Brooding Phylogenomics: Target-Capture Probe Sets for the Analysis of Ultraconserved Elements in the Peracarida

Area of Science:

• Genomics
• Evolutionary Biology
• Crustacean Research

Background:

• Target capture sequencing using ultraconserved elements (UCEs) is effective for phylogenetic studies in many taxa.
• Genomic data for diverse crustacean groups, particularly Peracarida (Amphipoda, Isopoda), remain limited despite research intensity.

Purpose of the Study:

• To develop and validate generalized probe sets for UCE target capture in Amphipoda and Isopoda.
• To enhance phylogenomic analyses and resolve evolutionary relationships within the Peracarida.

Main Methods:

• Design of probe sets targeting ~10,000 UCE loci for Peracarida.
• In silico analysis of probe set performance and locus recovery.
• In vitro target capture sequencing and phylogenetic analysis of selected amphipod and isopod families.

Main Results:

• In silico analysis recovered an average of 5087 loci, with 4633 retained post-filtering.
• In vitro analysis yielded up to 4864 unique loci, averaging 1897 loci per taxon, an order-of-magnitude increase over previous methods.
• Phylogenetic analyses produced well-supported trees, resolving relationships at both deep and shallow taxonomic levels within Peracarida.

Conclusions:

• The developed UCE probe sets are highly effective for phylogenomic research in Peracarida.
• These tools significantly improve the scale and resolution of evolutionary studies for Amphipoda and Isopoda.
• Further application of target enrichment will clarify poorly understood aspects of Peracarida evolutionary history.