A phylogenetic analysis of platypus, opossum and human OR genes for the new family 14 only. Opossum = black for intact genes, grey for pseudogenes. Platypus = red for intact genes, pink for pseudogenes. Human = blue. OR14 is an expansion of three ancestral OR gene subfamilies (A, B and C); the expansion, in both platypus and opossum, took place after speciation, whereas only one branch shows an orthologous relationship between platypus and human (marked with *). The tree was generated with MEGA4, using the nearest-neighbour-joining algorithm, and distances with the Poisson correction model. Bootstrap units are also indicated.34 This tree is grounded with the OR51E1 gene. Only genes with no more than two frame disruptions were considered in the analysis.

A phylogenetic analysis of one representative from each family of the human OR gene repertoire. In this tree, one can see the following: (1) a general guideline for how the different families relate to one another (although this is very general, and the branching is not always this well defined); (2) the numbers near each branch denote the OR family number; (3) each pie chart size is scaled to represent the number of the OR genes inside that family (black = functional genes, grey = pseudogenes, yellow = segregating pseudogenes [SPGs]). SPGs are genes that segregate in populations between intact genes and pseudogenes — due to a disruptive SNP.34 This disruptive mutation can introduce a stop codon, or alter a highly conserved amino acid that is important for proper function of the protein. In Tables 1–5, the SPGs are counted as ‘functional genes’ or ‘pseudogenes’, according to the Human Genome Project public version. Additional information can be found at the HORDE database (http://bioportal.weizmann.ac.il/HORDE/).