Biology Dept
Kenyon College
Chapter 9: Molecular Evolution
Fall Section Spring Section 1 Spring Section 2

Molecular Evolution
The study of molecular evolution--how gene sequences change and evolve over time--is an important part of bioinformatics, the study of DNA sequence information.

Spontaneous mutations occur in different individuals.
Each of us has a few unique mutations in our own germ-line DNA.  Our children will inherit them.

Different individuals pass on different mutations to their offspring.
If different populations of individuals breed separately, the sequences of their DNA will diverge.

The mutations most likely to remain without negative selection are silent or neutral mutations.
Silent mutations accumulate at an approximately constant rate over generations.

In current populations, we cannot distinguish between the original sequence and the versions that mutated.   However, by comparing DNA from current populations, we can calculate the most probable sequence of the original.


  • Position 1 shows A for each of the four current populations.  This position is highly conserved.  The original base probably was A. 
  • Position 5 shows C or T.  This position has diverged.  We cannot know whether the original base was C or T.  However, it probably was a pyrimidine, not a purine (A or G). 

Molecular evolution can be used to measure divergence of species. For example:


This dendrogram shows the relative time of divergence of different species of virus, including Apthovirus, the cause of foot and mouth disease (in the news--devastating cattle in England and Europe.)

Genes that have diverged by mutation from a common ancestor are called homologs.

Genes can diverge:

  • Between different species (orthologs).  Orthologs maintain basically the same function in the different species. 
  • Within a species (paralogs).  Paralogs have evolved different functions; otherwise, all but one would probably be lost through degenerative evolution (acquisition of deleterious mutations which eliminate function). 
  • Example:

    Homeobox genes were originally discovered in Drosophila.

    Homeobox Gene Database
    Hox in Limb Development

    The original homeobox (Hox) gene in invertebrates duplicated and evolved into several paralogs.
    Then during the transition to vertebrates, the entire Hox cluster duplicated into four copies.  These subsequently diverged, losing some of the paralogs and evolving others into novel functions in development.

    Homeobox Genes--A set of transgenic mice containing Hox gene "knockouts"

    The Human HoxA Cluster

    A homeobox gene HOX-A1 has been implicated as a key to autism.  See Patricia Rodier's article on Autism in Scientific American (February 2000).

    Molecular Biology of Color Vision -- HHMI Tutorial


    Rhodopsin illustration
    Rhodopsin, the receptor protein in rod cells, crosses the disk membrane seven times.  Retinal (which absorbs light) is shown in purple. The other colored balls represent amino acids that make up the rhodopsin structure.

    Cone cell receptors -- red, green, and blue opsin -- have nearly identical structure.  They differ only at a few key amino acid residues.

    Dr. Jeremy Nathans cloned a bovine rhodopsin gene obtained from cDNA from cow retinas.  He then used the bovine gene -- an ortholog of human rhodopsin -- as a probe to isolate clones of the red, green, and blue opsin genes (paralogs), using his own genomic DNA. (What kind of hybridization blot?)  He had to test his own color vision first, to make sure he was not color-deficient (estimates range from 7-30% of the male population.)

    The color receptor opsins all arose by gene duplication and subsequent divergent evolution into paralogs of different function.  Because the green opsin gene has a duplicate copy tandem to the red opsin gene, on the X chromosome, mistaken crossover can occur between these two genes.  The result is failure to distinguish red from green; or in rare cases, perception of an anomalous color.  In extremely rare cases, a female carrier of such a gene has been reported to "see" a fourth color.

    Dr. S's sci fi novel, Brain Plague depicts a mutant artist who sees four colors because her father was color-blind.

    Genome and Proteome
    One of the most exciting applications of gene cloning, PCR, and  rapid sequence analysis is the Human Genome Project.  Several other animal, plant, and microbial genomes have now been sequenced.  The human genome will take a bit longer, but we already have expressed sequence tags for most of the protein-encoding genes.

    Human mutations in disease: See Online Mendelian Inheritance in Man
    A sequence of a normal human gene can be compared statistically to that of other organisms--and to disease genes.
    A Genbank entry for human rhodopsin
    Example search on rhodopsin--BLAST program

    We can learn a lot about human genes by studying orthologs from model systems such as
    Drosophila and C. elegans. It's amazing how often genes from one species can complement defects in another.
    See Complementation (next week).

    The Model Worm -- C. elegans.
    Advanced topic: Worm or Yeast: What Makes a Eukaryote?
    Great web site: Wadsworth's Wonderful Worms
    Nobel winner Bob Horvitz, where Kenyon alumnus Brad Hersh did his PhD. 

    There are numerous ethical questions to consider; for example, whose DNA will be sequenced?   What ethnic classes will be considered "standard" or "normal"?  Will we neglect alleles of significance to certain ethnic groups?