A gene family is a set of genes defined by presumed homology, i.e. evidence that the genes evolved from a common ancestral gene. They generally share some biochemical activity. Genes are generally categorized into families based upon shared sequence motifs and similarities in structure.
Phylogenetic techniques can be used as a more rigorous test. The positions of introns within the coding sequence can be used to infer common ancestry. Knowing the sequence of the protein encoded by a gene can allow researchers to apply methods that find similarities among protein sequences that provide more information than similarities or differences among DNA sequences. Furthermore, knowledge of the protein's secondary structure gives further information about ancestry, since the organization of secondary structural elements presumably would be conserved even if the amino acid sequence changes considerably. These methods often rely upon predictions based upon the DNA sequence.
If the genes of a gene family encode proteins, the term protein family is often used in an analogous manner to gene family.
The expansion or contraction of gene families along a specific lineage can be due to chance, or can be the result of natural selection. To distinguish between these two cases is often difficult in practice. Recent work uses a combination of statistical models and algorithmic techniques to detect gene families that are under the effect of natural selection. The Evolution of Mammalian Gene Families
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