: Pertaining to phenotypic similarity, as in a phenetic classification.
phenotype: The morphological, physiological, biochemical, behavioral, and other properties of an organism manifested throughout its life; or any subset of such properties, especially those affected by a particular allele or other portion of the genotype.
phenotypic plasticity: The capacity of an organism to develop any of several phenotypic states, depending on the environment; usually this capacity is assumed to be adaptive.
phylogenetic species concept: Any of several related concepts of species as sets of populations that are diagnosably different from other populations.
phylogeny: The history of descent of a group of taxa such as species from their common ancestors, including the order of branching and sometimes the absolute times of divergence; also applied to the genealogy of genes derived from a common ancestral gene.
planktonic: Living in open water. Cf. benthic.
pleiotropy: A phenotypic effect of a gene on more than one character.
ploidy: The number of chromosome complements in an organism.
polygenic character: A character whose variation is based wholly or in part on allelic variation at more than a few loci.
polymorphism: The existence within a population of two or more genotypes, the rarest of which exceeds some arbitrarily low frequency (say, 1 percent); more rarely, the existence of phenotypic variation within a population, whether or not genetically based. Cf. monomorphic.
polyphenism: The capacity of a species or genotype to develop two or more forms, with the specific form depending on specific environmental conditions or cues, such as temperature or day length. A polyphenism is distinct from a polymorphism in that the former is the property of a single genotype, whereas the latter refers to multiple forms encoded by two or more different genotypes.
polyphyletic: Refers to a taxon, phylogenetic tree, or gene tree composed of members derived by evolution from ancestors in more than one ancestral taxon; hence, composed of members that do not share a unique common ancestor. Cf. monophyletic.
polyploid: Of a cell or organism, possessing more than two chromosome complements.
population: A group of conspecific organisms that occupy a more or less well defined geographic region and exhibit reproductive continuity from generation to generation; ecological and reproductive interactions are more frequent among these individuals than with members of other populations of the same species.
positive selection: Selection for an allele that increases fitness. Cf. purifying selection.
postzygotic: Occurring after union of the nuclei of uniting gametes; usually refers to inviability or sterility that confers reproductive isolation.
preadaptation: Possession of the necessary properties to permit a shift to a new niche, habitat, or function. A structure is preadapted for a new function if it can assume that function without evolutionary modification.
prezygotic: Occurring before union of the nuclei of uniting gametes; usually refers to events in the reproductive process that cause reproductive isolation.
primordium: A group of embryonic or larval cells destined to give rise to a particular adult structure.
processed pseudogene: A pseudogene that has arisen via the retrotransposition of mRNA into cDNA.
progenesis: A decrease during evolution of the duration of ontogenetic development, resulting in retention of juvenile features in the sexually mature adult. See also neoteny, paedomorphosis.
promoter: Usually refers to the DNA sequences immediately 5′ to (upstream of) a gene that are bound by the RNA polymerase and its cofactors and/or are required in order to transcribe the gene. Sometimes used interchangeably with enhancer.
provinciality: The degree to which the taxonomic composition of a biota is differentiated among major geographic regions.
pseudogene: A nonfunctional member of a gene family that has been derived from a functional gene. Cf. processed pseudogene.
punctuated equilibria: A pattern of rapid evolutionary change in the phenotype of a lineage separated by long periods of little change; also, a hypothesis intended to explain such a pattern, whereby phenotypic change transpires rapidly in small populations, in concert with the evolution of reproductive isolation.
purifying selection: Elimination of deleterious alleles from a population. Cf. positive selection.

Q

QTL: Quantitative trait locus (or loci); a chromosome region containing at least one gene that contributes to variation in a quantitative trait. QTL mapping is a procedure for determining the map positions of QTL on chromosomes.
quantitative trait: A phenotypic character that varies continuously rather than as discretely different character states.

R

race: A poorly defined term for a set of populations occupying a particular region that differ in one or more characteristics from populations elsewhere; equivalent to subspecies. In some writings, a distinctive phenotype, whether or not allopatric from others.
radiation: See adaptive radiation.
random genetic drift: See genetic drift.
recruitment: (1) In evolutionary genetics, the evolution of a new function for a gene other than the function for which that gene was originally adapted. (2) In population biology, refers to the addition of new adult (breeding) individuals to a population via reproduction (i.e., individuals born into the population that reach reproductive age).
recurrent mutation: Repeated origin of mutations of a particular kind within a species.
refugia: Locations in which species have persisted while becoming extinct elsewhere.
regression: In geology, withdrawal of sea from land, accompanying lowering of sea level; in statistics, a function that best predicts a dependent from an independent variable.
reinforcement: Evolution of enhanced reproductive isolation between populations due to natural selection for greater isolation.
relative fitness: The fitness of a genotype relative to (as a proportion of) the fitness of a reference genotype, which is often set at 1.0.
relict: A species that has been “left behind”; for example, the last survivor of an otherwise extinct group. Sometimes, a species or population left in a locality after extinction throughout most of the region.
replacement substitution: See nonsynonymous substitution.
reporter construct: A DNA segment in which a putative cis-regulatory sequence is spliced upstream of a gene whose expression can be easily assayed, such as β-galactosidase or green fluorescent protein.
reproductive effort: The proportion of energy or materials that an organism allocates to reproduction rather than to growth and maintenance.
response to selection: The change in the mean value of a character over one or more generations due to selection.
restriction enzyme: An enzyme that cuts double-stranded DNA at specific short nucleotide sequences. Genetic variation within a population results in variation in DNA sequence lengths after treatment with a restriction enzyme, or restriction fragment length polymorphism (RFLP).
reticulate evolution: Union of different lineages of a clade by hybridization.
RFLP: See restriction enzyme.

S

saltation: A jump; a discontinuous mutational change in one or more phenotypic traits, usually of considerable magnitude.
scala naturae: The “scale of nature, ” or Great Chain of Being: the pre-evolutionary concept that all living things were created in an orderly series of forms, from lower to higher.
selection: Nonrandom differential survival or reproduction of classes of phenotypically different entities. See natural selection, artificial selection.
selection coefficient: The difference between the mean relative fitness of individuals of a given genotype and that of a reference genotype.
selective advantage: The increment in fitness (survival and/or reproduction) provided by an allele or a character state.
selective sweep: Reduction or elimination of DNA sequence variation in the vicinity of a mutation that has been fixed by natural selection relatively recently.
selfing: Self-fertilization; union of female and male gametes produced by the same genetic individual. Cf. outcrossing.
“selfish DNA”: A DNA sequence that has the capacity for its own replication, or replication via other self-replicating elements, but has no immediate function (or is deleterious) for the organism in which it resides.
semelparous: Pertaining to a life history in which individuals (especially females) reproduce only once. Cf. iteroparous.
semispecies: One of several groups of populations that are partially but not entirely isolated from one another by biological factors (isolating mechanisms).
serial homology: A relationship among repeated, often differentiated, structures of a single organism, defined by their similarity of developmental origin; for example, the several legs and other appendages of an arthropod.
sex-linked: Of a gene, being carried by one of the sex chromosomes; it may be expressed phenotypically in both sexes.
sexual reproduction: Production of offspring whose genetic constitution is a mixture of those of two potentially genetically different gametes.
sexual selection: Differential reproduction as a result of variation in the ability to obtain mates.
sibling species: Species that are difficult or impossible to distinguish by morphological characters, but may be discerned by differences in ecology, behavior, chromosomes, or other such characters.
silent substitution: See synonymous substitution.
single nucleotide polymorphism (SNP): Variation in the identity of a nucleotide base pair at a single position in a DNA sequence, within or among populations of a species.
sister taxa: Two species or higher taxa that are derived from an immediate common ancestor, and are therefore each other’s closest relatives.
speciation: Evolution of reproductive isolation within an ancestral species, resulting in two or more descendant species.
species: In the sense of biological species, the members of a group of populations that interbreed or potentially interbreed with one another under natural conditions; a complex concept (see Chapter 15). Also, a fundamental taxonomic category to which individual specimens are assigned, which often but not always corresponds to the biological species. See also biological species, phylogenetic species concept.
species selection: A form of group selection in which species with different characteristics increase (by speciation) or decrease (by extinction) in number at different rates because of a difference in their characteristics.
stability: Often used to mean constancy; more often in this book, the propensity to return to a condition (a stable equilibrium) after displacement from that condition.
stabilizing selection: Selection against phenotypes that deviate in either direction from an optimal value of a character.
standard deviation: The square root of the variance.
stasis: Absence of evolutionary change in one or more characters for some period of evolutionary time.
stochastic: Random. Cf. deterministic.
strata: Layers of sedimentary rock that were deposited at different times.
subfunctionalization: Divergence of duplicate genes whereby each retains only a subset of the several functions of the ancestral gene. Cf. neofunctionalization.
subspecies: A named geographic race; a set of populations of a species that share one or more distinctive features and occupy a different geographic area from other subspecies.
substitution: The complete replacement of one allele by another within a population or species over evolutionary time. Cf. fixation.
superspecies: A group of semispecies.
symbiosis: An intimate, usually physical, association between two or more species.
sympatric: Of two species or populations, occupying the same geographic locality so that the opportunity to interbreed is presented.
synapomorphy: A derived character state that is shared by two or more taxa and is postulated to have evolved in their common ancestor.
synonymous substitution: Fixation of a base pair change that does not alter the amino acid in the protein product of a gene; also called silent substitution. Cf. nonsynonymous substitution.

T

target gene: In developmental genetics, a gene regulated by a transcription factor of interest. This regulation may be direct or indirect.
taxon (plural: taxa): The named taxonomic unit (e.g., Homo sapiens, Hominidae, or Mammalia) to which individuals, or sets of species, are assigned. Higher taxa are those above the species level. Cf. category.
teleology: The belief that natural events and objects have purposes and can be explained by their purposes.
territory: An area or volume of habitat defended by an organism or a group of organisms against other individuals, usually of the same species; territorial behavior is the behavior by which the territory is defended.
trade-off: The existence of both a fitness benefit and a fitness cost of a mutation or character state, relative to another.
transcription factor: A protein that interacts with a regulatory DNA sequence and affects the transcription of the associated gene.
transition: A mutation that changes a nucleotide to another nucleotide in the same class (purine or pyrimidine). Cf. transversion.
translocation: The transfer of a segment of a chromosome to another, nonhomologous, chromosome; the chromosome formed by the addition of such a segment.
transposable element: A DNA sequence, copies of which become inserted into various sites in the genome.
trans-regulatory element: A nucleotide sequence, usually encoding a regulatory protein, that is not closely linked to the structural gene whose expression it regulates. Cf. cis-regulatory element.
transversion: A mutation that changes a nucleotide to another nucleotide in the opposite class (purine or pyrimidine). Cf. transition.

U

unstable equilibrium: An equilibrium to which a system does not return if disturbed.

V

variance (σ², s², V): The average squared deviation of an observation from the arithmetic mean; hence, a measure of variation. s² = [Σ(x_i − x)²]/(n − 1), where x is the mean and n the number of observations.
vertical transmission: See horizontal transmission.
vestigial: Occurring in a rudimentary condition as a result of evolutionary reduction from a more elaborated, functional character state in an ancestor.
viability: Capacity for survival; often refers to the fraction of individuals surviving to a given age, and is contrasted with inviability due to deleterious genes.
vicariance: Separation of a continuously distributed ancestral population or species into separate populations due to the development of a geographic or ecological barrier.
virulence: Usually, the damage inflicted on a host by a pathogen or parasite; sometimes, the capacity of a pathogen or parasite to infect and develop in a host.

W

wild-type: The allele, genotype, or phenotype that is most prevalent (if there is one) in wild populations; with reference to the wild-type allele, other alleles are often termed mutations.

Z

zygote: A single-celled individual formed by the union of gametes. Occasionally used more loosely to refer to an offspring produced by sexual reproduction.