Ecological diversification preceded geographical expansion during the evolutionary radiation of Cataglyphis desert ants

Biological diversity often arises as organisms adapt to new ecological conditions (i.e. ecological opportunities) or colonise suitable areas (i.e. spatial opportunities). Cases of geographical expansion followed by local ecological divergence are well described; they result in clades comprising ecologically heterogeneous subclades. In contrast, nothing is known about evolutionary radiation events in which ecological opportunities preceded spatial spread. Here, we show that the desert ant genus Cataglyphis likely originated in open grassland habitats in the Middle East ~18 million years ago and became a taxon of diverse species specialising in prey of different masses. Around 9 million years ago, southern Europe and northern Africa experienced aridification and were colonised by Cataglyphis, which was preadapted to the harsh environmental conditions. The result was the rapid accumulation of species, and the appearance of local assemblages containing species from different lineages that s...,
We employed ultra-conserved elements (UCE) phylogenomics. We sent tissue samples to Rapid Genomics, Florida, USA, where the DNA was extracted. The genomic libraries were then prepared and enriched using 31,829 baits targeting 2,590 UCE loci conserved across ants (Hymenoptera 2.5Kv2). Sequencing was performed utilising an Illumina NovaSeq 2x150 system. We used one to five individuals per species.
We cleaned and processed the resulting reads using PHYLUCE software (v. 1.7.1.). We trimmed raw reads for adapter contamination using Illumiprocessor v. 2.0, which incorporates Trimmomatic . Trimmed reads were assembled de novo into contigs using SPAdes.
Next, we added assemblies for 11 outgroup species that were obtained from previous studies. To identify and extract UCE contigs from the bulk set of contigs for all 47 species, we employed a PHYLUCE program (match_contigs_to_probes) that uses Lastz v. 1.0 to match probe sequences to contig sequences and to create a database of hits. Our min-ide..., , # UCE sequencing Cataglyphis ants

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This dataset contents files resulting from the analysis of the sequencing of ultra-conserved elements (UCE) in 36 Cataglyphis ants (as well as 11 outgroups that were sequenced by previous studies, namely Formica fuscocinerea, Iberoformica subrufa, Polyergus vinosus, Proformica mongolica, Rossomyrmex minuchae, Nylanderia terricola, Paratrechina longicornis, Lasius arizonicus, Myrmecocystus pyramicus, Myrmelachista joycei, Gnamptogenys simulans).

We have submitted SPAdes assembly contigs for 47 species (genus_species_contigs.fasta), a concatenated UCE matrix (UCE_conca_75p.charsets and UCE_conca_75p.phylip), tree files (75p_method.treefile), and a UCE bait sequence file (hymenoptera-v2-PRINCIPAL-bait-set.fasta.txt).

All datafiles can be viewed in a standard text editor. 

## Description of the data and file structure

### SPAdes assembly contigs

The files 'genus_species_contigs.fasta' contain SPAdes assembly contigs. First, 36 Cataglyphis samples...