Two species are compared at a gene that evolves at a rate of 2 neutral substitutions per million years. Their sequences differ at 200 positions. What is the estimated divergence time?
A50 million years ago
B100 million years ago
C200 million years ago
D25 million years ago
You must divide by 2 because the 200 differences accumulated independently in BOTH lineages after divergence. Each lineage accumulated 100 changes over the elapsed time. At 2 substitutions/Myr, each lineage took 50 Myr — so divergence was 50 Mya. The common mistake is forgetting to divide by 2, which gives 100 Mya (double the correct answer).
Question 2 Multiple Choice
A researcher wants to date a divergence event estimated at roughly 500 million years ago. Which gene choice is most appropriate for the molecular clock analysis?
AA slowly evolving gene like histone H3, which has minimal functional divergence over long timescales
BA rapidly evolving gene like fibrinopeptides, which accumulates many substitutions quickly
CMitochondrial control region, because it evolves faster than nuclear genes
DAny gene, because all genes tick at the same rate for any timescale
Fast-evolving sequences become saturated over long timescales — so many substitutions have occurred at the same site that you can no longer accurately count them, causing systematic underestimates of divergence. Slowly evolving genes like histones preserve signal over hundreds of millions of years. Conversely, slow genes would be useless for dating recent divergences because too few substitutions would have accumulated to measure.
Question 3 True / False
The molecular clock must be calibrated against at least one independently dated event (such as a fossil) before it can give absolute divergence times.
TTrue
FFalse
Answer: True
True. Sequence differences alone give only a relative measure of divergence (more differences = more time). To convert that to an absolute time in years, you need to know the substitution rate per year, which requires anchoring to at least one event with a known age from an independent source like the fossil record. Without calibration, a clock tells you the ratio of divergence times between pairs of species, not the actual dates.
Question 4 True / False
Because neutral mutations accumulate at a constant rate per year, organisms with longer generation times (like elephants) should have the same molecular clock rate as organisms with shorter generation times (like mice).
TTrue
FFalse
Answer: False
False. Most mutations arise during DNA replication in the germline. Organisms with shorter generation times replicate their germline DNA more frequently per year, accumulating more mutations per unit of calendar time. Rodents typically evolve much faster molecularly than elephants per million years. This 'generation time effect' is a major source of rate variation across lineages that relaxed clock models must account for.
Question 5 Short Answer
Why must you divide the observed number of sequence differences by 2 when estimating divergence time from the molecular clock?
Think about your answer, then reveal below.
Model answer: After two lineages split from a common ancestor, each lineage independently accumulates mutations. The total number of observed differences between the two species represents changes in both lineages combined. To find how much time has elapsed since the split, you need the number of changes in just one lineage — so you divide by 2. Failing to do so doubles the estimated divergence time.
This is a fundamental bookkeeping issue in molecular dating. The observed divergence D = 2·r·t, where r is the substitution rate and t is time since divergence (each lineage accumulates r·t changes independently). Solving for t gives t = D/(2r). Dividing by 2 corrects for the fact that the total divergence counts evolution in both descendant lineages, not just one.