Molecular Clocks: Neutral Theory, Calibration, and Rate Variation

All flashcards

What is a molecular clock?

A method that uses molecular differences and an estimated rate of change to infer when evolutionary lineages diverged.

What is node calibration?

A method that constrains the age of a phylogenetic-tree node using time evidence, often fossils.

What is tip calibration?

A method that treats fossils as taxa at tree tips and combines molecular and morphological data.

What is a relaxed molecular clock?

A clock model that allows molecular rates to vary among lineages.

Why can neutral mutations produce a clock-like rate in a simple haploid population?

The expected fixation rate equals the per-individual neutral mutation rate because new mutations and their fixation probability multiply to that rate.

Quiz questions

1. Why does a molecular clock need calibration to estimate absolute divergence times?Answer: Molecular differences alone generally do not provide an absolute timescale.
2. How is an oldest known fossil commonly used in node calibration?Answer: It provides a minimum age constraint for the relevant clade's ancestor.
3. What distinguishes tip calibration from node calibration?Answer: Tip calibration treats fossils as taxa and combines their morphology with molecular data.
4. What does expansion calibration use as a time reference?Answer: The timing of a documented population expansion.
5. What assumption distinguishes a strict molecular clock from a relaxed clock?Answer: A strict clock assumes a common rate across lineages; a relaxed clock allows rate differences.