A deeper meaning for shallow‐level phylogenomic studies: nested anchored hybrid enrichment offers great promise for resolving the tiger moth tree of life (Lepidoptera: Erebidae: Arctiinae)

Abstract

Anchored hybrid enrichment (AHE) has emerged as a powerful tool for uncovering the evolutionary relationships within many taxonomic groups. AHE probe sets have been developed for a variety of insect groups, though none have yet been shown to be capable of simultaneously resolving deep and very shallow (e.g., intraspecific) divergences. In this study, we present NOC1, a new AHE probe set (730 loci) for Lepidoptera specialized for tiger moths and assess its ability to deliver phylogenetic utility at all taxonomic levels. We test the NOC1 probe set with 142 individuals from 116 species sampled from all the major lineages of Arctiinae (Erebidae), one of the most diverse groups of noctuoids (>11 000 species) for which no well‐resolved, strongly supported phylogenetic hypothesis exists. Compared to previous methods, we generally recover much higher branch support (BS), resulting in the most well‐supported, well‐resolved phylogeny of Arctiinae to date. At the most shallow‐levels, NOC1 confidently resolves species‐level and intraspecific relationships and potentially uncovers cryptic species diversity within the genus Hypoprepia. We also implement a ‘sensitivity analysis’ to explore different loci combinations and site sampling strategies to determine whether a reduced probe set can yield results similar to those of the full probe set. At both deep and shallow levels, only 50–175 of the 730 loci included in the complete NOC1 probe set were necessary to resolve most relationships with high confidence, though only when the more rapidly evolving sites within each locus are included. This demonstrates that AHE probe sets can be tailored to target fewer loci without a significant reduction in BS, allowing future studies to incorporate more taxa at a lower per‐sample sequencing cost. NOC1 shows great promise for resolving long‐standing taxonomic issues and evolutionary questions within arctiine lineages, one of the most speciose clades within Lepidoptera.

The (non) accuracy of mitochondrial genomes for family level phylogenetics: the case of erebid moths (Lepidoptera; Erebidae)

“…The clade composed by Cyana sp., Paraona staudingeri, Vamuna virilis, Eilema ussuricum and Brunia antica, representing the tribe Lithosiini, is placed as the sister group to the rest of the subfamily. This position of Lithosiini is in concordance with previously published studies (Zahiri et al 2012;Zaspel et al 2014;Rönkä et al 2016;Dowdy et al 2020). Also, the position of Amerila astreus (Amerilini), even though it is not supported, and the relationship of Callimorphina and Arctiina subtribes are similar to the afore mentioned studies.…”

Adding leaves to the Lepidoptera tree: capturing hundreds of nuclear genes from old museum specimens

“…AHE has also been used successfully for recently collected Lepidoptera material (e.g. Breinholt et al ., 2018; Espeland et al ., 2018; Homziak et al ., 2019; Dowdy et al ., 2020), but see also St Laurent et al . (2018) and Hamilton et al .…”

“…Although taxon sampling has increased, the need for fresh material in transcriptome‐based studies or well preserved relatively recent material for AHE, has so far made it impossible to include several highly interesting and rarely collected taxa, for which recently collected material may not be available (Kawahara et al ., 2019). Very recently, target enrichment kits specialized for specific Lepidoptera taxa have appeared, such as for butterflies (Espeland et al ., 2018), Arctiinae (Erebidae) (Dowdy et al ., 2020), Bombycoidea (Hamilton et al ., 2019) and Helicoverpa armigera Hübner (Noctuidae) (McGaughran, 2020), which likely only provide partially overlapping data.…”

Historical biogeography of Heteropterinae skippers via Beringian and post‐Tethyan corridors

“…Recent progress in phylogenomics and museomics ( i.e . use of DNA from old museum specimens) have allowed a better understanding of Lepidoptera systematics, phylogenetics and evolution (Allio et al., 2020; Breinholt et al., 2018; Dowdy et al., 2020; Espeland et al., 2018; Hamilton et al., 2019; Homziak et al., 2019; Kawahara et al., 2019; Li et al., 2019; St Laurent et al., 2018; Toussaint et al., 2018). Among butterflies (Lepidoptera, Papilionoidea), increasingly well sampled and strongly supported trees‐of‐life are facilitating new evolutionary insights thanks to the application of new methods.…”