Loss of phylogenetic information in chorion gene families of Bombyx mori gene conversion

The silkmoth chorion has provided a stimulating model for the study ofevolution and developmental regulation of gene families. Previous attemptsat inferring relationships among chorion sequences have been based onpairwise comparisons of overall similarity, a potentially problematicapproach. To remedy this, we identified the alignable regions of lowsequence variability and then analyzed this restricted database byparsimony and neighbor-joining methods. At the deepest level, the chorionsequence tree is split into two branches, called "alpha" and "beta." Withineach branch, early- and late-expressing genes each constitute monophyleticgroups, while the situation with middle-expressing genes remains uncertain.The HcB gene family appears to be the most basal beta-branch group, butthis conclusion is qualified because the effect of gene conversion onbranching order is unknown. Previous studies by Eickbush and colleagueshave strongly suggested that ErA, HcA, and HcB families undergo geneconversion within a gene family, whereas the ErB family does not. Theoccurrence of conversion correlates with a particular tree structure;namely, branch lengths are much greater at the base of the family than athigher internodes and terminal branches. These observations raise thepossibility that chorion gene families are defined by gene conversionevents (reticulate evolution) rather than by descent with modification(synapomorphy).