Museomics reveal origins of East African Pleophylla forest chafers and Miocene forest connectivity

Here we present a nearly complete species-level phylogeny including 23 of the 25 known species of the forest-dwelling herbivorous scarab chafer beetle genus Pleophylla (Coleoptera: Scarabaeidae: Sericinae), based on the analysis of 950 nuclear genes (metazoan-level universal single-copy orthologs; mzl-USCOs). DNA sequences were obtained from freshly collected, ethanol-preserved samples and from dried museum specimens by target enrichment or genome shotgun sequencing. Alignment completeness of mzl-USCOs newly obtained here by target DNA enrichment of ethanol samples were very heterogenous and lower (29-62%) than in Dietz et al. (2023), while that of sequences recovered from dried samples was even lower (~19%). Alignment completeness of the sequences obtained from low coverage shotgun sequencing was highest (~92%). We used the resulting phylogeny to reconstruct the historical biogeography of the group. To estimate a time-calibrated tree, we combined the mzl-USCO data of Pleophylla with a nucleotide alignment from an available transcriptomic dataset of Scarabaeoidea and used two different sets of secondary calibration points. Despite the problems associated with the capture rate of mzl-USCO sequences from museum specimens, we were able to infer a well-resolved phylogeny of the genus Pleophyllathat also provided reliable estimates of the phylogenetic position of species for which we had little sequence data. Our study clearly identified South Africa as the geographic origin of Pleophylla. Timing and biogeographic history confirm a persistent fragmentation of forests since the Eocene. The occurrence of only one long-distance dispersal event from southern Africa to the Eastern African Arc even during the Miocene highlights the limited dispersal possibilities for these forest-adapted chafers, which do not seem to have had important northerly range expansions along hypothetical forest corridors during the Pleistocene.

Methods
Sequencing was done via targeted enrichment or whole-genome shotgun sequencing from ethanol preserved or dry museum specimens of Pleophylla beetles. Reads were then mapped against reference mzl-USCO sequences with bwa and diploid consensus sequences extracted with samtools. Maximum-likelihood phylogenetic trees were then calculated with IQ-TREE, calibrated trees were created with MCMCtree, and biogeographic analyses were performed with BioGeoBEARS.