Molecular phylogenetic analysis is a method of estimating phylogenetic relationships by comparing the amino acid sequences of DNA and proteins. Using the concept of a molecular clock, divergence times can also be estimated.
Basic Knowledge
Principle of molecular phylogenetic analysis: More closely related organisms have more similar homologous DNA sequences and protein amino acid sequences. The size of sequence differences is proportional to the time since divergence. A phylogenetic tree (molecular phylogenetic tree) is constructed from the sequences compared.
Molecular clock: If the rate of amino acid substitution in a particular gene is constant, the divergence time can be estimated from sequence differences between two species.
Neutral theory of molecular evolution by Motoo Kimura: Most changes at the molecular level are nearly neutral with respect to natural selection, and substitutions occur at a constant rate dependent on the mutation rate. This is the theoretical basis of the molecular clock.
How to read a phylogenetic tree: Outgroup = an organism outside the group used as a comparison standard. Monophyletic group = a common ancestor and all of its descendants. Polyphyletic group = an artificial group containing different lineages. Paraphyletic group = a group that includes a common ancestor but excludes some descendants.
Phylogenetic analysis using rRNA (ribosomal RNA): Carl Woese proposed the three-domain system in 1977 by comparing 16S rRNA sequences.
Explain why Motoo Kimura's neutral theory provides a theoretical basis for the molecular clock.
Answer: According to neutral theory, most molecular-level mutations are neutral with respect to natural selection and become fixed in populations at a constant rate determined by the mutation rate. If the mutation rate is constant, sequence differences that accumulate after divergence are proportional to time, so the elapsed time since divergence (the divergence time) can be estimated from sequence differences between two species. This is the principle of the molecular clock.
- Molecular phylogenetic tree = phylogeny estimated by comparing DNA and protein sequences
- Molecular clock = sequence differences are proportional to time → estimation of divergence time
- Neutral theory = Motoo Kimura; most molecular changes are neutral
- Three-domain system = proposed by Woese from comparison of 16S rRNA (1977)
- Monophyletic group = common ancestor + all descendants
- Polyphyletic group = artificial group containing different lineages
- Outgroup = organism outside the group used as a comparison standard in phylogenetic analysis
Points to Note
① The molecular clock is not universally applicable. Because substitution rates differ among genes, it should be tested using multiple genes. ② Reptiles are a paraphyletic group in the traditional sense because birds are excluded. ③ Neutral theory and natural selection are not contradictory. Many molecular-level changes are neutral, whereas natural selection acts strongly on changes that appear in phenotypes.
Practice
- Explain what a molecular clock is using the terms “mutation rate” and “sequence difference.”
- State the content of the neutral theory proposed by Motoo Kimura.
- What molecule was compared to propose the three-domain system, and who proposed it?