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

Abstract

Museum collections around the world contain billions of specimens, including rare and extinct species. If their genetic information could be retrieved at a large scale, this would dramatically increase our knowledge of genetic and taxonomic diversity information, and support evolutionary, ecological and systematic studies. We here present a target enrichment kit for 2953 loci in 1753 orthologous nuclear genes + the barcoding region of cytochrome C oxidase 1, for Lepidoptera and demonstrate its utility to obtain a large number of nuclear loci from dry, pinned museum material collected from 1892 to 2017. We sequenced enriched libraries of 37 museum specimens across the order Lepidoptera, many from higher taxa not yet included in high‐throughput molecular studies, showing that our kit can be used to generate comparable data across the order, and provides resolution both for shallower and deeper nodes. The filtered datasets (172 taxa, 234 464 amino acid positions and corresponding nucleotides from 1835 CDS regions) were used to infer a phylogeny of Lepidoptera, which is largely congruent in topology to recent phylogenomic studies, but with the addition of some key taxa. We furthermore present our TEnriAn (Target Enrichment Analysis) workflow for processing and combining target enrichment, transcriptomic and genomic data.

The unresolved phylogenomic tree of butterflies and moths (Lepidoptera): assessing the potential causes and consequences

“…1) span the whole breadth of the lepidopteran tree of life and if they are all present in all of the resulting topologies, we can conclude that there is enough phylogenetic signal in our dataset to infer these relationships. We compare our results to the two most recent published studies, which have similar taxon sampling to ours: Kawahara et al (2019) (2098 genes) and Mayer et al (2021) (1753 genes). As Heterobathmioidea are not sampled in Mayer et al (2021) and the support for Angiospermivora can therefore not be assessed, we focus on the remaining nine clades in this set of comparisons.…”

“…We compare our results to the two most recent published studies, which have similar taxon sampling to ours: Kawahara et al (2019) (2098 genes) and Mayer et al (2021) (1753 genes). As Heterobathmioidea are not sampled in Mayer et al (2021) and the support for Angiospermivora can therefore not be assessed, we focus on the remaining nine clades in this set of comparisons. When evaluating strength of branch support, we consider values of UFB=>95 or bootstrap=>90 to denote strong support.…”

“…Molecular data have shed much light on the phylogenetic relationships of the families in this large group (Regier et al 2009; Mutanen et al 2010; Regier et al 2013; Heikkilä et al 2015), and the latest datasets based on transcriptomes and target enrichment appear to be converging on a consensus of the deeper relationships within the order (Bazinet et al 2013; Kawahara and Breinholt 2014; Bazinet et al 2017; Kawahara et al 2019; Mayer et al 2021). These datasets are based on single copy orthologous protein-coding genes, ranging from 741 (Bazinet et al 2013) to 1753 in Mayer et al (2021), 2098 (Kawahara et al 2019), 2696 (Kawahara and Breinholt 2014), and 2948 genes (Breinholt et al 2018). The phylogenomic studies support many of the surprising results obtained in previous Sanger sequencing based studies, such as the position of Pyraloidea as the sister to the so-called macro-moths (Macroheterocera), and butterflies as a lineage unrelated to the macro-moths.…”

“…The most striking conflict is within Apoditrysia – a large clade including the well-known lepidopterans such as butterflies, macro-moths, leaf-rollers, snout moths, and many others. One of the apoditrysian groups, plume moths (Pterophoroidea), is found to be in a clade with Thyridoidea and Gelechioidea in Bazinet et al (2013), Kawahara et al (2019), and Mayer et al (2021), but in a clade with leaf-rollers (Tortricoidea) and Urodoidea in Kawahara and Breinholt (2014) and Breinholt et al (2018). The position of other apoditrysian groups, such as the Cossoidea–Zygaenoidea complex, is also unstable (Mitter et al 2017).…”

“…The position of other apoditrysian groups, such as the Cossoidea–Zygaenoidea complex, is also unstable (Mitter et al 2017). Similarly, some conflicts exist in the relationships of the macro-moths, such as inchworms and relatives (Geometroidea) being sister to owlet moths (Noctuoidea) with full support in Kawahara and Breinholt (2014), while in Bazinet et al (2013), Kawahara et al (2019), and Mayer et al (2021) Geometroidea is sister to silk moths and relatives (Bombycoidea + Lasiocampoidea). Some of these discrepancies could perhaps be explained by very low taxon sampling in the earliest phylogenomic studies (e.g.…”