DOI: 10.5061/dryad.wdbrv15x3
title: Data from: Evolution across the adaptive landscape in a hyperdiverse beetle radiation

description: The extraordinary diversification of beetles on Earth is a textbook
 example of adaptive evolution. Yet the tempo and drivers of this
 super-radiation remain largely unclear. Here, we address this problem by
 investigating the macroevolutionary dynamics in darkling beetles
 (Coleoptera: Tenebrionidae), one of the most ecomorphologically diverse
 beetle families (with &gt;30k species). Using genomic datasets and
 multiple approaches, we resolve the long-standing inconsistency over deep
 relationships in the family. In conjunction with a landmark-based dataset
 of body shape morphology, we show that the evolutionary history of
 darkling beetles is marked by ancient rapid radiations, frequent
 ecological transitions, and rapid bursts of morphological diversification.
 On a global scale, our analyses uncovered a significant pulse of
 phenotypic diversification proximal to the K/Pg mass extinction and
 remarkable convergence of body shape associated with ecological
 specialization. On a regional scale, two major Australasian radiations,
 the Adeliini and the heleine clade, exhibited contrasting patterns of
 ecomorphological diversification, representing a clear contrast of
 phylogenetic niche conservatism versus adaptive radiation. Our findings
 align with the Simpsonian model of adaptive evolution across the
 macroevolutionary landscape and highlight a significant role of ecological
 opportunity in driving the immense ecomorphological diversity in a
 hyperdiverse beetle group.
description: # Data from: Evolution across the adaptive landscape in a hyperdiverse
 beetle radiation 
 [https://doi.org/10.5061/dryad.wdbrv15x3](https://doi.org/10.5061/dryad.wdbrv15x3) ## Description of the data and file structure 01_probe_design: TENEB_ExonCapture_OrthoRef_v1.sqlite # Exon-capture reference database for Orthograph TENEB_ExonCapture_probes.fas # Exon-capture probe sequences 02_alignment: 556loci_332taxa_NT_v11_supermatrix.fas # M1 matrix, 556loci,332taxa 556loci_332taxa_NT_v11_partition.txt # partition file for the M1 matrix 556loci_332taxa_tip_mapping.csv # tip name mapping file for the M1 matrix 2030loci_95taxa_NT_v10_supermatrix.fas # M2 matrix, 2030loci,95taxa 2030loci_95taxa_NT_v10_partition.txt # partition file for the M2 matrix 2030loci_95taxa_tip_mapping.csv # tip name mapping file for the M2 matrix 2586loci_105taxa_NT_supermatrix.fas # M3 matrix, 2586loci,105taxa 2586loci_105taxa_NT_partition.txt # partition file for the M3 matrix 03_trees: ASTRAL # summary-coalescent trees from ASTRAL IQTREE # Maximum-likelihood trees from IQTREE MCMCTREE # MCMCTREE results 04_landmark: TENEB_bodyshape_v15_aligned.tps # aligned landmark coordinates TENEB_landmark_specimen_database.csv # database of specimens used for geometric morphometrics 05_macroevolution: ./BayesTraits/raw_data: # folder containing BayesTraits input data 556loci_201taxa_timetree_T1_{calibration scheme}_rescaled.nex # NEXUS-format dated phylogeny of 201 tips, calibrated using {calibration scheme}: fossilsetA_root1.7, fossilsetA_root2, fossilsetF_root1.7, fossilsetF_root2 backbone_201taxa_bodyshape_PC12.txt # PC1 and PC2 values of body shape data in tab-delimited format backbone_VarRates_control.txt # BayesTraits control file BayesTraits/results: # folder containing BayesTraits results BayesTraitsVR_T1_{calibration scheme}_201taxa_bodyshape_multiVar.Rdata # Multivariate BayesTraits results based on {calibration scheme}: fossilsetA_root1.7, fossilsetA_root2, fossilsetF_root1.7, fossilsetF_root2 BayesTraitsVR_T1_{calibration scheme}_201taxa_bodyshape_uniVar.Rdata # Univariate BayesTraits results based on {calibration scheme}: fossilsetA_root1.7, fossilsetA_root2, fossilsetF_root1.7, fossilsetF_root2 ./Convergence/raw_data: # folder containing SURFACE and l1ou input data 556loci_201taxa_timetree_T1_{calibration scheme}_rescaled.tre # NEWICK-format dated phylogeny of 201 tips, calibrated using {calibration scheme}: fossilsetA_root1.7, fossilsetA_root2, fossilsetF_root1.7, fossilsetF_root2 backbone_201taxa_bodyshape_PC12.csv # PC1 and PC2 values of body shape data in csv format ./Convergence/results: # folder containing SURFACE and l1ou results l1ou_T1_{calibration scheme}_201taxa_bodyshape_PC12_conv_AICc.RData # Convergent regimes estimated by l1ou based on {calibration scheme}: fossilsetA_root1.7, fossilsetA_root2, fossilsetF_root1.7, fossilsetF_root2 l1ou_T1_{calibration scheme}_201taxa_bodyshape_PC12_shift_AICc.RData # Regime shifts estimated by l1ou based on {calibration scheme}: fossilsetA_root1.7, fossilsetA_root2, fossilsetF_root1.7, fossilsetF_root2 surface_T1_{calibration scheme}_201taxa_bodyshape_PC12_fwd.RData # forward phase of SURFACE analyses based on {calibration scheme}: fossilsetA_root1.7, fossilsetA_root2, fossilsetF_root1.7, fossilsetF_root2 surface_T1_{calibration scheme}_201taxa_bodyshape_PC12_bwd.RData # backward phase of SURFACE analyses based on {calibration scheme}: fossilsetA_root1.7, fossilsetA_root2, fossilsetF_root1.7, fossilsetF_root2 06_scripts: ./Bioinformatics: # folder containing scripts for sequence data processing 1_trim_v4.0.sh # deduplicate and quality trim raw reads, an example command-line to run the script on clusters: sbatch -a 0-{num} 1_trim_v4.0.sh 2.0_spades_v2.0.sh # assemble trimmed reads using Spades, an example command-line to run the script on clusters: sbatch -a 0-{num} 2.0_spades_v2.0.sh 2.1_trinity_v2.0.sh # assemble trimmed reads using Trinity, an example command-line to run the script on clusters: sbatch -a 0-{num} 2.1_trinity_v2.0.sh 3_orthograph.sh # ortholog search using Orthograph, see the original tutorial at [https://github.com/mptrsen/Orthograph](https://github.com/mptrsen/Orthograph) 4_change_header.py # change headers of FASTA-format orthologs generated by Orthograph, an example command-line to run the script: python 4_change_header.py 5_alignment.sh # align sequences using mafft and pal2nal, an example command-line to run the script on clusters: sbatch 5_alignment.sh ./Macroevolution: # folder containing scripts for macroevolutionary analyses BayesTraits.R # script for processing BayeTraits results in R Convergence.R # script for surface and l1ou analyses in R DiscreteTraits.R # script for ancestral state reconstructions in R Morphospace.R # script for geometric morphometric analyses in R 07_extra_assemblies_ANIC: Five transcriptome assemblies with unpublished raw data