Background 
Higher-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 Findings 
483 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 / Significance 
Support 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

/pdf/a-large-scale-higher-level-molecular-phylogenetic-study-of-3b9wt785go.pdf

A Large-Scale, Higher-Level, Molecular Phylogenetic Study of the Insect Order Lepidoptera (Moths and Butterflies)

Towards a mitogenomic phylogeny of Lepidoptera.

Progress toward understanding the dynamics of ancient plant-insect associations has addressed major patterns in the ecology and evolution of herbivory and pollination. This advancement involves development of more analytical ways of describing plant-insect associational patterns in time and space and an assessment of the role that the environment and internal biological processes have in their control. Current issues include the deep origins of terrestrial herbivory, the spread of herbivory across late Paleozoic landscapes, recoveries from sudden major crises, reaction to and accommodation of protracted environmental perturbations, and the nature of herbivory and pollination before the appearance of angiosperms during the mid-Mesozoic. These and other exploratory research themes provide a more complete account of a great nexus of ecological activity that has been wedged between the two most diverse organismic groups on land for the past 410 million years.

The Fossil Record of Plant-Insect Dynamics

Pest control service provided by bats in Mediterranean rice paddies: linking agroecosystems structure to ecological functions

Ditrysia comprise close to 99 % of all butterflies and moths. The evolutionary relationships among the ditrysian superfamilies have received considerable attention in phylogenetic studies based on DNA and transcriptomic data, but the deepest divergences remain for large parts unresolved or contradictory. To obtain complementary insight into the evolutionary history of the clade, and to test previous hypotheses on the subdivision of Ditrysia based on morphology, we examine the morphology of larvae, pupae and adult males and females of 318 taxa representing nearly all ditrysian superfamilies and families. We present the most comprehensive morphological dataset on Ditrysia to date, consisting of over 500 morphological characters. The data are analyzed alone and combined with sequence data (one mitochondrial and seven nuclear protein-coding gene regions, sequenced from 422 taxa). The full dataset consists of 473 exemplar species. Analyses are performed using maximum likelihood methods, and parsimony methods for the morphological dataset. We explore whether combining morphological data and DNA-data can stabilize taxa that are unstable in phylogenetic studies based on genetic data only. Morphological characters are found phylogenetically informative in resolving apical nodes (superfamilies and families), but characters serving as evidence of relatedness of larger assemblages are few. Results include the recovery of a monophyletic Tineoidea, Sesioidea and Cossoidea, and a stable position for some unstable taxa (e.g. Epipyropidae, Cyclotornidae, Urodoidea + Schreckensteinioidea). Several such taxa, however, remain unstable even though morphological characters indicate a position in the tree (e.g. Immidae). Evidence supporting affinities between clades are suggested, e.g. a novel larval synapomorphy for Tineidae. We also propose the synonymy of Tineodidae with Alucitidae, syn. nov.
 The large morphological dataset provides information on the diversity and distribution of morphological traits in Ditrysia, and can be used in future research on the evolution of these traits, in identification keys and in identification of fossil Lepidoptera. The “backbone” of the phylogeny for Ditrysia remains largely unresolved. As previously proposed as an explanation for the scarcity of molecular signal in resolving the deeper nodes, this may be due to the rapid radiation of Ditrysia in the Cretaceous.

/pdf/elusive-ditrysian-phylogeny-an-account-of-combining-3kci2z5od3.pdf

Elusive ditrysian phylogeny: an account of combining systematized morphology with molecular data (Lepidoptera)

Pyraloidea, one of the largest superfamilies of Lepidoptera, comprise more than 15 684 described species worldwide, including important pests, biological control agents and experimental models. Understanding of pyraloid phylogeny, the basis for a predictive classification, is currently provisional. We present the most detailed molecular estimate of relationships to date across the subfamilies of Pyraloidea, and assess its concordance with previous morphology-based hypotheses. We sequenced up to five nuclear genes, totalling 6633 bp, in each of 42 pyraloids spanning both families and 18 of the 21 subfamilies, plus up to 14 additional genes, for a total of 14 826 bp, in 21 of those pyraloids plus all 24 outgroups. Maximum likelihood analyses yield trees that, within Pyraloidea, differ little among datasets and character treatments and are strongly supported at all levels of divergence (83% of nodes with bootstrap ≥80%). Subfamily relationships within Pyralidae, all very strongly supported (>90% bootstrap), differ only slightly from a previous morphological analysis, and can be summarized as Galleriinae + Chrysauginae (Phycitinae (Pyralinae + Epipaschiinae)). The main remaining uncertainty involves Chrysauginae, of which the poorly studied Australian genera may constitute the basal elements of Galleriinae + Chrysauginae or even of Pyralidae. In Crambidae the molecular phylogeny is also strongly supported, but conflicts with most previous hypotheses. Among the newly proposed groupings are a 'wet-habitat clade' comprising Acentropinae + Schoenobiinae + Midilinae, and a provisional 'mustard oil clade' containing Glaphyriinae, Evergestinae and Noordinae, in which the majority of described larvae feed on Brassicales. Within this clade a previous synonymy of Dichogaminae with the Glaphyriinae is supported. Evergestinae syn. n. and Noordinae syn. n. are here newly synonymized with Glaphyriinae, which appear to be paraphyletic with respect to both. Pyraustinae and Spilomelinae as Re-use of this article is permitted in accordance with the Terms and Conditions set out at http://wileyonlinelibrary.com/onlineopen#OnlineOpen_

A molecular phylogeny for the pyraloid moths (Lepidoptera: Pyraloidea) and its implications for higher-level classification

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A molecular phylogeny for the pyraloid moths (Lepidoptera: Pyraloidea) and its implications for higher-level classification