Facilitating taxonomy and phylogenetics: An informative and cost-effective protocol integrating long amplicon PCRs and third-generation sequencing

Phylogenetic inference has become a standard technique in integrative taxonomy and systematics, as well as in biogeography and ecology. DNA barcodes are often used for phylogenetic inference, despite being strongly limited due to their low number of informative sites. Also, because current DNA barcodes are based on a fraction of a single, fast-evolving gene, they are highly unsuitable for resolving deeper phylogenetic relationships due to saturation. In recent years, methods that analyse hundreds and thousands of loci at once have improved the resolution of the Tree of Life, but these methods require resources, experience and molecular laboratories that most taxonomists do not have. This paper introduces a PCR-based protocol that produces long amplicons of both slow- and fast-evolving unlinked mitochondrial and nuclear gene regions, which can be sequenced by the affordable and portable ONT MinION platform with low infrastructure or funding requirements. As a proof of concept, we inferred a phylogeny of a sample of 63 spider species from 20 families using our proposed protocol. The results were overall consistent with the results from approaches based on hundreds and thousands of loci, while requiring just a fraction of the cost and labour of such approaches, making our protocol accessible to taxonomists worldwide.

Phylogenomic analysis provides diagnostic tools for the identification of Anastrepha fraterculus (Diptera: Tephritidae) species complex

Insect pests cause tremendous impact to agriculture worldwide. Species identification is crucial for implementing appropriate measures of pest control but can be challenging in closely related species. True fruit flies of the genus Anastrepha Schiner (Diptera: Tephritidae) include some of the most serious agricultural pests in the Americas, with the Anastrepha fraterculus (Wiedemann) complex being one of the most important due to its extreme polyphagy and wide distribution across most of the New World tropics and subtropics. The eight morphotypes described for this complex as well as other closely related species are classified in the fraterculus species group, whose evolutionary relationships are unresolved due to incomplete lineage sorting and introgression. We performed multifaceted phylogenomic approaches using thousands of genes to unravel the evolutionary relationships within the A. fraterculus complex to provide a baseline for molecular diagnosis of these pests. We used a methodology that accommodates variable sources of data (transcriptome, genome, and whole-genome shotgun sequencing) and developed a tool to align and filter orthologs, generating reliable datasets for phylogenetic studies. We inferred 3031 gene trees that displayed high levels of discordance. Nevertheless, the topologies of the inferred coalescent species trees were consistent across methods and datasets, except for one lineage in the A. fraterculus complex. Furthermore, network analysis indicated introgression across lineages in the fraterculus group. We present a robust phylogeny of the group that provides insights into the intricate patterns of evolution of the A. fraterculus complex supporting the hypothesis that this complex is an assemblage of closely related cryptic lineages that have evolved under interspecific gene flow. Despite this complex evolutionary scenario, our subsampling analysis revealed that a set of as few as 80 loci has a similar phylogenetic resolution as the genome-scale dataset, offering a foundation to develop more efficient diagnostic tools in this species group.

First Discovery of the North American Leaf-Mining Moth Chrysaster ostensackenella (Lepidoptera: Gracillariidae) in Russia: The Genetic Diversity of a Novel Pest in Invaded vs. Native Range

Here, we report the first detection of the North American leaf-mining moth Chrysaster ostensackenella (Fitch, 1859) (Lepidoptera: Gracillariidae) on North American black locust Robinia pseudoacacia (Fabaceae) in Primorsky Krai (the Russian Far East) in July 2022. Overall, six moths were reared from the leaf mines and identified based on adult morphology (forewing pattern and male genitalia) and three of them were DNA barcoding. Description of the leaf mines that allowed us to distinguish the damage of Ch. ostensackenella from other gracillariids associated with R. pseudoacacia is provided. The phylogeographic analysis comparing the DNA barcodes from Russia with those from other invaded countries in Europe (Italy) and East Asia (South Korea and Japan) and from the native range (North America) was performed. Intraspecific genetic diversity reached 3.29%. Altogether, 10 haplotypes were revealed among 21 studied specimens in the Holarctic. The detection of one haplotype common for Japan and the USA (North Carolina) suggests that the invasion to East Asia could have happened from the USA directly, rather than through Europe. A shared haplotype defined for Japan and the Russian Far East points at a possible moth species' spread to Primorsky Krai from earlier invaded Hokkaido. Further distribution of Ch. ostensackenella in East Asia and Europe is expected, bearing in mind the wide planting of R. pseudoacacia in these continents. Furthermore, an accidental introduction of the moth to the Southern Hemisphere, where black locust was introduced, is not ruled out.

Taxonomic Delineation of the Old World Species Stomphastis thraustica (Lepidoptera: Gracillariidae) Feeding on Jatropha gossypiifolia (Euphorbiaceae) that Was Collected in the New World and Imported as a Biocontrol Agent to Australia

We provide the identification and species delineation of this biocontrol agent as Stomphastis thraustica (Meyrick in Trans Ent Soc Lond 80(1):107-120, 1908) belonging to the family Gracillariidae. We clarify the distribution pattern of S. thraustica, its host plant preferences, and present taxonomic and molecular diagnoses based on original morphological and genetic data as well as data retrieved from historic literature and genetic databases. Following our own collecting efforts in three continents Africa, South America, and Australia as well as our study of historic museum collection material, we present many new distribution records of S. thraustica for countries and territories in the world including the new discovery of this species in the Neotropical region and we report its introduction in Australia as a biocontrol agent. Using mitogenomic and COI gene data, we clarified that the closest relative of S. thraustica is Stomphastis sp. that occurs in Madagascar and Australia and feeds on the same host plant as S. thraustica - Jatropha gossypiifolia L. (Euphorbiaceae). The molecular sequence divergence in the mitochondrial DNA barcode fragment between these two closely related species S. thraustica and Stomphastis sp. is over 5.7% supporting that they are different species.

A workflow for expanding DNA barcode reference libraries through 'museum harvesting' of natural history collections

Natural history collections are the physical repositories of our knowledge on species, the entities of biodiversity. Making this knowledge accessible to society - through, for example, digitisation or the construction of a validated, global DNA barcode library - is of crucial importance. To this end, we developed and streamlined a workflow for 'museum harvesting' of authoritatively identified Diptera specimens from the Smithsonian Institution's National Museum of Natural History. Our detailed workflow includes both on-site and off-site processing through specimen selection, labelling, imaging, tissue sampling, databasing and DNA barcoding. This approach was tested by harvesting and DNA barcoding 941 voucher specimens, representing 32 families, 819 genera and 695 identified species collected from 100 countries. We recovered 867 sequences (> 0 base pairs) with a sequencing success of 88.8% (727 of 819 sequenced genera gained a barcode > 300 base pairs). While Sanger-based methods were more effective for recently-collected specimens, the methods employing next-generation sequencing recovered barcodes for specimens over a century old. The utility of the newly-generated reference barcodes is demonstrated by the subsequent taxonomic assignment of nearly 5000 specimen records in the Barcode of Life Data Systems.

CO1 barcodes resolve an asymmetric biphyletic clade for Diabrotica undecimpunctata subspecies and provide nucleotide variants for differentiation from related lineages using real-time PCR

Diabrotica undecimpunctata is a multivoltine polyphagous beetle species that has long been documented as a significant agricultural pest throughout its native range in North America. This beetle can vector bacterial and viral plant pathogens that result in major losses to crops such as cucumber and soybean. Many countries outside the Americas treat D. undecimpunctata as a species of quarantine importance, while in the USA only the subspecies D. u. duodecimnotata is subject to quarantine, to prevent introduction from Mexico. Identification of D. undecimpunctata on the basis of morphology alone can be complicated given the use of conflicting characters in the description of some subspecific taxa. To better understand relationships among D. undecimpunctata subspecies and other related species, we sequenced mitochondrial cytochrome oxidase 1 (CO1) and nuclear internal transcribed spacer 2 (ITS2) DNA from individuals in different subspecific taxa and across different parts of the species range using museum samples and interceptions. When our data were combined with publicly available Diabrotica data, no pattern of divergence consistent with the currently recognized subspecific designations was found. In addition, we compared phylogenetic patterns in CO1 data from the congener D. virgifera to demonstrate the utility of mitochondrial data in resolving subspecies. From the CO1 data, a diagnostic real-time PCR assay was developed that could successfully identify all haplotypes within the large D. undecimpunctata clade for use in surveys and identification at ports of entry. These findings underscore the need to resolve molecular and morphological datasets into cogent, lineage-based groupings. Such efforts will provide an evolutionary context for the study of agriculturally important attributes of Diabrotica such as host preferences, xenobiotic metabolism, and natural and anthropogenic patterns of dispersal.

DNA Barcode Library of Megadiverse Lepidoptera in an Alpine Nature Park (Italy) Reveals Unexpected Species Diversity

Species inventories are a prerequisite for biodiversity monitoring and conservation, particularly in protected areas. However, the possibilities of a standardized survey of species diversity using DNA barcoding have so far hardly been implemented, especially in species-rich groups. A first-time molecular-based and nearly complete inventory of the megadiverse insect order Lepidoptera in a protected area in the Alps (Cottian Alps, Italy) was intended to test the possibilities and reliability of DNA-based identifications. From voucher material collected between 2019 and 2022, we successfully sequenced 1213 morphospecies that grouped into 1204 BINs (barcode index numbers), whereas DNA barcoding failed for another 18 species. A total of 35 species shared a BIN with one or more taxa, but a majority of 19 species could still be discriminated by divergent sequences. A total of 12 morphospecies split into two BINs. These species and a further 22 taxa with unique BINs and barcode divergences >2% to the nearest neighbor require taxonomic re-assessment. Two additional cryptic species from the study area were described recently. Finally, 16 species are newly recorded for Italy. Our study, therefore, demonstrates the importance of DNA barcoding for both faunistics and the discovery of cryptic diversity, even in apparently well-studied protected areas.

Integrative Taxonomy Approach Reveals Cryptic Diversity within the Phoretic Pseudoscorpion Genus Lamprochernes (Pseudoscorpiones: Chernetidae)

Pseudoscorpions represent an ancient, but homogeneous group of arachnids. The genus Lamprochernes comprises several morphologically similar species with wide and overlapping distributions. We implemented an integrative approach combining molecular barcoding (cox1), with cytogenetic and morphological analyses in order to assess species boundaries in European Lamprochernes populations. The results suggest ancient origins of Lamprochernes species accompanied by morphological stasis within the genus. Our integrative approach delimited three nominal Lamprochernes species and one cryptic lineage Lamprochernes abditus sp. nov. Despite its Oligocene origin, L. abditus sp. nov. can be distinguished from its closest relative only by molecular and cytogenetic differences, or alternatively, by a complex multivariate morphometric analysis involving other Lamprochernes species. The population structure and common haplotype sharing across geographically distant populations in most Lamprochernes species suggest that a phoretic manner of dispersal is efficient in this group.

Invasion Genetics of the Horse-Chestnut Leaf Miner, Cameraria ohridella (Lepidoptera: Gracillariidae), in European Russia: A Case of Successful Involvement of Citizen Science in Studying an Alien Insect Pest

Based on the intensive monitoring conducted by our team and volunteers in 2021, the secondary range of an alien horse-chestnut leaf miner, Cameraria ohridella Deschka & Dimić, 1986 (Lepidoptera: Gracillariidae), was specified in European Russia. This invasive pest was confirmed in 24 out of 58 administrative regions of Russia, which it has occupied for approximately 16 years. Analysis of the COI mtDNA gene sequenced in 201 specimens collected in 21 regions of the European part of Russia indicates the occurrence of two haplotypes (A and B), which are also present in the secondary range of C. ohridella in Eastern and Western Europe. The haplotype A dominated and was present in 87.5% of specimens from European Russia. In 2021, C. ohridella produced spectacular outbreaks in Aesculus hippocastanum in southern Russia, where it damaged more than 50% of the leaves in trees in 24 out of 30 distant localities. In the south of the country, the pest infested Acer pseudoplatanus, whereas other species of Acer of European, East Asian, and North American origin showed no signs of attacks. Taking into account that Ae. hippocastanum is present in most regions of European Russia, we expect a further range expansion of C. ohridella up to the Ural Mountains.

DNA barcoding and nutritional profiling of underutilized native indigenous plant species of Karnataka, India

BACKGROUND

Locally adapted native indigenous plant species (NIPS) could restore the crop diversity in sustainable agriculture.

METHODS

Here, we report the molecular identification and nutritional profiling of some five NIPS of Karnataka; Musa paradisiaca cv. Nanjangud rasabale, Piper betle L. cv. Mysore betel leaf, Jasminum grandiflorum cv Mysore mallige, Solanum melongena L. cv. Udupi Mattu Gulla and S. melongena L. cv. Erangere badane of which the first four are Geographical Indication (GI) tagged. The samples were procured, authenticated and sequenced using two standard DNA barcodes: nuclear ITS2 and plastid rbcl.

RESULTS

The phylogenetic analysis using Neighborhood joining method revealed all the ITS2 tree topologies with higher genetic divergence than rbcl. All the rbcl tree topologies were monophyletic indicating sequence conservation. Though the concatenated ITS2 + rbcl trees had higher bootstrap support (> 98% except Solanum sp.) differences were observed because of the lack of available sequence deposition at species level. The proximate and nutritional profiling of the NIPS displayed superiority in terms of their nutritional profile and their potential application in phytopharmaceutical sector as nutritional supplements.

CONCLUSION

To our best knowledge this is the first study reporting the screening of five NIPS plant species of Karnataka for phylogeny and nutritional analysis. We also anticipate that if research towards the identification of NIPS species is accelerated, these nutritionally enhanced crops could be used as a safe and sustainable food in changing global climatic conditions.

Genomic evidence for contrasting patterns of host-associated genetic differentiation across shared host-plant species in leaf- and bud-galling sawflies

Resource specialization and ecological speciation arising through host-associated genetic differentiation (HAD) are frequently invoked as an explanation for the high diversity of plant-feeding insects and other organisms with a parasitic lifestyle. While genetic studies have demonstrated numerous examples of HAD in insect herbivores, the rarity of comparative studies means that we still lack an understanding of how deterministic HAD is, and whether patterns of host shifts can be predicted over evolutionary timescales. We applied genome-wide single nucleotide polymorphism and mitochondrial DNA sequence data obtained through genome resequencing to define species limits and to compare host-plant use in population samples of leaf- and bud-galling sawflies (Hymenoptera: Tenthredinidae: Nematinae) collected from seven shared willow (Salicaceae: Salix) host species. To infer the repeatability of long-term cophylogenetic patterns, we also contrasted the phylogenies of the two galler groups with each other as well as with the phylogeny of their Salix hosts estimated based on RADseq data. We found clear evidence for host specialization and HAD in both of the focal galler groups, but also that leaf gallers are more specialized to single host species compared with most bud gallers. In contrast to bud gallers, leaf gallers also exhibited statistically significant cophylogenetic signal with their Salix hosts. The observed discordant patterns of resource specialization and host shifts in two related galler groups that have radiated in parallel across a shared resource base indicate a lack of evolutionary repeatability in the focal system, and suggest that short- and long-term host use and ecological diversification in plant-feeding insects are dominated by stochasticity and/or lineage-specific effects.

DNA Barcoding of Lepidoptera Species from the Maltese Islands: New and Additional Records, with an Insight into Endemic Diversity

This work presents the first outcomes resulting from a DNA barcode reference library of lepidopteran species from Malta. The library presented here was constructed from the specimens collected between 2015 and 2019 and covers the genetic barcodes of 146 species (ca. 25% of lepidopterous Maltese fauna), including four newly recorded Lepidoptera species from the Maltese islands: Apatema baixerasi, Bostra dipectinialis, Oiketicoides lutea, and Phereoeca praecox. The DNA reference barcode library constructed during this study was analyzed in conjunction with publicly available DNA barcodes and used to assess the ability of the local DNA barcodes to discriminate species. Results showed that each species occupies a different BOLD BIN; therefore, DNA barcoding was able to discriminate between the studied species. Our data led to the formation of 12 new BOLD BINs—that is, OTUs that were identified during this work—while nearly 46% of the barcodes generated during this study were never recorded on conspecifics, further indicating the uniqueness of genetic diversity on these central Mediterranean islands. The outcomes of this study highlight the integrative taxonomic approach, where molecular taxonomy plays an important role for biodiversity investigation in its entirety.

Saint Peter and Saint Paul Archipelago barcoded: Fish diversity in the remoteness and DNA barcodes reference library for metabarcoding monitoring

In order to monitor the effects of anthropogenic pressures in ecosystems, molecular techniques can be used to characterize species composition. Among molecular markers capable of identifying species, the cytochrome c oxidase I (COI) is the most used. However, new possibilities of biodiversity profiling have become possible, in which molecular fragments of medium and short-length can now be analyzed in metabarcoding studies. Here, a survey of fishes from the Saint Peter and Saint Paul Archipelago was barcoded using the COI marker, which allowed the identification of 21 species. This paved the way to further investigate the fish biodiversity of the archipelago, transitioning from barcoding to metabarcoding analysis. As preparatory steps for future metabarcoding studies, the first extensive COI library of fishes listed for these islands was constructed and includes new data generated in this survey as well as previously available data, resulting in a final database with 9,183 sequences from 169 species and 63 families of fish. A new primer specifically designed for those fishes was tested in silico to amplify a region of 262 bp. The new approach should guarantee a reliable surveillance of the archipelago and can be used to generate policies that will enhance the archipelago’s protection.

Notes on the distribution of Dalmatinella simonae (Gastropoda: Hydrobiidae) in Croatia and the utility of barcoding in its determination

Dalmatinella simonae is a recently described species from Lake Sladinac and the river Cetina (Croatia). New findings from the rivers Cetina, Neretva and Ruda indicate a wider distribution of this species especially in comparison with its relative D. fluviatilis, known only from a short section of the river Zrmanja. Its occurrence is also probable in the river Neretva in Bosnia and Herzegovina. Barcoding analysis, using mitochondrial cytochrome oxidase subunit I (COI), confirmed the occurrence of this species in new sites, and the nearly complete lack of genetic divergence.

Underestimated cryptic diversity in the Caryocolumtricolorella species complex (Lepidoptera, Gelechiidae)

The taxonomy of the Caryocolumtricolorella species complex, an informal subsection of the diverse Caryocoluminteralbicella species group, is revised and four species are separated from DNA barcodes of the mitochondrial COI (cytochrome c oxidase subunit 1) gene and adult morphology: C.tricolorella (Haworth, 1812), C.fibigerium Huemer, 1988, C.herwigvanstaai sp. nov., and C.olekarsholti sp. nov. These species show a vicariant distribution pattern, with C.tricolorella widely distributed in Central and Northern Europe, C.fibigerium restricted to the Iberian Peninsula and southern France, C.herwigvanstaai sp. nov. to the Italian Peninsula, and C.olekarsholti sp. nov. to the Balkans. All species are described in detail, and the adults and genitalia of both sexes are illustrated.

Tracing the invasion of a leaf-mining moth in the Palearctic through DNA barcoding of historical herbaria

The lime leaf-miner, Phyllonorycter issikii is an invasive micromoth with an unusually higher number of haplotypes in the invaded area (Europe, Western Siberia) compared to its putative native region (East Asia). The origin of the genetic diversity in the neocolonized region remains unclear. We surveyed over 15 thousand herbarium specimens of lime trees (Tilia spp.) collected across the Palearctic over a period of 252 years (1764-2016) looking for preserved larvae within the archival leaf mines. We found 203 herbarium specimens with leaf mines of Ph. issikii collected in East Asia, one of them dating back to 1830, i.e. 133 years before the description of the species. In contrast, only 22 herbarium specimens collected in the West Palearctic in the last three decades (1987-2015) carried leaf mines. DNA barcoding of archival specimens revealed 32 haplotypes out of which 23 were novel (not known from modern populations) and found exclusively in East Asia. Six haplotypes are shared between both native and invaded areas and only two were responsible for the recent invasion of the Western Palearctic. The remarkable number of newly discovered haplotypes in archival populations supports East Asia as the native region and the source area of invasion.

Integrative taxonomy reveals overlooked cryptic diversity in the conifer feeding Batrachedra pinicolella (Zeller, 1839) (Lepidoptera, Batrachedridae)

During efforts to generate DNA barcodes for all European Lepidoptera, Batrachedrapinicolella (Zeller, 1839) was found to comprise two genetically distinct clusters. Morphological investigation and results from two nuclear markers and ddRAD sequencing furthermore support the existence of two distinct taxa which we treat as two separate species, B.pinicolella and B.confusellasp. nov. A lectotype for B.pinicolella is designated. Available data indicate that the biology of both species also differs, with Piceaabies (L.) Karsten as a proved host-plant for B.pinicolella and Pinussylvestris L. for B.confusellasp. nov. Both species are mainly distributed on the European continent with B.pinicolella occurring in boreal parts of North and Central Europe and introduced to Canada, reflecting a boreo-montane distribution pattern. Batrachedraconfusellasp. nov. is more widely distributed in temperate Northern and Central Europe.

Taxonomical Evaluation of Plant Chloroplastic Markers by Bayesian Classifier

DNA barcodes are standardized sequences that range between 400 and 800 bp, vary at different taxonomic levels, and make it possible to assign sequences to species that have been previously taxonomically characterized. Several DNA barcodes have been postulated for plants, nonetheless, their classification potential has not been evaluated for metabarcoding, and as a result, it would appear as none of them excels above the others in this area. One tool that has been widely used and served as a baseline when evaluating new approaches is Naïve Bayesian Classifiers (NBC). The present study aims at evaluating the classification power of several plant chloroplast genetic markers that have been proposed as barcodes (trnL, rpoB, rbcL, matK, psbA-trnH, and psbK) using an NBC. We performed the classification at different taxonomic levels, and identified problematic genera when resolution was desired. We propose matK and trnL as potential candidate markers with resolution up to genus level. Some problematic genera within certain families could lead to the misclassification no matter which marker is used (i.e., Aegilops, Gueldenstaedtia, Helianthus, Oryza, Shorea, Thysananthus, and Triticum). Finally, we suggest recommendations for the taxonomic identification of plants in samples with potential mixtures.

Current State of DNA Barcoding of Sciaroidea (Diptera)—Highlighting the Need to Build the Reference Library

Simple Summary

DNA barcoding is a method by which a specific region of the mitochondrial genome is used to quantify genetic distances within and between animal species. Most DNA barcodes of the world are assembled on the Barcode of Life online database BoldSystems (BOLD). There, machine-generated barcode index numbers (BINs) are automatically assigned to clusters of specimens thought to represent species. I review the current state of DNA barcoding of the superfamily Sciaroidea, a diverse insect group consisting of close to 16,000 described fly species in eight families. To date, over 1.2 million specimens of Sciaroidea have been barcoded and the 56,648 assigned BINs on BOLD already represent 3.5 times the number of described species. Still, 95% of the BINs have currently no associated scientific name and very little effort has been put into building a quality-checked reference library where named species are linked to the BINs on BOLD. In the Nordic region, however, substantial progress is made towards building a complete reference library. While DNA barcoding has tremendous potential for advancing the knowledge for many diverse groups of insects, its potential will never be fully reached absent more engagement of trained taxonomists to build voucher collections, curate the reference libraries, and describe new species.

Abstract

DNA barcoding has tremendous potential for advancing species knowledge for many diverse groups of insects, potentially paving way for machine identification and semi-automated monitoring of whole insect faunas. Here, I review the current state of DNA barcoding of the superfamily Sciaroidea (Diptera), a diverse group consisting of eight understudied fly families where the described species in the world makes up some 10% (≈16,000 species) of all Diptera. World data of Sciaroidea were extracted from the Barcode of Life online database BoldSystems (BOLD) and contrasted with results and experiences from a Nordic project to build the reference library. Well over 1.2 million (1,224,877) Sciaroidea specimens have been submitted for barcoding, giving barcode-compliant sequences resulting in 56,648 so-called barcode index numbers (BINs, machine-generated proxies for species). Although the BINs on BOLD already represent 3.5 times the number of described species, merely some 2850 named species (described or interim names, 5% of the BINs) currently have been assigned a BIN. The other 95% remain as dark taxa figuring in many frontier publications as statistics representing proxies for species diversity within a family. In the Nordic region, however, substantial progress has been made towards building a complete reference library, currently making up 55% of all named Sciaroidea BINs on BOLD. Another major source (31%) of named Sciaroidea BINs on BOLD comes from COI sequences mined from GenBank, generated through phylogenetic and integrative studies outside of BOLD. Building a quality reference library for understudied insects such as Sciaroidea requires heavy investment, both pre sequence and post sequence, by trained taxonomists to build and curate voucher collections, to continually improve the quality of the data and describe new species. Only when the BINs are properly calibrated by a rigorously quality-checked reference library can the great potential of both classical taxonomic barcoding, metabarcoding, and eDNA ecology be realized.

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

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

DNA barcoding for bio-surveillance of emerging pests and species identification in Afrotropical Prioninae (Coleoptera, Cerambycidae)

DNA barcoding has been succesfully used for bio-surveillance of forest and agricultural pests in temperate areas, but has few applications in the tropics and particulary in Africa. Cacoscelesnewmannii (Coleoptera: Cerambycidae) is a Prioninae species that is locally causing extensive damage in commercially-grown sugarcane in the KwaZulu-Natal Province in South Africa. Due to the risk of spread of this species to the rest of southern Africa and to other sugarcane growing regions, clear and easy identification of this pest is critical for monitoring and for phytosanitary services. The genus Cacosceles Newman, 1838 includes four species, most being very similar in morphology. The damaging stage of the species is the larva, which is inherently difficult to distinguish morphologically from other Cerambycidae species. A tool for rapid and reliable identification of this species was needed by plant protection and quarantine agencies to monitor its potential abundance and spread. Here, we provide newly-generated barcodes for C.newmannii that can be used to reliably identify any life stage, even by non-trained taxonomists. In addition, we compiled a curated DNA barcoding reference library for 70 specimens of 20 named species of Afrotropical Prioninae to evaluate DNA barcoding as a valid tool to identify them. We also assessed the level of deeply conspecific mitochondrial lineages. Sequences were assigned to 42 different Barcode Index Numbers (BINs), 28 of which were new to BOLD. Out of the 20 named species barcoded, 11 (52.4%) had their own unique Barcode Index Number (BIN). Eight species (38.1%) showed multiple BINs with no morphological differentiation. Amongst them, C.newmannii showed two highly divergent genetic clusters which co-occur sympatrically, but further investigation is required to test whether they could represent new cryptic species.