Tailoring ultraconserved element (UCE) probe set design to focal taxa has been demonstrated to improve locus recovery and phylogenomic inference. However, beyond conducting expensive in vitro testing, it remains unclear how best to determine whether an existing UCE probe set is likely to suffice for phylogenomic inference, or if tailored probe design will be desirable. Here we investigate the utility of eight different UCE probe sets for the in silico phylogenomic inference of scarabaeoid beetles. Probe sets tested differed in terms of (1) how phylogenetically distant from Scarabaeoidea taxa those used during probe design are, (2) breadth of phylogenetic inference probe set was designed for, and (3) method of probe design. As part of this study, two new UCE probe sets are produced for the beetle family Scarabaeidae and superfamily Hydrophiloidea. We find that, predictably, probe set utility decreases with increasing phylogenetic distance of design taxa from focal taxa, as well as with narrower breadth of phylogenetic inference probes were designed for. We also confirm previous findings regarding ways to optimize UCE probe design. Finally, we make suggestions regarding assessment of need for de novo probe design and reinforce previous proposed methods for maximizing UCE probe design to improve phylogenomic inference.

Tailoring ultraconserved element (UCE) probe set design to focal taxa has been demonstrated to improve locus recovery and phylogenomic inference. However, beyond conducting expensive in vitro testing, it remains unclear how best to determine whether an existing UCE probe set is likely to suffice for phylogenomic inference or whether tailored probe design will be desirable. Here we investigate the utility of 8 different UCE probe sets for the in silico phylogenomic inference of scarabaeoid beetles. Probe sets tested differed in terms of (i) how phylogenetically distant from Scarabaeoidea taxa those used during probe design are, (ii) breadth of phylogenetic inference probe set was designed for, and (iii) method of probe design. As part of this study, 2 new UCE probe sets are produced for the beetle family Scarabaeidae and superfamily Hydrophiloidea. We confirm that probe set utility decreases with increasing phylogenetic distance from target taxa. In addition, narrowing the phylogenetic breadth of probe design decreases the phylogenetic capture range. We also confirm previous findings regarding ways to optimize UCE probe design. Finally, we make suggestions regarding assessment of need for de novo probe design.

The Neotropical water scavenger beetle genus Chasmogenus Sharp, 1882 is a diverse lineage with 34 described species. Here, three new species from the southwestern margin of the Guiana Shield are described using an integrative approach combining adult morphology and molecular data: Chasmogenus clinatus sp. n. (Brazil: Amazonas, Venezuela: Amazonas), C. gironae sp. n. (Venezuela: Amazonas), and C. inpa sp. n. (Brazil: Amazonas). Examination of the male genitalia is essential for confident identifications and thus unassociated females may prove extremely difficult to identify. New distributional records in Brazil for C. acuminatus Smith & Short, 2020 are provided as well as habitus images of newly described species and an updated key to the species from Venezuela, Suriname, Guyana, French Guiana and northern Brazil.