Phylogeny of the mega-diverse Gelechioidea (Lepidoptera): adaptations and determinants of success

Systematics and evolutionary dynamics of insect-fern interactions in the specialized fern-spore feeding Cuprininae (Lepidoptera, Stathmopodidae)

Fern-spore-feeding (FSF) is rare and found in only four families of Lepidoptera. Stathmopodidae is the most speciose family that contains FSF species, and its subfamily Cuprininae exclusively specializes on FSF. However, three species of Stathmopodinae also specialize on FSF. To better understand the evolutionary history of FSF and, more generally, the significance of specialization on a peculiar host, a phylogenetic and taxonomic revision for this group is necessary. We reconstructed the most comprehensive molecular phylogeny, including one mitochondrial and four nuclear genes, of Stathmopodidae to date, including 137 samples representing 62 species, with a particular focus on the FSF subfamily, Cuprininae, including 33 species (41% of named species) from 6 of the 7 Cuprininae genera. Species from two other subfamilies, Stathmopodinae and Atkinsoniinae, were also included. We found that FSF evolved only once in Stathmopodidae and that the previous hypothesis of multiple origins of FSF was misled by inadequate taxonomy. Moreover, we showed that (1) speciation/extinction rates do not differ significantly between FSF and non-FSF groups and that (2) oligophage is the ancestral character state in Cuprininae. We further revealed that a faster rate of accumulating specialists over time, and thus a higher number of specialists, was achieved by a higher transition rate from oligophagages to specialists compared to the transition rate in the opposite direction. We finish by describing three new genera, Trigonodagen. nov., Petalagen. nov., and Pediformisgen. nov., and revalidating five genera: Cuprina, Calicotis, Thylacosceles, Actinoscelis, Thylacosceloides in Cuprininae, and we provide an updated taxonomic key to genera and a revised global checklist of Cuprininae.

First report of the genus Semioscopis Hbner and four species of Gelechioidea (Lepidoptera) from Korea with redescriptions

We report for the first time the presence of the genus Semioscopis Hbner, 1825 and four species of the superfamily Gelechioidea in Korea, namely Coleophora serinipennella Christoph, 1872 (Coleophoridae), Semioscopis japonicella Saito, 1989 (Depressariidae), Anarsia isogona Meyrick, 1913 (Gelechiidae) and Dichomeris syndyas Meyrick, 1926 (Gelechiidae). In addition, we provide redescription and diagnostic characteristics for each species, based on previous descriptions and additional morphological data acquired.

New species of Oecophoridae (Lepidoptera: Gelechioidea) from Chile

Nine new species of Oecophoridae are described from central and southern Chile: Corita morai Urra, Encolia flava Urra, Endrosis apablazai Urra, Gildita versicolora Urra, Glorita nahuelbutensis Urra, Nagehana maulina Urra, Nagehana parvula Urra, Pirquelia vidali Urra, Zulemita chimbarongensis Urra. Diagnostic characteristics, geographic distribution data, photographs of adults and illustrations of the genital structures of males and females are provided.  

Global Biodiversity of the Family Lecithoceridae (Gelechioidea) with a Brief Historical Review

The family Lecithoceridae (Lepidoptera, Gelechioidea) is one of the more poorly known groups of microlepidoptera, even though it is a highly diverse group containing more than 1430 known species so far. During the last two decades since the end of the 20th century, the author has intensively studied the family Lecithoceridae, especially for the less explored areas including southern Asia and the Oceanian and Afrotropical regions. Throughout these studies, the author (often with his co-authors) described the new subfamily Crocanthinae Park, 2015, 32 new genera, and over 540 new species of the family. In this article, a historical review for the taxonomic works of the family since the comprehensive study by Gozmány is briefly summarized, with a comparison of the number of genera/species of each subfamily, and the number of the species by the subfamily in each region of the world. All available information on the phylogeny, biology, morphological characters of subfamilies, and zoogeographical remarks for the distribution of family are listed and discussed.

Movement and olfactory signals: Sexually dimorphic antennae and female flightlessness in moths

Darwin argued a role for sexual selection in the evolution of male sensory structures, including insect antennae, the strength of which will depend upon the importance of early arrival at receptive females. There is remarkable variation in the nature and degree of sexual dimorphism in moth antennae, with males of some species having spectacular, feathery antennae. Although it is widely assumed that these elaborate structures provide greater sensitivity to chemical signals (sex pheromones), the factors underlying the interspecific diversity in male antennal structure and size are poorly understood. Because male antennal morphology may be affected by several female life–history traits, including flight ability, we conducted a phylogenetic comparative analysis to test how these traits are linked, using data from 93 species of moths across 11 superfamilies. Our results reveal that elaborate antennae in males have evolved more frequently in species where females are monandrous. Further, female loss of flight ability evolved more frequently in species where males have elaborate antennae. These results suggest that elaborate antennae have evolved in response to more intense male competition, arising from female monandry, and that the evolution of elaborate antennae in males has, in turn, shaped the evolution of female flightlessness.

Revision of Neotropical Scythrididae moths and descriptions of 22 new species from Argentina, Chile, and Peru (Lepidoptera, Gelechioidea)

The taxonomy of South American Scythrididae (Lepidoptera: Gelechioidea) is revised, based on external morphology, genitalia, male abdominal segment VIII, and DNA barcodes using genetic distances, BINs, and a tentative molecular phylogeny. Data include both historical and fresh specimens from Argentina, Brazil, Colombia, Chile, Ecuador, Paraguay, and Peru. Thirty-four species are recognised as valid, and the fauna classified in three genera. Type specimens and morphology of all species are described and figured in detail. DNA barcode sequences of the COI gene were successful for 22 species, the average genetic divergence between species being 5.1%. A key to Neotropical Scythrididae species is provided, based on the male genitalia and abdominal segment VIII, which show most and easily accessible interspecific differences. Our study revealed that the Scythridae fauna of South America is more or less completely unknown. As a result, 22 new species are described, increasing the number of South American Scythrididae species from 13 to 34. All new species are authored by Kari Nupponen (incertae sedis means the genus combination is uncertain and needs further research, country of the type locality is given in parentheses): Rhamphurasubdimota sp. nov. (Argentina), R.pozohondaensis sp. nov. (Argentina), R.spiniuncus sp. nov. (Argentina), R.angulisociella sp. nov. incertae sedis (Argentina), R.curvisociella sp. nov. incertae sedis (Argentina), R.tetrafasciella sp. nov. incertae sedis (Argentina), Landryiaankylosauroides sp. nov. incertae sedis (Argentina), L.chilensis sp. nov. incertae sedis (Chile), Scythrisdirectiphallella sp. nov. (Argentina), S.furciphallella sp. nov. (Argentina), S.manchaoensis sp. nov. (Argentina), S.salinasgrandensis sp. nov. (Argentina), S.angustivalvella sp. nov. (Argentina), S.caimancitoensis sp. nov. (Argentina), S.lequetepequensis sp. nov. (Peru), S.sanfriscoensis sp. nov. (Argentina), S.tigrensis sp. nov. (Argentina), S.bicoloristrigella sp. nov. incertae sedis (Argentina), S.saldaitisi sp. nov. incertae sedis (Argentina), S.wikstromi sp. nov. incertae sedis (Argentina), S.andensis sp. nov. incertae sedis (Argentina), S.mendozaensis sp. nov. incertae sedis (Argentina). The following new combinations are proposed: Scythrisdepressa Meyrick, 1931 and Scythrisdimota Meyrick, 1931 are transferred from Scythris Hübner, 1825 to Rhamphura Landry, 1991 comb. nov. Three species classified in Scythris earlier are now classified as Scythris (incertae sedis): Scythrisdividua Meyrick, 1916, S.medullata Meyrick, 1916 and S.notorrhoa Meyrick, 1921. The taxon Syntetrernisneocompsa Meyrick, 1933, recently classified in Scythrididae: Scythris, is excluded from Scythrididae and it is now classified in Cosmopterigidae incertae sedis.

Taxonomic study of the genus Punctulata Wang (Lepidoptera: Autostichidae) from China, with descriptions of two new species

The genus Punctulata Wang, 2006 is transferred from Oecophoridae to Autostichidae based on morphological characters and molecular data. Punctulata guangxiensis sp. nov. and P. novipalliptera sp. nov. are described as new based on the specimens collected in China. The females of P. palliptera Wang, 2006 and P. trunciformis Wang, 2006 are described for the first time. Images of male adults and male and female genitalia are provided for all the six Punctulata species along with a key to separate its species and a map showing their distribution.

Complete mitochondrial genome of Casmara patrona (Lepidoptera: Oecophoridae)

The complete mitochondrial genome of Casmara patrona (Lepidoptera: Oecophoridae) was sequenced for a future phylogenetic study of Lepidoptera. The circle genome of the moth is 15,393 bp in length with a pronounced base bias of A + T (79.3%), containing 13 protein-coding genes, 22 transfer RNAs, two ribosomal RNAs, and a putative control region. The coxI gene had a CGA start codon as most lepidopteran species, other PCGs use the typical ATN codons. All PCGs end with the complete stop codon TAA. Phylogenetic analyses showed that the monophyly of Oecophoridae was highly supported based on the concatenated sequence of the 13 PCGs. In addition, Oecophoridae and Xyloryctidae had the closest relationship.

High functionality of DNA barcodes and revealed cases of cryptic diversity in Korean curved-horn moths (Lepidoptera: Gelechioidea)

Curved-horn moths or gelechioid moths (Lepidoptera: Gelechioidea) represent one of the most diverse lepidopteran groups. Due to the large number of species, generally small size of adults and subtle morphological differences, their confident identification requires tenacious and long-term dedication on their diversity. Over the past decade, DNA barcoding has repeatedly been used to elucidate boundaries of species in many large and difficult groups. Here, we conducted a test of DNA barcoding with the diverse fauna of Korean Gelechioidea with very little prior information of COI gene region from the area. Altogether 509 specimens representing 154 morphospecies were included in the study. The species assignments of all three tested species delimitation methods (ABGD, bPTP and PTP) were consistent with morphological identifications for 117 species (75.97%). A threshold of 2.5% genetic divergence was observed to differentiate the morphological species efficiently. Careful morphological examination of morphospecies exceeding 2.5% intraspecific variability prove cryptic diversity in three species (Neoblastobasis biceratala, Evippe albidoesella and Promalactis atriplagata). One morphospecies, Promalactis odaiensis, showed high intraspecific divergence while consisted of only a single MOTU. Overall, DNA barcoding was shown to provide a powerful tool to discriminate species of Korean Gelechioidea and reveal cases of cryptic diversity.

DNA barcode library for European Gelechiidae (Lepidoptera) suggests greatly underestimated species diversity

For the first time, a nearly complete barcode library for European Gelechiidae is provided. DNA barcode sequences (COI gene – cytochrome c oxidase 1) from 751 out of 865 nominal species, belonging to 105 genera, were successfully recovered. A total of 741 species represented by specimens with sequences ≥ 500bp and an additional ten species represented by specimens with shorter sequences were used to produce 53 NJ trees. Intraspecific barcode divergence averaged only 0.54% whereas distance to the Nearest-Neighbour species averaged 5.58%. Of these, 710 species possessed unique DNA barcodes, but 31 species could not be reliably discriminated because of barcode sharing or partial barcode overlap. Species discrimination based on the Barcode Index System (BIN) was successful for 668 out of 723 species which clustered from minimum one to maximum 22 unique BINs. Fifty-five species shared a BIN with up to four species and identification from DNA barcode data is uncertain. Finally, 65 clusters with a unique BIN remained unidentified to species level. These putative taxa, as well as 114 nominal species with more than one BIN, suggest the presence of considerable cryptic diversity, cases which should be examined in future revisionary studies.

Phylogeny, host use, and diversification in the moth family Momphidae (Lepidoptera: Gelechioidea)

Insect herbivores and their hostplants constitute much of Earth's described biological diversity, but how these often-specialized associations diversify is not fully understood. We combined detailed hostplant data and comparative phylogenetic analyses of the lepidopteran family Momphidae to explore how shifts in the use of hostplant resources, not just hostplant taxon, contribute to the diversification of a phytophagous insect lineage. We inferred two phylogenetic hypotheses emphasizing relationships among species in the nominate genus, Mompha Hübner. A six-gene phylogeny was constructed with reared exemplars and collections from hostplants in the family Onagraceae from western and southwestern USA, and a cytochrome c oxidase subunit 1 (COI) phylogeny was inferred from collections and publicly available accessions in the Barcode of Life Data System. Species delimitation analyses combined with morphological data revealed ca. 56 undescribed species-level taxa, many of which are hostplant specialists on Onagraceae in the southwestern USA. Our phylogenetic reconstructions divided Momphidae into six major clades: 1) an Onagraceae flower- and fruit-boring clade, 2) a Melastomataceae-galling clade, 3) a leafmining clade A, 4) a leafmining clade B, 5) a Zapyrastra Meyrick clade, and 6) a monobasic lineage represented by Mompha eloisella (Clemens). Ancestral trait reconstructions using the COI phylogeny identified leafmining on Onagraceae as the ancestral state for Momphidae. Our study finds that shifts along three hostplant resource axes (plant taxon, plant tissue type, and larval feeding mode) have contributed to the evolutionary success and diversification of momphids.

Revision of the genus Megacraspedus Zeller, 1839, a challenging taxonomic tightrope of species delimitation (Lepidoptera, Gelechiidae)

The taxonomy of the Palearctic genus Megacraspedus Zeller, 1839 (Lepidoptera, Gelechiidae) is revised, based on external morphology, genitalia and DNA barcodes. An integrative taxonomic approach supports the existence of 85 species which are arranged in 24 species groups (disputed taxa from other faunal regions are discussed). Morphology of all species is described and figured in detail. For 35 species both sexes are described; for 46 species only the male sex is reported, in one species the male is unknown, whereas in three species the female adult and/or genitalia morphology could not be analysed due to lack of material. DNA barcode sequences of the COI barcode fragment with > 500 bp were obtained from 264 specimens representing 62 species or about three-quarters of the species. Species delimitation is particularly difficult in a few widely distributed species with high and allegedly intraspecific DNA barcode divergence of nearly 14%, and with up to 23 BINs in a single species. Deep intraspecific or geographical splits in DNA barcode are frequently not supported by morphology, thus indicating a complex phylogeographic history or other unresolved molecular problems. The following 44 new species (22 of them from Europe) are described: Megacraspedusbengtssoni sp. n. (Spain), M.junnilaineni sp. n. (Turkey), M.similellus sp. n. (Bulgaria, Romania, Turkey), M.golestanicus sp. n. (Iran), M.tokari sp. n. (Croatia), M.neli sp. n. (France, Italy), M.faunierensis sp. n. (Italy), M.gredosensis sp. n. (Spain), M.bidentatus sp. n. (Spain), M.fuscus sp. n. (Spain), M.trineae sp. n. (Portugal, Spain), M.skoui sp. n. (Spain), M.spinophallus sp. n. (Spain), M.occidentellus sp. n. (Portugal), M.granadensis sp. n. (Spain), M.heckfordi sp. n. (Spain), M.tenuiuncus sp. n. (France, Spain), M.devorator sp. n. (Bulgaria, Romania), M.brachypteris sp. n. (Albania, Greece, Macedonia, Montenegro), M.barcodiellus sp. n. (Macedonia), M.sumpichi sp. n. (Spain), M.tabelli sp. n. (Morocco), M.gallicus sp. n. (France, Spain), M.libycus sp. n. (Libya, Morocco), M.latiuncus sp. n. (Kazahkstan), M.kazakhstanicus sp. n. (Kazahkstan), M.knudlarseni sp. n. (Spain), M.tenuignathos sp. n. (Morocco), M.glaberipalpus sp. n. (Morocco), M.nupponeni sp. n. (Russia), M.pototskii sp. n. (Kyrgyzstan), M.feminensis sp. n. (Kazakhstan), M.kirgizicus sp. n. (Afghanistan, Kazakhstan, Kyrgyzstan), M.ibericus sp. n. (Portugal, Spain), M.steineri sp. n. (Morocco), M.gibeauxi sp. n. (Algeria, Tunisia), M.multipunctellus sp. n. (Turkey), M.teriolensis sp. n. (Croatia, Greece, Italy, Slovenia), M.korabicus sp. n. (Macedonia), M.skulei sp. n. (Spain), M.longivalvellus sp. n. (Morocco), M.peslieri sp. n. (France, Spain), M.pacificus sp. n. (Afghanistan), and M.armatophallus sp. n. (Afghanistan). Nevadia Caradja, 1920, syn. n. (homonym), Cauloecista Dumont, 1928, syn. n., Reichardtiella Filipjev, 1931, syn. n., and Vadenia Caradja, 1933, syn. n. are treated as junior synonyms of Megacraspedus. Furthermore the following species are synonymised: M.subdolellus Staudinger, 1859, syn. n., M.tutti Walsingham, 1897, syn. n., and M.grossisquammellus Chrétien, 1925, syn. n. of M.lanceolellus (Zeller, 1850); M.culminicola Le Cerf, 1932, syn. n. of M.homochroa Le Cerf, 1932; M.separatellus (Fischer von Röslerstamm, 1843), syn. n. and M.incertellus Rebel, 1930, syn. n. of M.dolosellus (Zeller, 1839); M.mareotidellus Turati, 1924, syn. n. of M.numidellus (Chrétien, 1915); M.litovalvellus Junnilainen, 2010, syn. n. of M.imparellus (Fischer von Röslerstamm, 1843); M.kaszabianus Povolný, 1982, syn. n. of M.leuca (Filipjev, 1929); M.chretienella (Dumont, 1928), syn. n., M.halfella (Dumont, 1928), syn. n., and M.arnaldi (Turati & Krüger, 1936), syn. n. of M.violacellum (Chrétien, 1915); M.escalerellus Schmidt, 1941, syn. n. of M.squalida Meyrick, 1926. Megacraspedusribbeella (Caradja, 1920), comb. n., M.numidellus (Chrétien, 1915), comb. n., M.albella (Amsel, 1935), comb. n., M.violacellum (Chrétien, 1915), comb. n., and M.grisea (Filipjev, 1931), comb. n. are newly combined in Megacraspedus.

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.

Complete mitochondrial genome of the gelechioid Stathmopoda auriferella (Lepidoptera: Stathmopodidae)

Although Gelechioidea is the second most species-rich group of Lepidoptera, comprising ∼18,000 species, mitochondrial genomes (mitogenomes) have been sequenced from only eight species. In this study, we determined the complete mitogenomic sequence of the gelechioid Stathmopoda auriferella (Lepidoptera: Stathmopodidae) for a future phylogenetic study of Lepidoptera. The 15,456-bp-long S. auriferella genome was the largest among sequenced gelechioids. The cytochrome c oxidase subunit I (COI) gene had a CGA start codon as most other lepidopteran species do, including the eight gelechioid species for which datasets are available. An A + T-rich region (375 bp in length) harbored blocks of conserved sequences, which are typically found in lepidopteran insects. Bayesian inference (BI) phylogeny using 13 protein-coding genes (PCGs) indicated that S. auriferella belongs to the Stathmopodidae family and is grouped together with the within-familial species Hieromantis kurokoi with a strong nodal support (Bayesian posterior probabilities =0.95).

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.

Evolution of larval life mode of Oecophoridae (Lepidoptera: Gelechioidea) inferred from molecular phylogeny

Phylogenetic relationships within family Oecophoridae have been poorly understood. Consequently the subfamily and genus level classifications with this family problematic. A comprehensive phylogenetic analysis of Oecophoridae, the concealer moths, was performed based on analysis of 4444 base pairs of mitochondrial COI, nuclear ribosomal RNA genes (18S and 28S) and nuclear protein coding genes (IDH, MDH, Rps5, EF1a and wingless) for 82 taxa. Data were analyzed using maximum likelihood (ML), parsimony (MP) and Bayesian (BP) phylogenetic frameworks. Phylogenetic analyses indicated that (i) genera Casmara, Tyrolimnas and Pseudodoxia did not belong to Oecophoridae, suggesting that Oecophoridae s. authors was not monophyletic; (ii) other oecophorids comprising two subfamilies, Pleurotinae and Oecophorinae, were nested within the same clade, and (iii) Martyringa, Acryptolechia and Periacmini were clustered with core Xyloryctidae. They appeared to be sister lineage with core Oecophoridae. BayesTraits were implemented to explore the ancestral character states to infer historical microhabitat patterns and sheltering strategy of larvae. Reconstruction of ancestral microhabitat of oecophorids indicated that oecophorids might have evolved from dried plant feeders and further convergently specialized. The ancestral larva sheltering strategy of oecophorids might have used a silk tube by making itself, shifting from mining leaves.

Complete mitochondrial genome of the gelechioid Hieromantis kurokoi (Lepidoptera: Stathmopodidae)

Although the Gelechioidea is the second most species-rich group of Lepidoptera, comparatively few mitochondrial genomes (mitogenomes) have been sequenced in this superfamily. Here, we determined the complete mitogenomic sequence of the gelechioid Hieromantis kurokoi (Lepidoptera: Stathmopodidae) as the basis for a future study of the phylogeny of butterflies and moths (clade Ditrysia). The H. kurokoi genome was 15,208 bp with a typical set of genes (13 protein-coding genes [PCGs], two rRNA genes and 22 tRNA genes) and one major non-coding A + T-rich region. The cytochrome c oxidase subunit 1 (COI) gene had a CGA start codon, which is the start codon for this gene in the majority of lepidopteran species, whereas other PCGs began with an ATN codon. A 360 bp-long A + T-rich region harbored the blocks of conserved sequences that are typically found in lepidopteran insects. Phylogenetic analysis using the 13 PCGs and Bayesian inference (BI) and maximum-likelihood (ML) methods indicated that H. kurokoi belonged to the family Stathmopodidae and grouped together with the within-familial species Atrijuglans hetaohei with the highest nodal support (BI, 1.0; ML, 100%).

Complete mitochondrial genomes of two gelechioids, Mesophleps albilinella and Dichomeris ustalella (Lepidoptera: Gelechiidae), with a description of gene rearrangement in Lepidoptera

We sequenced the entire mitochondrial genome (mitogenome) of two gelechioids, Mesophleps albilinella and Dichomeris ustalella, and compared their genome organization and sequence composition to those of available gelechioid mitogenomes for an enhanced understanding of Gelechioidea genomic characteristics. We compared all available lepidopteran mitogenome arrangements, including that of M. albilinella, which is unique in Gelechioidea, to comprehend the extensiveness and mechanisms of gene rearrangement in Lepidoptera. The genomes of M. albilinella and D. ustalella are 15,274 and 15,410 bp in size, respectively, with the typical sets of mitochondrial (mt) genes. The COI gene begins with CGA (arginine) in all sequenced gelechioids, including M. albilinella and D. ustalella, reinforcing the feature as a synapomorphic trait, at least in the Gelechioidea. Each 353- and 321-bp long A + T-rich region of M. albilinella and D. ustalella contains one (D. ustalella) or two (M. albilinella) tRNA-like structures. The M. albilinella mitogenome has a unique gene arrangement among the Gelechioidea: ARNESF (the underline signifies an inverted gene) at the ND3 and ND5 junction, as opposed to the ARNSEF that is found in ancestral insects. An extensive search of available lepidopteran mitogenomes, including that of M. albilinella, turned up six rearrangements that differ from those of ancestral insects. Most of the rearrangements can be explained by the tandem duplication-random loss model, but inversion, which requires recombination, is also found in two cases, including M. albilinella. Excluding the MIQ rearrangement at the A + T-rich region and ND2 junction, which is found in nearly all Ditrysia, most of the remaining rearrangements found in Lepidoptera appear to be independently derived in that they are automorphic at several taxonomic scales, although current mitogenomic data are limited, particularly for congeneric data.

The Complete Mitochondrial Genome of Brachmia macroscopa (Lepidoptera: Gelechiidae) and Its Related Phylogenetic Analysis

The sweet potato leaf folder, Brachmia macroscopa, is an important pest in China. The complete mitogenome, which consists of 13 protein-coding genes (PCGs), 22 transfer RNA genes, two ribosomal RNA genes, and an A + T-rich region, was sequenced and found to be 15,394 bp in length (GeneBank no. KT354968). The gene order and orientation of the B. macroscopa mitogenome were similar to those of other sequenced lepidopteran species. All of the PCGs started with ATN as the canonical start codon except for cox1, which started with CGA. In regard to stop codons, most PCGs stopped at TAA except for cox2, which stopped at TA, and nad4, which stopped at a single T. Thirteen PCGs of the available species (33 taxa) were used to demonstrate phylogenetic relationships. The ditrysian cluster was supported as a monophyletic clade at high levels by using maximum likelihood and Bayesian methods. The apoditrysian group, covering the Gelechioidea, formed a monophyletic clade with a bootstrap value of 88% and a posterior probability of 1.00. The superfamily Gelechioidea was supported as a monophyletic lineage by a posterior probability of 1.00.

Mitochondrial genome characterization of Tecia solanivora (Lepidoptera: Gelechiidae) and its phylogenetic relationship with other lepidopteran insects

The complete mitogenome of the potato tuber moth Tecia solanivora (Lepidoptera: Gelechiidae) was sequenced, annotated, characterized and compared with 140 species of the order Lepidoptera. The circular genome is 15,251 bp, containing 37 genes (13 protein-coding genes (PCGs), two rRNA genes, 22 tRNA genes and an A+T-rich region). The gene arrangement was identical to other lepidopteran mitogenomes but different from the ancestral arrangement found in most insects for the tRNA-Met gene (A+T-region, tRNA-I, tRNA-Q, tRNA-M). The mitogenome of T. solanivora is highly A+T-biased (78.2%) and exhibits negative AT- and GC-skews. All PCGs are initiated by canonical ATN start codons, except for Cytochrome Oxidase subunit 1 (COI), which is initiated by CGA. Most PCGs have a complete typical stop codon (TAA). Only NAD1 has a TAG stop codon and the COII and NAD5 genes have an incomplete stop codon consisting of just a T. The A+T-rich region is 332 bp long and contains common features found in lepidopteran mitogenomes, including the 'ATAGA' motif, a 17 bp poly (T) stretch and a (AT)8 element preceded by the 'ATTTA' motif. Other tandem repeats like (TAA)4 and (TAT)7 were found, as well as (T)6 and (A)10 mononucleotide repeat elements. Finally, this mitogenome has 20 intergenic spacer regions. The phylogenetic relationship of T. solanivora with 28 other lepidopteran families (12 superfamilies) showed that taxonomic classification by morphological features coincides with the inferred phylogeny. Thus, the Gelechiidae family represents a monophyletic group, suggesting that T. solanivora and Pectinophora gossypiella have a recent common ancestor.

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

BACKGROUND

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.

RESULTS

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.

CONCLUSIONS

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.

Delineating species with DNA barcodes: a case of taxon dependent method performance in moths

The accelerating loss of biodiversity has created a need for more effective ways to discover species. Novel algorithmic approaches for analyzing sequence data combined with rapidly expanding DNA barcode libraries provide a potential solution. While several analytical methods are available for the delineation of operational taxonomic units (OTUs), few studies have compared their performance. This study compares the performance of one morphology-based and four DNA-based (BIN, parsimony networks, ABGD, GMYC) methods on two groups of gelechioid moths. It examines 92 species of Finnish Gelechiinae and 103 species of Australian Elachistinae which were delineated by traditional taxonomy. The results reveal a striking difference in performance between the two taxa with all four DNA-based methods. OTU counts in the Elachistinae showed a wider range and a relatively low (ca. 65%) OTU match with reference species while OTU counts were more congruent and performance was higher (ca. 90%) in the Gelechiinae. Performance rose when only monophyletic species were compared, but the taxon-dependence remained. None of the DNA-based methods produced a correct match with non-monophyletic species, but singletons were handled well. A simulated test of morphospecies-grouping performed very poorly in revealing taxon diversity in these small, dull-colored moths. Despite the strong performance of analyses based on DNA barcodes, species delineated using single-locus mtDNA data are best viewed as OTUs that require validation by subsequent integrative taxonomic work.

Towards a mitogenomic phylogeny of Lepidoptera

The backbone phylogeny of Lepidoptera remains unresolved, despite strenuous recent morphological and molecular efforts. Molecular studies have focused on nuclear protein coding genes, sometimes adding a single mitochondrial gene. Recent advances in sequencing technology have, however, made acquisition of entire mitochondrial genomes both practical and economically viable. Prior phylogenetic studies utilised just eight of 43 currently recognised lepidopteran superfamilies. Here, we add 23 full and six partial mitochondrial genomes (comprising 22 superfamilies of which 16 are newly represented) to those publically available for a total of 24 superfamilies and ask whether such a sample can resolve deeper lepidopteran phylogeny. Using recoded datasets we obtain topologies that are highly congruent with prior nuclear and/or morphological studies. Our study shows support for an expanded Obtectomera including Gelechioidea, Thyridoidea, plume moths (Alucitoidea and Pterophoroidea; possibly along with Epermenioidea), Papilionoidea, Pyraloidea, Mimallonoidea and Macroheterocera. Regarding other controversially positioned higher taxa, Doidae is supported within the new concept of Drepanoidea and Mimallonidae sister to (or part of) Macroheterocera, while among Nymphalidae butterflies, Danainae and not Libytheinae are sister to the remainder of the family. At the deepest level, we suggest that a tRNA rearrangement occurred at a node between Adeloidea and Ditrysia+Palaephatidae+Tischeriidae.

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.

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.