Molecular evolution

Molecular evolution is inherited change in molecules such as DNA and proteins across generations. Mutations introduce new variants; natural selection and genetic drift influence which variants persist. Comparing a nucleotide sequence or protein sequence between lineages therefore supplies evidence about their history as well as their present chemistry.

An important early example was the comparison of cytochrome c from different organisms. Emanuel Margoliash's 1963 report connected differences in protein primary structure to evolutionary relationships. The experimental input was the ordered amino acid residues of the proteins, rather than only their bulk composition or their shared function. Placing corresponding positions side by side made molecular differences countable.^[ref]

For a deliberately simplified example, suppose two already aligned sequences have $k=8$ differing positions among $n=100$ compared positions. Their observed difference fraction is $k/n=0.08$. That statistic is not itself a divergence time. If both lineages split $t$ time units ago and each accumulates substitutions at the same constant rate $r$ per position per unit time, their expected accumulated pairwise molecular divergence isThe factor two counts the two descendant branches. At low divergence, the observed difference fraction can approximate $d$; repeated changes at one position can conceal earlier changes, and unequal branch rates invalidate the equal-rate simplification. A molecular clock additionally needs a rate or time calibration to turn molecular differences into dates.

Sequence identity is a measured agreement between aligned positions. homology is a historical relationship of common descent; it is not a percentage. Orthology and paralogy further distinguish relationships associated with lineage splitting and gene duplication. These distinctions matter when a phylogenetic tree is inferred from a chosen gene rather than directly observed.

The neutral theory of molecular evolution provides a complementary population-level explanation: molecular change need not always be an adaptive improvement. Motoo Kimura's 1968 argument emphasized the potential importance of neutral changes and genetic drift, while leaving room for natural selection.^[ref]

Pairwise molecular divergence measures the accumulated evolutionary change separating two homologous molecular sequences. For aligned DNA sequences, a model-based distance $d$ is commonly expressed as the estimated number of nucleotide substitutions per site along the path connecting the sequences. It differs from the observed fraction of mismatching sites: a site may have changed more than once, including changes that restore the starting base.^[ref]

For example, 20 mismatches among 1,000 usable aligned sites give an observed mismatch fraction $p=0.020$. That is a count of present-day differences. An ancestral A that changed to G and then back to A contributes two historical substitutions but no endpoint mismatch. Sequence alignment and an explicit nucleotide substitution model are therefore needed to turn observed differences into an evolutionary interpretation.

The Kimura two-parameter model distinguishes nucleotide transitions from nucleotide transversions. If $P$ and $Q$ are their observed fractions among compared sites, respectively, its corrected pairwise estimate isFor $P=0.01$ and $Q=0.01$, this gives approximately $0.02028$ substitutions per site, slightly above the observed mismatch fraction $P+Q=0.020$. The correction accounts for hidden changes under the model's assumptions; it is not a direct count of every event. Both logarithm arguments must be positive for this finite real-valued estimate.^[ref]

Under a constant, equal per-lineage molecular clock rate $r$ and a split $T$ time units ago, the two branches contribute $d=2rT$. A pairwise divergence $d=0.02$ at $r=10^{-9}$ substitutions per site per year corresponds to $T=10^7$ years in that idealized model. The factor of two counts both lineages. Without a rate calibration or another time constraint, distance alone does not identify elapsed time.^[ref]

The neutral theory of molecular evolution proposes that much molecular evolutionary change arises from mutations with little or no effect on biological fitness, whose fates are governed largely by genetic drift. It concerns molecular substitutions and variation; it does not require adaptive traits or natural selection to be absent. Motoo Kimura argued in 1968 that observed molecular substitution rates were difficult to explain if all such changes were advantageous.^[ref]

The basic neutral calculation is especially revealing. In an idealized diploid biological population of size $N$, a neutral mutation rate $\mu$ per gene copy produces $2N\mu$ new copies per generation. Each has fixation probability $1/(2N)$, so the substitution rate isMore new mutations in a larger population are offset by the lower fixation chance of each one. This is a model prediction with explicit neutrality and population assumptions, not a claim that every mutation is neutral.