Ancient gene linkages and ultraconserved elements disentangle Acari interrelationships.

Area of Science:

• Genomics
• Evolutionary Biology
• Arachnology

Background:

• The evolutionary history of Acari, encompassing mites (Acariformes) and ticks/parasitic mites (Parasitiformes), remains a subject of extensive debate.
• Resolving higher-level relationships within Acari is crucial for understanding arachnid evolution.

Purpose of the Study:

• To elucidate the higher-level phylogenetic relationships among major Acari groups.
• To investigate the monophyly of Acariformes and Parasitiformes using genomic data.
• To explore the utility of rare genomic changes, specifically ancestral linkage groups (AcarLGs), in resolving deep evolutionary nodes.

Main Methods:

• Interrogation of 90 Arachnida genomes using a custom Chelicerata-wide ultraconserved elements bait set.
• Analysis of datasets with varying locus occupancy thresholds and partitioning schemes.
• Exploration of 27 Acari-specific ancestral linkage groups (AcarLGs) to identify rare genomic changes and syntenic patterns.

Main Results:

• Genomic analyses strongly supported the monophyly of both Acariformes and Parasitiformes, including their major subgroups.
• Acari-specific ancestral linkage groups (AcarLGs) revealed distinct chromosomal fusion patterns, providing robust phylogenetic signals for deeper nodes.
• Syntenic signal was observed to be less clear in miniaturized parasitic taxa, such as Tetranychus and Eriophyidae.

Conclusions:

• The study confirms the monophyly of Acariformes and Parasitiformes, settling long-standing debates in Acari systematics.
• Chromosomal fusion patterns identified through AcarLGs offer a powerful phylogenetic character for resolving deep evolutionary relationships across diverse karyotypes.
• Synteny analysis holds significant potential for overcoming limitations in molecular phylogenetics, especially in resolving relationships among miniaturized or highly diverged taxa.