Phylogenomics illuminates the complex evolutionary history of Bibionomorpha (Diptera)

Bibionomorpha is a large and diverse dipteran infraorder, of which its composition and family-level relationships have long been debated. In this study, we constructed a phylogenomic tree of Bibionomorpha using an extensive dataset of transcriptomic, genomic, and anchored hybrid enrichment data. To further investigate the evolutionary timeline of the group, we also generated a fossil-calibrated timetree using data-driven calibration priors. Different data types and models were utilized to produce a robust backbone phylogeny. Bibionomorpha, comprising Bibionoidea, Sciaroidea, Anisopodoidea, and Scatopsoidea, is recovered as the sister group to Brachycera. Axymyiidae and Perissommatidae, which have been considered part of Bibionomorpha by some authorities, are instead recovered as sister to the Bibionomorpha + Brachycera. We discuss recalcitrant nodes within the infraorder, particularly regarding the placements of Bolitophilidae and Cecidomyiidae. Phylogenetic network analysis suggests a ..., , # Data from: Phylogenomics illuminates the complex evolutionary history of Bibionomorpha (Diptera)

Dataset DOI: [10.5061/dryad.vq83bk472](https://doi.org/10.5061/dryad.vq83bk472)

### Description of the data and file structure

Sequence assemblies, alignments, tree files, and log files accompanying the paper: \"Phylogenomics illuminate complex evolutionary history of Bibionomorpha\".

#### **Files and variables**

##### **File: transcriptome_assemblies.zip**

**Description:** Collection of transcriptome assemblies generated in the current study.

We used transcriptomes sequenced as part of the 1K Insect Transcriptome Evolution (1KITE) Project (Misof et al., 2014) together with the publicly available transcriptome and genome sequences from GenBank. 1KITE transcriptome samples were collected in RNAlater and were sequenced at BGI (Beijing Genomic Institute, China) with the Illumina HiSeq 2000 (Illumina, San Diego, CA, USA) platform, following the protocol of Misof et al. (2014) and Peters e..., ,