Ultraconserved element data from Integrating morphology with phylogenomics to describe four Siculo-Maltese endemic Temnothorax species (Hymenoptera, Formicidae)

Temnothorax (Myrmicinae, Crematogastrini) is one of the most diverse Holarctic ant genera, and new taxonomic advancements are still frequent worldwide. The Mediterranean region, a global biodiversity hotspot characterized by a complex geographic history, is home to a substantial portion of its described diversity. Sicily is the region’s largest island and, as ongoing investigations are revealing, it is inhabited by a long-overlooked but highly diverse ant fauna that combines multiple biogeographic influences. We combined qualitative and quantitative morphology of multiple castes with phylogenomic analysis based on ultra-conserved elements (UCEs) to describe four Temnothorax species endemic to Sicily and the neighboring Maltese Islands (Sicilian Channel). Three of these species, T. marae sp. nov., T. poldii sp. nov. and T. vivianoi sp. nov., are new to science, while a redescription clarifies the identity of T. lagrecai (Baroni Urbani, 1964). These descriptions provide an opportunity to ..., DNA was extracted nondestructively from adult worker ants using a DNeasy Blood & Tissue Kit (Qiagen, Inc.) following the manufacturer’s protocols. Up to 50 ng of DNA was used as input, sheared to a target fragment size of 400–600 bp into a genomic DNA library preparation protocol for targeted enrichment of ultraconserved elements (UCEs) following Faircloth et al. (2015) as modified by Branstetter et al. (2017) using a unique combination of iTru barcoding adapters for each sample (Glenn et al. 2019; see Supplementary Table S2 for a list of the adapters used). Enrichments were performed on pooled libraries using the custom version of the Hym 2.5Kv2A ant-specific RNA probes (Branstetter et al. 2017; ArborBiosciences, Ann Arbor, MI), which target 2524 UCE loci in the Formicidae. The library enrichment procedures for the probe kit were followed, except that the RNA probe concentration was reduced to 0.1X (note that this step is only necessary for the custom kit; the currently available c..., , # Ultraconserved Element data from Integrating morphology with phylogenomics to describe four Siculo-Maltese endemic Temnothorax species (Hymenoptera, Formicidae)

## Description of the data and file structure

The file contains three directories:

* 'input_alignment' contains the alignment used for both analyses (partition clustering and tree inference).
* 'IQTREE_partition_clustering' contains the input partition file (from the SWSC-EN analysis) and the output of the clustering analysis.
* 'IQTREE_tree_inference' contains the input partition file from the clustering analysis and the output from tree inference in IQTREE.