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.

Assessing the enormous diversity of Southern Ocean benthic species and their evolutionary histories is a central task in the era of global climate change. Based on mitochondrial markers, it was recently suggested that the circumpolar giant sea spider Colossendeis megalonyx comprises a complex of at least six cryptic species with mostly small and non-overlapping distribution ranges. Here, we expand the sampling to include over 500 mitochondrial COI sequences of specimens from around the Antarctic. Using multiple species delimitation approaches, the number of distinct mitochondrial OTUs increased from six to 15–20 with our larger dataset. In contrast to earlier studies, many of these clades show almost circumpolar distributions. Additionally, analysis of the nuclear internal transcribed spacer region for a subset of these specimens showed incongruence between nuclear and mitochondrial results. These mito-nuclear discordances suggest that several of the divergent mitochondrial lineages can hybridize and should not be interpreted as cryptic species. Our results suggest survival of C. megalonyx during Pleistocene glaciations in multiple refugia, some of them probably located on the Antarctic shelf, and emphasize the importance of multi-gene datasets to detect the presence of cryptic species, rather than their inference based on mitochondrial data alone.

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Pallenopsis patagonica (Hoek, 1881) is one of the most taxonomically problematic and variable pycnogonid species, and is distributed around the southern South American coast, and the Subantarctic and Antarctic areas. We conducted a phylogenetic analysis of mitochondrial cytochrome c oxidase subunit I (COI) sequences of 47 Pallenopsis specimens, including 39 morphologically identified as P. patagonica, five Pallenopsis pilosa (Hoek, 1881), one Pallenopsis macneilli Clark, 1963, one Pallenopsis buphtalmus Pushkin, 1993, and one Pallenopsis latefrontalis Pushkin, 1993. Furthermore, we studied morphological differences between the different COI lineages using light and scanning electron microscopy, including also material from Loman's and Hedgpeth's classical collections, as well as Hoek's type material of P. patagonica from 1881. The molecular results unambiguously reveal that P. patagonica is a complex of several divergent clades, which also includes P. macneilli, P. buphtalmus, and P. latefrontalis. Based on the material available, two major clades could be identified, namely a 'Falkland' clade, to which we assign the nominal P. patagonica, and a 'Chilean' clade, which is distinct from the 'Falkland' clade. We describe the 'Chilean' clade as new species, Pallenopsis yepayekae sp. nov. Weis, 2013. All molecular results are confirmed by specific morphological characteristics that are discussed in detail and compared with Pallenopsis species closely related to the P. patagonica complex. Our results reveal that P. patagonica is a species-rich complex that is in need for a thorough taxonomic revision, using both morphological and genetic approaches.