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Showing 961–990 of 1709 reference entries

BiologyGene flow by migrant replacement

If migrants form a specified fraction of a population's allele pool, the post-migration allele frequency is a weighted average of resident and migrant frequencies.

Model
BiologyRecurrent mutation and purifying selection

Recurrent mutation can replenish a deleterious allele that purifying selection removes.

Approximation
BiologyNeutral fixation and substitution rate

In the ideal neutral diploid population, a new single-copy allele has eventual fixation probability 1/(2N).

Model
BiologyMolecular divergence, calibration and clock limits

Under equal constant lineage-specific substitution rates, the expected substitutions separating two descendant lineages accumulate over both branches since their common ancestor.

Model
ChemistryCoordination geometry and chirality

Coordination compounds can share composition while differing in ligand connectivity or spatial arrangement.

Definition
ChemistryMetal valence-electron counting and the 18-electron heuristic

Neutral-fragment and oxidation-state counting consistently allocate ligand and metal electrons when their conventions are used throughout.

Method
ChemistryLigand substitution, lability and thermodynamic stability

Dissociative ligand substitution loses a ligand before addition, while an associative route adds an incoming ligand before loss.

Model
ChemistryCovalent ligand fields and metal–ligand π interactions

Ligand-field MO models combine metal and ligand orbitals with compatible symmetry, adding covalent interactions beyond a point-charge crystal field.

Model
ChemistryIonic hydrides and hydrogen-compound acid/base character

Hydrogen in an ionic hydride is formally H− and can act as a strong base or reducing species; proton transfer with water produces hydrogen gas and hydroxide.

Model
ChemistryBoron Lewis acidity and silicon–oxygen frameworks

Boron trihalides have trigonal-planar molecular reference structures and can accept donor electron pairs; BF3 and fluoride form BF4−.

Model
ChemistryNitrogen oxides, electron parity and equilibrium

Nitrogen forms oxides with several formal oxidation states.

Model
ChemistryPhosphorus oxides, halides and phase-dependent structure

Phosphorus(III) and phosphorus(V) oxides have different oxygen content and formal oxidation states.

Model
ChemistryOxygen species and sulfur redox breadth

Oxide O²−, peroxide O₂²− and superoxide O₂− contain different numbers and arrangements of oxygen atoms and electrons.

Model
ChemistryHalogen redox and limits of noble-gas inertness

Halogens and halides have distinct oxidizing and reducing roles; for example, chlorine can oxidize bromide under suitable solution conditions.

Model
ChemistryHydroboration–oxidation and stereochemical complementarity

In the elementary alkene hydroboration model, C–H and C–B bonds form together from the same face without a free carbocation intermediate.

Model
ChemistryAlkyne hydration and enol-to-carbonyl conversion

Adding hydration equivalents to an alkyne initially produces an enol, which can tautomerize to a carbonyl compound.

Model
ChemistryActivated aromatic addition–elimination substitution

A nucleophile can add to an activated aryl system, forming an anionic intermediate before leaving-group elimination restores aromaticity.

Model
ChemistryAmine protonation and nitrogen lone-pair availability

An amine's basicity can be described by the acidity of its conjugate ammonium species under specified conditions.

Model
ChemistryActive-centre chain-growth polymerization

In chain-growth polymerization, monomer addition regenerates a growing active centre.

Model
ChemistryFunctional-group step-growth polymerization

Step-growth polymerization joins compatible functional groups on monomers and oligomers rather than requiring all growth at one persistent chain centre.

Model
Chemistry · BiologySingle-site binding, free ligand and affinity

For a reversible one-to-one receptor/ligand interaction at equilibrium, the dissociation constant relates free receptor, free ligand and complex concentrations.

Model
Chemistry · BiologyAllosteric coupling and cooperative binding

Ligand binding at one site can alter affinity or activity at another through coupling of protein states.

Model
ChemistryCoulometry and reaction-specific charge accounting

Coulometry infers reacting amount from integrated charge and electron stoichiometry.

Method
ChemistryVoltammetry, transport and electrode-current evidence

Voltammetry records current while controlling the working-electrode potential relative to a reference; a counter electrode carries the balancing current.

Method
ChemistryFluorescence yield and analytical linearity

Fluorescence emission follows optical excitation while competing with nonradiative relaxation.

Method
BiologyEvidence for organelle endosymbiotic ancestry

Mitochondrial and plastid ancestry is supported by bacterial affinities in molecular machinery and genes, organelle reproduction and transfer of many organelle-derived genes into nuclear genomes.

Model
BiologyBryophyte gametophytes and dependent sporophytes

Mosses, liverworts and hornworts illustrate gametophyte-dominant land-plant life cycles.

Model
BiologySeedless vascular plants and alternation of generations

Lycophytes and fern-related lineages have vascular sporophytes and life cycles that produce gametophytes through spores.

Model
BiologyAncestral polymorphism and gene/species-tree disagreement

Gene lineages need not coalesce at a population or species split.

Model
BiologyPhylogenetic covariance and comparative trait methods

Species traits can be correlated because related lineages share evolutionary history.

Method
ModelSource checked

Molecular divergence, calibration and clock limits

Biology

Under equal constant lineage-specific substitution rates, the expected substitutions separating two descendant lineages accumulate over both branches since their common ancestor.

Key knowledge

Under equal constant lineage-specific substitution rates, the expected substitutions separating two descendant lineages accumulate over both branches since their common ancestor. Converting sequence divergence to elapsed time requires a substitution model and a calibrated rate or independent time constraints. Rate variation, repeated hits and gene-tree ancestry prevent treating observed mismatches as an automatic species-divergence date.

Values and equations

E[d] = 2rt

d
inferred substitutions per site between lineages substitutions per site
r
constant per-lineage substitution rate site⁻¹ time-unit⁻¹
t
time since common ancestry in the same time unit time unit

Conditions and scope

  • The displayed expectation assumes equal rate r on both lineages and correctly inferred substitutions per site.
  • The time to a gene's common ancestor can precede population/species separation; no universal molecular clock is claimed.
Sources · 2

References

Sources retain their recorded scope. A source link alone does not establish verification of every statement.

  1. Lecture 11: Two-Lineage Divergence and Constraint, slides 4–9Graham Coop — UC Davis, undergraduate Population and Quantitative Genetics EVE 102 (2016)Textbook chapter · PDFgcbias.orgRead source
  2. Figures of Incomplete Lineage Sorting: ancestral-polymorphism simulations and captionsGraham Coop, University of California Davis, 2015Textbook chaptergcbias.orgRead source

Evidence and review

Read Lecture 11 slides 4–9 2Tμ neutral-clock expression and rate/constraint discussion, and the directly inspected ILS simulation captions tracing ancestral polymorphism through population separation. The captions support a gene-ancestry limitation, not a universal fixed probability or a reconstructed history for every species.

2026-10-10 · Independent AI editorial review: All 115 actual compact claims, hypotheses, equation/variable/unit tables and 251 origin semantic links independently read. All exact author source-binding rows and disclosed extents assessed; targeted original bodies or specifically identified indexed primary passages rechecked below. All retained biology compact records read for combined breadth. Independent AI editorial content and practical common-core inventory review; no human specialist, degree/laboratory proficiency, whole-textbook certification or experimental replication. Receipt: biology-independent-content-inventory-review.1.

Entry detailsPermanent link to this entry ↗
Record identity
uni-bio-molecular-clock
Revision
core.1
Structured reference record
University core expansion