Ancient gene linkages and ultraconserved elements disentangle Acari interrelationships

The interrelationships among Acari groups, Acariformes (mites) and Parasitiformes (ticks and parasitic mites) have been debated for long. We interrogated 90 genomes of Arachnida through a customized Chelicerata-wide ultraconserved elements bait set to resolve higher-level relationships of these two orders, including the first genome of Opilioacaridae, the putative sister group to the remaining Parasitiformes. Datasets with variable locus occupancy thresholds and partitioning schemes supported the monophyly of Acariformes and Parasitiformes, including their major subgroups. Exploration for rare genomic changes as potential character systems was done using a custom 27 Acari-specific ancestral linkage group (AcarLGs). AcarLGs revealed distinct chromosomal fusion patterns within subsets of both orders, indicating robust signal at deeper nodes, supporting their respective monophyly. Syntenic signal is blurred in miniaturized parasitic taxa (e.g., <i>Tetranychus</i>, Eriophyidae). We discuss the strong potential of synteny as a phylogenetic character to overcome limitations posed by molecular phylogenies at deeper nodes across karyotypic diversity.