Evidence for Evolution: Comparative Genomics
Biological evolution is a change in the allele frequency of a population's gene pool over successive generations. Heritable characteristics are encoded by genes and transferred between generations as alleles (alternative forms of a gene) — so evolution is cumulative change in a population from one generation to the next.
Comparative genomics is the comparison of the DNA and proteins of different species to determine how closely related they are. It works because some genes are highly conserved: their products perform jobs essential for life across many species (for example, cellular respiration), so the same gene can be lined up across very different organisms. The general rule is that more closely related species have fewer differences in their sequences.
COMPARATIVE ANATOMY
Before molecular tools existed, Darwin compared the anatomical features of different species. Structures with different functions but the same underlying plan are called homologous structures, and they suggest a common origin. The classic example is the pentadactyl (five-digit) limb, shared by mammals, birds, amphibians and reptiles:
- Human hands - adapted for tool manipulation (power and precision grips).
- Bird and bat wings - adapted for flying.
- Horse hooves - adapted for galloping.
- Whale and dolphin fins - adapted for swimming.
THE MOLECULAR CLOCK
Mutations accumulate over time at a roughly steady, calculable rate. The number of differences in a shared gene or protein therefore acts as a molecular clock: the more differences there are, the more time has passed since the two species shared a common ancestor. Different sequence types change at different rates:
| Sequence compared | Rate of change | Why |
|---|---|---|
| Non-coding DNA | Fastest — the best means of comparison | Mutations accumulate freely without disrupting a protein |
| Gene sequences | Slower | Base changes may affect protein structure and function |
| Amino acid sequences | Slowest | Codon degeneracy — several codons give the same amino acid |
SEQUENCING COMMON PROTEINS
Every protein has a primary structure that can be sequenced directly, or deduced from the gene that encodes it. The most commonly compared protein is cytochrome c, which is involved in aerobic respiration and is highly conserved across species. Haemoglobin is another conserved protein used in the same way.
DNA-DNA HYBRIDISATION
This technique measures how similar two genomes are by how strongly their strands bind to each other — the strength of binding reflects the number of complementary bases the two species share. The procedure has four steps:
- Heat the DNA above 90 °C to separate the strands — heating breaks the hydrogen bonds between complementary bases.
- Mix the DNA of the two species being compared.
- Cool the mixture to 50–60 °C so that complementary strands join into hybrid double helices.
- Gradually reheat to separate the hybrid strands again. The higher the temperature needed, the more complementary base pairing there was — and therefore the more similar (and more recently separated) the species.
DNA-DNA hybridisation: separate, mix, cool to form hybrid helices, then reheat. The melting temperature measures the degree of complementary base pairing.
OTHER DNA SOURCES AND TECHNIQUES
| Source or technique | Key point |
|---|---|
| DNA sequencing | The base sequence itself is compared against databases holding the equivalent DNA of many species |
| rRNA gene sequencing | Used especially to distinguish prokaryote (bacterial) species — rRNA is a highly conserved ribosome component that still shows variation between species |
| Mitochondrial DNA | Inherited only from the mother; generally high sequence variation between species; widely used to trace human evolutionary history |
PHYLOGENETIC TREES
The results of these comparisons are drawn as a phylogenetic tree — a diagram of evolutionary relationships. Three rules apply when reading one:
- The species of interest sit at the tips of the branches.
- Every branch point (junction) represents a common ancestor.
- Branch lengths can be drawn to scale to represent the time since divergence.
Trees can be built from amino acid similarity, DNA similarity, or the presence or absence of key characteristics (for example, hair or mammary glands). The same data can be drawn in different tree styles with exactly the same meaning.
Species sit at the tips and branch points are common ancestors. A and B diverged most recently, so they are the most closely related.
In summary: Fewer sequence differences → more recent common ancestor → more closely related species