DNA and proteins hold the keys to our evolutionary past. By comparing genetic sequences across species, scientists uncover hidden relationships and trace our shared ancestry. This molecular evidence complements fossils and anatomy, painting a fuller picture of life's history.

Mutations drive evolution at the molecular level, creating genetic variation for natural selection to act upon. From single nucleotide changes to whole gene duplications, these alterations can lead to new traits, adaptations, and even species over time.

DNA and Protein Evidence for Evolution

DNA sequences as evolutionary evidence

• DNA and protein sequence similarities reveal evolutionary relationships higher similarity indicates closer relatedness
• Conserved sequences across species suggest common ancestry (histones, ribosomal RNA)
• Comparative genomics analyzes whole genomes between species identifies homologous genes and sequences
• Phylogenetic trees constructed from genetic similarities visualize evolutionary relationships (primates)
• Molecular homology demonstrates common ancestry through orthologous genes similar genes in different species (hemoglobin) and paralogous genes similar genes within species from duplication (α and β globin)
• Protein structure conservation indicates common ancestry similar structures across species (cytochrome c) functional domains preserved through evolution

Molecular clocks for evolutionary timing

• Molecular clock concept assumes constant mutation rate over time calibrated using fossil record or geological events
• Types include protein-based clocks and DNA-based clocks
• Calculation methods:
  1. Determine rate of nucleotide or amino acid substitutions
  2. Estimate divergence time using formula: $T = K / (2r)$ T: time since divergence, K: genetic distance, r: substitution rate
• Applications date speciation events (human-chimpanzee split) estimate origins of genetic innovations (color vision in primates)
• Limitations include rate variation among lineages generation time differences selection pressures affecting mutation rates

Molecular vs other evolutionary evidence

• Molecular evidence advantages provides direct genetic information allows study of organisms without fossils (bacteria) reveals cryptic species (morphologically similar but genetically distinct)
• Fossil record strengths offers physical evidence of past life forms (dinosaurs) provides morphological details allows direct observation of evolutionary transitions (whale evolution)
• Comparative anatomy contributions reveals structural homologies (vertebrate limbs) demonstrates adaptive radiations (Darwin's finches) identifies vestigial structures (human appendix)
• Synergies between evidence types molecular data corroborates fossil-based phylogenies anatomical features support genetic relationships
• Discrepancies resolved through integrative approaches combining molecular and morphological data (resolving mammal phylogeny)

Mutations in molecular evolution

• Mutation types: point mutations (substitutions, insertions, deletions) chromosomal mutations (inversions, translocations, duplications)
• Genetic variation sources: mutation recombination gene flow
• Natural selection at molecular level: positive selection (lactase persistence) negative selection (lethal mutations) neutral theory (genetic drift of neutral mutations)
• Molecular adaptation changes protein function or regulation (antibiotic resistance) gene duplication and neofunctionalization (olfactory receptor genes)
• Evolutionary rates vary fast-evolving regions (immune genes) vs. conserved regions (ribosomal genes) influenced by factors like generation time and population size
• Codon bias and synonymous mutations impact translation efficiency (E. coli) selection on synonymous sites