Phylogenomics of the leaf-footed bug subfamily Coreinae (Hemiptera: Coreidae): applicability of ultraconserved elements at shallower depths

Abstract

24Baits targeting invertebrate ultraconserved elements (UCEs) are becoming more common 25 for phylogenetic studies. Recent studies have shown that invertebrate UCEs typically encode 26 proteinsand thus, are functionally different from more conserved vertebrate UCEs -can 27 resolve deep divergences (e.g., superorder to family ranks). However, the ability of the 28 invertebrate UCE baits to robustly resolve relationships at shallower phylogenetic scales (i.e., 29 tribes and congeners) has been generally limited to Coleoptera and Hymenoptera. Here, we 30 assessed the ability of a recently designed Hemiptera UCE bait set to reconstruct more recent 31 phylogenetic relationships in the largest leaf-footed bug subfamily, the Coreinae (Hemiptera: 32Coreidae), using a taxon-rich sample representing 21 of the 32 coreine tribes. Many well-33 supported, novel relationships were congruent in maximum likelihood and summary coalescent 34 analyses. We also found evidence for the para-and polyphyly of several tribes and genera of 35Coreinae, as well as the subfamilies Coreinae and Meropachyinae. Our study, along with other 36 recent UCE studies, provides evidence that UCEs can produce robust and novel phylogenetic 37 hypotheses at various scales in invertebrates. Additionally, we used different DNA extraction 38 and target enrichment protocols and recovered more UCE data using a touch-down hybridization 39 approach. 40 41

Extracting ‘legacy loci’ from an invertebrate sequence capture data set

“…(2019). We then retrieved raw sequence reads from 148 additional taxa published in recent sequence capture studies (Emberts et al., 2020; Forthman et al., 2019, 2020).…”

“…(2019), while another 13 taxa were subjected to protocols in Forthman et al. (2020). The remaining taxa were subjected to the same DNA extraction and library construction protocols in Forthman et al.…”

“…The remaining taxa were subjected to the same DNA extraction and library construction protocols in Forthman et al. (2020), but the touchdown sequence capture protocol was modified in the following ways: (a) bait–target hybridization was performed at 65°C for 12 hr, followed by 62°C for 12 hr and then 60°C for 12 hr, (b) bait‐target products were washed at 60°C, and (c) enriched libraries were amplified for 16–17 cycles before final pooling and sequenced at the University of Florida's Interdisciplinary Center for Biotechnology Research (ICBR) on a single Illumina HiSeq 3000 lane (2 × 100 run). Newly generated sequence reads were demultiplexed by ICBR.…”

“…For the newly generated sequence reads and those retrieved from Forthman et al. (2019, 2020) and Emberts et al. (2020), adapters were trimmed from sequence reads with illumiprocessor (Bolger et al., 2014; Faircloth et al., 2013).…”

“…Here, we integrated Forthman et al. 's (2020) UCE sequence capture data from 124 taxa with legacy locus data obtained from two sources (i.e. those extracted from our focal taxa and those retrieved from NCBI) to test the most recent phylogenetic hypothesis of Coreidae based on UCEs (Forthman et al., 2020).…”