REAGENT or RESOURCE	SOURCE	IDENTIFIER
Deposited data
SPAdes assembly contigs, concatenated UCE matrices, tree files, and the UCE bait sequence file	This study	Dryad: https://doi.org/10.5061/dryad.sbcc2frck
Raw Illumina reads – deposited to NCBI	This study	NCBI BioProject: PRJNA1087578 and Data S1
Experimental models: Organisms/strains
Cataglyphis species	This study	Data S1
Software and algorithms
PHYLUCE pipeline	Faircloth	https://phyluce.readthedocs.io/en/latest/
AMAS	Borowiec	https://github.com/marekborowiec/AMAS
IQ-TREE v. 2.0	Minh et al.31	http://www.iqtree.org/
SWSC-EN	Tagliacollo and Lanfear54	https://github.com/Tagliacollo/PFinderUCE-SWSC-EN
ASTRAL-III	Zhang et al.28	https://github.com/smirarab/ASTRAL
Newick utilities	Junier and Zdobnov55	https://github.com/tjunier/newick_utils
Clocklikeness script	Borowiec et al.34	https://github.com/marekborowiec/metazoan_phylogenomics
BEAST v. 2.6.2	Bouckaert et al.33	https://www.beast2.org/
Infomap Bioregions	Edler et al.40	https://www.mapequation.org/bioregions/