Scarab beetles (Scarabaeidae) are a diverse and ecologically important group of angiosperm-associated insects. As conventionally understood, scarab beetles comprise two major lineages: dung beetles and the phytophagous Pleurosticti. However, previous phylogenetic analyses have not been able to convincingly answer the question whether or not the two lineages form a monophyletic group. Here we report our results from phylogenetic analyses of more than 4,000 genes mined from transcriptomes of more than 50 species of Scarabaeidae and non-scarabaeid Scarabaeoidea. Our results provide convincing support for the monophyly of Scarabaeidae, confirming the debated sister group relationship of dung beetles and phytophagous pleurostict scarabs. Supermatrix-based maximum likelihood and multispecies coalescent phylogenetic analyses strongly imply the subfamily Melolonthinae as currently understood being paraphyletic. We consequently suggest various changes in the systematics of Melolonthinae: Sericinae Kirby, 1837 stat. rest. and sensu n. to include the tribes Sericini, Ablaberini and Diphucephalini, and Sericoidinae Erichson, 1847 stat. rest. and sensu n. to include the tribes Automoliini, Heteronychini, Liparetrini, Maechidiini, Scitalini, Sericoidini, and Phyllotocini. Both subfamilies appear to consistently form a monophyletic sister group to all remaining subfamilies so far included within pleurostict scarabs except Orphninae. Our results represent a major step towards understanding the diversification history of one of the largest angiosperm-associated radiations of beetles.

Universal single-copy orthologs (USCOs) on the Endopterygota level as well as Coleoptera-specific orthologs were extracted from transcriptomes of scarabaeoid beetles with Orthograph and aligned using two different programs (MAFFT and hmmalign). Alignments were analysed both on the nucleotide and amino-acid level, and additionally reduced datasets were generated that include only positions present in at leats 70% of individuals. Phylogenetic trees were created with IQ-TREE both for concatenated alignments and for individual genes, and coalescent-based analyses were done with ASTRAL based on the individual gene trees.

All alignments, including SNP datasets, are in FASTA format and can be opened with standard alignment viewers. Phylogenetic trees are in NEWICK format, files including multiple named trees are in NEXUS format. Both can be opened in a standard phylogenetic tree viewer such as FigTree.