Genes separated by speciation are called orthologs.

Genes separated by gene duplication events are called paralogs.

In a gene family with so many births and deaths as the P450s, it can be difficult to assign true orthology (homologous genes separated by speciation events). Paralogs (homologous genes separated by duplication) can blur the picture by differential loss. The somewhat looser term “orthologous group” can therefore be quite useful (Gabaldon and Koonin 2013). An example in arthropod CYPomes is the case of the neopteran insect CYP4G genes which despite multiple births and deaths have maintained two clearly distinguishable orthologous groups (Feyereisen, 2020). Mounting evidence shows that they have also maintained essentially the same function in cuticular hydrocarbon biosynthesis over 400 MY.

Arthropod CYPome phylogeny reveals a number of such conserved orthologous groups. There were about equal numbers of orthologous groups in each of the four major clans (9 in clan 2, 12 in clan 3, 12 in clan 4 and 12 in the mito clan). No P450 has a strict 1:1 ortholog in all species surveyed. Of the 47 orthologous groups described by Dermauw et al.(2020), only 24 are strict 1:1 orthologs, and 23 are 1 to more. Some are found in virtually all arthropods (CYP18, CYP302, CYP307, CYP314, CYP315), or in all Mandibulata (CYP306). Some are found in all Neoptera (CYP4G1, CYP4G15) or are restricted to an order, where they are highly conserved. See Figure 12A from Dermauw et al., 2020 below, with species abbreviation as in that paper.

The study of genomes from closely related species provides an excellent opportunity to identify orthologs. This was done byGood et al., 2014 who have followed the fate of the 77 P450 genes inferred from the ancestral Drosophila genome on the species tree of 12 extant species. Of these 77 genes, 30 were considered evolutionarily “stable”, (“meaning that they have only one gene from each of the 12 species”). Given the fine grain of the Good et al. study, we can extend their definition to infer that “stable” genes are those incurring no documented gene gain or losses in the branches of the tree under study. These 30 genes can therefore be considered 1:1 orthologs in the strictest sense, although Good et al., simply called them stable genes, following Thomas (2007). Although the loss or duplication of a conserved gene in one lineage removes this gene from the stable category, loss of a gene does not negate the probable orthology of the remaining genes of that group.