How do DNA and protein sequences help scientists compare species?

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Scientists use DNA and protein sequences as "informational macromolecules" to compare species and reconstruct their evolutionary history. Because these molecules are composed of linear sequences of units—nucleotides in DNA and amino acids in proteins—researchers can quantify the degree of difference between organisms by counting how many of these units differ.12

Key ways these sequences help in taxonomy and phylogeny include:

  • Measuring Divergence: The number of differences between homologous molecules serves as an indicator of how long ago two species diverged from a common ancestor.21
  • Molecular Clocks: Because mutations occur over time, these sequences can act as "molecular clocks." By comparing the number of substitutions, scientists can estimate the timing of branching events in a lineage.3
  • Quantifiable Comparisons: Unlike comparative anatomy, which can be subjective, molecular data is easily quantified and allows for comparisons between highly diverse organisms, such as bacteria and humans, that share homologous genes.1
  • Multiplicity: Because organisms possess thousands of genes and proteins, researchers can analyze multiple independent "clocks" to resolve complex evolutionary relationships.31

While powerful, scientists must select the appropriate gene for the specific taxonomic level being studied, as different molecules evolve at different rates.24