Rhytiphora Audinet-Serville is the most speciose longhorn beetle (Cerambycidae) genus in Australia, with about 200 species (from nearly 40 former genera, now synonymised into one) distributed across the entire continent. We used mitochondrial genome data from whole genome shotgun sequencing and COI barcoding of museum specimens to reconstruct the phylogeny of 68 Rhytiphora species, and analyse their morphological diversity and biogeographic history. We recovered a monophyletic Rhytiphora containing two distinct clades, within which all of the former genera (except Achriotypa) are paraphyletic. Nine morphological traits (including body size and the male setose ‘sex patches’) show strong phylogenetic signal and can be used to differentiate between the two clades. One clade is mainly restricted to Australia’s tropical north, while the other, larger clade has many species along the mesic east coast. Both clades have experienced multiple biome shifts, displaying a remarkable flexibility in habitat occupancy.

Alignment files

Rhyt_WGS_core_aa.nex (core dataset (31 taxa) concatenated alignment of amino acids)

Rhyt_WGS_core_deg.nex (core dataset concatenated alignment of degeneracy-recoded nucleotides)

Rhyt_WGS_core_nt.nex (core dataset concatenated alignment of nucleotides)

Rhyt_WGS_exp_aa.nex (expanded dataset (96 taxa) concatenated alignment of amino acids)

Rhyt_WGS_exp_deg.nex (expanded dataset concatenated alignment of degeneracy-recoded nucleotides)

Rhyt_WGS_exp_nt.nex (expanded dataset concatenated alignment of nucleotides)

Rhyt_WGS_exp_nt_pruned (pruned dataset (70 taxa) concatenated alignment of nucleotides)

Maximum likelihood phylogenies (IQ-TREE)

Rhyt_WGS_core_aa.tree (Newick-format tree from core amino acid dataset)

Rhyt_WGS_core_deg.tree (Newick-format tree from core degeneracy-recoded nucleotide dataset)

Rhyt_WGS_core_nt.tree (Newick-format tree from core nucleotide dataset)

Rhyt_WGS_exp_aa.tree (Nexus-format tree from expanded amino acid dataset)

Rhyt_WGS_exp_deg.tree (Nexus-format tree from expanded degeneracy-recoded nucleotide dataset)

Rhyt_WGS_exp_nt-149.tree (Nexus-format tree from expanded nucleotide dataset, tree search #149)

Rhyt_WGS_exp_nt-201.tree (Nexus-format tree from expanded nucleotide dataset, tree search #201)

Rhyt_WGS_exp_nt-476.tree (Nexus-format tree from expanded nucleotide dataset, tree search #476)

Bayesian phylogeny (BEAST2)

Rhyt_WGS_exp_nt_BEAST.tree (Nexus-format tree from pruned nucleotide dataset)

Other files

Rhyt_WGS_BGB_biomes.txt (input file for BioGeoBEARS analyses)

Rhyt_WGS_morph.csv (morphological data file for R statistical analyses)

README file

README_Rhytiphora_WGS_Dryad_metadata.txt (detailed information on the data package)