Testing ultra-conserved elements for phylogenetic inference across Bivalvia (Mollusca)

Bivalves are among the Mollusca groups that have rapidly joined the phylogenomic movement. While transcriptomes provide dense gene coverage, recent advances in ultraconserved elements (UCEs) have expanded the scope of genomic research. This paper presents the development and validation of a UCE probe set for Bivalvia, consisting of 19,588 baits, and capturing a total of 1,513 UCE loci. In the in vitro validation, the UCEs were extracted from 94 samples including species collected in the last 25 years, DNA already extracted in 2008, and museum species up to 1872. Phylogenetic analyses of both all bivalves and specifically the family Donacidae show the usefulness of this UCE probe set in resolving relationships between species and genera within a bivalve family, and how it allowed the inclusion of old museum samples that were not amplified in the previous Sanger-based study.