Additional file 1: of Genome sequencing of Rhinorhipus Lawrence exposes an early branch of the Coleoptera
Creators: name: Kusy, Dominik
name: Motyka, Michal
name: Andujar, Carmelo
name: Bocek, Matej
name: Masek, Michal
name: Sklenarova, Katerina
name: Kokas, Filip
name: Bocakova, Milada
name: Vogler, Alfried
name: Bocak, Ladislav
Publisher: name: figshare
Year: 2018
Subjects: subject: Microbiology
subject: FOS: Biological sciences
subject: FOS: Biological sciences
subject: Cell Biology
subject: Genetics
subject: Molecular Biology
subject: Evolutionary Biology
subject: 59999 Environmental Sciences not elsewhere classified
subject: FOS: Earth and related environmental sciences
subject: FOS: Earth and related environmental sciences
subject: Ecology
subject: 69999 Biological Sciences not elsewhere classified
subject: Cancer
subject: Inorganic Chemistry
subject: FOS: Chemical sciences
subject: FOS: Chemical sciences
subject: 110309 Infectious Diseases
subject: FOS: Health sciences
subject: FOS: Health sciences
subject: Plant Biology

description: Text the morphology-based classifications of Rhinorhipidae. Table S1. The list of taxa included in the LSU rRNA, SSU rRNA, rrnL, and cox1 mitochondrial DNA dataset with GenBank accession and voucher ID numbers. Table S2. The list of taxa included in the mitogenomic analysis with GenBank accession numbers. Table S3. The list of taxa included in the LSU rRNA, SSU rRNA, and six nuclear protein coding genes. Table S4. The list of taxa included in the 65-gene dataset. Table S5. The list of markers in the 95-gene dataset with information on multi-copy genes. Table S6. The list of taxa included in the phylotranscriptomic dataset and the number of sequences available for each taxon. Table S7. Overview of official gene sets of six reference species used for transcript ortholog assessment, including the source, version and number of genes. Table S8. Gene descriptions for the 4220 ortholog groups (OGs) as present in. OrthoDB 9.1. Each OG contains one gene of each of the 6 reference species. Table S9. Success of transcript assignment to ortholog groups (OGs) of Rhinorhipus, published beetles transcriptomes and genomes. Table S10. The models and partition selections recovered with ModelFinder for the maximum likelihood analysis of the LSU rRNA, SSU rRNA, rrnL mtDNA, and cox1 mtDNA dataset. Table S11. Identification of the best partition scheme and models for the mitochondrial DNA dataset. Table S12. The LSU rRNA, SSU rRNA, and six nuclear protein coding genes dataset: characteristics, partition scheme and models of DNA evolution. Table S13. The transcriptomic supermatrix 3: partition scheme and models of DNA evolution (amino acid dataset, 4220 orthologs). Table S14. The transcriptomic supermatrix 4: partition scheme and models of DNA evolution (amino acid dataset, 943 orthologs). Figure S1. Maximum likelihood tree for Rhinorhipus, 517 Elateriformia and 46 outgroups recovered from the LSU rRNA, SSU rRNA, rrnL mtDNA and cox1 mtDNA dataset. Figure S2. Maximum likelihood tree for 83 species of beetles recovered from 15 mitochondrial genes. Figure S3. Maximum likelihood tree for 139 species of beetles recovered from the. LSU rRNA, SSU rRNA and six nuclear protein coding genes. Figure S4. Bayesian tree for 139 species of beetles recovered from the LSU rRNA, SSU rRNA and six nuclear protein coding genes. Figure S5. Maximum likelihood (RaxML) tree for 372 species of beetles and for outgroups recovered from the 66-gene amino acid dataset. Figure S6. Maximum likelihood (iQ) tree for 372 species of beetles and for outgroups recovered from the 66-gene amino acid dataset. Figure S7. Maximum likelihood (iQ) tree for 372 species of beetles and for outgroups recovered from the 66-gene nucleotide dataset. Figure S8. Tree network obtained from the separate maximum likelihood analyses of 968 orthologs 590. Figure S9. Dated phylogenetic tree of beetle relationships inferred from the Bayesian analysis of mitogenomic dataset using maximum likelihood topology. Figure S10. Dated phylogenetic tree of beetle relationships inferred from the Bayesian analysis of mitogenomic dataset using Bayesian topology. Figure S11. Dated phylogenetic tree of beetle relationships inferred from the Bayesian analysis of eight-gene dataset using constrained Bayesian topology and two calibration points (A, B) and verified by mapping of nineteen fossil records reported by Toussaint et al. (2016). The bottom diagram shows accumulation of the number of extant beetle families (red dots on the tree). Time line relates the tree to extinction events and geologic periods. Red bars designate the origin of Rhinorhipidae. (PDF 30160 kb)