7.2 Molecular clocks and estimating divergence times

Molecular clocks measure evolutionary time through genetic changes, assuming constant rates of molecular evolution. This concept, rooted in neutral theory, helps estimate species divergence times by comparing DNA sequences and calculating genetic distances.

Accuracy depends on factors like generation time, metabolic rate, and selection pressure. Calibration uses fossils, biogeographic events, and cross-validation techniques. Relaxed clock models allow for rate variation, improving estimates across diverse lineages.

Molecular Clock Fundamentals

Concept of molecular clocks

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• Molecular clock measures evolutionary time through genetic changes accumulating at relatively constant rates
• Assumes constant rate of molecular evolution across lineages and over time
• Neutral theory of molecular evolution underpins concept positing most mutations are neutral and don't significantly affect fitness
• Constant mutation rate over time assumed, though can vary between species
• Similar generation times across lineages expected, but not always true (mice vs. elephants)
• Strict molecular clock assumes uniform rate across all lineages
• Relaxed molecular clock allows for rate variation between different branches (primates vs. rodents)

Molecular clocks for divergence times

• Process estimates divergence by comparing DNA sequences between species
• Genetic distance calculated using substitution models (Jukes-Cantor, Kimura)
• Mutation rate applied to convert genetic distance to time
• Molecular clock equation: $T = D / (2R)$ calculates time since divergence
• Phylogenetic trees constructed with branch lengths representing genetic distances
• Bayesian methods incorporate uncertainty in rate estimates and prior knowledge

Factors and Calibration

Factors affecting clock accuracy

• Generation time variations impact mutation accumulation (bacteria vs. redwoods)
• Metabolic rate differences potentially influence mutation rates (hummingbirds vs. tortoises)
• Population size effects genetic drift intensity in small populations (island species)
• Selection pressure variations accelerate evolutionary rates in certain genes (immune system genes)
• DNA repair efficiency affects mutation accumulation (human vs. naked mole rat)
• Environmental factors like UV radiation or chemical mutagens increase mutation rates
• Gene function influences evolutionary rate with essential genes evolving more slowly (ribosomal genes)

Calibration of molecular clocks

• Fossil calibration uses dated fossils as minimum age constraints (Archaeopteryx for bird-dinosaur split)
• Biogeographic events provide calibration points (Isthmus of Panama formation)
• Secondary calibrations utilize previously estimated divergence times from other studies
• Tip-dating methods incorporate extinct taxa into phylogenetic analyses
• Cross-validation techniques test consistency across multiple calibration points
• Relaxed clock models allow for rate variation across lineages (mammals vs. insects)
• Molecular dating software like BEAST, MrBayes, and PhyloBayes implement various calibration methods