Museomics of a rare taxon: placing Whalleyanidae in the Lepidoptera Tree of Life

Abstract

Museomics is a valuable tool that utilises the diverse biobanks that are natural history museums. The ability to sequence genomes from old specimens has expanded not only the variety of interesting taxa available to study but also the scope of questions that can be investigated in order to further knowledge about biodiversity. Here we present whole genome sequencing results from the enigmatic genus Whalleyana, as well as the families Callidulidae and Hyblaeidae. Library preparation was carried out on four museum specimens and one existing DNA extract and sequenced with Illumina short reads. De novo assembly resulted in highly fragmented genomes with the N50 ranging from 317 - 2,078 bp. Mining of a manually curated gene set of 332 genes from these draft genomes had an overall gene recovery rate of 64 - 90%. Phylogenetic analysis places Whalleyana as sister to Callidulidae, and Hyblaea as sister to Pyraloidea. Since the former sister-group relationship turns out to be also supported by ten morphological synapomorphies, we propose to formally assign the Whalleyanidae to the superfamily Calliduloidea. These results highlight the usefulness of not only museum specimens, but also existing DNA extracts, for whole genome sequencing and gene mining for phylogenomic studies.

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

“…Twort et al . (2020), based on maximum likelihood analyses of a 332 gene dataset derived from shotgun sequencing also found a non‐monophyletic GAPTECC clade, but except for a clade consisting of Calliduloidea, Thyridoidea and Whalleyaneoidea, relationships are not supported. Kawahara et al .…”

“…Cong et al ., 2017b; Li et al ., 2019; Zhang et al ., 2019a,b; Allio et al ., 2020), but see Twort et al . (2020). Most recently, a comprehensive higher‐level phylogeny of Lepidoptera based on transcriptome data and available genome data was published (Kawahara et al ., 2019).…”

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

“…Although Lepidoptera are relatively well sampled compared to other insect groups, and even most animal groups, we believe that what is needed at this stage to improve the resolution of the tree of life of butterflies and moths is an increase in taxon sampling even if it means sampling only hundreds of genes instead of thousands. Recent studies have given us tool sets for doing just that by using specimens in museum collections (Twort et al 2020; Call et al 2021; Mayer et al 2021) and we expect that museomics will play an increasingly important role in phylogenomics.…”

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

“…In this study old DNA extracts, obtained over 10 years ago, were used to generate libraries following the protocol in Twort et al (2020). Briefly, DNA quality was superficially checked using electrophoretic agarose gels and the high molecular weight samples were sonicated to approx.…”