Abstract The G elechioidea (>18 000 species), one of the largest superfamilies of L epidoptera, are a major element of terrestrial ecosystems and include important pests and biological model species. Despite much recent progress, our understanding of the classification, phylogeny and evolution of G elechioidea remains limited. Building on recent molecular studies of this superfamily and a recently revised family/subfamily classification, we provide an independent estimate of among‐family relationships, with little overlap in gene sample. We analysed up to five nuclear genes, totalling 6633 bp, for each of 77 gelechioids, plus up to 14 additional genes, for a total of 14 826 bp, in 45 of those taxa and all 19 outgroup taxa. Our maximum‐likelihood ( ML ) analyses, like those of previous authors, strongly support monophyly for most multiply‐sampled families and subfamilies, but very weakly support most relationships above the family level. Our tree looks superficially divergent from that of the most recent molecular study of gelechioids, but when the previous tree is re‐rooted to accord maximally with ours, the two phylogenies agree entirely on the deepest‐level divergences in G elechioidea, and strongly though incompletely on among‐family relationships within the major groups. This concordance between independent studies is evidence that the groupings (or at least the unrooted branching order) are probably accurate, despite the low bootstrap values. After re‐rooting, both trees divide the families into three monophyletic groups: a ‘ G elechiid A ssemblage,’ consisting of G elechiidae and C osmopterigidae; a ‘ S cythridid A ssemblage,’ consisting of S tathmopodidae, S cythrididae, B lastobasidae, E lachistidae, M omphidae, C oleophoridae and B atrachedridae; and a ‘ D epressariid A ssemblage,’ consisting of A utostichidae, X yloryctidae, L ecithoceridae, O ecophoridae, D epressariidae and L ypusidae. Within the largest family, Gelechiidae, our results strongly support the pairing of A nomologinae with G elechiinae, in accordance with a recent study of this family. Relationships among the other subfamilies, however, conflict moderately to strongly between studies, leaving the intrafamily phylogeny unsettled. Within the ‘ S cythridid A ssemblage,’ both trees support an ‘ SSB clade’ consisting of B lastobasidae + ( S cythrididae + S tathmopodidae), strongly resolved only in our results. Coleophoridae + B atrachedridae is supported, albeit weakly, in both trees, and only M omphidae differ in position between studies. Within the ‘ D epressariid A ssemblage,’ both trees support an ‘ AXLO ’ clade consisting of A utostichidae, X yloryctidae, L ecithoceridae and O ecophoridae. The monophyly of this clade and relationships therein are supported weakly in previous results but strongly in ours. The recently re‐defined family D epressariidae is paraphyletic in our tree, but the evidence against depressariid monophyly is very weak. There is moderate support for a core group of D epressariidae consisting, among the seven subfamilies we sampled, of D epressariinae, A eolanthinae and H ypertrophinae. We show that gelechioids have a higher total number and percentage of species that are saprophagous as larvae than any other apoditrysian superfamily, that saprophagy is concentrated primarily in the ‘ AXLO clade,’ and that the ancestral gelechioid condition was probably feeding on live plants. Among the living‐plant feeders, concealed external feeding was probably the ancestral state. The multiple origins of internal feeding of various kinds, including leaf mining (otherwise almost unknown in A poditrysia), are restricted mostly to the S cythridid and G elechiid A ssemblages. The traits that predispose or permit lineages to adopt these unusual life histories are worthy of study.
Figure S4. Distribution of DeepSuperSAGE tag frequencies and p-value vs. fold change (FC) of tags. Left panel: Normalized tag counts per million tags (tpm) in treatment and control libraries. Right panel: Relationship between tag FC (ratio of tpm counts) and p-value of significance. Up- and down-regulated tags (p Log2FC > 1) are marked in red and green, respectively. Of those, the best BLASTN hits to a transcript, according to bit score and e-value, were used to assess the transcript expression value. (a) cooled (C) vs. uncooled (UC) library. (b) TPA treated (T) vs. untreated (UT) library. (ZIP 946 kb)
Table S4. Table of 605 cold related differentially expressed H. euphorbiae tags. Assignment with BLASTN transcript hits and annotated protein sequence descriptions (nr protein database version 09/2016). (XLSX 169Â kb)
Significance Eyespots are a widespread form of antipredator defense that have long captured the imagination of evolutionary biologists, geneticists, psychologists, and artists. These markings are particularly common within Lepidoptera, and eyespots on caterpillars have been shown to deter avian predators; however, why eyespots have evolved in particular caterpillar species, and why they are not even more widespread, remain unclear. Here we answer this question using a powerful three-pronged approach. Our phylogenetically controlled analysis of hawkmoths demonstrates that eyespots are typically restricted to large caterpillars, and our field and laboratory experiments provide an explanation for this. Eyespots are costly to small caterpillars because they enhance detectability without providing a protective advantage, but they are beneficial to large caterpillars because they deter predators.
Table S2. List of the total taxa included in the phylogenetic analyses. Specimen names refer to tip names and include the specimen accession number and preliminary taxonomy. These specimen names can be used to identify a specimenâ s specific molecular data in the supplemental data. Other pieces of information included: taxonomy (family, subfamily, tribe, genus, and species â per Kitching et al., (12)); storage method of the tissues; whether the data came from an AHE probe set, transcriptome, or genome; and collecting date. (XLSX 16 kb)
Abstract Phylogenomics seeks to use next‐generation data to robustly infer an organism's evolutionary history. Yet, the practical caveats of phylogenomics motivate investigation of improved efficiency, particularly when quality of phylogenies are questionable. To achieve improvements, one goal is to maintain or enhance the quality of phylogenetic inference while severely reducing dataset size. We approach this by assessing which kinds of loci in phylogenomic alignments provide the majority of support for a phylogenetic inference of cockroaches in Blaberoidea. We examine locus substitution rate, saturation, evolutionary divergence, rate heterogeneity, stabilizing selection, and a priori information content as traits that may determine optimality. Our controlled experimental design is based on 265 loci for 102 blaberoidean taxa and 22 outgroup species. Loci with high substitution rate, low saturation, low sequence distance, low rate heterogeneity, and strong stabilizing selection derive more support for phylogenetic relationships. We found that some phylogenetic information content estimators may not be meaningful for assessing information content a priori . We use these findings to design concatenated datasets with an optimized subsample of 100 loci. The tree inferred from the optimized subsample alignment was largely identical to that inferred from all 265 loci but with less evidence of long branch attraction, improved statistical support, and potential 4‐6x improvements to computation time. Supported by phylogenetic and morphological evidence, we erect three newly named clades (Anallactinae Evangelista & Wipfler subfam. nov. , Orkrasomeria tax. nov. Evangelista, Wipfler, & Béthoux and Hemithyrsocerini Evangelista tribe nov .) and propose other taxonomic modifications. The diagnosis of Pseudophyllodromiidae Grandcolas, 1996 is modified to accommodate Anallactinae and Pseudophyllodromiinae Vickery & Kevan, 1983. The diagnosis of Ectobiidae Brunner von Wattenwyl, 1865 is modified to add novel morphological characters.
A new species of cicinnine Mimallonidae, Cicinnus chambersi sp. nov. , is described from the Sky Islands Region of southern Arizona, USA. The new species is closely related to C. mexicana (Druce), type locality Veracruz, Mexico, based on morphology and genetics. The other Cicinnus species known from the United States, the common C. melsheimeri (type locality Pennsylvania, USA) is morphologically and genetically distinct from both C. chambersi and C. mexicana . The new species is compared to C. mexicana and C. melsheimeri , as well as other Mexican Cicinnus . The life history of C. chambersi is unknown, but its description should facilitate future studies on this rarely reported North American mimallonid, a species which may have only recently become established in the United States. Cicinnus chambersi is the fifth known Mimallonidae species from the United States, and the first described from the country in nearly half a century.
Caddisflies (Trichoptera) are among the most diverse groups of freshwater animals with more than 16 000 described species. They play a fundamental role in freshwater ecology and environmental engineering in streams, rivers and lakes. Because of this, they are frequently used as indicator organisms in biomonitoring programmes. Despite their importance, key questions concerning the evolutionary history of caddisflies, such as the timing and origin of larval case making, remain unanswered owing to the lack of a well-resolved phylogeny. Here, we estimated a phylogenetic tree using a combination of transcriptomes and targeted enrichment data for 207 species, representing 48 of 52 extant families and 174 genera. We calibrated and dated the tree with 33 carefully selected fossils. The first caddisflies originated approximately 295 million years ago in the Permian, and major suborders began to diversify in the Triassic. Furthermore, we show that portable case making evolved in three separate lineages, and shifts in diversification occurred in concert with key evolutionary innovations beyond case making.
The diverse, largely Neotropical subtribe Euptychiina (Satyrinae, Nymphalidae) is widely regarded as one of the most taxonomically challenging groups among all butterflies. Over the last two decades, morphological and molecular studies have revealed widespread paraphyly and polyphyly among genera, and a comprehensive, robust phylogenetic hypothesis is needed to build a firm generic classification to support ongoing taxonomic revisions at the species level. Here, we generated a dataset which includes sequences for up to nine nuclear genes and the mitochondrial COI 'barcode' for a total of 1280 specimens representing 449 described and undescribed species of Euptychiina and 39 outgroups, resulting in the most complete phylogeny for the subtribe to date. In combination with a recently developed genomic backbone tree this dataset resulted in a topology with strong support for most branches.
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