Genomic insights into the phylogeny and evolutionary history of scale insects (Hemiptera: Coccoidea): Resolving family-level relationships

Scale insects (Hemiptera: Coccoidea), comprising archaeococcoids and neococcoids, represent the fourth largest superfamily within the order Hemiptera and are recognized as significant agricultural and forestry pests. Despite the increasing availability of insect genomic data, systematic phylogenetic studies of scale insects at the family level have been limited due to challenges in specimen collection, identification, and sequencing. In this study, we sequenced the genomes of 46 species representing 20 families and integrated this data with publicly available sequences to encompass 22 families, representing 95% of Coccoidea taxa. Notably, 14 of these families are sequenced for the first time. This work establishes a robust phylogenetic framework for scale insects. Our findings clarified the phylogenetic relationships of archaeococcoids, confirming Matsucoccidae as the most primitive extant group of scale insects and identifying Putoidae as a transitional lineage between archaeococcoids and neococcoids. We further demonstrated that Xenococcidae belongs to the neococcoids, distinct from Pseudococcidae, and revealed that Coccidae form a paraphyletic group, with Aclerdidae nested within Coccidae. Using MCMCTree analysis, we estimated the divergence times of various Coccoidea families and proposed a comprehensive evolutionary framework for scale insects. This study addresses key gaps in the phylogenetic and evolutionary understanding of Coccoidea, providing a valuable genomic resource and advancing our knowledge of their phylogeny and evolutionary history.