DOI: 10.5061/dryad.4j0zpc8kz
title: Data from: Museomics reveal origins of East African Pleophylla forest chafers and Miocene forest connectivity

description: 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.
description: 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.
description: # 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
 ([d.ahrens@leibniz-lib.de](mailto:d.ahrens@leibniz-lib.de)) or Lars Dietz
 ([l.dietz@leibniz-lib.de](mailto:l.dietz@leibniz-lib.de)) 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_alignments.zip: DNA alignments of
 individual USCO loci of 95 Pleophylla individuals and three outgroups. In
 these alignments, ambiguity codes (R, Y, W, S, M, K) stand for positions
 inferred to be heterozygous. pleophylla_gene_trees.zip: Maximum-likelihood
 phylogenetic trees in NEWICK format based on DNA alignments of individual
 USCO loci of 95 Pleophylla individuals and three outgroups. In these
 alignments, ambiguity codes (R, Y, W, S, M, K) stand for positions
 inferred to be heterozygous pleophylla_scarab_gene_alignments.zip: DNA
 alignments of individual USCO loci from 24 Pleophylla/Omaloplia
 individuals with transcriptomic sequences from 58 other scarabaeoid and
 outgroup taxa. pleophylla_eogs_skim2.fas: Concatenated alignment in FASTA
 format of USCO genes of 95 Pleophylla individuals and three outgroups.
 pleophylla_eogs_skim.charset.nex: Partition file in NEXUS format for
 concatenated alignment of USCO genes of 95 Pleophylla individuals and
 three outgroups. pleophylla_skim_RUN_24.treefile: Maximum-likelihood
 phylogenetic tree created with IQ-TREE from concatenated USCO dataset of
 95 Pleophylla individuals and three outgroups. pleophylla_skim_astral.tre:
 Coalescent-based tree created with ASTRAL based on phylogenetic trees of
 individual USCO loci of 95 Pleophylla individuals and three outgroups.
 pleophylla_partitions.phy: Partitioned alignment in PHYLIP format of USCO
 sequences from 24 Pleophylla/Omaloplia individuals with transcriptomic
 sequences from 58 other scarabaeoid and outgroup taxa.
 pleophylla_mcmctree_ahrens2_FigTree.tre: Calibrated tree of Scarabaeoidea
 transcriptomic dataset including 24 Pleophylla/Omaloplia individuals
 calculated with MCMCTREE according to calibration points from Ahrens et
 al. (2014). pleophylla_mcmctree_mckenna2_FigTree.tre: Calibrated tree of
 Scarabaeoidea transcriptomic dataset including 24 Pleophylla/Omaloplia
 individuals calculated with MCMCTREE according to calibration points from
 McKenna et al. (2019). pleophylla_areas_adjacency2.txt: Areas-adjacency
 matrix used for BioGeoBEARS analysis. 1 indicates adjacency between areas,
 0 indicates non-adjacency. Abbreviations: Ca: Cape, Na: Natal, Ka:
 Kalahari, ZS: Zambesia (South), ZN: Zambesia (North), Sh: Shaba.
 pleophylla_biogeo_table3.txt: Table containing distribution ranges of
 Pleophylla species used for BioGeoBEARS analysis. Rows stand for species,
 columns for areas. 1 indicates occurrence of species within area, 0
 indicates non-occurrence. Species are indicated by first three letters of
 their name, see Fig. 2 for full species names. Abbreviations for areas:
 Ca: Cape, Na: Natal, Ka: Kalahari, ZS: Zambesia (South), ZN: Zambesia
 (North), Sh: Shaba.
 Pleophylla_BAYAREALIKE_vs_BAYAREALIKE+J_M0_unconstrained_v1.pdf: Trees
 showing inferred ancestral ranges from BioGeoBEARS analysis using the
 models BAYAREALIKE and BAYAREALIKE+J.
 Pleophylla_DEC_vs_DEC+J_M0_unconstrained_v1.pdf: Trees showing inferred
 ancestral ranges from BioGeoBEARS analysis using the models DEC and DEC+J.
 Pleophylla_DIVALIKE_vs_DIVALIKE+J_M0_unconstrained_v1.pdf: Trees showing
 inferred ancestral ranges from BioGeoBEARS analysis using the models
 DIVALIKE and DIVALIKE+J. restable_AIC_rellike_formatted.txt: Likelihood,
 estimated parameter values, and weight of each model used in BioGeoBEARS
 according to Akaike Information Criterion (AIC). Rows stand for models,
 columns for parameters. Abbreviations: LnL: logarithm of likelihood,
 numparams: number of parameters, d: dispersal parameter, e: extinction
 parameter, j: jump parameter, AIC: Akaike Information Criterion, AIC_wt:
 weight of model according to AIC. restable_AICc_rellike_formatted.txt:
 Likelihood, estimated parameter values, and weight of each model used in
 BioGeoBEARS according to corrected Akaike Information Criterion (AICc).
 Rows stand for models, columns for parameters. Abbreviations: LnL:
 logarithm of likelihood, numparams: number of parameters, d: dispersal
 parameter, e: extinction parameter, j: jump parameter, AICc: corrected
 Akaike Information Criterion, AICc_wt: weight of model according to AICc.
 ## Sharing/Access information Data was derived from the following sources:
 * Raw reads from hybrid enrichment and genomic shotgun sequencing of
 Pleophylla/Omaloplia spp. (NCBI SRA) * Transcriptome assemblies of
 scarabaeoid beetles from Dietz et al. (2023b):
 [https://www.ncbi.nlm.nih.gov/bioproject/PRJNA906571/](https://www.ncbi.nlm.nih.gov/bioproject/PRJNA906571/) ## Code/Software trinity_longest_d.pl: This script creates filtered versions of Trinity assembly results, containing only the longest variant of each contig. Requires, in that order, the input folder containing assemblies in FASTA format, and an output folder for filtered assemblies. Names of assembly files must end in .fasta. Example: trinity_longest_d.pl input_folder/ output_folder/ hmmalign_cut2_d.pl: This script removes all positions not covered by the HMM from hmmalign protein alignments (STOCKHOLM format), and the nucleotide alignments (FASTA format) based on them. As part of this process, the STOCKHOLM format of the protein alignments is converted to FASTA. Requires, in that order, the paths to the folder containing input protein alignments, the folder containing input nucleotide alignments, an output folder for protein alignments, and an output folder for nucleotide alignments. Names of protein and nucleotide alignments must be identical, with the former ending in .sth and the latter in .fas. Example: hmmalign_c2ut_d.pl input_prot/ input_nuc/ output_prot/ output_nuc/ extract_codpos_d.pl: This script removes the third codon position from all nucleotide alignments (FASTA format) in a folder. Requires, in that order, the paths to the folder containing input alignments and an output folder for modified alignments. Names of alignment files must end in .fas. Example: extract_codpos_d.pl input_folder/ output_folder/ concat_eogs_part_d.pl: This script creates a concatenated alignment FASTA file from all alignments (FASTA format) in a folder. It also creates a partition file in NEXUS format listing each alignment as a partition. Requires, in that order, the path to the folder containing input alignments, a name for the concatenated output alignment, and the partition file. Names of alignment files must end in .fas. Example: concat_eogs_part_d.pl input_folder/ concat.fas partition.nex sam_coverage_d.pl: This script calculates the average coverage for a set of genes weighted by their length based on the output of the samtools "coverage" function. Requires, in that order, a folder containing the samtools output files in txt format, and an name for the output table. Example: sam_coverage_d.pl input_folder/ output.txt