Molecular biology, the study of biological activity at the molecular level, provides fundamental and quantifiable evidence for the theory of evolution. By focusing on DNA, RNA, and proteins, scientists can directly compare the genetic blueprints of different organisms. This approach offers concrete, verifiable data that traces the history of life on Earth, moving beyond anatomical comparisons. Shared molecular characteristics across all species point to a single, common origin, with differences accumulating over time.
Shared Genetic Machinery
The most compelling molecular argument for common descent is the near-universal nature of core biological processes. Every known organism, from the simplest bacterium to complex humans, uses deoxyribonucleic acid (DNA) as its hereditary material. This DNA is structured as a double helix and is composed of the same four nucleotide bases: adenine, guanine, cytosine, and thymine.
Organisms share the exact same mechanism for translating genetic information into proteins. The genetic code is a triplet code, meaning that a sequence of three nucleotides (a codon) specifies a single amino acid. With only minor exceptions, the same codons specify the same amino acids across virtually all life forms, a phenomenon known as the universality of the genetic code. This suggests the code was established very early in the history of life, in the last universal common ancestor (LUCA), and has been conserved.
Additional molecular components are also universally conserved. These include the use of adenosine triphosphate (ATP) as the energy currency for cellular reactions. Ribosomes, the complex molecular machines responsible for protein synthesis, are structurally and functionally similar in all organisms. This deep-seated conservation of machinery makes it highly probable that all life descended from a single ancestral cell that possessed these foundational traits.
Comparing Protein and DNA Sequences
The theory of evolution predicts that species sharing a more recent common ancestor will have fewer differences in their DNA and protein sequences than those that diverged long ago. Comparative genomics and proteomics test this prediction by aligning the sequences of homologous genes and proteins across different species. This analysis provides a precise, numerical measure of evolutionary relatedness.
For example, the human genome is approximately 98% identical to that of a chimpanzee, reflecting a recent divergence time. Comparisons with more distant relatives show a predictable increase in sequence differences; the human genome is about 92% similar to that of a mouse. This aligns with the fossil record’s estimates of when those lineages separated, and the pattern corresponds to the established evolutionary tree.
Specific proteins that perform fundamental cellular tasks are highly conserved across vast evolutionary distances. Cytochrome c, a protein essential for cellular respiration in nearly all organisms, shows remarkable homology. The human sequence differs by only one amino acid from that of a chimpanzee, but by 44 amino acids from the Cytochrome c found in yeast. The alpha and beta chains of hemoglobin in vertebrates are also structurally related, having evolved from a common ancestral globin gene through gene duplication events hundreds of millions of years ago.
Estimating Evolutionary Timelines
The accumulation of genetic differences between species can be used to estimate the time elapsed since their divergence from a common ancestor. This technique, called the molecular clock, is based on the premise that mutations accumulate in DNA at a relatively constant rate over geological time. The mutation rate is particularly constant in non-functional or non-coding regions of the genome, where changes are less likely to be removed by natural selection.
To use the molecular clock, scientists count the accumulated genetic differences between two species in a specific gene or DNA segment. This number is then divided by a known, calibrated mutation rate for that sequence. The rate is calibrated using known divergence events found in the fossil record, where geological dating provides an absolute time estimate for a split between lineages.
The application of the molecular clock provides dates for evolutionary events that are consistent with those derived from geology and paleontology. For instance, it estimates that the split between the hominin and chimpanzee lineages occurred between 6 and 8 million years ago. Molecular clocks can be applied to rapidly-evolving genes for recent divergences and slowly-evolving genes, like those for ribosomal RNA, to date ancient splits between major groups of life.
Fossilized Genetic Footprints
Within the non-coding regions of the genome lie “genetic fossils” that serve as markers of shared ancestry. These sequences are remnants of genes or viral infections that occurred in a shared ancestor and have been passed down through generations. Their presence and identical location in the genomes of different species provide powerful evidence for common descent.
One example is pseudogenes, which are former genes disabled by mutation. Humans, chimpanzees, and other primates cannot synthesize vitamin C because they possess a non-functional copy of the L-gulono-gamma-lactone oxidase (\(GULO\)) gene. The shared defect, which includes identical disabling mutations at the same location, is most simply explained by a single inactivating mutation event that occurred in the common ancestor of these primate groups.
Another example comes from Endogenous Retroviruses (ERVs), which are viral DNA sequences integrated into the germline DNA of an organism. If a retrovirus infects a sperm or egg cell, the viral DNA becomes a permanent part of the host’s genome and is inherited by descendants. Humans and chimpanzees share the exact same ERV insertions at hundreds of chromosomal locations. Since viral insertions are essentially random, the probability of two species independently acquiring the same ERV at the identical chromosomal spot is astronomically low, making shared ERVs a molecular scar of a shared ancestral infection.