How genomes change over time
Point mutation
Nucleotides
Models of nucleotide substitution
Proteins
Mediated by the genetic code
Represented by amino acid substitution matrices or models
Indels - insertions and deletions
Gene duplication and loss
Rearrangement
Sex, hybridization, genetic exchange, and chimaeras
DNA duplication can lead to the formation of gene families
Several mechanisms of DNA duplication are known, and they can lead to the duplication of segments of DNA ranging in size from a few nucleotides to a gene, a large piece of a chromosome, or even an entire genome.
Bear in mind that sexual reproduction in eukaryotes involves periodic separation and recombination of entire genomes, and that bacteria and archaea exchange DNA in a number of ways.
Examples of duplication
Mitochondrial genome in Arabidopsis
Globin genes in humans and other mammals
Homeobox genes in animals
MADS box genes in land plants
tufA in Coleochaete (a green algal relative of land plants)
COG - clusters of orthologous groups
Blast analysis was not designed for this kind of comparison, and there are some theoretical concerns, but blast has been widely used to compare genomes and examine the relationships among their genes.
One-to-one, one-to-many, and many-to-one BLAST hits
The fate of duplicated genes
Loss of function probably occurs in the vast majority of cases
Sometimes subfunctionalization can occur
Even when no subfunctionalization occurs, the presence of a duplicate gene may lead to a temporary increase in the rate of sequence evolution because of the relative relaxation of selection on a single locus.
Concerted evolution
Best documented in ribosomal RNA genes (rRNA)
rRNA genes in eukaryotes are typically encoded in a tandem array with ca. 120-600 copies
Exceptions include Plasmodium (3 copies, differentially expressed) and Tetrahymena (one copy, but amplified in the macronucleus).
This tandem array of rRNA genes evolved early in the history of eukaryotes
Despite the large number of rRNA genes, their sequences are typically very simiar to each other, even when compared to the sequences in close relatives.
Concerted evolution serves to homogenize these sequences. The mechanism is still under investigation, but seems to involve unequal crossing-over, at least in part.
Bacteria and Archaea typically have one or a small number of rRNA genes, but if more than one is present, these often seem to undergo concerted evolution.
Related issues in molecular evolution
Exon shuffling
Alternate splicing
RNA editing
Mobile elements
Gene transfer
Pseudogene
Concerted evolution
Tandem array
Inverted repeat
Special cases of homology:
Orthology
Paralogy
Xenology
Supplementary Reading
Li, W.-H. 1997. Molecular Evolution. Sinauer Associates, Inc., Sunderland, MA.
Heinemann, J. A., and G. F. Sprague, Jr. 1989. Bacterial conjugative plasmids mobilize DNA transfer between bacteria and yeast. Nature 340: 205-209.
Tatusov, R. L., E. V. Koonin, and D. J. Lipman. 1997. A genomic perspective on protein families. Science 278: 631-637. [There are many important publications that refer to this article, not all of which agree with its conclusions -- see science citation index.]
Rieseberg, L. H., B. Sinervo, C. R. Linder, M. C. Ungerer, and D. M. Arias. 1996. Role of gene interactions in hybrid speciation: Evidence from ancient and experimental hybrids. Science 272: 741-745. [This is one part of a rich thread of articles by the same authors.]