Independent Evolutionary Origin of <i>fem</i> Paralogous Genes and Complementary Sex Determination in Hymenopteran Insects

<div><p>The primary signal of sex determination in the honeybee, the <i>complementary sex determiner</i> (<i>csd</i>) gene, evolved from a gene duplication event from an ancestral copy of the <i>fem</i> gene. Recently, other paralogs of the <i>fem</i> gene have been identified in several ant and bumblebee genomes. This discovery and the close phylogenetic relationship of the paralogous gene sequences led to the hypothesis of a single ancestry of the <i>csd</i> genetic system of complementary sex determination in the Hymenopteran insects, in which the <i>fem</i> and <i>csd</i> gene copies evolved as a unit in concert with the mutual transfers of sequences (concerted evolution). Here, we show that the paralogous gene copies evolved repeatedly through independent gene duplication events in the honeybee, bumblebee, and ant lineage. We detected no sequence tracts that would indicate a DNA transfer between the <i>fem</i> and the <i>fem1/csd</i> genes between different ant and bee species. Instead, we found tracts of duplication events in other genomic locations, suggesting that gene duplication was a frequent event in the evolution of these genes. These and other evidences suggest that the <i>fem1/csd</i> gene originated repeatedly through gene duplications in the bumblebee, honeybee, and ant lineages in the last 100 million years. Signatures of concerted evolution were not detectable, implicating that the gene tree based on neutral synonymous sites represents the phylogenetic relationships and origins of the <i>fem</i> and <i>fem1/csd</i> genes. Our results further imply that the <i>fem1</i> and <i>csd</i> gene in bumblebees, honeybees, and ants are not orthologs, because they originated independently from the <i>fem</i> gene. Hence, the widely shared and conserved complementary sex determination mechanism in Hymenopteran insects is controlled by different genes and molecular processes. These findings highlight the limits of comparative genomics and emphasize the requirement to study gene functions in different species and major hymenopteran lineages.</p>