Museomics: Phylogenomics of the Moth Family Epicopeiidae (Lepidoptera) Using Target Enrichment

Abstract

Billions of specimens can be found in natural history museum collections around the world, holding potential molecular secrets to be unveiled. Among them are intriguing specimens of rare families of moths that, while represented in morphology-based works, are only beginning to be included in genomic studies: Pseudobistonidae, Sematuridae, and Epicopeiidae. These three families are part of the superfamily Geometroidea, which has recently been defined based on molecular data. Here we chose to focus on these three moth families to explore the suitability of a genome reduction method, target enrichment (TE), on museum specimens. Through this method, we investigated the phylogenetic relationships of these families of Lepidoptera, in particular the family Epicopeiidae. We successfully sequenced 25 samples, collected between 1892 and 2001. We use 378 nuclear genes to reconstruct a phylogenetic hypothesis from the maximum likelihood analysis of a total of 36 different species, including 19 available transcriptomes. The hypothesis that Sematuridae is the sister group of Epicopeiidae + Pseudobistonidae had strong support. This study thus adds to the growing body of work, demonstrating that museum specimens can successfully contribute to molecular phylogenetic studies.

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 (Call et al, 2021; Mayer et al, 2021; Twort et al, 2021) and we expect that museomics will play an increasingly important role in phylogenomics.…”

Delimiting Continuity: Comparison of Target Enrichment and ddRAD for Delineating Admixing Parapatric Melitaea Butterflies

“…Furthermore, the locus dropout effect also increases with divergence, leading to non-random patterns of missing data (Arnold et al 2013). RADseq methods also require high quality material, i.e., better preserved tissue to successfully extract enough amounts of DNA, while it is possible to recover genomic data from old museum material using target enrichment (Call et al 2021; Mayer et al 2021). In addition, probes used for hybrid enrichment can enrich regions containing up to 30% mismatches to the probe sequences and thus can efficiently capture the loci also if the variation is higher, while ddRAD requires exact matches of short k-mers for restriction enzymes to make cuts consistently across individuals (Banker et al 2020).…”

The phylogenetic placement of an enigmatic moth Egybolis vaillantina based on museomics

“…Consequently, molecular approaches have been restricted, on one hand, to sequencing technologies (e.g., Sanger sequencing) (Hajibabaei, Singer and Hickey, 2006; Hebert et al ., 2013), and on the other hand, were limited to quality materials (e.g., freshly collected samples, proper killing agent, etc.). However, recently, next-generation sequencing (NGS) technologies have made the DNA in museum specimens more accessible, either through whole-genome sequencing (WGS) (Sproul and Maddison, 2017; Allio et al ., 2019; Call et al ., 2021; Twort et al ., 2021) or genome reduction methods (Suchan et al ., 2016; Breinholt et al ., 2018; Mayer et al ., 2021). These advanced sequencing approaches have opened up a new field with great potential for studying the evolutionary history of taxa that are difficult to collect: museomics (Call et al ., 2021).…”