Supergenes are groups of tightly linked loci whose variation is inherited as a single Mendelian locus and are a common genetic architecture for complex traits under balancing selection [1, 2, 3, 4, 5, 6, 7, 8].
Supergenes are clusters of physically linked, co-evolving genes that often control complex traits.
We note that although supergenes are concatenated loci, we estimated supergene trees using partitioned analyses where each gene was put in a different partition.
Our splitting procedure is based on the assumption that the higher the BBH score is between a pair of supergenes, the greater is the chance that these BBH supergenes are orthologs and they are not false BBH bridges.
However, the mechanism governing the formation of supergenes is not well understood and poses the paradox of establishing divergent functional haplotypes in the face of recombination.
A1A2 is the strongest BBH, the arrangement of other supergenes is A3A4B1B2B3B4, and the first "filled" orthologous group is A1A2A3A4.
From all BBHs that are not included in this orthologous group, B1B2 is the strongest BBH, the arrangement of other supergenes is B3B4.
Therefore, the CDS alignments of each of the 276 gene families were separated into three datasets corresponding to each of the three codon positions in the CDS, and another three supergenes were assembled and used to estimate phylogeny.
The supergene is inherited as a single unit, the biologists report in the current issue of Nature.
If the mother and father have different wing patterns, the offspring will display the pattern of whichever version of the supergene is dominant.
