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The currently recognized robust support for the monophyly of the Lepidoptera (and the superorder Amphiesmenoptera comprising Lepidoptera + Trichoptera) is outlined, and the phylogeny of the principal lineages within the order is reviewed succinctly. The state of the taxonomic inventory of Lepidoptera is discussed separately for ‘micro-moths’, ‘macro-moths’ and butterflies, three assemblages on which work has followed historically somewhat different paths. While currently there are about 160,000 described species of Lepidoptera, the total number of extant species is estimated to be around half a million. On average, just over one thousand new species of Lepidoptera have been described annually in recent years. Allowing for the new synonyms simultaneously established, the net increase in species numbers still exceeds 800/year. Most of the additions are foreseeable in the micro-moth grade, but even for butterflies ca 100 species are added annually. Examples of particularly interesting new high-rank taxa that have been described (or whose significance has become realized) since the middle of the 20th century include the non-glossatan lineages represented by Agathiphaga and Heterobathmia and the heteroneuran families Andesianidae, Palaephatidae, Hedylidae and Micronoctuidae. Some thoughts on how present and future systematic lepidopterology might be prioritised are presented.

The proliferation of DNA data is revolutionizing all fields of systematic research. DNA barcode sequences, now available for millions of specimens and several hundred thousand species, are increasingly used in algorithmic species delimitations. This is complicated by occasional incongruences between species and gene genealogies, as indicated by situations where conspecific individuals do not form a monophyletic cluster in a gene tree. In two previous reviews, non-monophyly has been reported as being common in mitochondrial DNA gene trees. We developed a novel web service “Monophylizer” to detect non-monophyly in phylogenetic trees and used it to ascertain the incidence of species non-monophyly in COI (a.k.a. cox1) barcode sequence data from 4977 species and 41,583 specimens of European Lepidoptera, the largest data set of DNA barcodes analyzed from this regard. Particular attention was paid to accurate species identification to ensure data integrity. We investigated the effects of tree-building method, sampling effort, and other methodological issues, all of which can influence estimates of non-monophyly. We found a 12% incidence of non-monophyly, a value significantly lower than that observed in previous studies. Neighbor joining (NJ) and maximum likelihood (ML) methods yielded almost equal numbers of non-monophyletic species, but 24.1% of these cases of non-monophyly were only found by one of these methods. Non-monophyletic species tend to show either low genetic distances to their nearest neighbors or exceptionally high levels of intraspecific variability. Cases of polyphyly in COI trees arising as a result of deep intraspecific divergence are negligible, as the detected cases reflected misidentifications or methodological errors. Taking into consideration variation in sampling effort, we estimate that the true incidence of non-monophyly is ∼23%, but with operational factors still being included. Within the operational factors, we separately assessed the frequency of taxonomic limitations (presence of overlooked cryptic and oversplit species) and identification uncertainties. We observed that operational factors are potentially present in more than half (58.6%) of the detected cases of non-monophyly. Furthermore, we observed that in about 20% of non-monophyletic species and entangled species, the lineages involved are either allopatric or parapatric—conditions where species delimitation is inherently subjective and particularly dependent on the species concept that has been adopted. These observations suggest that species-level non-monophyly in COI gene trees is less common than previously supposed, with many cases reflecting misidentifications, the subjectivity of species delimitation or other operational factors.