Increased gene sampling strengthens support for higher-level groups within leaf-mining moths and relatives (Lepidoptera: Gracillariidae)

Novel insight into lepidopteran phylogenetics from the mitochondrial genome of the apple fruit moth of the family Argyresthiidae

BACKGROUND

The order Lepidoptera has an abundance of species, including both agriculturally beneficial and detrimental insects. Molecular data has been used to investigate the phylogenetic relationships of major subdivisions in Lepidoptera, which has enhanced our understanding of the evolutionary relationships at the family and superfamily levels. However, the phylogenetic placement of many superfamilies and/or families in this order is still unknown. In this study, we determine the systematic status of the family Argyresthiidae within Lepidoptera and explore its phylogenetic affinities and implications for the evolution of the order. We describe the first mitochondrial (mt) genome from a member of Argyresthiidae, the apple fruit moth Argyresthia conjugella. The insect is an important pest on apples in Fennoscandia, as it switches hosts when the main host fails to produce crops.

RESULTS

The mt genome of A. conjugella contains 16,044 bp and encodes all 37 genes commonly found in insect mt genomes, including 13 protein-coding genes (PCGs), two ribosomal RNAs, 22 transfer RNAs, and a large control region (1101 bp). The nucleotide composition was extremely AT-rich (82%). All detected PCGs (13) began with an ATN codon and terminated with a TAA stop codon, except the start codon in cox1 is ATT. All 22 tRNAs had cloverleaf secondary structures, except trnS1, where one of the dihydrouridine (DHU) arms is missing, reflecting potential differences in gene expression. When compared to the mt genomes of 507 other Lepidoptera representing 18 superfamilies and 42 families, phylogenomic analyses found that A. conjugella had the closest relationship with the Plutellidae family (Yponomeutoidea-super family). We also detected a sister relationship between Yponomeutoidea and the superfamily Tineidae.

CONCLUSIONS

Our results underline the potential importance of mt genomes in comparative genomic analyses of Lepidoptera species and provide valuable evolutionary insight across the tree of Lepidoptera species.

Multi-gene phylogeny of North American clear-winged moths (Lepidoptera: Sesiidae): a foundation for future evolutionary study of a speciose mimicry complex

Sesiids are a diverse group of predominantly diurnal moths, many of which are Batesian mimics of Hymenoptera. However, their diversity and relationships are poorly understood. A multi-gene phylogenetic analysis of 48 North American sesiid species confirmed the traditional taxonomic tribal ranks, demonstrated the paraphyly of Carmenta and Synanthedon with respect to several other genera and ultimately provided minimal phylogenetic resolution within and between North American and European groups. Character support from each gene suggested inconsistency between the phylogenetic signal of the CAD gene and that of the other four genes. However, removal of CAD from subsequent phylogenetic analyses did not substantially change the initial phylogenetic results or return Carmenta and Synanthedon as reciprocally monophyletic, suggesting that it was not impacting the overall phylogenetic signal. The lack of resolution using genes that are typically informative at the species level for other lepidopterans suggests a surprisingly rapid radiation of species in Carmenta/Synanthedon. This group also exhibits a wide range of mimicry strategies and hostplant usage, which could be fertile ground for future study.

Phylogeny of gracillariid leaf-mining moths: evolution of larval behaviour inferred from phylogenomic and Sanger data

Gracillariidae is the most taxonomically diverse cosmopolitan leaf-mining moth family, consisting of nearly 2000 named species in 105 described genera, classified into eight extant subfamilies. The majority of gracillariid species are internal plant feeders as larvae, creating mines and galls in plant tissue. Despite their diversity and ecological adaptations, their phylogenetic relationships, especially among subfamilies, remain uncertain. Genomic data (83 taxa, 589 loci) were integrated with Sanger data (130 taxa, 22 loci), to reconstruct a phylogeny of Gracillariidae. Based on analyses of both datasets combined and analyzed separately, monophyly of Gracillariidae and all its subfamilies, monophyly of the clade "LAMPO" (subfamilies: Lithocolletinae, Acrocercopinae, Marmarinae, Phyllocnistinae, and Oecophyllembiinae) and relationships of its subclade "AMO" (subfamilies: Acrocercopinae, Marmarinae, and Oecophyllembiinae) were strongly supported. A sister-group relationship of Ornixolinae to the remainder of the family, and a monophyletic leaf roller lineage (Callicercops Vári + Parornichinae) + Gracillariinae, as sister to the "LAMPO" clade were supported by the most likely tree. Dating analyses indicate a mid-Cretaceous (105.3 Ma) origin of the family, followed by a rapid diversification into the nine subfamilies predating the Cretaceous-Palaeogene extinction. We hypothesize that advanced larval behaviours, such as making keeled or tentiform blotch mines, rolling leaves and galling, allowed gracillariids to better avoid larval parasitoids allowing them to further diversify. Finally, we stabilize the classification by formally re-establishing the subfamily ranks of Marmarinae stat.rev., Oecophyllembiinae stat.rev. and Parornichinae stat.rev., and erect a new subfamily, Callicercopinae Li, Ohshima and Kawahara to accommodate the enigmatic genus Callicercops.

DNA barcodes combined with multi-locus data of representative taxa can generate reliable higher-level phylogenies

Taxa are frequently labeled incertae sedis when their placement is debated at ranks above the species level, such as their subgeneric, generic, or subtribal placement. This is a pervasive problem in groups with complex systematics due to difficulties in identifying suitable synapomorphies. In this study, we propose combining DNA barcodes with a multilocus backbone phylogeny in order to assign taxa to genus or other higher-level categories. This sampling strategy generates molecular matrices containing large amounts of missing data that are not distributed randomly: barcodes are sampled for all representatives, and additional markers are sampled only for a small percentage. We investigate the effects of the degree and randomness of missing data on phylogenetic accuracy using simulations for up to 100 markers in 1000-tips trees, as well as a real case: the subtribe Polyommatina (Lepidoptera: Lycaenidae), a large group including numerous species with unresolved taxonomy. Our simulation tests show that when a strategic and representative selection of species for higher-level categories has been made for multigene sequencing (approximately one per simulated genus), the addition of this multigene backbone DNA data for as few as 5–10% of the specimens in the total data set can produce high-quality phylogenies, comparable to those resulting from 100% multigene sampling. In contrast, trees based exclusively on barcodes performed poorly. This approach was applied to a 1365-specimen data set of Polyommatina (including ca. 80% of described species), with nearly 8% of representative species included in the multigene backbone and the remaining 92% included only by mitochondrial COI barcodes, a phylogeny was generated that highlighted potential misplacements, unrecognized major clades, and placement for incertae sedis taxa. We use this information to make systematic rearrangements within Polyommatina, and to describe two new genera. Finally, we propose a systematic workflow to assess higher-level taxonomy in hyperdiverse groups. This research identifies an additional, enhanced value of DNA barcodes for improvements in higher-level systematics using large data sets. [Birabiro; DNA barcoding; incertae sedis; Kipepeo; Lycaenidae; missing data; phylogenomic; phylogeny; Polyommatina; supermatrix; systematics; taxonomy]

Global phylogeography suggests extensive eucosmopolitanism in Mesopelagic Fishes (Maurolicus: Sternoptychidae)

Fishes in the mesopelagic zone (200–1000 m) have recently been highlighted for potential exploitation. Here we assess global phylogeography in Maurolicus, the Pearlsides, an ecologically important group. We obtained new sequences from mitochondrial COI and nuclear ITS-2 from multiple locations worldwide, representing 10 described species plus an unknown central South Pacific taxon. Phylogenetic analyses identified five geographically distinct groupings, three of which comprise multiple described species. Species delimitation analyses suggest these may represent four species. Maurolicus muelleri and M. australis are potentially a single species, although as no shared haplotypes are found between the two disjunct groups, we suggest maintenance of these as two species. Maurolicus australis is a predominantly southern hemisphere species found in the Pacific, Indian and southern South Atlantic Oceans, comprising five previously allopatric species. M. muelleri (previously two species) is distributed in the North Atlantic and Mediterranean Sea. Maurolicus weitzmani (previously two species) inhabits the eastern equatorial Atlantic, Gulf of Mexico and western North and South Atlantic. Maurolicus mucronatus is restricted to the Red Sea. No Maurolicus have previously been reported in the central South Pacific but we have identified a distinct lineage from this region, which forms a sister group to Maurolicus from the Red Sea.

Sequence capture across large phylogenetic scales by using pooled PCR-generated baits: A case study of Lepidoptera

Sequence capture across large phylogenetic scales is not easy because hybridization capture is only effective when the genetic distance between the bait and target is small. Here, we propose a simple but effective strategy to tackle this issue: pooling DNA from a number of selected representative species of different clades to prepare PCR-generated baits to minimize the genetic distance between the bait and target. To demonstrate the utility of this strategy, we newly developed a set of universal nuclear markers (including 94 nuclear protein-coding genes) for Lepidoptera, a superdiverse insect group. We used a DNA pool from six lepidopteran species (representing six superfamilies) to prepare PCR baits for the 94 markers. These homemade PCR baits were used to capture sequence data from 43 species of 17 lepidopteran families, and 94% of the target loci were recovered. We constructed two data sets from the obtained data (one containing ~90 kb target coding sequences and the other containing ~120 kb target + flanking coding sequences). Both data sets yielded highly similar and well-resolved trees with 90% of nodes having >95% bootstrap support. Our capture experiment indicated that using DNA mixtures pooled from different clade-representative species of Lepidoptera to prepare PCR baits can reliably capture a large number of targeted nuclear markers across different Lepidoptera lineages. We hope that this newly developed nuclear marker set will serve as a new phylogenetic tool for Lepidoptera phylogenetics, and the PCR bait preparation strategy can facilitate the application of sequence capture techniques by researchers to accelerate data collection.

Overlooked gall-inducing moths revisited, with the description of Andescecidiumparrai gen. et sp. n. and Olierasaizi sp. n. from Chile (Lepidoptera, Cecidosidae)

There are still many gall systems associated with larvae of Lepidoptera in which the true gall-inducers have not been identified to species. Reports on misidentification of gall inducers have been recurrent for these galls, particularly in complex gall-systems that may include inquilines, kleptoparasites, and cecidophages, among other feeding guilds such as predators and parasitoid wasps. Here we describe and illustrate the adults, larvae, pupae and galls, based on light and scanning microscopy, of Andescecidiumparraigen. et sp. n. and Olierasaizisp. n., two sympatric cecidosid moths that are associated with Schinuspolygamus (Cav.) Cabrera (Anacardiaceae) in central Chile. Adults, immatures, and galls of the former did not conform to any known cecidosid genus. Galls of A.parrai are external, spherical, and conspicuous, being known for more than one century. However, their induction has been mistakenly associated with either unidentified Coleoptera (original description) or Olieraargentinana Brèthes (recently), a distinct cecidosid species with distribution restricted to the eastern Andes. Galls of O.saizi had been undetected, as they are inconspicuous. They occur under the bark within swollen stems, and may occur on the same plant, adjacent to those of A.parrai. We also propose a time-calibrated phylogeny using sequences from mitochondrial and nuclear loci, including specimens of the new proposed taxa. Thus in addition to clarifying the taxonomy of the Chilean cecidosid species we also tested their monophyly in comparison to congeneric species and putative specimens of all genera of Neotropical and African cecidosids.

Phylogeographic pattern of the plane leaf miner, Phyllonorycter platani (STAUDINGER, 1870) (Lepidoptera: Gracillariidae) in Europe

Background

The plane leaf miner, Phyllonorycter platani is a widely distributed insect species on plane trees and has a well-documented colonisation history in Europe over the last century. However, phylogeographic data of the species are lacking.

Results

We analysed 284 individuals from 38 populations across Europe, Asia, and North America. A 1242 bp fragment of the mitochondrial COI gene and an 893 bp fragment of the 28S rDNA has been Sanger sequenced. Twenty-four haplotypes were detected on the COI gene, and two alleles were identified on the 28S rDNA. We revealed two distinct clades for both markers reflecting the geographic origins, Asia and Europe. The genetic distance between the two main clades is 2.08% on the COI gene and 0.10% on the nuclear DNA.

An overlapping zone of the two clades was found across Eastern Europe and the Anatolian Peninsula. We detected heterozygote individuals of the 28S rDNA gene in Moldavia, Ukraine and in the southern part of Turkey. These suggest that the two clades can hybridise. Furthermore, the presence of European type homozygote individuals has been confirmed in the southern part of Turkey as well.

Conclusions

We have shown that both post-glacial recolonization and recent expansion events influenced the present genetic structure of P. platani. The genetic patterns revealed at least two refugia during the last ice age: one in the Balkan Peninsula and the other in the Caucasus region. Recent expansion was detected in some European and Central Asian populations. The two main clades (Europe/Asia) show definite genetic differences; however, several hybrid individuals were found in the overlapping zone as well (stretching over Eastern Europe and the Anatolian Peninsula). Discrepancies in mitochondrial and nuclear data indicate introgressions in the southern part of the Anatolian Peninsula.

Electronic supplementary material

The online version of this article (10.1186/s12862-018-1240-z) contains supplementary material, which is available to authorized users.

Resolving Relationships among the Megadiverse Butterflies and Moths with a Novel Pipeline for Anchored Phylogenomics

The advent of next-generation sequencing technology has allowed for thecollection of large portions of the genome for phylogenetic analysis. Hybrid enrichment and transcriptomics are two techniques that leverage next-generation sequencing and have shown much promise. However, methods for processing hybrid enrichment data are still limited. We developed a pipeline for anchored hybrid enrichment (AHE) read assembly, orthology determination, contamination screening, and data processing for sequences flanking the target "probe" region. We apply this approach to study the phylogeny of butterflies and moths (Lepidoptera), a megadiverse group of more than 157,000 described species with poorly understood deep-level phylogenetic relationships. We introduce a new, 855 locus AHE kit for Lepidoptera phylogenetics and compare resulting trees to those from transcriptomes. The enrichment kit was designed from existing genomes, transcriptomes, and expressed sequence tags and was used to capture sequence data from 54 species from 23 lepidopteran families. Phylogenies estimated from AHE data were largely congruent with trees generated from transcriptomes, with strong support for relationships at all but the deepest taxonomic levels. We combine AHE and transcriptomic data to generate a new Lepidoptera phylogeny, representing 76 exemplar species in 42 families. The tree provides robust support for many relationships, including those among the seven butterfly families. The addition of AHE data to an existing transcriptomic dataset lowers node support along the Lepidoptera backbone, but firmly places taxa with AHE data on the phylogeny. Combining taxa sequenced for AHE with existing transcriptomes and genomes resulted in a tree with strong support for (Calliduloidea $+$ Gelechioidea $+$ Thyridoidea) $+$ (Papilionoidea $+$ Pyraloidea $+$ Macroheterocera). To examine the efficacy of AHE at a shallow taxonomic level, phylogenetic analyses were also conducted on a sister group representing a more recent divergence, the Saturniidae and Sphingidae. These analyses utilized sequences from the probe region and data flanking it, nearly doubled the size of the dataset; resulting trees supported new phylogenetics relationships, especially within the Saturniidae and Sphingidae (e.g., Hemarina derived in the latter). We hope that our data processing pipeline, hybrid enrichment gene set, and approach of combining AHE data with transcriptomes will be useful for the broader systematics community.

Phylogeny and Evolution of Lepidoptera

Until recently, deep-level phylogeny in Lepidoptera, the largest single radiation of plant-feeding insects, was very poorly understood. Over the past two decades, building on a preceding era of morphological cladistic studies, molecular data have yielded robust initial estimates of relationships both within and among the ∼43 superfamilies, with unsolved problems now yielding to much larger data sets from high-throughput sequencing. Here we summarize progress on lepidopteran phylogeny since 1975, emphasizing the superfamily level, and discuss some resulting advances in our understanding of lepidopteran evolution.

Genomic Mining of Phylogenetically Informative Nuclear Markers in Bark and Ambrosia Beetles

Deep level insect relationships are generally difficult to resolve, especially within taxa of the most diverse and species rich holometabolous orders. In beetles, the major diversity occurs in the Phytophaga, including charismatic groups such as leaf beetles, longhorn beetles and weevils. Bark and ambrosia beetles are wood boring weevils that contribute 12 percent of the diversity encountered in Curculionidae, one of the largest families of beetles with more than 50000 described species. Phylogenetic resolution in groups of Cretaceous age has proven particularly difficult and requires large quantity of data. In this study, we investigated 100 nuclear genes in order to select a number of markers with low evolutionary rates and high phylogenetic signal. A PCR screening using degenerate primers was applied to 26 different weevil species. We obtained sequences from 57 of the 100 targeted genes. Sequences from each nuclear marker were aligned and examined for detecting multiple copies, pseudogenes and introns. Phylogenetic informativeness (PI) and the capacity for reconstruction of previously established phylogenetic relationships were used as proxies for selecting a subset of the 57 amplified genes. Finally, we selected 16 markers suitable for large-scale phylogenetics of Scolytinae and related weevil taxa.

Phylogenetic test of speciation by host shift in leaf cone moths (Caloptilia) feeding on maples (Acer)

The traditional explanation for the exceptional diversity of herbivorous insects emphasizes host shift as the major driver of speciation. However, phylogenetic studies have often demonstrated widespread host plant conservatism by insect herbivores, calling into question the prevalence of speciation by host shift to distantly related plants. A limitation of previous phylogenetic studies is that host plants were defined at the family or genus level; thus, it was unclear whether host shifts predominate at a finer taxonomic scale. The lack of a statistical approach to test the hypothesis of host-shift-driven speciation also hindered studies at the species level. Here, we analyze the radiation of leaf cone moths (Caloptilia) associated with maples (Acer) using a newly developed, phylogeny-based method that tests the role of host shift in speciation. This method has the advantage of not requiring complete taxon sampling from an entire radiation. Based on 254 host plant records for 14 Caloptilia species collected at 73 sites in Japan, we show that major dietary changes are more concentrated toward the root of the phylogeny, with host shift playing a minor role in recent speciation. We suggest that there may be other roles for host shift in promoting herbivorous insect diversification rather than facilitating speciation per se.

PCR primers for 30 novel gene regions in the nuclear genomes of Lepidoptera

We report primer pairs for 30 new gene regions in the nuclear genomes of Lepidoptera that can be amplified using a standard PCR protocol. The new primers were tested across diverse Lepidoptera, including nonditrysians and a wide selection of ditrysians. These new gene regions give a total of 11,043 bp of DNA sequence data and they show similar variability to traditionally used nuclear gene regions in studies of Lepidoptera. We feel that a PCR-based approach still has its place in molecular systematic studies of Lepidoptera, particularly at the intrafamilial level, and our new set of primers now provides a route to generating phylogenomic datasets using traditional methods.

A new genus and species of leaf-mining moth from the French Alps, Mercantouria neli gen. n., sp. n. (Lepidoptera, Gracillariidae)

The Alps are a hotspot of biodiversity in Europe with many Lepidoptera species still to be discovered. Here we describe a new gracillariid genus and species, Mercantourianeligen. n. and sp. n. The morphology of the male genitalia is highly differentiated with unique features. DNA barcodes show that its nearest neighbor is the North American species ‘Caloptilia’ scutellariella (Braun, 1923). Mercantourianeli is known from four adults (two males and two females) collected at two localities in the French Alps. Its host plant and life cycle remain unknown.

Color Pattern on the Forewing of Micropterix (Lepidoptera: Micropterigidae): Insights into the Evolution of Wing Pattern and Wing Venation in Moths

Wing patterns are key taxonomic characters that have long been used in descriptions of Lepidoptera; however, wing pattern homologies are not understood among different moth lineages. Here, we examine the relationship between wing venation and wing pattern in the genus Micropterix, among the most basal extant Lepidoptera, in order to evaluate the two existing predictive models that have the potential to establish wing pattern element homologies for the order. The location of wing pattern elements along the costal margin of the wing in Micropterix is consistent with the predictions of the model proposed for Tortricidae by Brown and Powell in 1991, later modified by Baixeras in 2002. The predictive power of this model for such distantly related taxa suggests that the model may hold across various superfamilies within Lepidoptera, and supports the long-held notion that fasciae, not spots, are the most likely primitive wing pattern elements for the order. In addition, the location of wing pattern elements suggests that the wing vein commonly termed Sc1 may in fact be a different vein, which Comstock identified in Trichoptera and referred to as "a."

Correlation between the green-island phenotype and Wolbachia infections during the evolutionary diversification of Gracillariidae leaf-mining moths

Internally feeding herbivorous insects such as leaf miners have developed the ability to manipulate the physiology of their host plants in a way to best meet their metabolic needs and compensate for variation in food nutritional composition. For instance, some leaf miners can induce green-islands on yellow leaves in autumn, which are characterized by photosynthetically active green patches in otherwise senescing leaves. It has been shown that endosymbionts, and most likely bacteria of the genus Wolbachia, play an important role in green-island induction in the apple leaf-mining moth Phyllonorycter blancardella. However, it is currently not known how widespread is this moth-Wolbachia-plant interaction. Here, we studied the co-occurrence between Wolbachia and the green-island phenotype in 133 moth specimens belonging to 74 species of Lepidoptera including 60 Gracillariidae leaf miners. Using a combination of molecular phylogenies and ecological data (occurrence of green-islands), we show that the acquisitions of the green-island phenotype and Wolbachia infections have been associated through the evolutionary diversification of Gracillariidae. We also found intraspecific variability in both green-island formation and Wolbachia infection, with some species being able to form green-islands without being infected by Wolbachia. In addition, Wolbachia variants belonging to both A and B supergroups were found to be associated with green-island phenotype suggesting several independent origins of green-island induction. This study opens new prospects and raises new questions about the ecology and evolution of the tripartite association between Wolbachia, leaf miners, and their host plants.

Phylotranscriptomics: saturated third codon positions radically influence the estimation of trees based on next-gen data

Recent advancements in molecular sequencing techniques have led to a surge in the number of phylogenetic studies that incorporate large amounts of genetic data. We test the assumption that analyzing large number of genes will lead to improvements in tree resolution and branch support using moths in the superfamily Bombycoidea, a group with some interfamilial relationships that have been difficult to resolve. Specifically, we use a next-gen data set that included 19 taxa and 938 genes (∼1.2M bp) to examine how codon position and saturation might influence resolution and node support among three key families. Maximum likelihood, parsimony, and species tree analysis using gene tree parsimony, on different nucleotide and amino acid data sets, resulted in largely congruent topologies with high bootstrap support compared with prior studies that included fewer loci. However, for a few shallow nodes, nucleotide and amino acid data provided high support for conflicting relationships. The third codon position was saturated and phylogenetic analysis of this position alone supported a completely different, potentially misleading sister group relationship. We used the program RADICAL to assess the number of genes needed to fix some of these difficult nodes. One such node originally needed a total of 850 genes but only required 250 when synonymous signal was removed. Our study shows that, in order to effectively use next-gen data to correctly resolve difficult phylogenetic relationships, it is necessary to assess the effects of synonymous substitutions and third codon positions.

Three new cecidogenous species of Palaeomystella Fletcher (Lepidoptera, Momphidae) from the Brazilian Atlantic Rain Forest

Three new cecidogenous species of Palaeomystella Fletcher (Lepidoptera, Momphidae) from the Brazilian Atlantic Rain Forest are described. Larvae of P. fernandesi Moreira & Becker, sp. n., P. rosaemariae Moreira & Becker, sp. n. and P. tavaresi Becker & Moreira, sp. n. induce galls, respectively, on Tibouchina sellowiana (Cham.) Cogn., T. asperior (Cham.) Cogn. and T. fissinervia (Schrank & Mart. ex DC.) Cogn. (Melastomataceae). Adults, immature stages and galls are illustrated, and data on life history and a preliminary analysis of mitochondrial DNA sequences, including related species, are also provided.

A gateway for phylogenetic analysis powered by grid computing featuring GARLI 2.0

We introduce molecularevolution.org, a publicly available gateway for high-throughput, maximum-likelihood phylogenetic analysis powered by grid computing. The gateway features a garli 2.0 web service that enables a user to quickly and easily submit thousands of maximum likelihood tree searches or bootstrap searches that are executed in parallel on distributed computing resources. The garli web service allows one to easily specify partitioned substitution models using a graphical interface, and it performs sophisticated post-processing of phylogenetic results. Although the garli web service has been used by the research community for over three years, here we formally announce the availability of the service, describe its capabilities, highlight new features and recent improvements, and provide details about how the grid system efficiently delivers high-quality phylogenetic results. [garli, gateway, grid computing, maximum likelihood, molecular evolution portal, phylogenetics, web service.]

Can RNA-Seq resolve the rapid radiation of advanced moths and butterflies (Hexapoda: Lepidoptera: Apoditrysia)? An exploratory study

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.

Convergent evolution of morphology and habitat use in the explosive Hawaiian fancy case caterpillar radiation

Species occurring in unconnected, but similar habitats and under similar selection pressures often display strikingly comparable morphology, behaviour and life history. On island archipelagos where colonizations and extinctions are common, it is often difficult to separate whether similar traits are a result of in situ diversification or independent colonization without a phylogeny. Here, we use one of Hawaii's most ecologically diverse and explosive endemic species radiations, the Hawaiian fancy case caterpillar genus Hyposmocoma, to test whether in situ diversification resulted in convergence. Specifically, we examine whether similar species utilizing similar microhabitats independently developed largely congruent larval case phenotypes in lineages that are in comparable, but isolated environments. Larvae of these moths are found on all Hawaiian Islands and are characterized by an extraordinary array of ecomorphs and larval case morphology. We focus on the 'purse cases', a group that is largely specialized for living within rotting wood. Purse cases were considered a monophyletic group, because morphological, behavioural and ecological traits appeared to be shared among all members. We constructed a phylogeny based on nuclear and mitochondrial DNA sequences from 38 Hyposmocoma species, including all 14 purse case species and 24 of non-purse case congeners. Divergence time estimation suggests that purse case lineages evolved independently within dead wood and developed nearly identical case morphology twice: once on the distant Northwest Hawaiian Islands between 15.5 and 9 Ma and once on the younger main Hawaiian Islands around 3.0 Ma. Multiple ecomorphs are usually found on each island, and the ancestral ecomorph of Hyposmocoma appears to have lived on tree bark. Unlike most endemic Hawaiian radiations that follow a clear stepwise progression of colonization, purse case Hyposmocoma do not follow a pattern of colonization from older to younger island. We postulate that the diversity of microhabitats and selection from parasitism/predation from endemic predators may have shaped case architecture in this extraordinary endemic radiation of Hawaiian insects.

Evolution of Manduca sexta hornworms and relatives: biogeographical analysis reveals an ancestral diversification in Central America

The hawkmoth genus Manduca is a diverse group of very large, conspicuous moths that has served as an important model across many biological disciplines. Two species in particular, the tobacco hornworm (Manduca sexta) and the tomato hornworm (Manduca quinquemaculatus) have been researched extensively. Studies across biological fields have referred to these two species as being closely related or even sister species, but the extent to which these two model organisms are related remains largely unknown. We conducted a comprehensive multi-gene phylogenetic analysis of Manduca, based on both an ML and Bayesian framework, which resulted in a monophyletic Manduca but only when two other genera, Dolba and Euryglottis are included. We tentatively conclude that the sister group to Manduca sexta comprises the Caribbean M. afflicta and M. johanni, and the sister lineage to this clade includes M. quinquemaculatus and the Hawaiian M. blackburni. Thus, M. sexta and M. quinquemaculatus are closely related, but are not sister species. Biogeographical analyses reveal an ancestral center of diversification in Central America, and Manduca appears to have subsequently colonized North and South America. Our phylogeny provides an important foundation for comparative studies of two model organisms and their relatives.

A new Brazilian Passiflora leafminer: Spinivalva gaucha, gen. n., sp. n. (Lepidoptera, Gracillariidae, Gracillariinae), the first gracillariid without a sap-feeding instar

Male, female, pupa, larva and egg of a new genus and species of Gracillariidae (Gracillariinae), Spinivalva gaucha Moreira and Vargas from southern Brazil are described and illustrated with the aid of optical and scanning electron microscopy. A preliminary analysis of mitochondrial DNA sequences including members of related lineages is also provided. The immature stages are associated with Passiflora actinia, Passiflora misera and Passiflora suberosa (Passifloraceae), and build mines on the adaxial leaf surface. Initially the mines are serpentine in shape, but later in larval ontogeny become a blotch type. Although the larvae are hypermetamorphic as in other Gracillariidae, there is no sap-feeding instar in Spinivalva gaucha; the larva feeds on the palisade parenchyma, thus producing granular frass during all instars. Pupation occurs outside the mine; prior to pupating, the larva excretes numerous bubbles that are placed in rows on the lateral margins of the cocoon external surface. This is the second genus of gracillariid moth described for the Atlantic Rain Forest, and the second gracillariid species known to be associated with Passifloraceae.

A large-scale, higher-level, molecular phylogenetic study of the insect order Lepidoptera (moths and butterflies)

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.

A molecular phylogeny for yponomeutoidea (insecta, Lepidoptera, ditrysia) and its implications for classification, biogeography and the evolution of host plant use

BACKGROUND

Yponomeutoidea, one of the early-diverging lineages of ditrysian Lepidoptera, comprise about 1,800 species worldwide, including notable pests and insect-plant interaction models. Yponomeutoids were one of the earliest lepidopteran clades to evolve external feeding and to extensively colonize herbaceous angiosperms. Despite the group's economic importance, and its value for tracing early lepidopteran evolution, the biodiversity and phylogeny of Yponomeutoidea have been relatively little studied.

METHODOLOGY/PRINCIPAL FINDINGS

Eight nuclear genes (8 kb) were initially sequenced for 86 putative yponomeutoid species, spanning all previously recognized suprageneric groups, and 53 outgroups representing 22 families and 12 superfamilies. Eleven to 19 additional genes, yielding a total of 14.8 to 18.9 kb, were then sampled for a subset of taxa, including 28 yponomeutoids and 43 outgroups. Maximum likelihood analyses were conducted on data sets differing in numbers of genes, matrix completeness, inclusion/weighting of synonymous substitutions, and inclusion/exclusion of "rogue" taxa. Monophyly for Yponomeutoidea was supported very strongly when the 18 "rogue" taxa were excluded, and moderately otherwise. Results from different analyses are highly congruent and relationships within Yponomeutoidea are well supported overall. There is strong support overall for monophyly of families previously recognized on morphological grounds, including Yponomeutidae, Ypsolophidae, Plutellidae, Glyphipterigidae, Argyresthiidae, Attevidae, Praydidae, Heliodinidae, and Bedelliidae. We also assign family rank to Scythropiinae (Scythropiidae stat. rev.), which in our trees are strongly grouped with Bedelliidae, in contrast to all previous proposals. We present a working hypothesis of among-family relationships, and an informal higher classification. Host plant family associations of yponomeutoid subfamilies and families are non-random, but show no trends suggesting parallel phylogenesis. Our analyses suggest that previous characterizations of yponomeutoids as predominantly Holarctic were based on insufficient sampling.

CONCLUSIONS/SIGNIFICANCE

We provide the first robust molecular phylogeny for Yponomeutoidea, together with a revised classification and new insights into their life history evolution and biogeography.

A molecular phylogeny for the leaf-roller moths (Lepidoptera: Tortricidae) and its implications for classification and life history evolution

BACKGROUND

Tortricidae, one of the largest families of microlepidopterans, comprise about 10,000 described species worldwide, including important pests, biological control agents and experimental models. Understanding of tortricid phylogeny, the basis for a predictive classification, is currently provisional. We present the first detailed molecular estimate of relationships across the tribes and subfamilies of Tortricidae, assess its concordance with previous morphological evidence, and re-examine postulated evolutionary trends in host plant use and biogeography.

METHODOLOGY/PRINCIPAL FINDINGS

We sequenced up to five nuclear genes (6,633 bp) in each of 52 tortricids spanning all three subfamilies and 19 of the 22 tribes, plus up to 14 additional genes, for a total of 14,826 bp, in 29 of those taxa plus all 14 outgroup taxa. Maximum likelihood analyses yield trees that, within Tortricidae, differ little among data sets and character treatments and are nearly always strongly supported at all levels of divergence. Support for several nodes was greatly increased by the additional 14 genes sequenced in just 29 of 52 tortricids, with no evidence of phylogenetic artifacts from deliberately incomplete gene sampling. There is strong support for the monophyly of Tortricinae and of Olethreutinae, and for grouping of these to the exclusion of Chlidanotinae. Relationships among tribes are robustly resolved in Tortricinae and mostly so in Olethreutinae. Feeding habit (internal versus external) is strongly conserved on the phylogeny. Within Tortricinae, a clade characterized by eggs being deposited in large clusters, in contrast to singly or in small batches, has markedly elevated incidence of polyphagous species. The five earliest-branching tortricid lineages are all species-poor tribes with mainly southern/tropical distributions, consistent with a hypothesized Gondwanan origin for the family.

CONCLUSIONS/SIGNIFICANCE

We present the first robustly supported phylogeny for Tortricidae, and a revised classification in which all of the sampled tribes are now monophyletic.