Molecular Biology and Evolution

DNA and Genetic Code

The universal nature of DNA and the genetic code across all living organisms is strong evidence for common ancestry:

• All known living organisms use DNA as their genetic material, with the same four nucleotides (A, T, C, G) forming the basis of genetic information.
• The genetic code (how DNA sequences are translated into proteins) is nearly identical in all species. For example, the codon UUU codes for phenylalanine in bacteria, archaea, and eukaryotes alike.
• Rare exceptions to the standard genetic code exist, such as in some mitochondria. For instance, in human mitochondria, AUA codes for methionine instead of isoleucine, and UGA codes for tryptophan instead of being a stop codon. These variations can be explained by evolutionary divergence.

Protein Homology

Similarities in protein sequences across species provide evidence of shared ancestry:

• Cytochrome c, a protein involved in electron transport, shows increasing differences in amino acid sequence as species become more distantly related. Specific examples include:
  • Humans and chimpanzees share 100% identical cytochrome c sequences.
  • Humans and rhesus monkeys have a single amino acid difference in their cytochrome c sequences.
  • Humans and horses differ by 12 amino acids in their cytochrome c sequences.
  • Humans and tuna differ by 21 amino acids in their cytochrome c sequences.
• The histone H4 protein, crucial for DNA packaging, is 98% identical between peas and cows, despite these species having diverged over a billion years ago.

Gene Duplication and Divergence

The process of gene duplication followed by divergence explains the evolution of new gene functions:

• Hemoglobin and myoglobin likely evolved from a common ancestral oxygen-binding protein. They share about 45% sequence identity, suggesting a duplication event occurred about 800 million years ago.
• The human olfactory receptor gene family has undergone extensive duplication and divergence, resulting in about 400 functional genes and 600 pseudogenes. This family represents the largest gene family in the human genome, comprising about 3% of our genes.
• The HOX gene cluster, crucial for body plan development, has undergone multiple duplication events. Fruit flies have a single cluster of 8 HOX genes, while humans have four clusters (HOXA, HOXB, HOXC, HOXD) totaling 39 HOX genes.

Pseudogenes

Pseudogenes, non-functional gene sequences, provide evidence of evolutionary history:

• The GULOP (L-gulonolactone oxidase) gene, responsible for vitamin C synthesis, is non-functional in humans and other primates but functional in most other mammals. In humans, it has accumulated multiple mutations, including a 28-base-pair deletion in exon X, rendering it non-functional.
• Olfactory receptor pseudogenes in whales and dolphins reflect their aquatic adaptation and reduced reliance on smell. For example, the bottlenose dolphin has 830 olfactory receptor genes, but only 26 are functional, while the remainder are pseudogenes.
• The human genome contains about 20,000 pseudogenes, including about 8,000 processed pseudogenes. For instance, the ψARF1 pseudogene on chromosome 17 is derived from the functional ARF1 gene on chromosome 1, but lacks introns and contains a poly-A tail, indicating it arose through reverse transcription of mRNA.

Molecular Clocks

The concept of molecular clocks allows estimation of divergence times between species:

• The rate of neutral mutations in DNA can be used to estimate when species diverged. For example, the mitochondrial DNA mutation rate in humans is estimated at about 1.7 × 10^-8 substitutions per site per year.
• Molecular clock analyses suggest that the last common ancestor of humans and chimpanzees lived about 5-7 million years ago. This is based on a 1.2% difference in DNA sequences between the two species, assuming a mutation rate of about 1 × 10^-9 substitutions per site per year.
• The divergence of placental mammals has been dated to about 100-120 million years ago using molecular clock techniques applied to multiple nuclear genes.

Horizontal Gene Transfer

The transfer of genetic material between unrelated species provides evidence for evolution:

• Many bacteria have acquired antibiotic resistance genes through horizontal gene transfer. For example, the mecA gene, which confers methicillin resistance in Staphylococcus aureus, is believed to have been acquired from another species of Staphylococcus.
• Some eukaryotic genes originated from bacteria. For instance, the gene for the enzyme cellulase in ruminants, crucial for cellulose digestion, likely originated from bacteria. The bovine genome contains at least 10 cellulase genes that show high similarity to bacterial cellulases.
• About 8% of the human genome consists of endogenous retroviruses (HERVs), which are remnants of ancient viral infections that became integrated into our genome. Some HERVs, like HERV-W, have been co-opted for important functions like placental development.

Endosymbiosis

The endosymbiotic theory, supported by molecular evidence, explains the origin of mitochondria and chloroplasts:

• Mitochondrial and chloroplast DNA are more similar to bacterial DNA than to eukaryotic nuclear DNA. For example, mitochondrial DNA is circular, like bacterial DNA, and lacks histones.
• These organelles have their own ribosomes, which are more similar to bacterial ribosomes than to eukaryotic cytoplasmic ribosomes. Mitochondrial ribosomes are sensitive to antibiotics that target bacterial ribosomes, such as chloramphenicol.
• The gene for the small subunit ribosomal RNA (16S rRNA) in chloroplasts is more similar to that of cyanobacteria than to nuclear rRNA genes. For instance, the 16S rRNA gene of spinach chloroplasts shares about 90% sequence identity with that of cyanobacteria.

Conclusion

The field of molecular biology has provided numerous, independent lines of evidence that strongly support the theory of evolution. From the universality of DNA to the intricate details of protein structures and gene functions, molecular data consistently points to the shared ancestry of all life on Earth and the ongoing process of evolutionary change. The specific examples provided here represent just a fraction of the overwhelming molecular evidence for evolution.

Further Reading

• DNA Structure and Function
• Evolution of protein molecules
• An integrated map of genetic variation from 1,092 human genomes
• Gene duplication and evolutionary innovations in animals