Gene duplications, paralogs etc, a phylogenetic phantom menace

Hurles, M., 2004. Gene Duplication: The Genomic Trade in Spare Parts. PLoS Biol 2(7): e206. DOI:10.1371/journal.pbio.0020206.

Here's a nice paper in PLOS about how gene duplications come about as a "major opportunities from which new genes evolve". Part of the research I do is based on paralogues of genes and how such phenomena can confound certain issues in IgE-binding capacity. The more I delve into this issue, I feel that gene duplication will be important in functional genomics. Gene duplications are really a fundamental toolkit in evolutionary genetics and the reductionists need to really take variation into consideration. Paralogs are a phylogeneticist's nightmare.

Orthologs are genes that divide via speciation so have counterparts in other species while paralogs are genes that arise through duplication.

See also this correspondence in Genome Biology - Orthologs and paralogs - we need to get it right. Jensen does a great job at teasing out the nitty gritty of the definitions, which when given enough thought can be really more profound than we'd normally imagine it to be.