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 ..., 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., , # Data from: Museomics reveal origins of East African Pleophylla forest chafers and Miocene forest connectivity

Supplementary files for study \"Museomics reveal origins of East African Arc forest chafers and Miocene forest connectivity\", L. Dietz et al., submitted

For questions, contact Dirk Ahrens ([[e-mail]](mailto:[e-mail])) or Lars Dietz ([[e-mail]](mailto:[e-mail]))

All alignments, except for the one used for the MCMCtree analysis, are in FASTA format and can be opened with standard alignment viewers.

Phylogenetic trees are in NEWICK format and can be opened in a standard phylogenetic tree viewer such as FigTree. Partition files for concatenated alignments are in NEXUS format for use in IQ-TREE.

Figures showing BioGeoBEARS results are in PDF format and can be opened e.g. with Adobe Acrobat Reader. All other files can be opened with a standard text editor.

## Description of the data and file structure

pleophylla_gene_al...,