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.

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.

Asexual reproduction occurs widely in plants and animals, particularly in insects. Aphid species usually reproduce by cyclic parthenogenesis, but many species include obligate asexual lineages. We recently showed that the leaf-curl plum aphid, Brachycaudus helichrysi, actually encompasses two lineages, B. helichrysi H1 and H2. Ecological data suggest that these lineages have different life cycles. We conducted a large population genetics study, based on 14 microsatellite loci, to infer their respective life cycles and investigate their population structure and geographical distribution. Brachycaudus helichrysi H1 displayed the genetic signature of cyclical parthenogenesis, using plum trees as primary hosts for sexual reproduction, as classically described for B. helichrysi. This global survey showed that the Central Asian population of H1 was clearly differentiated from American-European populations. By contrast, B. helichrysi H2 displayed the typical signature of obligate asexual reproduction. H2 encompassed at least eight highly successful genotypes or superclones. This lack of ability to undergo sexual reproduction was confirmed for one of the superclones by sex induction experiments. We found only one B. helichrysi H2 population that underwent sexual reproduction, which was collected from peach trees, in Northern India. Our results confirm that H1 and H2 have different life cycles. Brachycaudus helichrysi H1 is clearly heteroecious using plum trees as primary hosts, while B. helichrysi H2 encompasses several anholocyclic lineages, and some heteroecious populations that until now have only been found associated with peach trees as primary hosts. We discuss implications of these findings for the pest status of B. helichrysi lineages.