Leaving X: How scale insects evolved alternatives to chromosomal sex determination

Reproduction is a core feature of life, which makes understanding the reproductive diversity of organisms a fundamental goal of evolutionary biology. It is still unclear why sex determination systems are faithfully conserved for hundreds of millions of years in some taxa but repeatedly turn over in others. A prime example is the true bugs, Hemiptera. The vast majority of families employ a conserved X sex chromosomal system, but in scale insects (Coccomorpha), sex determination systems are far more varied. Different families may retain X chromosomes, employ a rare form of haplodiploidy known as paternal genome elimination (PGE), or forgo sexual reproduction in favor of simultaneous hermaphroditism. While these systems have been known for decades, only recently has non-model genomics enabled their study with modern bioinformatic methods. We collected and sequenced representatives of rare, early-diverging scale insects to study genomic changes that coincide with transitions between sex determination systems. Using ancillary expression data, we also explored sex-biased gene expression in a subset of scale insects on both sides of one transition. In a newly updated molecular phylogeny, we recovered two independent losses of X chromosomal sex determination, once in the family Monophlebidae and a second time at the base of the families that employ PGE. In the former, genomic rearrangements begin before the X is lost and any previously X-linked orthologs have been absorbed into one of two massive, shuffled autosomes in the hermaphrodites. In the latter, the X chromosome itself is faithfully preserved in early diverging PGE taxa; it appears to have merely lost its sex determination function. We analyze ortholog conservation across these transitions and find few genes lost, with only one orthogroup lost in both transitions, and a number of orthogroups gained, suggesting these large transitions did not require large changes to the gene content of the X chromosome. Expression data suggests that extreme sexual dimorphism of gene expression predates sex determination turnover and may have helped enable it. Together these new observations illustrate the multiple routes to sex determination turnover, help refine hypotheses for its causes, and provide a wealth of new resources for the modern genomic study of scale insects.