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