Fig. 2. Schematic illustration of pseudogene identification and ancestral states reconstruction.

Flowchart of pseudogene analysis. OG1, OG2, and OG3 refer to three different homologous gene family IDs assigned by OrthoFinder. Pseudogenes with all query ORFs from the same gene family are “strict-consistent” and those with >1/2 of their query ORFs clustered into the same gene family are “relaxed-consistent”. “Inconsistent” pseudogenes do not have >1/2 of query ORFs clustered into one family. Only strict- and relaxed-consistent pseudogenes were assigned to corresponding gene families. “Multi-state” gene families contain both ORFs and pseudogenes from the same genome, while in “single-state” gene families, either ORFs or pseudogenes are present in each of the involved genome. Only single-state gene families were selected for ancestral reconstructions of genetic and ecological traits.