Evolutionary Biology: Key Terms and Glossary

The expected number of offspring a genotype contributes to the next generation, which governs whether the population grows or shrinks and need not match that genotype’s change in frequency.

A trait shaped by selection for the function under study, which these notes treat as a hypothesis that experiment, comparative origins, or a quantitative prediction can reject.

An allele whose heterozygote lies between the two homozygotes, so selection can see it at every frequency and, when selection is weak, frequency changes fastest in the middle of the range.

A plant genome that joins the chromosomes of two species, usually with a further doubling so that pairing at meiosis is possible, and that is isolated from both parents in that step.

The egg that lets a vertebrate complete its life cycle away from open water, a Carboniferous step that follows limbs already present in Late Devonian animals whose lives were still mostly aquatic.

A similarity of function that was not inherited from an ancestor which already possessed the trait, as when bat, bird, and insect wings are compared as wings.

The contrast between costly eggs and cheap sperm, which usually leaves the sex that invests less per offspring with the higher variance in mating success.

The geological eon whose rounded limits are about 4.0 and about 2.5 billion years ago. Cellular life that is widely accepted is older than about 3.4 billion years and therefore falls inside this eon, on an Earth about 4.54 billion years old, and no fossil is treated here as the first cell.

Mating between the expanding *Homo sapiens* lineage and archaic humans. Living people outside Africa carry Neanderthal ancestry of a few percent, Denisovan ancestry also reaches a few percent in the groups where it is highest, and neither source is the main ancestor of any living population.

Reshaping of a population because a person, not the organism’s own survival and mating, decides which individuals breed, as in Darwin’s pigeons.

Pairing by phenotype rather than by pedigree, which raises homozygosity at the loci that build the chosen trait and does not by itself change allele frequencies.

An African hominin grade, including *Australopithecus afarensis*, that walked bipedally while the brain was still ape-sized, so a large brain did not come first.

Doubling of a single species’ chromosome set, which isolates the new plant because a cross back to the diploid parent yields largely sterile triploids.

Neutral variants disappear because they sit next to deleterious mutations that selection removes, so local diversity falls even though no advantageous mutation has been fixed.

Mayr’s criterion that species are natural populations which actually or potentially interbreed and are reproductively cut off from other such groups, a test built for sexual animals in contact and not for asexuals, fossils, or bacteria as stated.

A sharp fall in numbers inside a population that was already there, which loses rare alleles first and can leave gene diversity low after the census has grown back.

The response of the offspring mean equals narrow-sense heritability times the selection differential, R = h²S, so there is no response if either factor is zero.

An early-Cambrian increase, fast by geological standards, in fossilised animal forms, bilaterian layout, and mineralised skeletons. It is a radiation of bodies that can be preserved, preceded by Ediacaran life, and not a start of animals from a blank.

The impact structure dated to the end-Cretaceous boundary, the one mass extinction among the big five whose cause these notes treat as established.

An ancestor and every descendant of that ancestor, which is the group a single node on a tree names.

A geographic gradient in allele frequency, maintained where dispersal opposes local selection, and, in humans, the gradual geographic pattern these notes accept instead of discrete racial types.

The correspondence, in many animals, between the order of *Hox* genes along the cluster and the order of their expression along the anterior–posterior axis.

Absence, correlation, or developmental cost of the variation a selective story would need, whether the limit is inherited history, the way embryos are built, or a genetic correlation.

Separate lineages arriving at a similar job, which shows that a repeated demand can shape a repeated outcome and which mis-groups organisms if that outcome is used as the only shared character.

A shared developmental gene or circuit, older than the organs that now use it, which is a weaker claim than homology of those organs.

An archaic sister group of Neanderthals, diagnosed mainly from genomes and from very few bones, and given no formal species name in these notes.

A difference, associated with a trait, in survival to breeding, mating, fecundity, or offspring survival, which is the third Darwin–Wallace condition and is not the same thing as strength.

Selection that favours one tail, so the mean of the trait moves, without any promise that the same direction will continue.

Founding of a population by colonists that cross a barrier already in place, after which ordinary selection and drift can yield speciation; a founder-effect shift is possible and not required.

Selection that favours both extremes, which increases variance and splits a randomly mating population only if mating also becomes non-random with respect to the trait.

The ratio of nonsynonymous to synonymous substitution rates: a value below 1 is the usual sign of purifying selection, a value of about 1 is the neutral case, and a value above 1 suggests positive selection. The figure compares rates and is not a proof by itself, and a gene-wide average can hide the opposite pattern at a minority of sites.

Hybrid unfitness that appears only when alleles which were each fit on their own population’s background meet for the first time, so neither parent population had to pass through an unfit genotype.

The developmental relation that decides whether a rare allele is expressed in heterozygotes, and therefore whether selection can see it while it is rare.

The macroscopic biota that precedes the Cambrian, much of it of uncertain affinity, which shows that large organisms were already present before the famous hard-part faunas.

The census of an idealised Wright–Fisher population whose sampling error would match the drift of the real population, nearly always below a head count when crashes, a skewed sex ratio, or uneven family size are present.

A retroviral sequence inserted in the germline and thereafter inherited like any other insertion; the same site in two species is evidence of an insertion in their common ancestor, not of a shared present need.

The acquisition of mitochondria from alphaproteobacteria and of the primary chloroplast from cyanobacteria, each organelle descending from a free-living cell that became resident in a host.

* A hypoxia-inducible-factor subunit gene. In Tibet a haplotype close to Denisovan sequence is the favoured case of introgression then selection, and it is tied to a smaller climb in haemoglobin when oxygen is scarce, while Andean and Ethiopian altitude adaptations use other variants.

The combination of overlapping generations, cooperative brood care, and a caste that reproduces little or not at all. High relatedness among hymenopteran sisters does not by itself explain it, because many haplodiploid species are not eusocial and some eusocial animals are diploid.

A trait used for a job other than the one for which selection first built it, or a trait co-opted after arising without that function, as when feathers precede flight and are later refined for it.

Arrival of an allele at frequency 1, where it remains if mutation does not restore an alternative; for a neutral allele the chance of that outcome equals the frequency it already has.

The older doctrine that each species was formed essentially as it is now, so that a nested classification recorded similarity rather than branching descent.

The accidental sample of alleles carried by the few individuals that start a new population, which is drift at small size and not an established genetic revolution.

An index of allele-frequency difference among populations, scaled by how much variation is found inside them. Under the island model the neutral balance is about 1 / (1 + 4 Ne m), a statement about markers in that model and not a claim that a single migrant each generation saves a declining population.

Movement of alleles between populations when migrants breed, which homogenises frequencies and can either swamp a locally favoured allele or deliver one that selection then spreads.

The nearly universal mapping from codons to amino acids, with only a modest list of exceptions, whose shared form is evidence of common ancestry because chemistry does not force that one mapping.

Random change in allele frequency because each generation draws a finite sample of gene copies, a walk that ends at loss or fixation rather than hovering about a stable mean.

The cell lineage destined to make gametes, separated from the body cells in animals, so that an alteration in muscle or skeleton is not copied into the DNA of sperm or eggs.

Oxygenic photosynthesis by cyanobacteria raised oxygen about 2.4 billion years ago, yet concentrations stayed much lower than they are now for a long interval afterwards. The rise allowed aerobic metabolism and does not, alone, account for the later expansion of animal body plans.

When hybrid offspring of only one sex are absent, scarce, or unable to breed, that sex is the one carrying two unlike sex chromosomes. Recessive incompatibilities exposed on a sex chromosome are the leading account, and the pattern is not a claim that sterility always traces to one locus.

The condition rB > C, under which an allele spreads if relatedness times the fitness benefit to the recipient exceeds the fitness cost to the actor, with relatedness a regression of breeding value. The rule is that comparison; a high pedigree relatedness among hymenopteran sisters does not, by itself, explain eusociality.

The null for an autosomal locus at which, with no selection, mutation, migration, or drift, and with random mating, genotype frequencies are p², 2pq, and q² and allele frequencies do not change.

The average of fluctuating population sizes that long-term effective size tracks, pulled towards the smallest generations so that one crash outweighs many large ones.

The degree to which offspring resemble parents because of genes; in the quantitative relation these notes use, narrow-sense heritability is the additive-genetic fraction of phenotypic variance.

A change, between ancestor and descendant, in when or how fast a feature develops, so the descendant’s adult resembles some other stage of the ancestor; without that comparison the word has nothing to mean.

Balancing selection in which the heterozygote out-reproduces both homozygotes, as with sickle-cell haemoglobin where malaria penalises the common homozygote and disease penalises the sickling homozygote, so severe disease keeps the equilibrium well below one half.

The rise of neutral variants that ride on the haplotype of a spreading beneficial allele, the association lasting longer where recombination is rarer.

In the modern use of these notes, the great-ape clade that includes humans, a wider group than the hominin branch and not the mid-century name for that branch.

Every lineage on the human side of the fork with chimpanzees and bonobos, a split placed at about 6–7 million years ago; living chimpanzees are the sister group, not ancestral humans.

* A hominin species, in the broad sense used here, with more human-like body proportions and the first unmistakable range outside Africa, overlapping later *Homo* rather than standing as a single middle rung.

Similarity of a structure, gene, or behaviour that is shared because a common ancestor already had it, such as the bone pattern of the tetrapod forelimb under many different jobs.

Similarity that is not homology, whether by convergence, parallelism, or reversal, so that the character must be specified before the likeness is used as evidence of a clade.

A homeodomain transcription-factor gene from the shared bilaterian set that distinguishes anterior from posterior. Animal architectures differ mainly by shifting when and where these genes are used, not by each phylum inventing its own axis.

The region where distinct populations meet and interbreed, which may be a tension zone balanced by dispersal and hybrid unfitness, a track of an environmental boundary, or a contact that will later fuse.

The chance that the two copies of a locus in one individual both descend from one ancestral copy, which thins out heterozygotes by that fraction and leaves allele frequency unchanged.

The loss of fitness that commonly follows a rise in homozygosity, mostly because partly recessive deleterious alleles are exposed rather than because heterozygote advantage is the usual cause.

A bookkeeping of effects on an actor’s own offspring plus effects on other individuals’ offspring, each weighted by relatedness, and not a second kind of fitness substance.

Ancestral alleles still unsorted by drift, so the tree of one gene need not follow the order in which populations split, particularly if that ancestor was large and the splits were close together.

Melanic morphs of *Biston betularia* became common in sooty Britain and rarer again as the air cleared, a frequency change recorded in collections and traps. Kettlewell’s releases, too dense and often placed on trunks rather than under branches, were a flawed predation experiment and do not undo that historical change.

Lamarck’s claim that a change produced by use is passed to offspring, which fails as a general mechanism because an animal germline is not rewritten by what the soma did. Short-lived epigenetic carry-over is not a substitute that builds complex adaptations.

Continued expression, in adults, of the enzyme that digests lactose, reached by different regulatory mutations in several dairying populations rather than by one shared mutation.

A short stretch of geological time in which lineages end far faster than the usual trickle, across many groups at once, and the cast of ecosystems changes. Five such Phanerozoic episodes are listed together here, and published percentages of species lost are rough conventions rather than inventories.

The joining of Mendelian inheritance to selection, with continuous variation understood as many loci of small effect and with drift and geographic speciation kept beside selection.

The tendency of strictly neutral substitutions to accumulate at the neutral mutation rate, because population size cancels, which yields a calibrated estimate with error and not a fossil date or a metronome.

The property of a group that contains an ancestor and all of that ancestor’s descendants.

Delimiting species by form, which is what fossils and many asexuals allow, and which is misled by polymorphism, sexual dimorphism, plasticity, and cryptic species.

A new sequence, the only source of an allele the species has never had, random with respect to usefulness and not equally likely at every base.

The frequency at which mutation puts a deleterious allele back as fast as selection removes it, about the square root of μ/s for a complete recessive and about μ/(hs) when heterozygotes carry most of the harm, which is reintroduction and not an advantage when rare.

A large-brained archaic population of Europe and western Asia, sister to the modern-human lineage rather than a failed draft of it, and a source of a few percent of ancestry in living non-African genomes.

Ohta’s extension of the neutral null to alleles whose selection coefficients are small beside 1/Ne, so that a small population fixes some slightly deleterious changes a large population would remove.

Selection that favours a type when it is rare and thereby holds a polymorphism, without any need for the heterozygote to be the fittest genotype.

Evolution of a new function in one copy of a duplicate while the other copy keeps the ancestral job; the mere survival of two copies is not evidence that this has happened.

A slowing of somatic development relative to sexual maturation, so that juvenile features of the ancestor remain in the breeding adult, as in the axolotl, *Ambystoma mexicanum*. Thyroid hormone can still induce the terrestrial transition, so the larval body is an untriggered programme rather than evolution running backwards.

A null for sequences: most differences that become fixed between species are neutral or nearly neutral alleles fixed by drift, and for a strictly neutral allele that pace equals the rate at which such mutations arise. It does not claim that most new mutations are neutral, since those that alter function are usually eliminated by purifying selection and never become substitutions.

A point where a tree branches. The internal ones stand for inferred ancestors of the descendant tips, and a living species is a tip, not something to paste onto that ancestor.

The abandoned idea of an inner drive carrying a lineage along a fixed line, distinct from selection among varying individuals.

A gene copy whose separation from the copy in another species was produced by speciation, which is the comparison a species tree requires.

A lineage outside the group under study, used to propose which character states are ancestral, a polarity that stays a hypothesis if the outgroup is wrong.

A gene copy whose separation from another copy was produced by duplication, so that a tree of the survivors can group species by which copy was lost.

The property of a group that keeps an ancestor and only some of its descendants, as with traditional reptiles if birds are left out, or apes if humans are left out.

Hereditary factors that separate when gametes form and can pass through a heterozygote without being averaged away, so variation survives from one generation to the next.

Development carried past the ancestral adult condition, so that a descendant adult extends a trait the ancestor already showed when mature.

The fossil pattern in which a lineage changes more or less continuously, so that a complete rock record would contain the intermediate forms.

The smallest group that can be diagnosed, and in some versions that is monophyletic, which often splits populations before reproductive isolation is complete.

A hypothesis of ancestry drawn as a tree and read from which tips share a node, not from the order of those tips across the page.

A grouping by a similarity that the common ancestor did not have, so the members are united by convergence rather than by a clade.

A node with more than two immediate descendants, usually a split the data have not resolved and sometimes a genuinely simultaneous split.

Selection that favours a type because it is already common, which tends to fix that type and need not increase mean fitness.

A barrier that acts after a zygote exists, as hybrid inviability, hybrid sterility, or failure of later generations, and that reinforcement cannot repair once the hybrid is already unfit.

A barrier that acts before a zygote forms, including separation by habitat, time, courtship, mechanical fit, or gametes that fail to fertilise, and the class of barrier reinforcement can strengthen.

The eon opening at the close of the Archaean, near 2.5 billion years ago, and closing where the Cambrian begins, near 540 million years ago.

Change of form concentrated when a species first appears, after which form stays nearly still until the species ends. An interval that is only thousands of years long, or at most a few tens of thousands, looks instantaneous in strata but is ordinary time for selection or drift, and the pattern neither discards selection nor requires a macromutation.

Removal of deleterious mutations, read in a coding sequence when amino-acid changes are fixed less often than silent changes, which is the usual fate of a functional protein.

The reading that *Homo sapiens* arose in Africa and that most living non-African ancestry comes from a later African dispersal, with limited archaic admixture rather than separate descent from local *Homo erectus*.

Production of new combinations of alleles that already exist, by independent assortment and crossing over, which multiplies genotypes and does not create a novel sequence.

Selection for stronger mating barriers where hybrids are unfit, predicted to leave stronger discrimination in sympatry than in allopatry, and still a hypothesis when that geographic pattern is found.

Absolute fitness scaled to a reference genotype, usually the fittest, which is the quantity that decides whether an allele increases, even in a population that is shrinking.

Populations wrapped around a barrier so that each can breed with its neighbours while the two ends, where the chain meets, cannot. The familiar salamander and warbler rings have not had uninterrupted gene flow the whole way round, so they illustrate distance and are easy to over-read as pure sympatric speciation.

The oldest node of a tree; without it the diagram records only which branches connect, not which node came first.

Gain of a plastid by engulfing a eukaryote that already had one, which carries photosynthesis beyond the single clade that acquired the primary chloroplast.

The rise of one beneficial copy from rarity to fixation, carrying its haplotype and locally reducing linked neutral variation; not every valley of low diversity is this scar.

A pollen–stigma rejection system in which pollen that carries a matching allele fails, so a rare allele has more successful partners and many alleles are maintained without heterozygote advantage.

Differences in reproductive success that come from competition for mates, either within a sex or by mate choice, and that are stronger on the sex with the greater variance in mating success rather than on males as such.

The volcanic province that is the leading explanation of the end-Permian mass extinction, through a favoured chain of warming, anoxia, and acidification, without every chemical step treated as settled.

Two lineages that share an immediate common ancestor, so that each is the other’s closest relative among the tips being compared.

A character that is present because of neighbouring parts, the materials used, or what the lineage already had, and that may afterwards be co-opted, rather than a part whose present job explains why it exists.

A proposed sorting of species-level traits by differences in speciation or extinction rate, which is not established as a force alongside ordinary selection and is not sacrifice for the good of the species.

A difference among species in speciation or extinction that is produced by traits of their individual members, so the species-level tally is still organismal selection.

Selection that favours intermediate values, leaving the mean in place and reducing variance, which is active removal of extremes and not an absence of selection.

Alleles already segregating when an environmental challenge begins, able to respond without first surviving as a single new mutant on one haplotype.

Little net morphological change through most of a species’ duration in the fossil record, the long interval that makes a punctuation stand out.

Division of an ancestral job between two duplicate genes, so that each copy loses a different part and both are then required, with no new function in either.

Splitting without an external geographic barrier, among individuals that can meet, which recombination prevents unless disruptive selection and assortative mating are both strong enough.

A shared ancestral character, once a novelty at a deeper node, which does not mark out a subgroup among the species that still retain it.

A novelty that members of a group share because their most recent shared ancestor already carried it, evidence for that node rather than a tag the trait keeps forever.

A fossil that combines traits no living species still combines, evidence of an intermediate character state and not a certified ancestor or a rung on a ladder.

Lamarck’s adaptive proposal that organs enlarge when they are used and waste when they are not, which is separate from the further claim that the acquired change is inherited.

A homologue reduced relative to the working organ in relatives, such as a whale pelvis that no longer supports a hind limb, whether or not a smaller job remains.

Division of an existing range by a new geographic barrier, after which the separated populations can diverge; the Isthmus of Panama and sister species of *Alpheus* are the picture used here, not a single dated rate.

A shortage of heterozygotes, relative to Hardy–Weinberg expectations from the average allele frequency, that appears when populations with different frequencies are pooled.

A faunal discontinuity with Bali on the Asian side of Lombok and Borneo on the Asian side of Sulawesi. Land vertebrates to the west are Asian and those further east are increasingly Australian, because deep water along this line stayed open at Pleistocene low sea level.