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 still displayed ancestral foraging specialties. These findings highlight that, in Cataglyphis, ecological diversification happened before the genus geographically spread into newly arisen suitable habitats, resulting in a clade composed of ecologically homogeneous subclades.

Methods

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-identity and min-coverage settings were 80. We aligned each UCE locus using MAFFT v. 7.130b and the default algorithm setting in PHYLUCE (FFT-NS-i). We tested different trimming strategies: (i) no trimming, (ii) edge trimming, and (iii) trimming internal and external alignment regions using GBLOCKS, implemented with reduced stringency parameters (b1:0.5, b2:0.5, b3:12, b4:7). Based on the descriptive statistics generated by PHYLUCE and AMAS, we decided to use the GBLOCKS strategy in further analyses because it achieved a good compromise between the number of informative sites and the percentage of missing data. We then concatenated all the loci to form a supermatrix and filtered the alignments for taxon occupancy, requiring the loci to be found in 0, 50, 75, 85, 90, 95, and 100% of the taxon. For each of the seven supermatrices, we generated descriptive statistics using PHYLUCE and AMAS. For further analyses, we decided to use the locus set filtered for 75% taxon occupancy because it achieved a good compromise between the number of informative sites and the percentage of missing data. The resulting matrix contained 2,294 loci (mean length = 1,159 bp), 560,008 informative sites, and a gaps/missing data level of 18.5%.