To design or not to design? Comparison of beetle ultraconserved element probe set utility based on phylogenetic distance, breadth, and method of probe design

Abstract

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.

From museum drawer to tree: historical DNA phylogenomics clarifies the systematics of rare dung beetles (Coleoptera: Scarabaeinae) from museum collections

“…The 50p dataset contained 1,497 UCE loci with a mean of 79.97 parsimony-informative sites per locus (Table S4), and the 70p dataset contained 289 UCE loci with a mean of 60.54 parsimony-informative sites per locus (Table S5). The conspicuous disparity among unfiltered, 50p and 70p datasets is due to large proportion of missing data present in the genomes retrieved from GenBank, which mostly served as outgroup taxa in our study (Gustafson et al (2023) Table S2 and Figs. S1-S5).…”

“…We used the tailored UCE Scarabaeinae probe-set Scarab 3Kv1 (Gustafson et al, 2023), a genome reduction approach for beetle genomes combining the Coleoptera 1.1Kv1 probeset (Faircloth, 2017) and Scarabaeinae-specific targeted loci (Gustafson et al, 2023), to generate sequence data for reconstruction of phylogenies (Fig. 1 and Figs.…”

“…UCE loci were then extracted from the sequenced data. We harvested UCE loci from the available whole beetle genomes on GenBank (Gustafson et al, 2023) (Table S1) using Phyluce and combined them with our newly sequenced data. The UCE loci were aligned in MAFFT (Katoh and Standley, 2013), using the default Phyluce settings, and the command -no-trim to provide internal trimming, as recommended for analysis of divergences over 50 million years old (Faircloth, 2016).…”

“…Finally, nine poorly-known taxa belonging to the endemic Madagascan genus Helictopleurus were represented by specimens from MZHF collected between 2003–2010. Our archival DNA extraction protocol yielded high quality DNA for successful UCE-sequencing using the recently designed probe set for scarab beetles (Gustafson et al, 2023). To elucidate the phylogenetic position of the selected enigmatic species, we expanded our taxon sampling by sequencing additional alcohol-preserved dung beetles using a standard DNA extraction protocol with a commercial kit.…”

Dung beetle tribal classification (Coleoptera: Scarabaeidae: Scarabaeinae): progress, problems, and prospects

“…Therefore, it is, perhaps, time to shift to phylogenomic methods that are less-demanding in terms of quality, such as target-enrichment procedures that focus on Ultraconserved Elements (UCEs), which are highly conserved regions within the genome that are shared among evolutionary distant taxa (Faircloth et al 2012, Faircloth 2017). In particular, 2 new UCEs probe sets have been recently designed for the subfamily Scarabaeinae (Scarabaeidae) and superfamily Hydrophiloidea (Gustafson et al 2023). Compared to similar methods, such as Anchored Hybrid Enrichment, BaitFisher (Mayer et al 2016), and Hyb-Seq (Weitemier et al 2014), UCEs have proven useful in resolving phylogenies at both shallow and deep phylogenetic scales in several groups of Coleoptera, including Adephaga (Baca et al 2017, 2021, Gustafson et al 2020), Elmidae (Kobayashi et al 2021), Carabidae (Sota et al 2022), Curculionidae (Van Dam et al 2017) and Scirtidae (Bradford et al 2022) although they have not yet been applied in dung beetles.…”