= Molecular evolution
{wiki}
\b[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.<Primary structure and evolution of cytochrome c by Emanuel Margoliash>[pp.672–679, cytochrome-c primary structures and evolutionary comparison]{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> is
$$
\boxed{d=2rt.}
$$
The 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 (biology)> 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>.<Evolutionary Rate at the Molecular Level by Motoo Kimura>[pp.624–626, molecular substitution rates and neutrality argument]{ref}
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