BackgroundHigher-level relationships within the Lepidoptera, and particularly within the species-rich subclade Ditrysia, are generally not well understood, although recent studies have yielded progress. We present the most comprehensive molecular analysis of lepidopteran phylogeny to date, focusing on relationships among superfamilies.Methodology / Principal Findings483 taxa spanning 115 of 124 families were sampled for 19 protein-coding nuclear genes, from which maximum likelihood tree estimates and bootstrap percentages were obtained using GARLI. Assessment of heuristic search effectiveness showed that better trees and higher bootstrap percentages probably remain to be discovered even after 1000 or more search replicates, but further search proved impractical even with grid computing. Other analyses explored the effects of sampling nonsynonymous change only versus partitioned and unpartitioned total nucleotide change; deletion of rogue taxa; and compositional heterogeneity. Relationships among the non-ditrysian lineages previously inferred from morphology were largely confirmed, plus some new ones, with strong support. Robust support was also found for divergences among non-apoditrysian lineages of Ditrysia, but only rarely so within Apoditrysia. Paraphyly for Tineoidea is strongly supported by analysis of nonsynonymous-only signal; conflicting, strong support for tineoid monophyly when synonymous signal was added back is shown to result from compositional heterogeneity.Conclusions / SignificanceSupport for among-superfamily relationships outside the Apoditrysia is now generally strong. Comparable support is mostly lacking within Apoditrysia, but dramatically increased bootstrap percentages for some nodes after rogue taxon removal, and concordance with other evidence, strongly suggest that our picture of apoditrysian phylogeny is approximately correct. This study highlights the challenge of finding optimal topologies when analyzing hundreds of taxa. It also shows that some nodes get strong support only when analysis is restricted to nonsynonymous change, while total change is necessary for strong support of others. Thus, multiple types of analyses will be necessary to fully resolve lepidopteran phylogeny.

Recent molecular phylogenetic studies of the insect order Lepidoptera have robustly resolved family-level divergences within most superfamilies, and most divergences among the relatively species-poor early-arising superfamilies. In sharp contrast, relationships among the superfamilies of more advanced moths and butterflies that comprise the mega-diverse clade Apoditrysia (ca. 145,000 spp.) remain mostly poorly supported. This uncertainty, in turn, limits our ability to discern the origins, ages and evolutionary consequences of traits hypothesized to promote the spectacular diversification of Apoditrysia. Low support along the apoditrysian “backbone” probably reflects rapid diversification. If so, it may be feasible to strengthen resolution by radically increasing the gene sample, but case studies have been few. We explored the potential of next-generation sequencing to conclusively resolve apoditrysian relationships. We used transcriptome RNA-Seq to generate 1579 putatively orthologous gene sequences across a broad sample of 40 apoditrysians plus four outgroups, to which we added two taxa from previously published data. Phylogenetic analysis of a 46-taxon, 741-gene matrix, resulting from a strict filter that eliminated ortholog groups containing any apparent paralogs, yielded dramatic overall increase in bootstrap support for deeper nodes within Apoditrysia as compared to results from previous and concurrent 19-gene analyses. High support was restricted mainly to the huge subclade Obtectomera broadly defined, in which 11 of 12 nodes subtending multiple superfamilies had bootstrap support of 100%. The strongly supported nodes showed little conflict with groupings from previous studies, and were little affected by changes in taxon sampling, suggesting that they reflect true signal rather than artifacts of massive gene sampling. In contrast, strong support was seen at only 2 of 11 deeper nodes among the “lower”, non-obtectomeran apoditrysians. These represent a much harder phylogenetic problem, for which one path to resolution might include further increase in gene sampling, together with improved orthology assignments.

Within the insect order Lepidoptera (moths and butterflies), the so-called nonditrysian superfamilies are mostly species-poor but highly divergent, offering numerous synapomorphies and strong morphological evidence for deep divergences. Uncertainties remain, however, and tests of the widely accepted morphological framework using other evidence are desirable. The goal of this paper is to test previous hypotheses of nonditrysian phylogeny against a data set consisting of 61 nonditrysian species plus 20 representative Ditrysia and eight outgroups (Trichoptera), nearly all sequenced for 19 nuclear genes (up to 14 700 bp total). We compare our results in detail with those from previous studies of nonditrysians, and review the morphological evidence for and against each grouping The major conclusions are as follows. (i) There is very strong support for Lepidoptera minus Micropterigidae and Agathiphagidae, here termed Angiospermivora, but no definitive resolution of the position of Agathiphagidae, although support is strongest for alliance with Micropterigidae, consistent with another recent molecular study. (ii) There is very strong support for Glossata, which excludes Heterobathmiidae, but weak support for relationships among major homoneurous clades. Eriocraniidae diverge first, corroborating the morphological clade Coelolepida, but the morphological clades Myoglossata and Neolepidoptera are never monophyletic in the molecular trees; both are contradicted by strong support for Lophocoronoidea + Hepialoidea, the latter here including Correspondence: Charles Mitter, †Deceased 6 December 2014. No conflicts of interest were discovered. © 2015 The Royal Entomological Society 671 672 J. C. Regier et al.Mnesarchaeoidea syn.n. (iii) The surprising grouping of Acanthopteroctetidae + Neopseustidae, although weakly supported here, is consistent with another recent molecular study. (iv) Heteroneura is very strongly supported, as is a basal split of this clade into Nepticuloidea + Eulepidoptera. Relationships within Nepticuloidea accord closely with recent studies based on fewer genes but many more taxa. (v) Eulepidoptera are split into a very strongly supported clade consisting of Tischeriidae + Palaephatidae + Ditrysia, here termed Euheteroneura, and a moderately supported clade uniting Andesianidae with Adeloidea. (vi) Relationships within Adeloidea are strongly resolved and Tridentaformidae fam.n. is described for the heretofore problematic genus Tridentaforma Davis, which is strongly supported in an isolated position within the clade. (vii) Within Euheteroneura, the molecular evidence is conflicting with respect to the sister group to Ditrysia, but strongly supports paraphyly of Palaephatidae. We decline to change the classification, however, because of strong morphological evidence supporting palaephatid monophyly. (viii) We review the life histories and larval feeding habits of all nonditrysian families and assess the implications of our results for hypotheses about early lepidopteran phytophagy. The first host record for ...

Abstract. The Tineoidea are the earliest-originating extant superfamily of the enormous clade Ditrysia, whose 152 000+ species make up 98% of the insect order Lepidoptera. Though more diverse than all non-ditrysian superfamilies put together (3719 vs 2604 species), the tineoids are not especially species-rich among ditrysian superfamilies. Their phylogenetic position, however, makes tineoids potentially important for understanding the causes of ditrysian hyperdiversity, through their effect on inferences about the traits of ancestral ditrysians. To reconstruct early ditrysian evolution, we need a firmly established ground plan for tineoids themselves, which in turn requires a robust knowledge of their biodiversity and phylogeny. Tineoid systematics is under-studied. The description of the world fauna remains very patchy, especially in the largest family, Tineidae, and phylogenetic studies within and among families have been few. Recently, molecular analyses have shown strong promise for advancing tineoid systematics. Here we present the largest tineoid molecular study to date, sampling five to 19 nuclear gene regions (6.6-14.7 kb) in 62 species, representing all tineoid groups ever assigned family rank, 25 of the 31 subfamilies recognized in recent classifications, and 40 genera spanning the morphological diversity of Tineidae, for which monophyly has not been established. Phylogenetic analysis used maximum likelihood, with synonymous substitutions alternatively included and excluded. The main findings confirm and extend those of other recent studies, as follows: (i) monophyly is strongly supported for Psychidae subsuming Arrhenophanidae, for Eriocottidae, and for Tineidae subsuming Acrolophidae but excluding Dryadaulinae and two genera previously assigned to Meessiinae; (ii) two new families are described, Dryadaulidae stat. rev. and Meessiidae stat. rev., based on subfamilies previously included in Tineidae but strongly excluded from this and all other families by our molecular results; (iii) Doleromorpha, formerly placed in Meessiinae sensu lato, is likewise here excluded from Tineidae, but left incertae sedis pending better characterization of what is potentially another new family; (iv) basal division of Tineidae sensu novo into 'tineine' and 'acrolophine' lineages is moderately to strongly supported, but most subfamily relationships within these lineages are very weakly supported, and polyphyly is confirmed for Meessiinae and Myrmecozelinae as previously defined; (v) basal division of Psychidae sensu novo into 'arrhenophanine' and 'psychine' lineages is moderately to strongly supported, as are most subfamily relationships within these lineages; (vi) Tineoidea are paraphyletic with respect to all other Ditrysia when synonymous substitutions are eliminated, with branching order (Meessiidae stat. rev. (Psychidae sensu novo ((Eriocottidae (Dryadaulidae stat. rev. + Doleromorpha)) (Tineidae sensu novo + all other Ditrysia)))). Support for tineoid non-monophyly varies, among the relevant nodes and among analyses...

Major progress has been made recently toward resolving the phylogeny of Noctuoidea, the largest superfamily of Lepidoptera. However, numerous questions and weakly supported nodes remain. In this paper we independently check and extend the main findings of multiple recent authors by performing maximum-likelihood analyses of 5-19 genes (6.7-18.6 kb) in 74 noctuoids representing all the families and a majority of the subfamilies. Our results strongly support the six family system of Zahiri et al., with the former Lymantriidae and Arctiidae subsumed within the huge family Erebidae, and Noctuidae restricted largely to the subfamilies with so-called trifine hindwing venation. Our data also strongly corroborate monophyly of the set of four families with quadrifid forewing venation, to the exclusion of Notodontidae, and removal from the latter of Oenosandridae. Other among-family relationships, however, remain unsettled. Our evidence is equivocal on the position of Oenosandridae, which are sister group to either Notodontidae alone or to all other noctuoids. Like other recent nuclear gene studies, our results also provide no strong support for relationships among the four quadrifid forewing families. In contrast, within families our analyses significantly expand the list of robustly resolved relationships, while introducing no strong conflicts with previous molecular studies. Within Notodontidae, for which we present the largest molecular taxon sample to date, we find strong evidence for polyphyly for some, or all, recent definitions of the subfamilies Thaumetopoeinae, Pygaerinae, Notodontinae and Heterocampinae. Deeper divergences are incompletely resolved but there is strong support for multiple 'backbone' nodes subtending most of the subfamilies studied. Within Erebidae, we find much agreement and no strong conflict with a recent previous study regarding relationships among subfamilies, and somewhat stronger support. Although many questions remain, the two studies together firmly resolve positions for over half the subfamilies. Within Noctuidae, we find no strong conflict with previous molecular studies regarding relationships among subfamilies, but much stronger resolution along the 'backbone' of the phylogeny. Combining information from multiple studies yields strongly resolved positions for most of the subfamilies. Finally, our results strongly suggest that the tribes Pseudeustrotiini and Prodeniini, currently assigned to the largest subfamily, Noctuinae, do not belong there. In sum, our results provide additional corroboration for the main outlines of family-level phylogeny in Noctuoidea, and contribute toward resolving relationships within families.