Identification of single-copy nuclear PCR targets for resolution of species-scale clades: a proof-of-concept using eupulmonate gastropods

To aid in the empirical evaluation of species hypotheses / concepts we present a strategy that uses NGS whole nuclear genome assemblies to identify novel single-copy universal PCR targets whose sequences discriminate species-scale clades. Our approach begins by identifying UCEs within partial Illumina genome assemblies across a strategically-chosen taxa set and culminates with experimental validation of appropriate single-copy nuclear DNA regions for PCR/Sanger sequencing. The highly diverse (~ 35 K species) group of eupulmonate gastropods was used as proof-of-concept. Among the ~ 24 K ultraconserved elements identified across 14 de novo and publicly-available genome assemblies spanning eupulmonate phylogeny, 61 informative universal PCR targets were ultimately identified. These allow for targeted sequence recovery from loci known to contain useful phylogenetic signal and permit efficient scaling to larger sample sizes, something that is immensely important when working with issues as complex as evolution and biodiversity.