Genomic outposts serve the phylogenomic pioneers: designing novel nuclear markers for genomic DNA extractions of lepidoptera

Mesoamerica is a cradle and the Atlantic Forest is a museum of Neotropical butterfly diversity: insights from the evolution and biogeography of Brassolini (Lepidoptera: Nymphalidae)

Regional species diversity is explained ultimately by speciation, extinction and dispersal. Here, we estimate dispersal and speciation rates of Neotropical butterflies to propose an explanation for the distribution and diversity of extant species. We focused on the tribe Brassolini (owl butterflies and allies), a Neotropical group that comprises 17 genera and 108 species, most of them endemic to rainforest biomes. We inferred a robust species tree using the multispecies coalescent framework and a dataset including molecular and morphological characters. This formed the basis for three changes in Brassolini classification: (1) Naropina syn. nov. is subsumed within Brassolina; (2) Aponarope syn. nov. is subsumed within Narope; and (3) Selenophanes orgetorix comb. nov. is reassigned from Catoblepia to Selenophanes. By applying biogeographical stochastic mapping, we found contrasting species diversification and dispersal dynamics across rainforest biomes, which might be explained, in part, by the geological and environmental history of each bioregion. Our results revealed a mosaic of biome-specific evolutionary histories within the Neotropics, where butterfly species have diversified rapidly (cradles: Mesoamerica), have accumulated gradually (museums: Atlantic Forest) or have diversified and accumulated alternately (Amazonia). Our study contributes evidence from a major butterfly lineage that the Neotropics are a museum and a cradle of species diversity.

Wolbachia affects mitochondrial population structure in two systems of closely related Palaearctic blue butterflies

The bacterium Wolbachia infects many insect species and spreads by diverse vertical and horizontal means. As co-inherited organisms, these bacteria often cause problems in mitochondrial phylogeny inference. The phylogenetic relationships of many closely related Palaearctic blue butterflies (Lepidoptera: Lycaenidae: Polyommatinae) are ambiguous. We considered the patterns of Wolbachia infection and mitochondrial diversity in two systems: Aricia agestis/Aricia artaxerxes and the Pseudophilotes baton species complex. We sampled butterflies across their distribution ranges and sequenced one butterfly mitochondrial gene and two Wolbachia genes. Both butterfly systems had uninfected and infected populations, and harboured several Wolbachia strains. Wolbachia was highly prevalent in A. artaxerxes and the host's mitochondrial structure was shallow, in contrast to A. agestis. Similar bacterial alleles infected both Aricia species from nearby sites, pointing to a possible horizontal transfer. Mitochondrial history of the P. baton species complex mirrored its Wolbachia infection and not the taxonomical division. Pseudophilotes baton and P. vicrama formed a hybrid zone in Europe. Wolbachia could obscure mitochondrial history, but knowledge on the infection helps us to understand the observed patterns. Testing for Wolbachia should be routine in mitochondrial DNA studies.

Description of a new genus and species for a common and widespread Amazonian satyrine butterfly (Lepidoptera: Nymphalidae: Satyrinae: Satyrini)

We here propose a new monotypic butterfly genus Scriptor Nakahara & Espeland, n. gen. to accommodate a new species, S. sphenophorus Lamas & Nakahara, n. sp., described and named herein. Scriptor sphenophorusn. gen. and n. sp.is a relatively common and widespread butterfly species which is recovered as a member of the so-called “Splendeuptychia clade” in the nymphalid subtribe Euptychiina, based on our molecular phylogenetic analysis using a maximum likelihood approach. Nevertheless, its sister group is not confidently resolved in any analysis, supporting a relatively distant relationship to any described genus as well as our decision to establish a new monotypic genus. We further discuss the proposed taxonomy in the light of frequent criticism of the description of monotypic taxa, as well as emphasize the importance of incorporating multiple evidence when describing new genera, illustrated by reference to several recent generic descriptions in this subtribe.

DNA barcodes for Aotearoa New Zealand Pyraloidea (Lepidoptera)

Identification of pyraloid species is often hampered by highly similar external morphology requiring microscopic dissection of genitalia. This becomes especially obvious when mass samples from ecological studies or insect monitoring have to be analysed. DNA barcode sequences could accelerate identification, but are not available for most pyraloid species from New Zealand. Hence, we are presenting a first DNA-barcode library for this group, providing 440 COI barcodes (cytochrome C oxidase I sequences) for 73 morphologically-identified species, which is 29% of Pyraloidea known from New Zealand. Results are analysed using the Barcode Index Number system (BIN) of BOLD and the Automatic Barcode Gap Discovery method (ABGD). Using BIN, the 440 barcodes reveal 82 clusters. A perfect match between BIN assignment and morphological identification was found for 63 species (86.3%). Four species (5.5%) share BINs, each with two species in one BIN, of which Glaucocharis epiphaea and Glaucocharis harmonica even share the same barcode. In contrast, six species (8.2%) split into two or more BINs, with the highest number of five BINs for Orocrambus ramosellus. The interspecific variation of all collected specimens of New Zealand Pyraloidea averages 12.54%. There are deep intraspecific divergences (> 2%) in seven species, for instance Orocrambus vulgaris with up to 6.6% and Scoparia ustimacula with 5.5%. Using ABGD, the 440 barcodes reveal 71 or 88 operational taxonomic units (OTUs), depending on the preferred partition. A perfect match between OTU and morphological identification was found for 56 species (76.7%) or 62 species (84.9%). ABGD delivers four or seven species sharing OTUs and four or ten species split into more than one OTU. Morphological re-examination, as well as the analysis of a concatenated dataset of COI and the nuclear markers EF1α and GADPH for species split into more than one BIN or OTU, do not support a higher number of species. Likewise, there is no evidence for Wolbachia infection as a trigger for these sequence variations.

A new species of Sacada Walker, 1862 from Thailand (Lepidoptera, Pyralidae, Pyralinae)

A new species of Sacada from northern Thailand is described: S. chaehomensissp. nov. Pellinen & Zahiri (Lepidoptera: Pyralidae, Pyralinae). Morphological characters and DNA barcode data are provided for the new species, with a morphological comparison to S. dzonguensis and S. umtasorensis, and a DNA-barcode comparison to S. ragonotalis and S. albioculalis, respectively. After this addition, the current number of valid species in the genus Sacada is 43.

Monopis jussii, a new species (Lepidoptera, Tineidae) inhabiting nests of the Boreal owl (Aegolius funereus)

Monopis jussii Kaila, Mutanen, Huemer, Karsholt & Autto, sp. nov. (Lepidoptera, Tineidae) is described as a new species. It is closely related to the widespread and common M. laevigella ([Denis & Schiffermüller], 1775), but differs in its distinct COI DNA barcode sequences, four examined nuclear loci as well as details in forewing coloration and pattern. Most reared specimens of M. jussii have emerged from the nest remnants of the Boreal owl (Aegolius funereus (Linnaeus, 1758)), but also nests of the Ural owl (Strix uralensis Pallas, 1771) and the Great tit (Parus major Linnaeus, 1758) have been observed as suitable habitats. Based on the present knowledge, the new species has a boreo-montane distribution as it is recorded only from northern Europe and the Alps. Several extensive rearing experiments from Strix spp. nest remnants from southern Finland did not produce any M. jussii, but thousands of M. laevigella, suggesting that the species is lacking in the area or, more unlikely, that the nest of these owl species do not serve as good habitat for the new species. This unexpected species discovery highlights, once again, the usefulness of DNA barcoding in revealing the cryptic layers of biodiversity. To serve stability we select a neotype for Tinea laevigella [Denis & Schiffermüller], 1775, and discuss the complicated synonymy and nomenclature of this species.

Spatial and temporal sex ratio bias and Wolbachia-infection in New Zealand Crambidae (Lepidoptera: Pyraloidea)

The New Zealand fauna of snout moths (Pyraloidea) predominantly consists of endemic species. During 2017 and 2018, 56 species of Pyraloidea in 1,749 individuals were collected at 14 localities. All species were screened for Wolbachia-infection, with specimens of eight species (14%) being positive, of which six species belong to Scopariinae. This is the first record of Wolbachia-infection amongst New Zealand Lepidoptera. The most common pyraloid species, Eudonia submarginalis and Orocrambus flexuosellus, were analysed for a larger set of individuals looking for sex ratio and Wolbachia-infection. There is a sex ratio bias towards females in both species, but it varies in space and time. Wolbachia is found in all populations of E. submarginalis with 10-80% of the tested individuals being positive, depending on locality. No Wolbachia-infection has been found in O. flexuosellus. Thus, sex ratio bias might be linked to Wolbachia-infection in E. submarginalis, but not in O. flexuosellus.

A complete time-calibrated multi-gene phylogeny of the European butterflies

With the aim of supporting ecological analyses in butterflies, the third most species-rich superfamily of Lepidoptera, this paper presents the first time-calibrated phylogeny of all 496 extant butterfly species in Europe, including 18 very localised endemics for which no public DNA sequences had been available previously. It is based on a concatenated alignment of the mitochondrial gene COI and up to eleven nuclear gene fragments, using Bayesian inferences of phylogeny. To avoid analytical biases that could result from our region-focussed sampling, our European tree was grafted upon a global genus-level backbone butterfly phylogeny for analyses. In addition to a consensus tree, the posterior distribution of trees and the fully concatenated alignment are provided for future analyses. Altogether a complete phylogenetic framework of European butterflies for use by the ecological and evolutionary communities is presented.

A multilocus analysis of Epicopeiidae (Lepidoptera, Geometroidea) provides new insights into their relationships and the evolutionary history of mimicry

The family Epicopeiidae is a small group of day-flying moths, known for mimicking many different groups of butterflies and moths. So far, there still lacks a reliable phylogenetic framework of Epicopeiidae that is necessary to our understanding of the evolutionary process of their mimicry. In this study, we sequenced 94 nuclear protein-coding markers for 56 epicopeiid samples and 11 outgroups, covering all ten genera of Epicopeiidae. We used homemade PCR-generated baits to capture target sequences, which allowed us to utilize old and dried specimens that were difficult to handle by conventional PCR + Sanger sequencing. Maximum likelihood and Bayesian analyses of the newly obtained dataset (86,388 bp) at both DNA and protein levels produced identical phylogenies with strong support. The non-mimicry genus Deuveia is the sister group of other epicopeiid genera. Epicopeia and Nossa are not monophyletic, and these two genera nest together to form a clade. We also estimated divergence times of Epicopeiidae and found that their initial diversification happened in Eocene about 41 million years ago. The ancestral state reconstruction of mimicry type for this family suggested that thelast common ancestor of epicopeiid moths is non-mimetic, and the Riodinidae-mimicry type evolved first. In summary, our work provides a comprehensive and robust time-calibrated phylogeny of Epicopeiidae that provides a sound framework for revising their classification and interpreting character evolution.

Hidden Genetic Variability, Can the Olive Moth Prays oleae (Lepidoptera: Yponomeutidae or Praydidae?) be a Species' Complex?

Prays oleae is the second most important pest in Mediterranean olive groves, causing substantial damage on olive production. We used mitochondrial [cytochrome c oxidase subunit I (COI), and NADH dehydrogenase subunit 5 (nad5)] and nuclear [ribosomal protein S5 (RpS5)] amplicons to assess the population variability in five main olive producing regions from Tunisia, to support or dismiss the existence of two non-monophyletic groups within the species, as found within Portugal. Our phylogenetic analysis with cytochrome c oxidase subunit I (COI) indeed displayed two distinct and well-supported clades of P. oleae, which were corroborated by the haplotype network reconstructed with both mitochondrial and nuclear amplicons. We were also able to dismiss the hypothesis that one of the clades would not develop on olive fruits. No correlation was observed between clades differentiation and geographic distribution. The existence of cryptic species can impact on the management of agroecosystems and on the perception of how these moths responds to environmental changes.

Cytogenetic markers applied to cytotaxonomy in two soybean pests: Anticarsia gemmatalis (Hübner, 1818) and Chrysodeixis includens (Walker, 1858)

Anticarsia gemmatalis (Hübner, 1818) and Chrysodeixis includens (Walker, 1858) are species of Lepidoptera that cause great damages in the soybean plantations of Brazil. Despite the importance they have in this regard, there are no studies on the chromosomal organization of these species and recently, A. gemmatalis, which belonged to the Noctuidae family, was allocated to the Erebidae family. Therefore, the objective of this paper was to analyze, through conventional and molecular cytogenetic markers, both species of Lepidoptera. A 2n = 62 was observed, with ZZ/ZW sex chromosome system and holokinetic chromosomes for both species. There was homogeneity in the number of 18S rDNA sites for both species. However, variations in heterochromatin distribution were observed between both species. The cytogenetic analyses enabled separation of the species, corroborating the transference of A. gemmatalis, from the family Noctuidae to the family Erebidae, suggesting new cytotaxonomic characteristics.

Incipient sympatric speciation via host race formation in Phengaris arion (Lepidoptera: Lycaenidae)

The plausibility of sympatric speciation is still debated despite increasing evidence, such as host races in insects. This speciation process may be occurring in the case of the two phenological forms of the obligatorily myrmecophilous Phengaris arion. The main goal of our research was to study the nature and causes of difference between these forms focusing primarily on the incipient speciation via host races. Molecular analyses based on highly variable microsatellites together with Wolbachia screening, male genitalia morphometrics and host ant studies were carried out on four syntopic sample pairs. Our results show that the two phenological forms of P. arion may meet the criteria for host plant races. They coexist in sympatry in certain parts of the species range which is allowed by the adaptation to the distinct phenology of the host plants. Negative selection acts against the intermediate individuals which are on the wing in the inappropriate time frame. Thus, disruptive selection affects and produces bimodal distributions of phenotypes. However, the phenology of food plants is not entirely distinct and fluctuates year by year. Therefore, the two forms can exchange genes occasionally depending on the length of the time slot when they can meet with each other. Consequently, the reproductive isolation could not be completed and the existence of the two arion forms may represent only an incipient stage of sympatric speciation. It is also clear that Wolbachia is likely not a driver of sympatric speciation in this case.

A glide over the Indo-Australian geological maze: repeated transgressions of Lydekker’s and Wallace’s Lines in archdukes, barons and dukes (Nymphalidae: Limenitidinae: Adoliadini)

Archdukes, barons, counts, dukes and marquises are forest-dwelling butterflies found in mainland Asia and most islands of the Indo-Australian archipelago west of Wallace’s Line, with only a few species occurring as far east as the Bismarck Archipelago. This pattern is unusual among butterfly groups of the region, which often present more widespread geographical ranges bearing little signature of Lydekker’s and Wallace’s Lines. Using a molecular multimarker matrix, we infer the first dated phylogeny for this clade and estimate its biogeographical history. We recover the Oriental genus Euthalia as polyphyletic, although other genera are monophyletic. The clade originated in continental Indomalaya in the late Oligocene ~24 Mya, when the Indo-Australian archipelago was at one of the most dynamic stages of its orogeny. Multiple independent colonization events towards the Lesser Sunda Islands, Moluccas, Australia and New Guinea suggest the relative permeability of Lydekker’s and Wallace’s Lines to these butterflies. Colonization of Melanesia took place twice, probably before the recent formation of Sulawesi. The study of Indo-Australian Adoliadini provides additional evidence that biogeographical barriers long thought to prevent exchange between the Asian and Australian biotas are, in fact, permeable especially to vagile insect lineages in the region.

Twenty-six new species of Hoploscopa (Lepidoptera, Crambidae) from South-East Asia revealed by morphology and DNA barcoding

Hoploscopa Meyrick (Lepidoptera: Crambidae) is a fern-feeding genus found in montane areas of South-East Asia and Melanesia, eastwards up to the Samoan Islands. It includes sixteen described species, with at least 70 further undescribed species known from scientific collections. An iterative approach including morphological and molecular characters was used in order to explore the diversity of Hoploscopa. The hitherto described species are revised, and descriptions authored by T. Léger and M. Nuss are provided for an additional 26 new species: H.agtuuganonensissp. nov., H.albipunctasp. nov., H.albomaculatasp. nov., H.anacanthasp. nov., H.boletasp. nov., H.cynodontasp. nov., H.danaoensissp. nov., H.gombongisp. nov., H.gracilissp. nov., H.ignitamaculaesp. nov., H.isarogensissp. nov., H.jubatasp. nov., H.kelamasp. nov., H.kinabaluensissp. nov., H.mallyisp. nov., H.marijoweissaesp. nov., H.matheaesp. nov., H.niveofasciasp. nov., H.pangrangoensissp. nov., H.parvimaculasp. nov., H.pseudometacrossasp. nov., H.sepanggisp. nov., H.sumatrensissp. nov., H.titikasp. nov., H.tonsepisp. nov., H.ypsilonsp. nov. Using a protocol specific for the amplification of DNA from old museum specimens, we recovered 101 COI barcodes for all but one of the newly described species, with 76 being barcode compliant (>487 bp). Species delimitation analyses suggest cryptic diversity, with six cases reflecting allopatric divergence, and two further cases found in sympatry.

Evolution and losses of spines in slug caterpillars (Lepidoptera: Limacodidae)

Larvae of the cosmopolitan family Limacodidae, commonly known as "slug" caterpillars, are well known because of the widespread occurrence of spines with urticating properties, a morpho-chemical adaptive trait that has been demonstrated to protect the larvae from natural enemies. However, while most species are armed with rows of spines ("nettle" caterpillars), slug caterpillars are morphologically diverse with some species lacking spines and thus are nonstinging. It has been demonstrated that the evolution of spines in slug caterpillars may have a single origin and that this trait is possibly derived from nonstinging slug caterpillars, but these conclusions were based on limited sampling of mainly New World taxa; thus, the evolution of spines and other traits within the family remains unresolved. Here, we analyze morphological variation in slug caterpillars within an evolutionary framework to determine character evolution of spines with samples from Asia, Australia, North America, and South America. The phylogeny of the Limacodidae was reconstructed based on a multigene dataset comprising five molecular markers (5.6 Kbp: COI, 28S, 18S, EF-1α, and wingless) representing 45 species from 40 genera and eight outgroups. Based on this phylogeny, we infer that limacodids evolved from a common ancestor in which the larval type possessed spines, and then slug caterpillars without spines evolved independently multiple times in different continents. While larvae with spines are well adapted to avoiding generalist predators, our results imply that larvae without spines may be suited to different ecological niches. Systematic relationships of our dataset indicate six major lineages, several of which have not previously been identified.

A comprehensive molecular phylogeny of Geometridae (Lepidoptera) with a focus on enigmatic small subfamilies

Our study aims to investigate the relationships of the major lineages within the moth family Geometridae, with a focus on the poorly studied Oenochrominae-Desmobathrinae complex, and to translate some of the results into a coherent subfamilial and tribal level classification for the family. We analyzed a molecular dataset of 1,206 Geometroidea terminal taxa from all biogeographical regions comprising up to 11 molecular markers that includes one mitochondrial (COI) and 10 protein-coding nuclear gene regions (wingless, ArgK, MDH, RpS5, GAPDH, IDH, Ca-ATPase, Nex9, EF-1alpha, CAD). The molecular data set was analyzed using maximum likelihood as implemented in IQ-TREE and RAxML. We found high support for the subfamilies Larentiinae, Geometrinae and Ennominae in their traditional scopes. Sterrhinae becomes monophyletic only if Ergavia Walker, Ametris Hübner and Macrotes Westwood, which are currently placed in Oenochrominae, are formally transferred to Sterrhinae. Desmobathrinae and Oenochrominae are found to be polyphyletic. The concepts of Oenochrominae and Desmobathrinae required major revision and, after appropriate rearrangements, these groups also form monophyletic subfamily-level entities. Oenochrominae s.str. as originally conceived by Guenée is phylogenetically distant from Epidesmia and its close relatives. The latter is hereby described as the subfamily Epidesmiinae Murillo-Ramos, Sihvonen & Brehm, subfam. nov. Epidesmiinae are a lineage of "slender-bodied Oenochrominae" that include the genera Ecphyas Turner, Systatica Turner, Adeixis Warren, Dichromodes Guenée, Phrixocomes Turner, Abraxaphantes Warren, Epidesmia Duncan & Westwood and Phrataria Walker. Archiearinae are monophyletic when Dirce and Acalyphes are formally transferred to Ennominae. We also found that many tribes were para- or polyphyletic and therefore propose tens of taxonomic changes at the tribe and subfamily levels. Archaeobalbini stat. rev. Viidalepp (Geometrinae) is raised from synonymy with Pseudoterpnini Warren to tribal rank. Chlorodontoperini Murillo-Ramos, Sihvonen & Brehm, trib. nov. and Drepanogynini Murillo-Ramos, Sihvonen & Brehm, trib. nov. are described as new tribes in Geometrinae and Ennominae, respectively.

Five nuclear protein-coding markers for establishing a robust phylogenetic framework of niphargid crustaceans (Niphargidae: Amphipoda) and new molecular sequence data

The data presented here includes selection of 5 successfully amplified protein-coding markers for inferring phylogenetic relationships of the family of amphipod crustaceans Niphargidae. These markers have been efficiently amplified from niphargid samples for the first time and present the framework for robust phylogenetic assessment of the family Niphargidae. They are useful for phylogenetic purposes among other amphipod genera as well. In detail, the data consists of two parts: 1. Information regarding markers, specific oligonucleotide primer pairs and conditions for PCR reaction that enables successful amplification of specific nucleotide fragments. Two pairs of novel oligonucleotide primers were constructed which enable partial sequence amplification of two housekeeping genes: arginine kinase (ArgKin) and glyceraldehyde phosphate dehydrogenase (GAPDH), respectively. Additionally, 3 existing combinations of oligonucleotide primer pairs for protein-coding loci for glutamyl-prolyl tRNA synthetase (EPRS), opsin (OP) and phosphoenolpyruvate carboxykinase (PEPCK) were proven to be suitable to amplify specific nucleotide fragments from selected amphipod specimens; 2. Information on novel nucleotide sequences from amphipod taxa of the family Niphagidae and related outgroup taxa. Unilocus phylogenetic trees were constructed using Bayesian analysis and show relationships among selected taxa. Altogether 299 new nucleotide sequences from 92 specimens of the family Niphargidae and related outgroup amphipod taxa are deposited in GenBank (NCBI) repository and available for further use in phylogenetic analyses.

Molecular phylogeny and historical biogeography of Parnara butterflies (Lepidoptera: Hesperiidae)

The butterfly genus Parnara (Hesperiinae: Baorini), of which some are major pests of economic crops (e.g., rice, wild rice stems and sugarcane), currently consists of 10 species and several subspecies and has a highly disjunct distribution in Australia, Africa, and Asia. We determined the systematic relationships and biogeographical history of the genus by reconstructing the phylogeny based on eight genes and 101 specimens representing all 10 recognized species. Four species delimitation methods (ABGD, bPTP, GMYC and BPP) were also employed to assess the taxonomic status of each species. Based on these results and analyses, we recognize 11 extant species in the genus. The status of the taxon P. naso poutieri (Boisduval, 1833) from Madagascar is revised as a distinct species, Parnara poutieri (Boisduval, 1833) stat. rev. The subspecies P. guttata mangala (Moore, 1866) syn. nov. is synonymized with P. guttata guttata (Bremer & Grey, 1853), while P. bada (Moore, 1878) is provisionally treated as a complex of two species, namely P. bada and P. apostata (Snellen, 1886). The monophyly of Parnara is strongly supported, with the following relationships: P. amalia + ((P. monasi + (P. poutieri + P. naso)) + ((P. kawazoei + P. bada complex) + (P. ganga + (P. ogasawarensis + (P. guttata + P. batta))))). Divergence time and ancestral range estimates indicate that the common ancestor of Parnara originated in an implausible area of Australia, Africa, and Oriental region in the mid-Oligocene and then differentiated in the late Miocene-late Pliocene. Dispersal and range expansion have played an important role in diversification of the genus in Asia and Afica. Relatively stable geotectonic plates at the time when most extant lineages appeared during the late Miocene-early Pliocene might have been the factor responsible for the relatively constant low dynamic rate of diversification within the group.

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.

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.

Pheromones and Barcoding Delimit Boundaries between Cryptic Species in the Primitive Moth Genus Eriocrania (Lepidoptera: Eriocraniidae)

Animal classification is primarily based on morphological characters, even though these may not be the first to diverge during speciation. In many cases, closely related taxa are actually difficult to distinguish based on morphological characters alone, especially when there is no substantial niche separation. As a consequence, the diversity of certain groups is likely to be underestimated. Lepidoptera –moths and butterflies– represent the largest group of herbivorous insects. The extensive diversification in the group is generally assumed to have its origin in the spectacular radiation of flowering plants and the resulting abundance of ecological niches. However, speciation can also occur without strong ecological divergence. For example, reproductive isolation can evolve as the result of divergence in mate preference and the associated pheromone communication system. We combined pheromone trapping and genetic analysis to elucidate the evolutionary relationships within a complex of primitive moth species (Lepidoptera: Eriocraniidae). Mitochondrial and nuclear DNA markers provided evidence that Eriocrania semipurpurella, as currently defined by morphological characters, includes three cryptic species in Northern and Western Europe. Male moths of these cryptic species, as well as of the closely related E. sangii, exhibited relative specificity in terms of their attraction to specific ratios of two major pheromone components, (2S,6Z)-nonen-2-ol and (2R,6Z)-nonen-2-ol. Our data suggest strong assortative mating in these species in the absence of apparent niche separation, indicating that Eriocrania moths may represent an example of non-ecological speciation. Finally, our study argues in favour of combining pheromone investigations and DNA barcoding as powerful tools for identifying and delimitating species boundaries.

A Revision of North American Lactura (Lepidoptera, Zygaenoidea, Lacturidae)

The Lactura Walker, 1854 fauna north of Mexico is revised. Six species are documented, one new species Lacturanalli Matson & Wagner, sp. n. is described, and two new synonymies are proposed: Lacturapsammitis (Zeller, 1872), syn. n. and L.rhodocentra (Meyrick, 1913), syn. n. One new subspecies Lacturasubfervenssapeloensis Matson & Wagner, ssp. n. is also described. Adult and larval stages, male and female genitalia, are illustrated, a preliminary phylogeny is presented based on nuclear and mitochondrial data, distribution records provided for verified specimens, and the biology and life history for each species is briefly characterized. Phylogenetic analyses, larval phenotypes, and life history information reveal that much of the historic taxonomic confusion rampant across this group in North America traces to the phenotypic variation in just one species, L.subfervens (Walker, 1854).

Global phylogeography reveals the origin and the evolutionary history of the gypsy moth (Lepidoptera, Erebidae)

We examined the global phylogeography of gypsy moth (Lymantria dispar L.) using molecular data based on mitochondrial and nuclear genes. Populations from all biogeographic regions of the native and introduced range of L. dispar, were sampled to fully document intraspecific and subspecies variation, identify potential cryptic species, and to clarify the relationships among major phylogeographic lineages. We recovered three major mtDNA lineages of L. dispar: Transcaucasia; East Asia + Japan; and Europe + Central Asia. The circumscription of these lineages is only partially consistent with the current taxonomic concept (i.e., L. dispar dispar; L. dispar asiatica; L. dispar japonica), with the following important discrepancies: (1) north-central Asian populations, including topotypical populations of L. dispar asiatica, may be more closely related to European rather than Asian segregates, which would require the synonymization of the taxon asiatica and establishment of a new name; (2) the Japanese populations (L. d. japonica) are not distinct from east Asian populations; (3) the presence of a distinct, unnamed mitogenomic lineage endemic to the Trancaucasus region. We demonstrated that the population from Transcaucasia contains the highest mitochondrial haplotype diversity among L. dispar, potentially indicative of an ancestral area for the entire dispar-group. Our study corroborates the endemic Hokkaido, Japan taxon Lymantria umbrosa (Butler) as the sister group to all other L. dispar populations, but the applicability of the names umbrosa versus hokkaidoensis Goldschmidt needs to be re-evaluated. The ancestral area analysis suggest that Japan was likely colonized via Sakhalin ∼1 Mya, in contrast to previous studies which have suggested colonization of the Japanese archipelago via the Korean Peninsula. Lastly, mitogenomic variation within L. dispar is incongruent with phylogenies based on nuclear DNA, as nDNA gene phylogenies did not recover the three major mtDNA lineages, and also failed to recover L. dispar and L. umbrosa as reciprocally monophyletic.

Revision of the genus Emphylica Turner, 1913 based on morphology and molecular data (Lepidoptera, Crambidae, Pyraustinae)

Moths of the genus Emphylica Turner, 1913 resemble species of Achyra Guenée, 1849, Loxostege Hübner, 1825 and Sitochroa Hübner, 1825 in having a conical frons. In order to examine the monophyly of Emphylica, and its relationship to other genera with a conical frons, a molecular phylogenetic framework is reconstructed based on sequence data of COI, 16S rRNA, 28S rRNA, EF-1α and Wg gene regions. The results robustly support the monophyly of Emphylica. Achyra + (Loxostege + Sitochroa) is in a sister position to Emphylica. A new species, E.crassihamatasp. n., is described from Southern China and two new combinations, E.diaphana (Caradja & Meyrick, 1934), comb. n. and E.cruoralis (Warren, 1895), comb. n., are proposed. An identification key based on males is provided for all Emphylica species. The adult habitus and genitalia of all species are figured.

Considerations on the Taxonomy of the Genus Arhuaco Adams and Bernard 1977, and its Relationships with the Genus Pronophila Doubleday [1849] (Nymphalidae, Satyrinae)

Arhuaco Adams & Bernard (1977) is one of the least known genera of Neotropical Satyrinae. It comprises two species and presents an unusual disjunct distribution, with A. ica Adams & Bernard (1977), endemic to the isolated Colombian Sierra Nevada de Santa Marta, and A. dryadina (Schaus 1913) found in the mountains of Costa Rica and Panama. Here, the female of A. dryadina is described, and a new generic diagnosis is presented. Affinities with other genera of the subtribe Pronophilina, in particular the potential closest relatives, such as Pronophila Doubleday (1849), are investigated based on morphological, molecular, ecological, and behavioral data. Results from molecular and morphological sources are incongruent. Molecular data indicate that Arhuaco is paraphyletic, with A. dryadina segregating within the Pronophila clade. Morphological data, by contrast, indicate a closer affinity between the two species currently placed in Arhuaco, favoring the monophyly of the genus, and show no consistent synapomorphies for Arhuaco + Pronophila. A vicariance biogeographical scenario is evaluated.

Cross-continental phylogeography of two Holarctic Nymphalid butterflies, Boloria eunomia and Boloria selene

Pleistocene glaciations had significant effects on the distribution and evolution of species inhabiting the Holarctic region. Phylogeographic studies concerning the entire region are still rare. Here, we compared global phylogeographic patterns of one boreo-montane and one boreo-temperate butterflies with largely overlapping distribution ranges across the Northern Hemisphere, but with different levels of range fragmentation and food specialization. We reconstructed the global phylogeographic history of the boreo-montane specialist Boloria eunomia (n = 223) and of the boreo-temperate generalist Boloria selene (n = 106) based on mitochondrial and nuclear DNA markers, and with species distribution modelling (SDM). According to the genetic structures obtained, both species show a Siberian origin and considerable split among populations from Nearctic and Palaearctic regions. According to SDMs and molecular data, both butterflies could inhabit vast areas during the moderate glacials. In the case of B. selene, high haplotype diversity and low geographic structure suggest long-lasting interconnected gene flow among populations. A stronger geographic structuring between populations was identified in the specialist B. eunomia, presumably due to the less widespread, heterogeneously distributed food resources, associated with cooler and more humid climatic conditions. Populations of both species show opposite patterns across major parts of North America and in the case of B. eunomia also across Asia. Our data underline the relevance to cover entire distribution ranges to reconstruct the correct phylogeographic history of species.

The Immature Stages, Biology, and Phylogenetic Relationships of Rotunda rotundapex (Lepidoptera: Bombycidae)

The life history, morphology, and biology of the immature stages and phylogenetic relationships of Rotunda rotundapex (Miyata & Kishida, 1990) are described and illustrated for the first time. The species is univoltine: eggs hatch in spring (March or April) and the life cycle from egg to adult is completed in about 3 wk, with larvae developing rapidly on young leaves of the host plants, Morus australis and to a lesser extent Broussonetia monoica (Moraceae), and adults emerging in April-May. Eggs are laid in clusters on twigs of the host plant, are covered by scales during female oviposition, and remain in diapause for the remainder of the year (i.e., for 10-11 mo). Larvae (all instars) are unique among the Bombycidae in that they lack a horn on abdominal segment 8. A strongly supported molecular phylogeny based on six genes (5.0 Kbp: COI, EF-1α, RpS5, CAD, GAPDH, and wgl) representing seven genera of Bombycinae from the Old World revealed that Rotunda is a distinct monotypic lineage sister to Bombyx. This phylogenetic position, together with morphological data of the immature stages (egg and larval chaetotaxy), supports the current systematic classification in which the species rotundapex has been placed in a separate genus (Rotunda) from Bombyx in which it was previously classified.

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.

Systematics of the new genus Spinosuncus Chen, Zhang & Li with descriptions of four new species (Lepidoptera, Crambidae, Pyraustinae)

The new genus Spinosuncusgen. n. is proposed for three known species, S.contractalis (Warren, 1896), comb. n., S.praepandalis (Snellen, 1890), comb. n., and S.aureolalis (Lederer, 1863), comb. n. and four new species, S.rectacutussp. n., S.brevacutussp. n., S.curvisetaceussp. n., and S.quadracutussp. n. from the Oriental Region. An identification key is provided for all species. The habiti and genitalia of all species are figured. The monophyly of the genus is well supported by a phylogenetic analysis based on sequence data of the COI, 16S rRNA, and EF-1α genes. The potential sister groups of the new genus, the interspecific relationships and some intraspecific variations within the genus are discussed.

Uncovered variability in olive moth (Prays oleae) questions species monophyly

The olive moth -Prays oleae Bern.- remains a significant pest of olive trees showing situation dependent changes in population densities and in severity of damages. The genetic variability of olive moth was assessed on three main olive orchards regions in Portugal by three different markers (COI, nad5 and RpS5), suggesting high species diversity albeit with no obvious relation with a regional pattern nor to an identified ecological niche. Selected COI sequences obtained in this study were combined with those available in the databases for Prays genus to generate a global dataset. The reconstruction of the Prays phylogeny based on this marker revealed the need to revise Prays oleae to confirm its status of single species: COI data suggests the co-existence of two sympatric evolutionary lineages of morphologically cryptic olive moth. We show, however, that the distinct mitochondrial subdivision observed in the partial COI gene fragment is not corroborated by the other DNA sequences. There is the need of understanding this paradigm and the extent of Prays variability, as the disclosure of lineage-specific differences in biological traits between the identified lineages is fundamental for the development of appropriate pest management practices.

A simple method for data partitioning based on relative evolutionary rates

BACKGROUND

Multiple studies have demonstrated that partitioning of molecular datasets is important in model-based phylogenetic analyses. Commonly, partitioning is done a priori based on some known properties of sequence evolution, e.g. differences in rate of evolution among codon positions of a protein-coding gene. Here we propose a new method for data partitioning based on relative evolutionary rates of the sites in the alignment of the dataset being analysed. The rates are inferred using the previously published Tree Independent Generation of Evolutionary Rates (TIGER), and the partitioning is conducted using our novel python script RatePartitions. We conducted simulations to assess the performance of our new method, and we applied it to eight published multi-locus phylogenetic datasets, representing different taxonomic ranks within the insect order Lepidoptera (butterflies and moths) and one phylogenomic dataset, which included ultra-conserved elements as well as introns.

METHODS

We used TIGER-rates to generate relative evolutionary rates for all sites in the alignments. Then, using RatePartitions, we partitioned the data into partitions based on their relative evolutionary rate. RatePartitions applies a simple formula that ensures a distribution of sites into partitions following the distribution of rates of the characters from the full dataset. This ensures that the invariable sites are placed in a partition with slowly evolving sites, avoiding the pitfalls of previously used methods, such as k-means. Different partitioning strategies were evaluated using BIC scores as calculated by PartitionFinder.

RESULTS

Simulations did not highlight any misbehaviour of our partitioning approach, even under difficult parameter conditions or missing data. In all eight phylogenetic datasets, partitioning using TIGER-rates and RatePartitions was significantly better as measured by the BIC scores than other partitioning strategies, such as the commonly used partitioning by gene and codon position. We compared the resulting topologies and node support for these eight datasets as well as for the phylogenomic dataset.

DISCUSSION

We developed a new method of partitioning phylogenetic datasets without using any prior knowledge (e.g. DNA sequence evolution). This method is entirely based on the properties of the data being analysed and can be applied to DNA sequences (protein-coding, introns, ultra-conserved elements), protein sequences, as well as morphological characters. A likely explanation for why our method performs better than other tested partitioning strategies is that it accounts for the heterogeneity in the data to a much greater extent than when data are simply subdivided based on prior knowledge.

Phylogenetics of moth-like butterflies (Papilionoidea: Hedylidae) based on a new 13-locus target capture probe set

The Neotropical moth-like butterflies (Hedylidae) are perhaps the most unusual butterfly family. In addition to being species-poor, this family is predominantly nocturnal and has anti-bat ultrasound hearing organs. Evolutionary relationships among the 36 described species are largely unexplored. A new, target capture, anchored hybrid enrichment probe set ('BUTTERFLY2.0') was developed to infer relationships of hedylids and some of their butterfly relatives. The probe set includes 13 genes that have historically been used in butterfly phylogenetics. Our dataset comprised of up to 10,898 aligned base pairs from 22 hedylid species and 19 outgroups. Eleven of the thirteen loci were successfully captured from all samples, and the remaining loci were captured from ≥94% of samples. The inferred phylogeny was consistent with recent molecular studies by placing Hedylidae sister to Hesperiidae, and the tree had robust support for 80% of nodes. Our results are also consistent with morphological studies, with Macrosoma tipulata as the sister species to all remaining hedylids, followed by M. semiermis sister to the remaining species in the genus. We tested the hypothesis that nocturnality evolved once from diurnality in Hedylidae, and demonstrate that the ancestral condition was likely diurnal, with a shift to nocturnality early in the diversification of this family. The BUTTERFLY2.0 probe set includes standard butterfly phylogenetics markers, captures sequences from decades-old museum specimens, and is a cost-effective technique to infer phylogenetic relationships of the butterfly tree of life.

Molecular evidence of hybridization in sympatric populations of the Enantia jethys complex (Lepidoptera: Pieridae)

Hybridization events are frequently demonstrated in natural butterfly populations. One interesting butterfly complex species is the Enantia jethys complex that has been studied for over a century; many debates exist regarding the species composition of this complex. Currently, three species that live sympatrically in the Gulf slope of Mexico (Enantia jethys, E. mazai, and E. albania) are recognized in this complex (based on morphological and molecular studies). Where these species live in sympatry, some cases of interspecific mating have been observed, suggesting hybridization events. Considering this, we employed a multilocus approach (analyses of mitochondrial and nuclear sequences: COI, RpS5, and Wg; and nuclear dominant markers: inter-simple sequence repeat (ISSRs) to study hybridization in sympatric populations from Veracruz, Mexico. Genetic diversity parameters were determined for all molecular markers, and species identification was assessed by different methods such as analyses of molecular variance (AMOVA), clustering, principal coordinate analysis (PCoA), gene flow, and PhiPT parameters. ISSR molecular markers were used for a more profound study of hybridization process. Although species of the Enantia jethys complex have a low dispersal capacity, we observed high genetic diversity, probably reflecting a high density of individuals locally. ISSR markers provided evidence of a contemporary hybridization process, detecting a high number of hybrids (from 17% to 53%) with significant differences in genetic diversity. Furthermore, a directional pattern of hybridization was observed from E. albania to other species. Phylogenetic study through DNA sequencing confirmed the existence of three clades corresponding to the three species previously recognized by morphological and molecular studies. This study underlines the importance of assessing hybridization in evolutionary studies, by tracing the lineage separation process that leads to the origin of new species. Our research demonstrates that hybridization processes have a high occurrence in natural populations.