Testing ultraconserved elements (UCEs) for phylogenetic inference across bivalves (Mollusca: Bivalvia)

Area of Science:

• Zoology
• Genomics
• Molecular Phylogenetics

Background:

• Bivalves are crucial for fisheries and cultural heritage, but their evolutionary relationships (phylogenetics) remain unclear due to conflicting data from different molecular methods.
• Existing genomic and transcriptomic approaches are costly and complex, limiting broad phylogenetic studies.

Purpose of the Study:

• To design and validate a novel ultraconserved elements (UCEs) probe set for efficient and cost-effective bivalve phylogenetics.
• To enable phylogenetic analysis using DNA from historical museum specimens, expanding the scope of bivalve evolutionary research.

Main Methods:

• Development and testing of a custom UCE probe set for the class Bivalvia.
• Capture of 1,513 UCE loci (263,800 bp total) across various bivalve species.
• Phylogenetic analyses using different data matrices and inference methods, including data from pre-1900 museum specimens.

Main Results:

• The UCE probe set successfully captured a substantial number of loci across Bivalvia.
• Phylogenetic analyses yielded robust results at multiple taxonomic levels, including within the Donacidae family.
• The probe set effectively retrieved UCEs from ancient DNA of historical museum specimens.

Conclusions:

• The developed UCE probe set is a valuable and novel resource for advancing bivalve phylogenetics.
• This method offers a cost-effective and accessible alternative to whole-genome or transcriptome sequencing for phylogenetic studies.
• The ability to analyze historical specimens opens new avenues for understanding bivalve evolutionary history.