Molecular phylogeny and biogeography of the aquatic dance fly subfamily Clinocerinae (Diptera: Empididae)

Supplementary Data for: Molecular phylogeny and biogeography of the aquatic dance fly subfamily Clinocerinae (Diptera: Empididae) Tanja Vojvoda Zeljko1, Martina Pavlek1, Emma Wahlberg2, Bradley J. Sinclair3, Marija Ivković4,* 1Ruđer Bošković Institute, Bijenička cesta 54, Zagreb, Croatia; 2Department of Zoology, Swedish Museum of Natural History, Stockholm, Sweden; 3Canadian National Collection of Insects and Canadian Food Inspection Agency, Ottawa, Canada; 4Division of Zoology, Department of Biology, Faculty of Science, University of Zagreb, Zagreb, Croatia *Correspondence: Marija Ivković, Division of Zoology, Department of Biology, Faculty of Science, University of Zagreb, Horvatovac 102A, 10000 Zagreb, Croatia. E-mail: [e-mail] This dataset is provided to enable replication of the phylogenetic analysis presented in the research article “Molecular phylogeny and biogeography of the aquatic dance fly subfamily Clinocerinae (Diptera: Empididae)” 1. Content and Description for the files used in the maximum – likelihood analysis: AlignmentFile.phy: This file contains the concatenated nucleotide sequences used in the study. Command_IqTree.txt: A text file detailing the commands executed in IQ-TREE for reproducing the phylogenetic analysis. Input_For_Partitions.txt: Contains information used to define partitions in the phylogenetic analysis, corresponding to different codon positions. Note.txt: Supplementary comments regarding the analysis or dataset. Partitions.txt.best_scheme.nex: Nexus file containing the best partitioning scheme as determined by ModelFinder within IQ-TREE, specifying how the dataset was divided into subsets for phylogenetic analysis. Partitions.txt.best_scheme.nex.best_model.nex: Nexus file detailing the best-fit evolutionary model for each partition identified by ModelFinder. Partitions.txt.best_scheme.nex.log: Log file documenting the progress and results of the IQ-TREE execution. Partitions.txt.best_scheme.nex.treefile: The final tree file produced by IQ-TREE, representing the best-scoring maximum likelihood phylogenetic tree. 2. Content and Description for the files used in the Bayesian inference analysis: Clinocer_alignm.nex - This file contains the concatenated nucleotide alignment used for Bayesian phylogenetic analysis with MrBayes. The file can be used to load it into MrBayes to initiate the Bayesian inference analysis. MrBayesRun0.pbs – a PBS script used to submit MrBayes analysis job to a high-performance computing cluster using the PBS queuing system. It includes a simple command for loading necessary modules, executing MrBayes, and specifying computational resources. Clinocer_alignm.con.tre - The final tree file produced by MrBayes