Target-capture probes for phylogenomics of the Caenogastropoda.

Abstract

Target-capture approaches have facilitated a rapid growth in the field of phylogenomics but few probe sets exist for mollusks, an exceptionally rich phylum with unparalleled ecological and morphological diversity. We designed and tested the first universal probe set using Phyluce to capture ultraconserved elements (UCEs) and exon loci from the Subclass Caenogastropoda - one of six major lineages of gastropods. The probe set consists of 29,441 probes designed to target 1,142 UCE loci and 1,933 exon loci (3,075 total). In silico analyses of our probe set yielded an average of 2,110 loci from genomes and 1,389 loci from transcriptomes of diverse caenogastropods, from which an average of 1,669 and 849 loci were retained respectively after screening to remove those that matched multiple contigs. Phylogenetic analyses of the loci extracted from transcriptomes produced well-supported trees very similar to those published based on transcriptomic analyses. Phylogenetic relationships estimated from loci extracted from genomes recover similar phylogenetic relationships, and indicate that the loci targeted with this probe set are informative for resolving deep phylogenetic relationships. An in vitro analysis of the probe set with the Epitoniidae, a diverse caenogastropod family of uncertain affinity and with poorly resolved evolutionary relationships, recovered a total of 2,850 loci. Although preliminary, the analysis of loci captured by our probe set for a small number of epitoniid taxa produced a well-resolved tree indicating that this probe set is also able to resolve relationships at shallower hierarchical scales. Together, the in silico and in vitro analyses indicate that target-capture enrichment with this probe set is a useful tool for reconstructing phylogenetic relationships across taxonomic levels and evolutionary time scales.