Information Dropout Patterns in Restriction Site Associated DNA Phylogenomics and a Comparison with Multilocus Sanger Data in a Species-Rich Moth Genus.

A rapid shift from traditional Sanger sequencing-based molecular methods to the phylogenomic approach with large numbers of loci is underway. Among phylogenomic methods, restriction site associated DNA (RAD) sequencing approaches have gained much attention as they enable rapid generation of up to thousands of loci randomly scattered across the genome and are suitable for nonmodel species. RAD data sets however suffer from large amounts of missing data and rapid locus dropout along with decreasing relatedness among taxa. The relationship between locus dropout and the amount of phylogenetic information retained in the data has remained largely uninvestigated. Similarly, phylogenetic hypotheses based on RAD have rarely been compared with phylogenetic hypotheses based on multilocus Sanger sequencing, even less so using exactly the same species and specimens. We compared the Sanger-based phylogenetic hypothesis (8 loci; 6172 bp) of 32 species of the diverse moth genus Eupithecia (Lepidoptera, Geometridae) to that based on double-digest RAD sequencing (3256 loci; 726,658 bp). We observed that topologies were largely congruent, with some notable exceptions that we discuss. The locus dropout effect was strong. We demonstrate that number of loci is not a precise measure of phylogenetic information since the number of single-nucleotide polymorphisms (SNPs) may remain low at very shallow phylogenetic levels despite large numbers of loci. As we hypothesize, the number of SNPs and parsimony informative SNPs (PIS) is low at shallow phylogenetic levels, peaks at intermediate levels and, thereafter, declines again at the deepest levels as a result of decay of available loci. Similarly, we demonstrate with empirical data that the locus dropout affects the type of loci retained, the loci found in many species tending to show lower interspecific distances than those shared among fewer species. We also examine the effects of the numbers of loci, SNPs, and PIS on nodal bootstrap support, but could not demonstrate with our data our expectation of a positive correlation between them. We conclude that RAD methods provide a powerful tool for phylogenomics at an intermediate phylogenetic level as indicated by its broad congruence with an eight-gene Sanger data set in a genus of moths. When assessing the quality of the data for phylogenetic inference, the focus should be on the distribution and number of SNPs and PIS rather than on loci.

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.

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.

The Elachista dispunctella (Duponchel) complex (Lepidoptera, Elachistidae) revisited, with exceptional level of synonymy.

The E. dispunctella and E. triseriatella complexes sensu Traugott-Olsen are merged. The newly delineated E. dispunctella complex is re-defined and diagnosed. Until now, a total of 64 species has been assigned to this species complex. The taxonomy of the constituent species has been obscure owing to their identities based on unvalidated traits, in particular subtle differences on branching points of forewing veins. The taxonomy of the E. dispunctella complex is revised on the basis of new material, new and reevaluated information obtained from morphology and biology, as well as from the standard barcode region of COI, with at least partial barcode data derived from 194 recently collected specimens and 33 holotypes. As a result, the number of species considered valid is markedly reduced, with only 19 species now recognized. The following 43 new synonymies are established: Elachista dispunctella (Duponchel, 1843) = E. cahorsensis Traugott-Olsen, 1992, syn. nov., E. imbi Traugott-Olsen, 1992, syn. nov., E. karsholti Traugott-Olsen, 1992, syn. nov., E. mannella Traugott-Olsen, 1992, syn. nov., E. multipunctella Traugott-Olsen, 1992, syn. nov., E. pocopunctella Traugott-Olsen, 1992, syn. nov., E. povolnyi Traugott-Olsen, 1992, syn. nov., E. punctella Traugott-Olsen, 1992, syn. nov., E. hallini Traugott-Olsen, 1992, syn. nov., E. intrigella Traugott-Olsen, 1992, syn. nov., E. skulei Traugott-Olsen, 1992 and E. nielspederi Traugott-Olsen, 1992, syn. nov.; E. tribertiella Traugott-Olsen, 1985 = E. toveella Traugott-Olsen, 1985, syn. nov., E. baldizzonella Traugott-Olsen, 1985, syn. nov., E. veletaella Traugott-Olsen, 1992, syn. nov., E. bazaella Traugott-Olsen, 1992, syn. nov. and E. louiseae Traugott-Olsen, 1992, syn. nov.; E. parvula Parenti, 1978 = E. minusculella Traugott-Olsen, 1992, syn. nov. and E. blancella Traugott-Olsen, 1992, syn. nov.; E. maboulella Chrétien, 1915 = E. catalunella Traugott-Olsen, 1992, syn. nov., E. gerdmaritella Traugott-Olsen, 1992, syn. nov. and E. gielisi Traugott-Olsen, 1992, syn. nov.; E. glaseri Traugott-Olsen, 1992 = E. rikkeae Traugott-Olsen, 1992, syn. nov., E. totanaensis Traugott-Olsen, 1992, syn. nov., E. olemartini Traugott-Olsen, 1992, syn. nov., E. bengtssoni Traugott-Olsen, 1992, syn. nov., E. senecai Traugott-Olsen, 1992, syn. nov., E. wadielhiraensis Traugott-Olsen, 1992, syn. nov., E. rissaniensis Traugott-Olsen, 1992, syn. nov. and E. michelseni Traugott-Olsen, 1992, syn. nov.; E. hispanica Traugott-Olsen, 1992 = E. vivesi Traugott-Olsen, 1992, syn. nov., E. cuencaensis Traugott-Olsen, 1992, syn. nov., E. vanderwolfi Traugott-Olsen, 1992, syn. nov., E. amparoae Traugott-Olsen, 1992, syn. nov., E. varensis Traugott-Olsen, 1992, syn. nov., E. luqueti Traugott-Olsen, 1992, syn. nov., E. occidentella Traugott-Olsen, 1992, syn. nov. and E. clintoni Traugott-Olsen, 1992, syn. nov.; E. berndtiella Traugott-Olsen, 1985 = E. casascoensis Traugott-Olsen, 1992, syn. nov.; E. triseriatella Stainton, 1854 = E. contisella Chrétien, 1922, syn. nov., E. gregori Traugott-Olsen, 1988, syn. nov., and E. lerauti Traugott-Olsen, 1992, syn. nov.; E. elsaella Traugott-Olsen, 1988 = E. svenssoni Traugott-Olsen, 1988, syn. nov.; E. galactitella (Eversmann, 1844) = E. madridensis Traugott-Olsen, 1992, syn. nov. E. deresyensis Traugott-Olsen, 1988 is resurrected as a valid species, stat. rev. Evidence from DNA barcodes suggests that there may exist further species, but in the absence of distinct morphological differences, they are not formally described as new.

Morphology reinforces proposed molecular phylogenetic affinities: a revised classification for Gelechioidea (Lepidoptera).

Gelechioidea are one of the most species rich and least studied superfamilies of Lepidoptera. We examine the interrelationships within the superfamily using the densest taxon sampling to date, combined with the most extensive ever morphological and molecular character data. We perform partitioned and combined analyses using maximum likelihood, Bayesian and parsimony approaches. The combined dataset consists of 155 exemplar species of Gelechioidea, representing nearly all subfamilies recognized in recent classifications. Parsimony analyses are performed with a dataset including 28 additional terminal taxa with only morphological data available. We use eight genes with a total of 6127 bp, and morphological data with 253 characters derived from larval, pupal, and adult morphology. The analyses of combined data yield more resolved trees and significantly better-supported groupings than either dataset when analysed alone. The recurrent monophyletic groupings in all our model-based analyses support a revision of the family classification. Deeper relationships vary between analyses and data partitions, leaving them ambiguous. The place of the root remains a challenge for future research. We propose a revised classification and suggest the division of Gelechioidea into 16 families. We redefine Depressariidae Meyrick, 1883 for a monophylum that includes Acriinae, Aeolanthinae, Cryptolechiinae, Depressariinae, Ethmiinae, Hypercalliinae, Hypertrophinae, Peleopodinae, Oditinae, Stenomatinae, Carcina, and a diversity of predominantly New World taxa previously excluded from Lypusidae (Amphisbatidae s. authors) but left without family position. A monophyletic Oecophoridae s. s., including Deuterogoniinae and Pleurotinae, is obtained for the first time with significant support. Elachistidae s. l. is found to be polyphyletic, and Elachistidae is restricted to comprise Agonoxeninae, Elachistinae, and Parametriotinae. Batrachedridae are polyphyletic, with several genera pending further study. Apart from the core Batrachedra, the taxa previously included in this family are grouped in an expanded Pterolonchidae, together with Coelopoetinae and Syringopainae. Lypusidae s. s. and Chimabachidae form a monophylum; Chimabachinae is united with Lypusidae as a subfamily, stat. n. Our results contradict the subfamily classifications of several families, notably Lecithoceridae and Autostichidae, but due to insufficient sampling of taxa we refrain from comprehensive taxonomic conclusions on the subfamily level, and encourage focused studies to resolve these groups.

Elachistadimicatella sensu auctt.-a complex of neglected species diversity (Lepidoptera, Elachistidae) from European mountain systems.

Elachistadimicatella Rebel, 1903, has so far been considered a species in Europe with restricted distribution from Ukraine to western France. The species occurs on mountainous regions. However, the in-depth analysis of a taxonomically uncertain species of Elachista from the Cottian Alps (Italy), especially through DNA barcoding and subsequent morphological studies, led to the realization that individuals previously identified as E.dimicatella from the Cottian Alps and the Pyrenees were misidentified. According to our research, a total of three species can be differentiated: E.dimicatella from Carpathians and its former junior synonym E.niphadophanes Meyrick, 1937, sp. rev., from the Pyrenees, as well as the newly described E.cottiella sp. nov. from southwestern Alps, hitherto incorrectly identified as E.dimicatella. Diagnostic features of the three species are discussed and illustrated. Elachistadimicatella and E.niphadophanes are redescribed.

Major lineages of Nolidae (Lepidoptera, Noctuoidea) elucidated by molecular phylogenetics.

To elucidate the evolutionary relationships of the major lineages within the moth family Nolidae, we analysed a molecular dataset comprising eight independent gene regions (6.4 kbp), cytochrome c oxidase subunit I (COI) from the mitochondrial genome, and elongation factor-1α (EF-1α), ribosomal protein S5 (RpS5), carbamoylphosphate synthase domain protein (CAD), cytosolic malate dehydrogenase (MDH), glyceraldehyde-3-phosphate dehydrogenase (GAPDH), isocitrate dehydrogenase (IDH) and wingless genes from the nuclear genome, using parsimony and model-based evolutionary methods (maximum likelihood and Bayesian inference). Our analyses revealed a well-resolved phylogenetic hypothesis, again recovering the six previously recognized families within Noctuoidea (i.e. Oenosandridae, Notodontidae, Euteliidae, Erebidae, Nolidae and Noctuidae), and monophyly of the quadrifid Noctuoidea (i.e. Euteliidae, Erebidae, Nolidae and Noctuidae). The family Nolidae is diagnosed and characterized by two synapomorphies from morphology: construction of a ridged boat-shaped cocoon that bears a vertical exit slit at one end; and two other morphological character states: elongation of the forewing retinaculum into a bar-like or digitate condition and possession of a postpiracular counter-tympanal hood. We present a new phylogenetic hypothesis for Nolidae consisting of eight strongly supported subfamilies, two of which are erected here: Diphtherinae, Risobinae, Collomeninae subfam. nov., Beaninae subfam. nov., Eligminae, Westermanniinae, Nolinae and Chloephorinae. Where we are able, each monophyletic lineage is diagnosed by morphological autapomorphies and within each subfamily, monophyletic tribes and subtribes are circumscribed, most of which are also diagnosable by morphological apomorphies. We also describe two new taxa: Gelastocerini trib. nov. and Etannina subtrib. nov. The Neotropical subfamily Diphtherinae, here newly circumscribed, is considered to be the plesiomorphic sister lineage to the rest of Nolidae. Diphtherinae are characterized by loss of the proximal pair of metatibial spurs in males and by the presence of a frontal tubercle, which is presumably associated with a derived strategy of emergence from the cocoon.

Identity of Eumenodora encrypta Meyrick, a cryptic Australian moth (Lepidoptera:Gelechioidea).

A hitherto neglected gelechioid moth genus Eumenodora Meyrick (Gelechioidea: Elachistidae; Cosmopterigidae; Xyloryctidae) is redescribed. The genus, originally assigned to the Elachistidae and later transferred to the Cosmopterigidae, is monotypic. The single constituent species, E. encrypta Meyrick, 1906, has long been known only from the holotype, collected in Brisbane, Queensland (Australia). The specimen lacks its abdomen. The genus is characterized and the single recognized species redescribed based on recently collected adult males and a female. Evidence from morphology, supported by DNA sequences, is provided to support the placement of the taxon in the Hierodoris group of the Xyloryctidae, in spite of its atypical external appearance.

The assignment of Prodidactidae to Hyblaeoidea, with remarks on Thyridoidea (Lepidoptera).

We examine the systematic position of the lepidopteran family Prodidactidae Epstein and Brown, 2003, which includes the single species Prodidactis mystica (Meyrick). We provide details on a morphological trait of the adult male hindcoxa that appears to link Prodidactidae with Hyblaeidae. This putative relationship is consistent with molecular data derived from five genes. Based on morphological and molecular evidence, we place Prodidactidae in Hyblaeoidea. Moreover, the apex of the larval spinneret is similarly modified in these families and in Thyrididae. This modification is unknown in other Lepidoptera and may prove to be a synapomorphy linking Thyridoidea and Hyblaeoidea. As the latter is not fully congruent with published molecular studies, we refrain from suggesting sister group position for Thyridoidea and Hyblaeoidea.

Cretaceous origin and repeated tertiary diversification of the redefined butterflies.

Although the taxonomy of the ca 18 000 species of butterflies and skippers is well known, the family-level relationships are still debated. Here, we present, to our knowledge, the most comprehensive phylogenetic analysis of the superfamilies Papilionoidea, Hesperioidea and Hedyloidea to date based on morphological and molecular data. We reconstructed their phylogenetic relationships using parsimony and Bayesian approaches. We estimated times and rates of diversification along lineages in order to reconstruct their evolutionary history. Our results suggest that the butterflies, as traditionally understood, are paraphyletic, with Papilionidae being the sister-group to Hesperioidea, Hedyloidea and all other butterflies. Hence, the families in the current three superfamilies should be placed in a single superfamily Papilionoidea. In addition, we find that Hedylidae is sister to Hesperiidae, and this novel relationship is supported by two morphological characters. The families diverged in the Early Cretaceous but diversified after the Cretaceous-Palaeogene event. The diversification of butterflies is characterized by a slow speciation rate in the lineage leading to Baronia brevicornis, a period of stasis by the skippers after divergence and a burst of diversification in the lineages leading to Nymphalidae, Riodinidae and Lycaenidae.

A molecular-based identification resource for the arthropods of Finland.

To associate specimens identified by molecular characters to other biological knowledge, we need reference sequences annotated by Linnaean taxonomy. In this study, we (1) report the creation of a comprehensive reference library of DNA barcodes for the arthropods of an entire country (Finland), (2) publish this library, and (3) deliver a new identification tool for insects and spiders, as based on this resource. The reference library contains mtDNA COI barcodes for 11,275 (43%) of 26,437 arthropod species known from Finland, including 10,811 (45%) of 23,956 insect species. To quantify the improvement in identification accuracy enabled by the current reference library, we ran 1000 Finnish insect and spider species through the Barcode of Life Data system (BOLD) identification engine. Of these, 91% were correctly assigned to a unique species when compared to the new reference library alone, 85% were correctly identified when compared to BOLD with the new material included, and 75% with the new material excluded. To capitalize on this resource, we used the new reference material to train a probabilistic taxonomic assignment tool, FinPROTAX, scoring high success. For the full-length barcode region, the accuracy of taxonomic assignments at the level of classes, orders, families, subfamilies, tribes, genera, and species reached 99.9%, 99.9%, 99.8%, 99.7%, 99.4%, 96.8%, and 88.5%, respectively. The FinBOL arthropod reference library and FinPROTAX are available through the Finnish Biodiversity Information Facility (www.laji.fi) at https://laji.fi/en/theme/protax. Overall, the FinBOL investment represents a massive capacity-transfer from the taxonomic community of Finland to all sectors of society.

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

The Gelechioidea, with 18,000 described and many more unnamed species ranks among the most diverse lepidopteran superfamilies. Nevertheless, their taxonomy has remained largely unresolved, and phylogenetic affinities among gelechioid families and lower taxa have been insufficiently understood. We constructed, for the first time, a comprehensive molecular phylogeny for the Gelechioidea. We sampled seven genes, in total 5466 base pairs, of 109 gelechioid taxa representing 32 of 37 recognized subfamilies, and two outgroup taxa. We used maximum likelihood methods and Bayesian inference to construct phylogenetic trees. We found that the families Autostichidae, Lecithoceridae, Xyloryctidae, and Oecophoridae s. str., in this order, are the most basally arising clades. Elachistidae s. l. was found to be paraphyletic, with families such as Gelechiidae and Cosmopterigidae nested within it, and Parametriotinae associated with several families previously considered unrelated to them. Using the phylogenetic trees, we examined patterns of life history evolution and determinants of the success of different lineages. Gelechioids express unusually wide variability in life-history strategies, including herbivorous, saprophagous, fungivorous, and carnivorous lineages. Most species are highly specialized in diet and other life history traits. The results suggest that either saprophagy was the ancestral feeding strategy from which herbivory evolved independently on multiple occasions, or that the ancestor was herbivorous with repeated origins of saprophagy. External feeding is an ancestral trait from which internal feeding evolved independently several times. In terms of species number, saprophages are dominant in Australia, while elsewhere several phytophagous lineages have extensively specialized and diversified. Internal feeding has remained a somewhat less generally adopted feeding mode, although in a few lineages significant radiations of leaf mining species have occurred. We conclude that diverse feeding modes, specialization among saprophages, repeated shifts to phytophagy, and a generally high specialization rate on single plant species (monophagy) are the major factors behind the success of the Gelechioidea.

Comprehensive gene and taxon coverage elucidates radiation patterns in moths and butterflies.

Lepidoptera (butterflies and moths) represent one of the most diverse animals groups. Yet, the phylogeny of advanced ditrysian Lepidoptera, accounting for about 99 per cent of lepidopteran species, has remained largely unresolved. We report a rigorous and comprehensive analysis of lepidopteran affinities. We performed phylogenetic analyses of 350 taxa representing nearly 90 per cent of lepidopteran families. We found Ditrysia to be a monophyletic taxon with the clade Tischerioidea + Palaephatoidea being the sister group of it. No support for the monophyly of the proposed major internested ditrysian clades, Apoditrysia, Obtectomera and Macrolepidoptera, was found as currently defined, but each of these is supported with some modification. The monophyly or near-monophyly of most previously identified lepidopteran superfamilies is reinforced, but several species-rich superfamilies were found to be para- or polyphyletic. Butterflies were found to be more closely related to 'microlepidopteran' groups of moths rather than the clade Macrolepidoptera, where they have traditionally been placed. There is support for the monophyly of Macrolepidoptera when butterflies and Calliduloidea are excluded. The data suggest that the generally short diverging nodes between major groupings in basal non-tineoid Ditrysia are owing to their rapid radiation, presumably in correlation with the radiation of flowering plants.

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.

Museomics identifies genetic erosion in two butterfly species across the 20th century in Finland.

Erosion of biodiversity generated by anthropogenic activities has been studied for decades and in many areas at the species level, using taxa monitoring. In contrast, genetic erosion within species has rarely been tracked, and is often studied by inferring past population dynamics from contemporaneous estimators. An alternative to such inferences is the direct examination of past genes, by analysing museum collection specimens. While providing direct access to genetic variation over time, historical DNA is usually not optimally preserved, and it is necessary to apply genotyping methods based on hybridization-capture to unravel past genetic variation. In this study, we apply such a method (i.e., HyRAD), to large time series of two butterfly species in Finland, and present a new bioinformatic pipeline, namely PopHyRAD, that standardizes and optimizes the analysis of HyRAD data at the within-species level. In the localities for which the data retrieved have sufficient power to accurately examine genetic dynamics through time, we show that genetic erosion has increased across the last 100 years, as revealed by signatures of allele extinctions and heterozygosity decreases, despite local variations. In one of the two butterflies (Erebia embla), isolation by distance also increased through time, revealing the effect of greater habitat fragmentation over time.

An annotated catalogue of Elachistinae of the World (Lepidoptera: Gelechioidea: Elachistidae).

An annotated catalogue of world species of Elachistinae (Lepidoptera: Gelechioidea: Elachistidae) is presented. The classification follows recent phylogenetic studies. Genera and the species within each genus are listed in alphabetical order. All family, genus and species-group names of Elachistinae published before 28 August 2018 are treated. Sixty-six genus-group names are listed, 60 of which are nomenclaturally available. In the classification followed in this catalogue the species are placed in 10 genera. There are 1016 nomenclaturally available and 106 unavailable species-group names. Of these, 805 names are currently considered to represent valid species. For each species the following data are given: the reference to the original publication and the page; type locality; deposition of the name-bearing types; in the genus Elachista, the taxonomic rank with the subgenus and the informal species group when applicable; distribution; larval host plants; references to essential illustrations, and remarks, when needed. Synonyms are listed under valid names; distribution with geographic area and country records, for Australia, Canada and U.S.A. territories, provinces and states are given; Russia is divided into subregions. Larval host plant records are listed with notes regarding uncertain records. When possible, original references that are considered trustworthy in later literature are given, as well as relevant literature references for illustrations for each species. Synonymies, incorrect subsequent spellings and misspellings are listed under each species with full reference. Alphabetical lists are given for subfamily and infra-generic groupings of species of the genus Elachista, to summarize the placement of each species in its subgenus and species group within the subgenera. 110 valid and one unavailable species-group names originally described to genera currently considered elachistines, but later removed, are listed. When known, their current identity is given. The following taxonomic changes are made: Elachista amseli (Parenti, 1981), a secondary junior homonym of E. amseli Rebel, 1933, is replaced with E. parentii nom. nov.; Hemiprosopa asiatica Sinev, 1998 = Elachista asiatica (Sinev, 1998) stat. nov., comb. nov.; E. bipunctella (Sinev Sruoga, 1995), a junior secondary homonym of E. bipunctella Treitschke, 1833, is replaced as E. ochropunctosa Kaila, nom. nov.; Elachista cerusella f. juncta Dufrane, 1957 is raised as species-rank name Elachista juncta Dufrane, 1957 stat. nov., a synonym of E. maculicerusella Bruand; Svenssonia corsicana Tautel Nel, 2010 is transferred to Elachista (Aphelosetia), comb. n.; E. cupreella Blanchard, 1852 is transferred to Perittia, comb. nov.; E. flammeaepennella Costa, 1836 is raised as valid species, stat. rev.; Illantis Meyrick, 1921 is considered a junior subjective synonym of Elachista, syn. nov.; I. picroleuca Meyrick, 1921 is transferred to Elachista, comb. nov.; E. kosteri Traugott-Olsen, 1995 = E. differens Parenti, 1978, syn. nov.; E. oritropha Bradley, 1965 = E. iriphaea (Meyrick, 1932), syn. nov.; Paraperittia Rebel, 1916 = Phaulernis Meyrick, 1895 (Epermeniidae) syn. nov.; P. uniformella Rebel, 1916 = Phaulernis dentella (Zeller, 1839), syn. nov.; and E. zernyi Hartig, 1941 = E. stelviella Amsel, 1932, syn. nov. A lectotype is designated for Paraperittia uniformella Rebel. Elachista macquartella Duponchel, 1840 is considered a nomen oblitum, stat. nov.

Characterization of Pleurotinae, with review of Pleurota species close to P. aristella (Linnaeus) from Morocco (Lepidoptera: Gelechioidea: Oecophoridae).

Morphological traits characterizing and delimiting Pleurotinae (Oecophoridae) are provided and discussed. The evidence supports the validity of the subfamily as suggested by recent molecular studies. The Pleurota aristella (Linnaeus, 1767) species group is characterized, and six new species belonging to the group from Morocco are described: Pleurota tricolor Tabell, sp. nov., P. pellicolor Tabell, sp. nov., P. lacteella Tabell, sp. nov., P. moroccoensis Tabell, sp. nov., P. ochreopalpella Tabell, sp. nov., and P. atlasensis Tabell, sp. nov. Habitus images and label data are provided for the types of P. goundafella Zerny, 1935; P. insignella Zerny, 1935; P. ochreostrigella Baker, 1885; P. macrosella Rebel, 1900; P. staintoniella Baker, 1888; P. mauretanica Baker, 1888; and P. algeriella Baker, 1885. DNA barcodes of the new species are compared with all available Pleurotinae sequences (BIN n = 117) in BOLD.

A review of the Elachista subula Parenti species complex (Lepidoptera, Elachistidae), with descriptions of nine new Palearctic species.

Taxonomy of the here established Elachista subula species complex is reviewed. This species complex is subordinate to the E. dispilella group sensu Kaila et al. (2015), in subgenus Aphelosetia. The E. subula species complex is exclusively Palearctic. Most of the currently recognized species occur in dry areas in Central Asia where they appear to form a significant part of the Elachista diversity. The constituent species are characterized by a phallus with bent and sharp-tipped apex, and the vesica with one weakly sclerotized plate-like cornutus that usually bears one blunt or spine-like tooth. Fourteen species are recognized, of which the following 9 are described as new: E. ameteria Kaila, sp. nov. (Type locality country Kazakhstan), E. cisoria Kaila, sp. nov. (Spain), E. cultella Kaila, sp. nov. (Mongolia), E. drepanella Kaila, sp. nov. (Russia: Tuva), E. marusiki Kaila, sp. nov. (Mongolia), E. perona Kaila, sp. nov. (Kyrgyzstan), E. platamodes Kaila, sp. nov. (Croatia), E. scalpra Kaila, sp. nov. (Turkey) and E. spinipyra Kaila, sp. nov. (Turkmenistan). Redescriptions are given to E. mus Parenti¸ E. bimaculata Parenti, E. semnani Parenti, E. subula Parenti and E. acutella Kaila.

A revision of the Elachista dispilella complex (Lepidoptera: Gelechioidea: Elachistidae).

The Elachista dispilella group and its subordinate E. dispilella species complex are characterized. Identity of the long confused oldest names applicable for taxa in the E. dispilella complex, i.e., E. dispilella Zeller, E. festucicolella Zeller, and E. distigmatella Frey, is resolved. Elachista dispilella Zeller is the valid name for the species often identified as E. festucicolella, E. steueri Traugott-Olsen, or E. manni Traugott-Olsen. Elachista distigmatella Frey is the valid name for the species regularly identified as E. dispilella. The identity of E. festucicolella Zeller, so far entirely dubious, is clarified. Nineteen species attributable to the E. dispilella complex sensu Traugott-Olsen are recognized. The following new synonymies are proposed: Elachista steueri Traugott-Olsen, 1990, syn. nov.; E. manni Traugott-Olsen, 1990, syn. nov.; E. jaeckhi Traugot-Olsen, 1990, syn. nov.; and E. gebzeensis Traugott-Olsen, 1990, syn. nov., are considered synonyms of E. dispilella Zeller, 1839. Elachista klimeschiella Parenti, 2002 is synonymized with E. festucicolella Zeller, 1853; and Elachista purella Sruoga, 2000 with E. levasi Sruoga, 1998, syn. nov. Identification keys for males and females are provided. All species are diagnosed, the lesser known are also redescribed. Four new species are described: Elachista implana Kaila, sp. nov., from Austria; E. ripai Kaila, sp. nov., from Kyrgyzstan; Elachista sitibunda Kaila, sp. nov., from Uzbekistan; and Elachista laterotis Kaila, sp. nov., from Turkey.

One species in eight: DNA barcodes from type specimens resolve a taxonomic quagmire.

Each holotype specimen provides the only objective link to a particular Linnean binomen. Sequence information from them is increasingly valuable due to the growing usage of DNA barcodes in taxonomy. As type specimens are often old, it may only be possible to recover fragmentary sequence information from them. We tested the efficacy of short sequences from type specimens in the resolution of a challenging taxonomic puzzle: the Elachista dispunctella complex which includes 64 described species with minuscule morphological differences. We applied a multistep procedure to resolve the taxonomy of this species complex. First, we sequenced a large number of newly collected specimens and as many holotypes as possible. Second, we used all >400 bp examine species boundaries. We employed three unsupervised methods (BIN, ABGD, GMYC) with specified criteria on how to handle discordant results and examined diagnostic bases from each delineated putative species (operational taxonomic units, OTUs). Third, we evaluated the morphological characters of each OTU. Finally, we associated short barcodes from types with the delineated OTUs. In this step, we employed various supervised methods, including distance-based, tree-based and character-based. We recovered 658 bp barcode sequences from 194 of 215 fresh specimens and recovered an average of 141 bp from 33 of 42 holotypes. We observed strong congruence among all methods and good correspondence with morphology. We demonstrate potential pitfalls with tree-, distance- and character-based approaches when associating sequences of varied length. Our results suggest that sequences as short as 56 bp can often provide valuable taxonomic information. The results support significant taxonomic oversplitting of species in the Elachista dispunctella complex.