Phylogenetic groups and ASVs recovered by COI
For the 42 sample libraries, MiSeq sequencing generated a total of 11,639,999 paired reads. We obtained from 108,583 to 419,903 reads in each direction by each sample. Of these, from 39,484 to 178,720 sequences remained after quality filtering (totalling 4,990,334). After read merging and sequence filtering to a length of 418 bp, each sample comprised from 33,609 to 155,634 sequences (totalling 4,305,390) remained. Taxonomic assignments with usearch showed high similarity for a wide range of arthropod species (Figure 2a). The 4,305,390 sequences included 1,277 ASVs (unique variants), divided in 385 ASVs in Diptera, 270 in Collembola, 155 in Arachnida, 136 in Coleoptera, 133 in Hymenoptera, 116 in Hemiptera, 51 in Myriapods, and 31 in Lepidoptera (Figure 2b). The number of lineages decreased while increasing the hierarchical clustering (Table S1). The GMYC threshold value obtained was 0.9% in Diptera, 2.9% in Collembola, 1.3% in Arachnida, 0.7% in Coleoptera, 1% in Hymenoptera, 1.8% in Hemiptera, 1.5% in Myriapoda, and 0.3% in Lepidoptera (Table S1).