Molecular phylogeny and biogeography of the aquatic dance fly subfamily Clinocerinae (Diptera: Empididae)
Bibliographic record
Abstract
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: marija.ivkovic@biol.pmf.hr 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
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How this classification was reachedexpand
Full frame machine prediction
Teacher imitationNot calibrated prevalence, not ground truth. Human validation pending. The Gemma side is a direct model label for every work in the frame, read from the title-only record. The Codex side is a classifier learned from the 10,348 direct Codex labels and calibrated to design-weighted sample rates; fields without enough sample support carry no Codex call. Candidate is the union of the two sides; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels.
Distilled classifier scores by category (both heads)
| Category | Codex | Gemma |
|---|---|---|
| Metaresearch | 0.002 | 0.011 |
| Meta-epidemiology (narrow) | 0.002 | 0.001 |
| Meta-epidemiology (broad) | 0.002 | 0.001 |
| Bibliometrics | 0.007 | 0.015 |
| Science and technology studies | 0.002 | 0.000 |
| Scholarly communication | 0.002 | 0.002 |
| Open science | 0.003 | 0.002 |
| Research integrity | 0.002 | 0.002 |
| Insufficient payload (model declined to judge) | 0.491 | 0.153 |
Machine scores (provisional)
The two teacher heads of the student model, read on this work. A score orders the frame for review; it never asserts a category, and the validation status ships verbatim with every row.
Baseline scores from an immature model (maturity gate not passed, 7 training rounds). Scores rank; they never assert a category.
score_only:v0-immature-baseline · verbatim from the scoring run: score_only means the number may rank works, and no category label ships from itClassification
machine, unvalidatedMachine predicted; a candidate call from one source (direct Gemma or distilled Codex), not a consensus.
How this classification was reached, model by model and score by score, is at the end of the page under "How this classification was reached".