Molecular Evolution Lab
Compare hemoglobin gene sequences across species to discover evolutionary relationships. Measure sequence similarity, compute Jukes-Cantor distances, introduce mutations to study their effects on protein translation, and build phylogenetic trees from molecular data.
Guided Experiment: Sequence Similarity Across Species
How do you think hemoglobin gene similarity will vary among humans, chimps, mice, chickens, and frogs? Which pairs will be most similar?
Write your hypothesis in the Lab Report panel, then click Next.
Sequence Comparison
Controls
Results
Protein Comparison
Hemoglobin Phylogenetic Tree (UPGMA)
This tree shows the evolutionary relationships of hemoglobin gene sequences across five species, built using UPGMA clustering on Jukes-Cantor distances.
Data Table
(0 rows)| # | Trial | Species Pair | Length(bp) | Matches | Mismatches | Gaps | Identity(%) | JC Distance |
|---|
Reference Guide
Molecular Phylogenetics
Closely related species share more DNA sequence similarity than distantly related species. By comparing gene sequences, we can reconstruct the evolutionary tree of life.
Hemoglobin is a conserved protein found in all vertebrates, making it ideal for comparing species across hundreds of millions of years of evolution.
Molecular data often confirms (and sometimes corrects) phylogenies based on morphological features and the fossil record.
Jukes-Cantor Model
Raw percent difference underestimates the true number of substitutions because some sites mutate more than once (multiple hits).
The Jukes-Cantor model assumes equal rates for all four types of substitution and equal base frequencies. It corrects for back-mutations and convergent substitutions.
The Molecular Clock
If DNA accumulates mutations at a roughly constant rate over time, the number of differences between two species is proportional to the time since they last shared a common ancestor.
This "molecular clock" can be calibrated using fossil dates to estimate divergence times for species that lack a fossil record.
UPGMA tree construction assumes a molecular clock. Branch lengths represent evolutionary time, and the root is placed at the midpoint.
Synonymous vs Nonsynonymous Mutations
Not all DNA mutations change the protein. Because the genetic code is degenerate (redundant), some mutations are "silent" or synonymous.
Synonymous (silent) mutations change the DNA but not the amino acid, usually at the third codon position.
Nonsynonymous mutations change the amino acid and may affect protein function. Natural selection acts on nonsynonymous mutations.
The ratio of nonsynonymous to synonymous mutations (dN/dS) indicates whether a gene is under purifying selection (<1), neutral evolution (=1), or positive selection (>1).