Molluscs are the second most diverse animal phylum and heterobranch gastropods present ~44,000 species. These comprise fascinating creatures with a huge morphological and ecological disparity. Such great diversity comes with even larger phylogenetic uncertainty and many taxa have been largely neglected in molecular assessments. Genomic tools have provided resolution to deep cladogenic events but generating large numbers of transcriptomes/genomes is expensive and usually requires fresh material. Here we leverage a target enrichment approach to design and synthesize a probe set based on available genomes and transcriptomes across Heterobranchia. Our probe set contains 57,606 70mer baits and targets a total of 2,259 ultra-conserved elements (UCEs). Post-sequencing capture efficiency was tested against 31 marine heterobranchs from major groups, including Acochlidia, Acteonoidea, Aplysiida, Cephalaspidea, Pleurobranchida, Pteropoda, Runcinida, Sacoglossa, and Umbraculida. The combined Trinity and Velvet assemblies recovered up to 2,211 UCEs in Tectipleura and up to 1,978 in Nudipleura, the most distantly related taxon to our core study group. Total alignment length was 525,599 bp and contained 52% informative sites and 21% missing data. Maximum-likelihood and Bayesian inference approaches recovered the monophyly of all orders tested as well as the larger clades Nudipleura, Panpulmonata, and Euopisthobranchia. The successful enrichment of diversely preserved material and DNA concentrations demonstrate the polyvalent nature of UCEs, and the universality of the probe set designed. We believe this probe set will enable multiple, interesting lines of research, that will benefit from an inexpensive and largely informative tool that will, additionally, benefit from the access to museum collections to gather genomic data.

Sampling impediments and paucity of suitable material for molecular analyses have precluded the study of speciation and radiation of deep-sea species in Antarctic ecosystems. This knowledge may serve to establish the framework for evaluating future anthropogenic alterations, particularly in a highly susceptible region like Antarctica. Here, we analyze genome-wide single nucleotide polymorphisms (SNPs) obtained from double digestion restriction site-associated DNA sequencing (ddRADseq) for most species in the family Antarctophilinidae and throughout the geographic distribution and bathymetric ranges of these marine snails. We also reevaluate the fossil record associated with this taxon. In light of the new data provided we discuss relevant diversification processes and biogeographic and bathymetric affinities. Novel approaches in finding genetic distinctive lineages, including unsupervised machine learning variational autoencoder (VAE) plots, are further used to establish species hypothesis frameworks aided by available morphological data. In this sense, two new species and a complex of cryptic species are here identified, suggesting allopatric speciation connected to geographic or bathymetric isolation. We further, observe that the shallow waters around the Scotia Arc and on the continental shelf in the Weddell Sea present high endemism and diversity. In contrast, likely due to the glacial pressure during the Cenozoic, a deep-sea group with fewer species emerged expanding over great areas in the South-Atlantic Antarctic Ridge. Our study exemplifies how diachronic paleoclimatic and current environmental factors shaped Antarctic communities both at the shallow and deep-sea levels, promoting Antarctica as the center of origin for numerous taxa such as gastropod mollusks.