Advancing taxonomy and bioinventories with DNA barcodes

Sea anemone (Anthozoa, Actiniaria) diversity in Mo'orea (French Polynesia)

Sea anemones (Order Actiniaria) are a diverse group of marine invertebrates ubiquitous across marine ecosystems. Despite their wide distribution and success, a knowledge gap persists in our understanding of their diversity within tropical systems, owed to sampling bias of larger and more charismatic species overshadowing cryptic lineages. This study aims to delineate the sea anemone diversity in Mo'orea (French Polynesia) with the use of a dataset from the Mo'orea Biocode's "BioBlitz" initiative, which prioritized the sampling of more cryptic and understudied taxa. Implementing a target enrichment approach, we integrate 71 newly sequenced samples into an expansive phylogenetic framework and contextualize Mo'orea's diversity within global distribution patterns of sea anemones. Our analysis corroborates the presence of several previously documented sea anemones in French Polynesia and identifies for the first time the occurrence of members of genera Andvakia and Aiptasiomorpha. This research unveils the diverse sea anemone ecosystem in Mo'orea, spotlighting the area's ecological significance and emphasizing the need for continued exploration. Our methodology, encompassing a broad BLAST search coupled with phylogenetic analysis, proved to be a practical and effective approach for overcoming the limitations posed by the lack of comprehensive sequence data for sea anemones. We discuss the merits and limitations of current molecular methodologies and stress the importance of further research into lesser-studied marine organisms like sea anemones. Our work sets a precedent for future phylogenetic studies stemming from BioBlitz endeavors.

Phytochemical and bioactive potentials of African Annonaceae species

This review aims to gather available information on the medicinal, nutritional, and bioactive profiles of Annonaceae species in the African continent, sponsoring their use worldwide and mainly in African communities, where access to food and medicines for basic health care is scarce. >60 medicinal taxa were compiled, belonging to 22 genera, namely Annickia, Annona, Anonidium, Artabotrys, Cleistochlamys, Cleistopholis, Dennettia, Duguetia, Greenwayodendron, Hexalobus, Isolona, Lettowianthus, Monanthotaxis, Monodora, Neostenanthera, Polyceratocarpus, Sphaerocoryne, Uvaria, Uvariastrum, Uvariodendron, Uvariopsis and Xylopia; the most diverse and economically important genera were the genera Annona, Uvaria and Xylopia with 7 species each. Annonaceae species hold a valuable nutritional profile, rich in proteins, fibers, and minerals, being also good sources of a wide range of bioactive compounds of high biological relevance. These compounds are especially important in developing countries, where most of these species are available for direct use as food and/or medicines by the most deprived populations.

Improving the gold standard in NCBI GenBank and related databases: DNA sequences from type specimens and type strains

Scientific names permit humans and search engines to access knowledge about the biodiversity that surrounds us, and names linked to DNA sequences are playing an ever-greater role in search-and-match identification procedures. Here, we analyze how users and curators of the National Center for Biotechnology Information (NCBI) are flagging and curating sequences derived from nomenclatural type material, which is the only way to improve the quality of DNA-based identification in the long run. For prokaryotes, 18,281 genome assemblies from type strains have been curated by NCBI staff and improve the quality of prokaryote naming. For Fungi, type-derived sequences representing over 21,000 species are now essential for fungus naming and identification. For the remaining eukaryotes, however, the numbers of sequences identifiable as type-derived are minuscule, representing only 739 species of arthropods, 1542 vertebrates, and 125 embryophytes. An increase in the production and curation of such sequences will come from (i) sequencing of types or topotypic specimens in museum collections, (ii) the March 2023 rule changes at the International Nucleotide Sequence Database Collaboration requiring more metadata for specimens, and (iii) efforts by data submitters to facilitate curation, including informing NCBI curators about a specimen's type status. We illustrate different type-data submission journeys and provide best-practice examples from a range of organisms. Expanding the number of type-derived sequences in DNA databases, especially of eukaryotes, is crucial for capturing, documenting, and protecting biodiversity.

Assessing arthropod biodiversity with DNA barcoding in Jinnah Garden, Lahore, Pakistan

Previous difficulties in arthropod taxonomy (such as limitations in conventional morphological approaches, the possibility of cryptic species and a shortage of knowledgeable taxonomists) has been overcome by the powerful tool of DNA barcoding. This study presents a thorough analysis of DNA barcoding in regards to Pakistani arthropods, which were collected from Lahore's Jinnah Garden. The 88 % (9,451) of the 10,792 specimens that were examined were able to generate DNA barcodes and 83% (8,974) of specimens were assigned 1,361 barcode index numbers (BINs). However, the success rate differed significantly between the orders of arthropods, from 77% for Thysanoptera to an astounding 93% for Diptera. Through morphological exams, DNA barcoding, and cross-referencing with the Barcode of Life Data system (BOLD), the Barcode Index Numbers (BINs) were assigned with a high degree of accuracy, both at the order (100%) and family (98%) levels. Though, identifications at the genus (37%) and species (15%) levels showed room for improvement. This underscores the ongoing need for enhancing and expanding the DNA barcode reference library. This study identified 324 genera and 191 species, underscoring the advantages of DNA barcoding over traditional morphological identification methods. Among the 17 arthropod orders identified, Coleoptera, Diptera, Hemiptera, Hymenoptera, and Lepidoptera from the class Insecta dominated, collectively constituting 94% of BINs. Expected malaise trap Arthropod fauna in Jinnah Garden could contain approximately 2,785 BINs according to Preston log-normal species distribution, yet the Chao-1 Index predicts 2,389.74 BINs. The Simpson Index of Diversity (1-D) is 0.989, signaling high species diversity, while the Shannon Index is 5.77, indicating significant species richness and evenness. These results demonstrated that in Pakistani arthropods, DNA barcoding and BOLD are an invaluable tool for improving taxonomic understanding and biodiversity assessment, opening the door for further eDNA and metabarcoding research.

Stepping towards pollen DNA metabarcoding: A breakthrough in forensic sciences

This review is engaged in determining the capability of plant pollen as a significant source of evidence for the linkage between suspects and crime location in forensic sciences. Research and review articles were collected from Google Scholar, the Web of Science, and PubMed. Articles were searched using specific keywords such as "Forensic Palynology," "Pollen metabarcoding," "Plant forensics," and "Pollen" AND "criminal investigation." Boolean logic was also utilized to narrow the articles to be included in this review article. Through the literature and exploratory research, it has been observed in the current study that with advancements in technology, forensic palynology has found its application in creating an association between the crime scene and suspected individuals to have a link to it, as pollen DNA is a long-lasting investigative tool that can effectively help forensic investigations. Moreover, the literature shows that the DNA of pollen and spores has helped forensic scientists link suspects to crime scenes, and the introduction of pollen DNA metabarcoding tools has eased the efforts of palynologists to analyze pollen DNA. The introduction of DNA metabarcoding techniques to analyze pollen from plants has helped identify the geological locations of the plants and ultimately identify the culprit.

Metabarcoding and applied ecology with hyperdiverse organisms: Recommendations for biological control research

Metabarcoding is revolutionizing fundamental research in ecology by enabling large-scale detection of species and producing data that are rich with community context. However, the benefits of metabarcoding have yet to be fully realized in fields of applied ecology, especially those such as classical biological control (CBC) research that involve hyperdiverse taxa. Here, we discuss some of the opportunities that metabarcoding provides CBC and solutions to the main methodological challenges that have limited the integration of metabarcoding in existing CBC workflows. We focus on insect parasitoids, which are popular and effective biological control agents (BCAs) of invasive species and agricultural pests. Accurately identifying native, invasive and BCA species is paramount, since misidentification can undermine control efforts and lead to large negative socio-economic impacts. Unfortunately, most existing publicly accessible genetic databases cannot be used to reliably identify parasitoid species, thereby limiting the accuracy of metabarcoding in CBC research. To address this issue, we argue for the establishment of authoritative genetic databases that link metabarcoding data to taxonomically identified specimens. We further suggest using multiple genetic markers to reduce primer bias and increase taxonomic resolution. We also provide suggestions for biological control-specific metabarcoding workflows intended to track the long-term effectiveness of introduced BCAs. Finally, we use the example of an invasive pest, Drosophila suzukii, in a reflective "what if" thought experiment to explore the potential power of community metabarcoding in CBC.

Genome skimming as an efficient tool for authenticating commercial products of the pharmaceutically important Paris yunnanensis (Melanthiaceae)

BACKGROUND

Paris yunnanensis (Melanthiaceae) is a traditional Chinese medicinal plant of significant pharmaceutical importance. Due to previous taxonomic confusion, a congeneric species, Paris liiana, has been mistaken for P. yunnanensis and cultivated on a large scale, leading to the mixing of commercial products (i.e., seedlings and processed rhizomes) of P. yunnanensis with those of P. liiana. This may have adverse effects on quality control in the standardization of P. yunnanensis productions. As the lack of PCR amplifiable genomic DNA within processed rhizomes is an intractable obstacle to the authentication of P. yunnanensis products using PCR-based diagnostic tools, this study aimed to develop a PCR-free method to authenticate commercial P. yunnanensis products, by applying genome skimming to generate complete plastomes and nrDNA arrays for use as the molecular tags.

RESULTS

Based on a dense intraspecies sampling of P. liiana and P. yunnanensis, the robustness of the proposed authentication systems was evaluated by phylogenetic inferences and experimental authentication of commercial seedling and processed rhizome samples. The results indicate that the genetic criteria of both complete plastomes and nrDNA arrays were consistent with the species boundaries to achieve accurate discrimination of P. yunnanensis and P. liinna. Owing to its desirable accuracy and sensitivity, genome skimming can serve as an effective and sensitive tool for monitoring and controlling the trade of P. yunnanensis products.

CONCLUSION

This study provides a new way to solve the long-standing problem of the molecular authentication of processed plant products due to the lack of PCR amplifiable genomic DNA. The proposed authentication system will support quality control in the standardization of P. yunnanensis products in cultivation and drug production. This study also provides molecular evidence to clarify the long-standing taxonomic confusion regarding the species delimitation of P. yunnanensis, which will contribute to the rational exploration and conservation of the species.

Using DNA barcodes to test the association of sexes and morphs in Calodesma spp. (Lepidoptera, Erebidae, Arctiinae, Arctiini, Pericopina) of Trinidad, West Indies, with an overview of the genus, taxonomic changes and a new species

Phalaena militta Stoll, [1781], currently in the combination Thyrgis militta, is transferred to the new combination Calodesma militta. Phalaena militta is the type species of Thyrgis Walker, 1854, and so Thyrgis is a junior synonym of Calodesma Hübner, [1820]. The reinstated genus Seileria Dognin, 1923 is the next available name for the genus previously known as Thyrgis, and the remaining eight species and their subspecies currently in Thyrgis are transferred to new combinations as species of Seileria: S. angustifascia (Hering, 1925), S. basipunctata (Hering, 1926), S. constrictifascia (Dognin, 1919), S. flavonigra (Dognin, 1910), S. investigatorum (Toulgoët, 1988), S. marginata (Butler, 1875), S. meres (Druce, 1911), S. phlegon (Druce, 1885), S. phlegon ruscia (Druce, 1895), S. tenuifascia (Hering, 1930) and S. tenuifascia daguana (Hering, 1930). Eucyanoides Toulgoët, 1988, currently a synonym of Thyrgis, is made a new subjective synonym of Seileria. Based on DNA barcodes, we recognise three very similar, sexually dimorphic and in two cases polymorphic South American species of Calodesma with some phenotypes in common but very similar male genitalia: C. militta (BOLD:AAK1660), C. sp. cf. collaris (BOLD:ABZ2392) and C. pseudocollaris Cock new species (BOLD:AEI2170). Calodesma militta is widespread in South America, with two male morphs (collaris and dioptis) and two female morphs with variable markings (white and orange morphs). Centronia plorator Kaye, [1923] and Thyrgis lacryma Dognin, 1919 are variants of the white female morph and are new synonyms of Calodesma militta. A third female morph with red markings was not sequenced and could not be allocated to a species. Calodesma sp. cf. collaris (BOLD:ABZ2392) occurs in southern South America with both male morphs but only a white female morph. Calodesma pseudocollaris new species (BOLD:AEI2170) is only known from Trinidad, with one male morph (collaris) and the white female morph. Although more than ten morphs relating to this complex have been described as species, they cannot be synonymised without more data on distribution of the different species or DNA barcodes from the type specimens. Collated life history information indicates species of this group are split between Malpighiaceae feeders and Bromeliaceae feeders, but more work is needed to define these differences. The morphism patterns observed are discussed in terms of Müllerian mimicry and mimicry rings, and we suggest that in Trinidad (and elsewhere) there is a loose mimicry ring of diurnal black species with white spots or transparent patches on the wings which are most conspicuous and frequently observed when feeding on white Asteraceae flowers.

Monitoring of benthic eukaryotic communities in two tropical coastal lagoons through eDNA metabarcoding: a spatial and temporal approximation

Tropical coastal lagoons are important ecosystems that support high levels of biodiversity and provide several goods and services. Monitoring of benthic biodiversity and detection of harmful or invasive species is crucial, particularly in relation to seasonal and spatial variation of environmental conditions. In this study, eDNA metabarcoding was used in two tropical coastal lagoons, Chacahua (CH) and Corralero (C) (Southern Mexican Pacific), to describe the benthic biodiversity and its spatial–temporal dynamics. The distribution of benthic diversity within the lagoons showed a very particular pattern evidencing a transition from freshwater to seawater. Although the two lagoon systems are similar in terms of the species composition of metazoans and microeukaryotes, our findings indicate that they are different in taxa richness and structure, resulting in regional partitioning of the diversity with salinity as the driving factor of community composition in CH. Harmful, invasive, non-indigenous species, bioindicators and species of commercial importance were detected, demonstrating the reach of this technique for biodiversity monitoring along with the continued efforts of building species reference libraries.

DNA Barcoding Medicinal Plant Species from Indonesia

Over the past decade, plant DNA barcoding has emerged as a scientific breakthrough and is often used to help with species identification or as a taxonomical tool. DNA barcoding is very important in medicinal plant use, not only for identification purposes but also for the authentication of medicinal products. Here, a total of 61 Indonesian medicinal plant species from 30 families and a pair of ITS2, matK, rbcL, and trnL primers were used for a DNA barcoding study consisting of molecular and sequence analyses. This study aimed to analyze how the four identified DNA barcoding regions (ITS2, matK, rbcL, and trnL) aid identification and conservation and to investigate their effectiveness for DNA barcoding for the studied species. This study resulted in 212 DNA barcoding sequences and identified new ones for the studied medicinal plant species. Though there is no ideal or perfect region for DNA barcoding of the target species, we recommend matK as the main region for Indonesian medicinal plant identification, with ITS2 and rbcL as alternative or complementary regions. These findings will be useful for forensic studies that support the conservation of medicinal plants and their national and global use.

DNA barcodes reveal striking arthropod diversity and unveil seasonal patterns of variation in the southern Atlantic Forest

The Atlantic Forest harbors 7% of global biodiversity and possesses high levels of endemism, but many of its component taxa remain unstudied. Due to the importance of tropical forests and the urgency to protect them, there is a compelling need to address this knowledge gap. To provide more information on its arthropod fauna, a Malaise trap was deployed for 12 months in a semi-degraded area of the southern Upper Paraná ecoregion of the Atlantic Forest. All specimens were DNA barcoded and the Barcode Index Number (BIN) system was employed to assign each specimen to a species proxy. DNA barcodes were obtained from 75,500 arthropods that included representatives of 8,651 BINs. Nearly 81% of these BINs were first records, highlighting the high rates of endemism and lack of study of arthropods from the Atlantic Forest. Diptera was the most abundant order, followed by Hemiptera, Lepidoptera and Hymenoptera. Diptera was also the most species-rich order, followed by Hymenoptera, Lepidoptera, and Coleoptera, a result consistent with studies in other biogeographic regions. Insects were most abundant in winter and most diverse in autumn and winter. This pattern, however, was caused mainly by the dynamics of dipteran diversity as other orders differed in their seasonal variation. The BIN composition of the insect community varied sharply through the year and also differed between the two consecutive summers included in the sampling period. The study of the 38 commonest BINs showed that seasonal patterns of abundance were not order-specific. Temperature had the strongest impact on seasonal abundance variation. Our results highlight the striking and understudied arthropod diversity of the highly fragmented Atlantic Forest, the predominance of dipterans, and the fact that abundance and richness in this insect community peak in the coolest months. Standardized studies like this generate fast and reliable biodiversity inventories and unveil ecological patterns, thus providing valuable information for conservation programs.

Barcoding of Antarctic Marine Invertebrates: From Field Sampling to Lab Procedures

DNA barcoding is a powerful and widespread method used to identify large numbers of species collected in the framework of sampling activities in the field. With the exception of research projects that may count on large teams characterized by tasks' delegation and where many activities may run in parallel, in the majority of cases the barcoding effort is handled by a limited number of persons. The guidelines here reported focus on this second case, with a special attention paid to field procedures, whose efficiency and smoothness are often overlooked.

DROP: Molecular voucher database for identification of Drosophila parasitoids

Molecular identification is increasingly used to speed up biodiversity surveys and laboratory experiments. However, many groups of organisms cannot be reliably identified using standard databases such as GenBank or BOLD due to lack of sequenced voucher specimens identified by experts. Sometimes a large number of sequences are available, but with too many errors to allow identification. Here, we address this problem for parasitoids of Drosophila by introducing a curated open-access molecular reference database, DROP (Drosophila parasitoids). Identifying Drosophila parasitoids is challenging and poses a major impediment to realize the full potential of this model system in studies ranging from molecular mechanisms to food webs, and in biological control of Drosophila suzukii. In DROP, genetic data are linked to voucher specimens and, where possible, the voucher specimens are identified by taxonomists and vetted through direct comparison with primary type material. To initiate DROP, we curated 154 laboratory strains, 856 vouchers, 554 DNA sequences, 16 genomes, 14 transcriptomes, and six proteomes drawn from a total of 183 operational taxonomic units (OTUs): 114 described Drosophila parasitoid species and 69 provisional species. We found species richness of Drosophila parasitoids to be heavily underestimated and provide an updated taxonomic catalogue for the community. DROP offers accurate molecular identification and improves cross-referencing between individual studies that we hope will catalyse research on this diverse and fascinating model system. Our effort should also serve as an example for researchers facing similar molecular identification problems in other groups of organisms.

Unraveling the plant diversity of the Amazonian canga through DNA barcoding

The canga of the Serra dos Carajás, in Eastern Amazon, is home to a unique open plant community, harboring several endemic and rare species. Although a complete flora survey has been recently published, scarce to no genetic information is available for most plant species of the ironstone outcrops of the Serra dos Carajás. In this scenario, DNA barcoding appears as a fast and effective approach to assess the genetic diversity of the Serra dos Carajás flora, considering the growing need for robust biodiversity conservation planning in such an area with industrial mining activities. Thus, after testing eight different DNA barcode markers (matK, rbcL, rpoB, rpoC1, atpF-atpH, psbK-psbI, trnH-psbA, and ITS2), we chose rbcL and ITS2 as the most suitable markers for a broad application in the regional flora. Here we describe DNA barcodes for 1,130 specimens of 538 species, 323 genera, and 115 families of vascular plants from a highly diverse flora in the Amazon basin, with a total of 344 species being barcoded for the first time. In addition, we assessed the potential of using DNA metabarcoding of bulk samples for surveying plant diversity in the canga. Upon achieving the first comprehensive DNA barcoding effort directed to a complete flora in the Brazilian Amazon, we discuss the relevance of our results to guide future conservation measures in the Serra dos Carajás.

Documenting trumpet leaf-miner moths (Tischeriidae): new Neotropical Coptotriche and Astrotischeria species, with notes on Sapindaceae as a host-plant family

Four new species of trumpet leaf-miner moths (Tischeriidae) are described from the Neotropics: Coptotriche serjaniphaga Remeikis Stonis, sp. nov., feeding on Serjania Mill. (Sapindaceae), Astrotischeria mystica Dikus Stonis, sp. nov., feeding on Verbesina L. (Asteraceae), A. yungasi Dikus Stonis, sp. nov., feeding on Oyedaea DC. (Asteraceae), and A. parapallens Dikus Stonis, sp. nov., feeding on Baccharis L. (Asteraceae). Records on Sapindaceae-feeding Tischeriidae are very rare and Serjania is a novel host-plant genus for Tischeriidae. It is hypothesized that Serjania, a diverse genus in the tropical and subtropical Americas, may be a host for many undiscovered species of specialized stenophagous Tischeriidae. The new species are illustrated with photographs of the adults, male and, if available, female genitalia, and the leaf mines. We briefly discuss the importance of new species descriptions as a part of biodiversity assessment.

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.

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

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

Rapid Identification of Tropilaelaps Mite (Mesostigmata: Laelapidae) Species Using a COI Barcode-HRM

Tropilaelaps mite (Mesostigmata: Laelapidae) is an ectoparasite of bees present, to date, only on the Asian continent. In the context of the threat of Tropilaelaps's introduction into new regions, accurate, rapid, and sensitive detection of the Tropilaelaps spp. is essential. In the present study, we developed a novel molecular method for bee mite's identification, which consists of a new real-time PCR method. A high-resolution melting analysis (HRM) was then performed on the amplified products to differentiate the species. PCR amplification was applied on the cytochrome c oxidase subunit I gene (580 bp). Short fragments from the most variable regions of this gene were identified in silico to amplify and discriminate among the four Tropilaelaps species. Four reference plasmids were synthesized to characterize species by well-distinguished melting curves. The method was then validated in terms of its specificity and sensitivity using a panel of 12 specimens. The results showed that an HRM method can be applied for the intended objective: for rapid and simultaneous identification of Tropilaelaps species. To our knowledge, this study reports the first direct HRM assay developed for the genome of a bee mite, specific for Tropilaelaps species. This COI barcode-HRM technique could be a promising tool for mite species identification.

Integrative ecological and molecular analysis indicate high diversity and strict elevational separation of canopy beetles in tropical mountain forests

Tropical mountain forests contribute disproportionately to terrestrial biodiversity but little is known about insect diversity in the canopy and how it is distributed between tree species. We sampled tree-specific arthropod communities from 28 trees by canopy fogging and analysed beetle communities which were first morphotyped and then identified by their DNA barcodes. Our results show that communities from forests at 1100 and 1700 m a.s.l. are almost completely distinct. Diversity was much lower in the upper forest while community structure changed from many rare, less abundant species to communities with a pronounced dominance structure. We also found significantly higher beta-diversity between trees at the lower than higher elevation forest where community similarity was high. Comparisons on tree species found at both elevations reinforced these results. There was little species overlap between sites indicating limited elevational ranges. Furthermore, we exploited the advantage of DNA barcodes to patterns of haplotype diversity in some of the commoner species. Our results support the advantage of fogging and DNA barcodes for community studies and underline the need for comprehensive research aimed at the preservation of these last remaining pristine forests.

Genetic structure of rice striped stem borer, Chilo suppressalis (Lepidoptera:Crambidae) in North of Iran

Information on the genetic structure of rice striped stem borer, Chilo suppressalis (Walker), is essential for an effective pest management program and can corporate with control program and prompt the modification of current control methods. In this study, the genetic structure of COI gene has been investigated for 18 populations of this pest in north of Iran. Chilo suppressalis specimens were collected from rice fields on rice and weeds in Guilan and Mazanderan provinces, at Caspian Sea coast at both seasonal activity (spring) and overwintering stage from May through October 2018 and identified using morphological characters. Genetic structure of 18 populations of the species was evaluated using polymerase chain reaction (PCR)-direct-sequencing of a fragment (869 bp) of mtDNA-COI gene. Results revealed that almost all specimens from different generations, hosts, and locations belong to a single haplotype very close to a South Korean haplotype. To the best our knowledge, it is the first comprehensive molecular typing of striped stem borer in both Northern provinces of the country and suggests a high gene flow among different populations of this pest in the region.

Using DNA-barcoded Malaise trap samples to measure impact of a geothermal energy project on the biodiversity of a Costa Rican old-growth rain forest

We report one year (2013-2014) of biomonitoring an insect community in a tropical old-growth rain forest, during construction of an industrial-level geothermal electricity project. This is the first-year reaction by the species-rich insect biodiversity; six subsequent years are being analyzed now. The site is on the margin of a UNESCO Natural World Heritage Site, Área de Conservación Guanacaste (ACG), in northwestern Costa Rica. This biomonitoring is part of Costa Rica's ongoing efforts to sustainably retain its wild biodiversity through biodevelopmental integration with its societies. Essential tools are geothermal engineering needs, entomological knowledge, insect species-rich forest, government-NGO integration, common sense, DNA barcoding for species-level identification, and Malaise traps. This research is tailored for integration with its society at the product level. We combine an academic view with on-site engineering decisions. This biomonitoring requires alpha-level DNA barcoding combined with centuries of morphology-based entomological taxonomy and ecology. Not all desired insect community analyses are performed; they are for data from subsequent years combined with this year. We provide enough analysis to be used by both guilds now. This biomonitoring has shown, for the first year, that the geothermal project impacts only the biodiversity within a zone less than 50 m from the project margin.

Nematode biodiversity assessments need vouchered databases: A BOLD reference library for plant-parasitic nematodes in the superfamily Criconematoidea

Nematodes are frequently cited as underrepresented in faunistic surveys using DNA barcoding with COI. This underrepresentation is generally attributed to a limited presence of nematodes in DNA databases which, in turn, is often ascribed to structural variability and high evolutionary rates in nematode mitochondrial genomes. Empirical evidence, however, indicates that many taxa are readily amplified with primer sets specifically targeted to different nematode families. Here we report the development of a COI reference library of 1726 specimens in the terrestrial plant parasitic nematode superfamily Criconematoidea. Specimens collected during an ecoregion survey of North America were individually photographed, measured, and PCR amplified to produce a 721 bp region of COI for taxonomic analysis. A neighbor-joining tree structured the dataset into 179 haplotype groups that generally conformed to morphospecies in traditional analysis or Barcode Index Numbers (BINs) in the BOLD system, although absent formal BIN membership due to insufficient overlap with the Folmer region of COI. Approximately one-third of the haplotype groups could be associated with previously described species. The geographic distribution of criconematid nematode species suggests a structure influenced by the major habitat types in the United States and Canada. All sequences collected in the ecoregion survey are deposited in BOLD.

The Molecular Data Organization for Publication (MDOP) R package to aid the upload of data to shared databases

Molecular identification methods, such as DNA barcoding, rely on centralized databases populated with morphologically identified individuals and their referential nucleotide sequence records. As molecular identification approaches have expanded in use to fields such as food fraud, environmental surveys, and border surveillance, there is a need for diverse international data sets. Although central data repositories, like the Barcode of Life Datasystems (BOLD), provided workarounds for formatting data for upload, these workarounds can be taxing on researchers with few resources and limited funding. To address these concerns, we present the Molecular Data Organization for Publication (MDOP) R package to assist researchers in uploading data to public databases. To illustrate the use of these scripts, we use the BOLD system as an example. The main intent of this writing is to assist in the movement of data, from academic, governmental, and other institutional computer systems, to public locations. The movement of these data can then better contribute to the global DNA barcoding initiative and other global molecular data efforts.

DNA barcoding of fogged caterpillars in Peru: A novel approach for unveiling host-plant relationships of tropical moths (Insecta, Lepidoptera)

The present study aimed to perform molecular identification of lepidopteran larvae from canopy fogging including gut-content analyses. A total of 130 lepidopteran larvae were selected from 37 fogging samples at the Panguana station, district Yuyapichis, province Puerto Inca, department Huánuco, Peru. Target trees were pre-identified and subsequently submitted to molecular confirmation of identity with three markers (rbcL, psbA and trnL-F). The COI gene of 119 lepidopteran larvae was successfully sequenced and found to belong to 92 species: Comparison of DNA barcodes with the reference database of adult moths resulted in 65 (55%) matches at species level, 32 (27%) at genus level, 19 (16%) at subfamily or family level, three just to order level. Three larvae could not be assigned to a family. For these larvae the fogged target tree now suggests a potential host-plant relationship. Molecular gut content analysis, based on High-Throughput-Sequencing was successfully tested for ten larvae corroborating feeding on the target plant in some cases but elucidating several other cases of potential 'alternative feeding'. We propose a larger-scale approach using this rapid and efficient method including molecular gut-content analyses for comprehensively testing the ratio of 'alternative feeders' and pitfalls caused by collateral fogging of larvae from neighboring trees.

A reference library for Canadian invertebrates with 1.5 million barcodes, voucher specimens, and DNA samples

The reliable taxonomic identification of organisms through DNA sequence data requires a well parameterized library of curated reference sequences. However, it is estimated that just 15% of described animal species are represented in public sequence repositories. To begin to address this deficiency, we provide DNA barcodes for 1,500,003 animal specimens collected from 23 terrestrial and aquatic ecozones at sites across Canada, a nation that comprises 7% of the planet's land surface. In total, 14 phyla, 43 classes, 163 orders, 1123 families, 6186 genera, and 64,264 Barcode Index Numbers (BINs; a proxy for species) are represented. Species-level taxonomy was available for 38% of the specimens, but higher proportions were assigned to a genus (69.5%) and a family (99.9%). Voucher specimens and DNA extracts are archived at the Centre for Biodiversity Genomics where they are available for further research. The corresponding sequence and taxonomic data can be accessed through the Barcode of Life Data System, GenBank, the Global Biodiversity Information Facility, and the Global Genome Biodiversity Network Data Portal.

Assessment of North American arthropod collections: prospects and challenges for addressing biodiversity research

Over 300 million arthropod specimens are housed in North American natural history collections. These collections represent a "vast hidden treasure trove" of biodiversity -95% of the specimen label data have yet to be transcribed for research, and less than 2% of the specimens have been imaged. Specimen labels contain crucial information to determine species distributions over time and are essential for understanding patterns of ecology and evolution, which will help assess the growing biodiversity crisis driven by global change impacts. Specimen images offer indispensable insight and data for analyses of traits, and ecological and phylogenetic patterns of biodiversity. Here, we review North American arthropod collections using two key metrics, specimen holdings and digitization efforts, to assess the potential for collections to provide needed biodiversity data. We include data from 223 arthropod collections in North America, with an emphasis on the United States. Our specific findings are as follows: (1) The majority of North American natural history collections (88%) and specimens (89%) are located in the United States. Canada has comparable holdings to the United States relative to its estimated biodiversity. Mexico has made the furthest progress in terms of digitization, but its specimen holdings should be increased to reflect the estimated higher Mexican arthropod diversity. The proportion of North American collections that has been digitized, and the number of digital records available per species, are both much lower for arthropods when compared to chordates and plants. (2) The National Science Foundation's decade-long ADBC program (Advancing Digitization of Biological Collections) has been transformational in promoting arthropod digitization. However, even if this program became permanent, at current rates, by the year 2050 only 38% of the existing arthropod specimens would be digitized, and less than 1% would have associated digital images. (3) The number of specimens in collections has increased by approximately 1% per year over the past 30 years. We propose that this rate of increase is insufficient to provide enough data to address biodiversity research needs, and that arthropod collections should aim to triple their rate of new specimen acquisition. (4) The collections we surveyed in the United States vary broadly in a number of indicators. Collectively, there is depth and breadth, with smaller collections providing regional depth and larger collections providing greater global coverage. (5) Increased coordination across museums is needed for digitization efforts to target taxa for research and conservation goals and address long-term data needs. Two key recommendations emerge: collections should significantly increase both their specimen holdings and their digitization efforts to empower continental and global biodiversity data pipelines, and stimulate downstream research.

Assembling a DNA barcode reference library for the spiders (Arachnida: Araneae) of Pakistan

Morphological study of 1,795 spiders from sites across Pakistan placed these specimens in 27 families and 202 putative species. COI sequences >400 bp recovered from 1,782 specimens were analyzed using neighbor-joining trees, Bayesian inference, barcode gap, and Barcode Index Numbers (BINs). Specimens of 109 morphological species were assigned to 123 BINs with ten species showing BIN splits, while 93 interim species included representatives of 98 BINs. Maximum conspecific divergences ranged from 0-5.3% while congeneric distances varied from 2.8-23.2%. Excepting one species pair (Oxyopes azhari-Oxyopes oryzae), the maximum intraspecific distance was always less than the nearest-neighbor (NN) distance. Intraspecific divergence values were not significantly correlated with geographic distance. Most (75%) BINs detected in this study were new to science, while those shared with other nations mainly derived from India. The discovery of many new, potentially endemic species and the low level of BIN overlap with other nations highlight the importance of constructing regional DNA barcode reference libraries.

Evolution of defences in large tropical plant genera: perspectives for exploring insect diversity in a tri-trophic context

Divergence and escalation in defences promote chemical diversity in plants, and consequently the diversity of insect herbivores. This diversification cascades to insect parasitoids through direct effects on host herbivore susceptibility, changes in herbivore community composition, or disparity in plant volatiles. Large tropical plant genera represent an ideal model for studying these trends due to the high diversity of sympatric species and their insects. Novel measures of chemical structural similarity should be used to analyse evolutionary trends in both direct and indirect defences. Host chemical data need to be combined with detailed herbivore and parasitoid data. This will help to identify truly active compounds. Furthermore, resolved genomic phylogenies for plants and insects should be included to assign directionality in the processes.

A highly-simplified and inexpensive MALDI-TOF mass spectrometry sample-preparation method with broad applicability to microorganisms, plants, and insects

Matrix-assisted laser-desorption and ionization time-of-flight mass spectrometry prepares proteins intact in the gas phase with predominantly a single positive charge. The times-of-flight of charged proteins along a tube held at high vacuum after acceleration in an electrical field are proportional to the square root of the mass-over-charge ratios for the proteins, thereby allowing a mass spectrum to be generated, which can then be used to characterize or identify a protein-containing sample. Several sample-preparation methods are currently available but not all of these are applicable to some forms of fungal biomass and few of these are well suited to the analysis of plant or insect material. We have therefore developed a simplified method that: lyses cells, selectively solubilizes basic proteins, dissolves matrix to a suitable concentration, generates spectra with good intensity and peak richness, costs no more (and generally less) than current methods, and is not constrained in terms of throughput by the availability of centrifuges. Using this method, and a reagent formulation comprising α-cyano-4-hydroxycinnamic acid matrix close to saturation in 60%–65% (v/v) acetonitrile in water containing 2.5% (v/v) trifluoroacetic acid, we have been able to differentiate between strains for a representative subset of aflatoxin-producing and aflatoxin-non-producing strains of Aspergillus fungi, to differentiate between Indian and Pakistani strains of Himalayan balsam rust, to differentiate between closely-related Crassula spp. and regional biotypes of Crassula helmsii, and to differentiate between rubbervine introduced into Australia and Brazil. We have also analyzed fall armyworm and stem-borer samples stored in 70% (v/v) ethanol and old dried insect specimens.

DNA barcoding reveals insect diversity in the mangrove ecosystems of Hainan Island, China

Insect diversity is an indicator of environmental conditions. Frequent outbreaks of mangrove pests have threatened the fragile mangrove ecosystem in China and the sustainable utilization of mangrove resources. The understanding of mangrove pests, as well as a fundamental knowledge of insect diversity, in mangrove forests in China has been hindered by the difficulty of morphological species delimitation because captured insect specimens are either larvae or incompletely preserved adults. DNA barcoding technology uses only a small amount of DNA to conduct species identification. Taking advantage of this, we investigated the entomofauna of mangrove forests on Hainan Island by using a barcode combining cytochrome c oxidase subunit I (COI) and cytochrome-b (Cytb). We collected 627 specimens at six localities around the island, which were identified as 219 insect species belonging to 11 orders and 72 families. Lepidoptera, Coleoptera, and Hymenoptera are the most species-rich and abundant taxa. We also identified 13 mangrove pests, 5 parasitoids, and 12 species of predators.

DNA barcodes reveal deeply neglected diversity and numerous invasions of micromoths in Madagascar 1

Madagascar is a prime evolutionary hotspot globally, but its unique biodiversity is under threat, essentially from anthropogenic disturbance. There is a race against time to describe and protect the Madagascan endangered biota. Here we present a first molecular characterization of the micromoth fauna of Madagascar. We collected 1572 micromoths mainly using light traps in both natural and anthropogenically disturbed habitats in 24 localities across eastern and northwest Madagascar. We also collected 1384 specimens using a Malaise trap in a primary rain forest at Andasibe, eastern Madagascar. In total, we DNA barcoded 2956 specimens belonging to 1537 Barcode Index Numbers (BINs), 88.4% of which are new to BOLD. Only 1.7% of new BINs were assigned to species. Of 47 different families found, Dryadaulidae, Bucculatricidae, Bedelliidae, Batrachedridae, and Blastobasidae are newly reported for Madagascar and the recently recognized Tonzidae is confirmed. For test faunas of Canada and Australia, 98.9%-99.4% of Macroheterocera BINs exhibited the molecular synapomorphy of a phenylalanine in the 177th complete DNA barcode codon. Non-macroheteroceran BINs could thus be sifted out efficiently in the Malaise sample. The Madagascar micromoth fauna shows highest affinity with the Afrotropics (146 BINs also occur in the African continent). We found 22 recognised pests or invasive species, mostly occurring in disturbed habitats. Malaise trap samples show high temporal turnover and alpha diversity with as many as 507 BINs collected; of these, astonishingly, 499 (98.4%) were novel to BOLD and 292 (57.6%) were singletons. Our results provide a baseline for future surveys across the island.

Tracking of Host Defenses and Phylogeny During the Radiation of Neotropical Inga-Feeding Sawflies (Hymenoptera; Argidae)

Coevolutionary theory has long predicted that the arms race between plants and herbivores is a major driver of host selection and diversification. At a local scale, plant defenses contribute significantly to the structure of herbivore assemblages and the high alpha diversity of plants in tropical rain forests. However, the general importance of plant defenses in host associations and divergence at regional scales remains unclear. Here, we examine the role of plant defensive traits and phylogeny in the evolution of host range and species divergence in leaf-feeding sawflies of the family Argidae associated with Neotropical trees in the genus Inga throughout the Amazon, the Guiana Shield and Panama. Our analyses show that the phylogenies of both the sawfly herbivores and their Inga hosts are congruent, and that sawflies radiated at approximately the same time, or more recently than their Inga hosts. Analyses controlling for phylogenetic effects show that the evolution of host use in the sawflies associated with Inga is better correlated with Inga chemistry than with Inga phylogeny, suggesting a pattern of delayed host tracking closely tied to host chemistry. Finally, phylogenetic analyses show that sister species of Inga-sawflies are dispersed across the Neotropics, suggesting a role for allopatric divergence and vicariance in Inga diversification. These results are consistent with the idea that host defensive traits play a key role not only in structuring the herbivore assemblages at a single site, but also in the processes shaping host association and species divergence at a regional scale.

Quillworts from the Amazon: A multidisciplinary populational study on Isoetes serracarajensis and Isoetes cangae

Isoetes are ancient quillworts members of the only genus of the order Isoetales. The genus is slow evolving but is resilient, and widespread worldwide. Two recently described species occur in the Eastern Brazilian Amazon, Isoetes serracarajensis and Isoetes cangae. They are found in the ironstone grasslands known as Canga. While I. serracarajensis is present mostly in seasonal water bodies, I. cangae is known to occur in a single permanent lake at the South mountain range. In this work, we undertake an extensive morphological, physiological and genetic characterization of both species to establish species boundaries and better understand the morphological and genetic features of these two species. Our results indicate that the morphological differentiation of the species is subtle and requires a quantitative assessment of morphological elements of the megaspore for diagnosis. We did not detect differences in microspore output, but morphological peculiarities may establish a reproductive barrier. Additionally, genetic analysis using DNA barcodes and whole chloroplast genomes indicate that although the plants are genetically very similar both approaches provide diagnostic characters. There was no indication of population structuring I. serracarajensis. These results set the basis for a deeper understanding of the evolution of the Isoetes genus.

Use of genetic, climatic, and microbiological data to inform reintroduction of a regionally extinct butterfly

Species reintroductions are increasingly used as means of mitigating biodiversity loss. Besides habitat quality at the site targeted for reintroduction, the choice of source population can be critical for success. The butterfly Melanargia russiae (Esper´s marbled white) was extirpated from Hungary over 100 years ago, and a reintroduction program has recently been approved. We used museum specimens of this butterfly, mitochondrial DNA data (mtDNA), endosymbiont screening, and climatic-similarity analyses to determine which extant populations should be used for its reintroduction. The species displayed 2 main mtDNA lineages across its range: 1 restricted to Iberia and southern France (Iberian lineage) and another found throughout the rest of its range (Eurasian lineage). These 2 lineages possessed highly divergent wsp alleles of the bacterial endosymbiont Wolbachia. The century-old Hungarian specimens represented an endemic haplotype belonging to the Eurasian lineage, differing by one mutation from the Balkan and eastern European populations. The Hungarian populations of M. russiae occurred in areas with a colder and drier climate relative to most sites with extant known populations. Our results suggest the populations used for reintroduction to Hungary should belong to the Eurasian lineage, preferably from eastern Ukraine (genetically close and living in areas with the highest climatic similarity). Materials stored in museum collections can provide unique opportunities to document historical genetic diversity and help direct conservation.

Generating DNA sequence data with limited resources for molecular biology: Lessons from a barcoding project in Indonesia

The advent of the DNA sequencing age has led to a revolution in biology. The rapid and cost-effective generation of high-quality sequence data has transformed many fields, including those focused on discovering species and surveying biodiversity, monitoring movement of biological materials, forensic biology, and disease diagnostics. There is a need to build capacity to generate useful sequence data in countries with limited historical access to laboratory resources, so that researchers can benefit from the advantages offered by these data. Commonly used molecular techniques such as DNA extraction, PCR, and DNA sequencing are within the reach of small laboratories in many countries, with the main obstacles to successful implementation being lack of funding and limited practical experience. Here we describe a successful approach that we developed to obtain DNA sequence data during a small DNA barcoding project in Indonesia.

One thousand DNA barcodes of piranhas and pacus reveal geographic structure and unrecognised diversity in the Amazon

Piranhas and pacus (Characiformes: Serrasalmidae) are a charismatic but understudied family of Neotropical fishes. Here, we analyse a DNA barcode dataset comprising 1,122 specimens, 69 species, 16 genera, 208 localities, and 34 major river drainages in order to make an inventory of diversity and to highlight taxa and biogeographic areas worthy of further sampling effort and conservation protection. Using four methods of species discovery-incorporating both tree and distance based techniques-we report between 76 and 99 species-like clusters, i.e. between 20% and 33% of a priori identified taxonomic species were represented by more than one mtDNA lineage. There was a high degree of congruence between clusters, with 60% supported by three or four methods. Pacus of the genus Myloplus exhibited the most intraspecific variation, with six of the 13 species sampled found to have multiple lineages. Conversely, piranhas of the Serrasalmus rhombeus group proved difficult to delimit with these methods due to genetic similarity and polyphyly. Overall, our results recognise substantially underestimated diversity in the serrasalmids, and emphasise the Guiana and Brazilian Shield rivers as biogeographically important areas with multiple cases of across-shield and within-shield diversifications. We additionally highlight the distinctiveness and complex phylogeographic history of rheophilic taxa in particular, and suggest multiple colonisations of these habitats by different serrasalmid lineages.

From water striders to water bugs: the molecular diversity of aquatic Heteroptera (Gerromorpha, Nepomorpha) of Germany based on DNA barcodes

With about 5,000 species worldwide, the Heteroptera or true bugs are the most diverse taxon among the hemimetabolous insects in aquatic and semi-aquatic ecosystems. Species may be found in almost every freshwater environment and have very specific habitat requirements, making them excellent bioindicator organisms for water quality. However, a correct determination by morphology is challenging in many species groups due to high morphological variability and polymorphisms within, but low variability between species. Furthermore, it is very difficult or even impossible to identify the immature life stages or females of some species, e.g., of the corixid genus Sigara. In this study we tested the effectiveness of a DNA barcode library to discriminate species of the Gerromorpha and Nepomorpha of Germany. We analyzed about 700 specimens of 67 species, with 63 species sampled in Germany, covering more than 90% of all recorded species. Our library included various morphological similar taxa, e.g., species within the genera Sigara and Notonecta as well as water striders of the genus Gerris. Fifty-five species (82%) were unambiguously assigned to a single Barcode Index Number (BIN) by their barcode sequences, whereas BIN sharing was observed for 10 species. Furthermore, we found monophyletic lineages for 52 analyzed species. Our data revealed interspecific K2P distances with below 2.2% for 18 species. Intraspecific distances above 2.2% were shown for 11 species. We found evidence for hybridization between various corixid species (Sigara, Callicorixa), but our molecular data also revealed exceptionally high intraspecific distances as a consequence of distinct mitochondrial lineages for Cymatia coleoptrata and the pygmy backswimmer Plea minutissima. Our study clearly demonstrates the usefulness of DNA barcodes for the identification of the aquatic Heteroptera of Germany and adjacent regions. In this context, our data set represents an essential baseline for a reference library for bioassessment studies of freshwater habitats using modern high-throughput technologies in the near future. The existing data also opens new questions regarding the causes of observed low inter- and high intraspecific genetic variation and furthermore highlight the necessity of taxonomic revisions for various taxa, combining both molecular and morphological data.

DNA Barcoding for the Identification and Authentication of Animal Species in Traditional Medicine

Animal-based traditional medicine not only plays a significant role in therapeutic practices worldwide but also provides a potential compound library for drug discovery. However, persistent hunting and illegal trade markedly threaten numerous medicinal animal species, and increasing demand further provokes the emergence of various adulterants. As the conventional methods are difficult and time-consuming to detect processed products or identify animal species with similar morphology, developing novel authentication methods for animal-based traditional medicine represents an urgent need. During the last decade, DNA barcoding offers an accurate and efficient strategy that can identify existing species and discover unknown species via analysis of sequence variation in a standardized region of DNA. Recent studies have shown that DNA barcoding as well as minibarcoding and metabarcoding is capable of identifying animal species and discriminating the authentics from the adulterants in various types of traditional medicines, including raw materials, processed products, and complex preparations. These techniques can also be used to detect the unlabelled and threatened animal species in traditional medicine. Here, we review the recent progress of DNA barcoding for the identification and authentication of animal species used in traditional medicine, which provides a reference for quality control and trade supervision of animal-based traditional medicine.

Phylogeography and DNA-based species delimitation provide insight into the taxonomy of the polymorphic rose chafer Protaetia (Potosia) cuprea species complex (Coleoptera: Scarabaeidae: Cetoniinae) in the Western Palearctic

The development of modern methods of species delimitation, unified under the "integrated taxonomy" approach, allows a critical examination and re-evaluation of complex taxonomic groups. The rose chafer Protaetia (Potosia) cuprea is a highly polymorphic species group with a large distribution range. Despite its overall commonness, its taxonomy is unclear and subject to conflicting hypotheses, most of which largely fail to account for its evolutionary history. Based on the sequences of two mitochondrial markers from 65 individuals collected across the species range, and a detailed analysis of morphological characters including a geometric morphometry approach, we infer the evolutionary history and phylogeography of the P. cuprea species complex. Our results demonstrate the existence of three separate lineages in the Western Palearctic region, presumably with a species status. However, these lineages are in conflict with current taxonomic concepts. None of the 29 analyzed morphological characters commonly used in the taxonomy of this group proved to be unambiguously species- or subspecies- specific. The geometric morphometry analysis reveals a large overlap in the shape of the analyzed structures (pronotum, meso-metaventral projection, elytra and aedeagus), failing to identify either the genetically detected clades or the classical species entities. Our results question the monophyly of P. cuprea in regard to P. cuprina, as well as the species status of P. metallica. On the other hand, we found support for the species status of the Sicilian P. hypocrita. Collectively, our findings provide a new and original insight into the taxonomy and phylogeny of the P. cuprea species complex. At the same time, the results represent the first attempt to elucidate the phylogeography of these polymorphic beetles.

Sorting specimen-rich invertebrate samples with cost-effective NGS barcodes: Validating a reverse workflow for specimen processing

Biologists frequently sort specimen-rich samples to species. This process is daunting when based on morphology, and disadvantageous if performed using molecular methods that destroy vouchers (e.g., metabarcoding). An alternative is barcoding every specimen in a bulk sample and then presorting the specimens using DNA barcodes, thus mitigating downstream morphological work on presorted units. Such a "reverse workflow" is too expensive using Sanger sequencing, but we here demonstrate that is feasible with an next-generation sequencing (NGS) barcoding pipeline that allows for cost-effective high-throughput generation of short specimen-specific barcodes (313 bp of COI; laboratory cost <$0.50 per specimen) through next-generation sequencing of tagged amplicons. We applied our approach to a large sample of tropical ants, obtaining barcodes for 3,290 of 4,032 specimens (82%). NGS barcodes and their corresponding specimens were then sorted into molecular operational taxonomic units (mOTUs) based on objective clustering and Automated Barcode Gap Discovery (ABGD). High diversity of 88-90 mOTUs (4% clustering) was found and morphologically validated based on preserved vouchers. The mOTUs were overwhelmingly in agreement with morphospecies (match ratio 0.95 at 4% clustering). Because of lack of coverage in existing barcode databases, only 18 could be accurately identified to named species, but our study yielded new barcodes for 48 species, including 28 that are potentially new to science. With its low cost and technical simplicity, the NGS barcoding pipeline can be implemented by a large range of laboratories. It accelerates invertebrate species discovery, facilitates downstream taxonomic work, helps with building comprehensive barcode databases and yields precise abundance information.

Filling reference gaps via assembling DNA barcodes using high-throughput sequencing-moving toward barcoding the world

Over the past decade, biodiversity researchers have dedicated tremendous efforts to constructing DNA reference barcodes for rapid species registration and identification. Although analytical cost for standard DNA barcoding has been significantly reduced since early 2000, further dramatic reduction in barcoding costs is unlikely because Sanger sequencing is approaching its limits in throughput and chemistry cost. Constraints in barcoding cost not only led to unbalanced barcoding efforts around the globe, but also prevented high-throughput sequencing (HTS)-based taxonomic identification from applying binomial species names, which provide crucial linkages to biological knowledge. We developed an Illumina-based pipeline, HIFI-Barcode, to produce full-length Cytochrome c oxidase subunit I (COI) barcodes from pooled polymerase chain reaction amplicons generated by individual specimens. The new pipeline generated accurate barcode sequences that were comparable to Sanger standards, even for different haplotypes of the same species that were only a few nucleotides different from each other. Additionally, the new pipeline was much more sensitive in recovering amplicons at low quantity. The HIFI-Barcode pipeline successfully recovered barcodes from more than 78% of the polymerase chain reactions that didn't show clear bands on the electrophoresis gel. Moreover, sequencing results based on the single molecular sequencing platform Pacbio confirmed the accuracy of the HIFI-Barcode results. Altogether, the new pipeline can provide an improved solution to produce full-length reference barcodes at about one-tenth of the current cost, enabling construction of comprehensive barcode libraries for local fauna, leading to a feasible direction for DNA barcoding global biomes.

Insect symbionts in food webs

Recent research has shown that the bacterial endosymbionts of insects are abundant and diverse, and that they have numerous different effects on their hosts' biology. Here we explore how insect endosymbionts might affect the structure and dynamics of insect communities. Using the obligate and facultative symbionts of aphids as an example, we find that there are multiple ways that symbiont presence might affect food web structure. Many symbionts are now known to help their hosts escape or resist natural enemy attack, and others can allow their hosts to withstand abiotic stress or affect host plant use. In addition to the direct effect of symbionts on aphid phenotypes there may be indirect effects mediated through trophic and non-trophic community interactions. We believe that by using data from barcoding studies to identify bacterial symbionts, this extra, microbial dimension to insect food webs can be better elucidated.

This article is part of the themed issue ‘From DNA barcodes to biomes’.

DNA barcoding of reef brittle stars (Ophiuroidea, Echinodermata) from the southwestern Indian Ocean evolutionary hot spot of biodiversity

In anticipation of the current biodiversity crisis, it has become critical to rapidly and accurately assess biodiversity. DNA barcoding has proved efficient in facilitating the discovery and description of thousands of species and also provides insight into the dynamics of biodiversity. Here, we sequenced a portion of the mitochondrial cytochrome c oxidase subunit I (COI) gene from all morphospecies of reef brittle stars collected during a large‐scale biodiversity survey in the southwestern Indian Ocean (SWIO). Three methods of species delineation (Automatic Barcode Gap Discovery, Generalized Mixed Yule Coalescent model, and Bayesian Poisson Tree Processes) showed concordant results and revealed 51 shallow reef species in the region. Mean intraspecific genetic distances (0.005–0.064) and mean interspecific genetic distances within genera (0.056–0.316) were concordant with previous echinoderm studies. This study revealed that brittle‐star biodiversity is underestimated by 20% within SWIO and by >40% when including specimens from the Pacific Ocean. Results are discussed in terms of endemism, diversification processes, and conservation implications for the Indo‐West Pacific marine biodiversity. We emphasize the need to further our knowledge on biodiversity of invertebrate groups in peripheral areas.

How many species and under what names? Using DNA barcoding and GenBank data for west Central African amphibian conservation

Development projects in west Central Africa are proceeding at an unprecedented rate, often with little concern for their effects on biodiversity. In an attempt to better understand potential impacts of a road development project on the anuran amphibian community, we conducted a biodiversity assessment employing multiple methodologies (visual encounter transects, auditory surveys, leaf litter plots and pitfall traps) to inventory species prior to construction of a new road within the buffer zone of Moukalaba-Doudou National Park, Gabon. Because of difficulties in morphological identification and taxonomic uncertainty of amphibian species observed in the area, we integrated a DNA barcoding analysis into the project to improve the overall quality and accuracy of the species inventory. Based on morphology alone, 48 species were recognized in the field and voucher specimens of each were collected. We used tissue samples from specimens collected at our field site, material available from amphibians collected in other parts of Gabon and the Republic of Congo to initiate a DNA barcode library for west Central African amphibians. We then compared our sequences with material in GenBank for the genera recorded at the study site to assist in identifications. The resulting COI and 16S barcode library allowed us to update the number of species documented at the study site to 28, thereby providing a more accurate assessment of diversity and distributions. We caution that because sequence data maintained in GenBank are often poorly curated by the original submitters and cannot be amended by third-parties, these data have limited utility for identification purposes. Nevertheless, the use of DNA barcoding is likely to benefit biodiversity inventories and long-term monitoring, particularly for taxa that can be difficult to identify based on morphology alone; likewise, inventory and monitoring programs can contribute invaluable data to the DNA barcode library and the taxonomy of complex groups. Our methods provide an example of how non-taxonomists and parataxonomists working in understudied parts of the world with limited geographic sampling and comparative morphological material can use DNA barcoding and publicly available sequence data (GenBank) to rapidly identify the number of species and assign tentative names to aid in urgent conservation management actions and contribute to taxonomic resolution.

A streamlined collecting and preparation protocol for DNA barcoding of Lepidoptera as part of large-scale rapid biodiversity assessment projects, exemplified by the Indonesian Biodiversity Discovery and Information System (IndoBioSys)

Here we present a general collecting and preparation protocol for DNA barcoding of Lepidoptera as part of large-scale rapid biodiversity assessment projects, and a comparison with alternative preserving and vouchering methods. About 98% of the sequenced specimens processed using the present collecting and preparation protocol yielded sequences with more than 500 base pairs. The study is based on the first outcomes of the Indonesian Biodiversity Discovery and Information System (IndoBioSys). IndoBioSys is a German-Indonesian research project that is conducted by the Museum für Naturkunde in Berlin and the Zoologische Staatssammlung München, in close cooperation with the Research Center for Biology - Indonesian Institute of Sciences (RCB-LIPI, Bogor).

A review of biodiversity-related issues and challenges in megadiverse Indonesia and other Southeast Asian countries

Indonesia is one of the ten member states of the economically and politically diverse regional organization of the Association of Southeast Asian Nations (ASEAN). Southeast Asia comprises four of the 25 global biodiversity hotspots, three of the 17 global megadiverse countries (Indonesia, Malaysia, and the Philippines) and the most diverse coral reefs in the world. All member states are Parties to the Convention on Biological Diversity (CBD). We discuss ASEAN-wide joint activities on nature conservation and sustainable use of biodiversity that do not stop at national borders.

The Indonesian archipelago comprises two of the world’s biodiversity hotspots (areas with a high degree of endemic species that are highly threatened by loss of habitats): Its insular character and complex geological history led to the evolution of a megadiverse fauna and flora on the global scale. The importance of biodiversity, e.g., in traditional medicine and agriculture, is deep-rooted in Indonesian society. Modern biodiversity pathways include new fields of application in technology, pharmacy and economy along with environmental policies. This development occurred not only in Indonesia but also in other biodiversity-rich tropical countries.

This review summarizes and discusses the unique biodiversity of Indonesia from different angles (science, society, environmental policy, and bioeconomy) and brings it into context within the ASEAN region. The preconditions of each member state for biodiversity-related activities are rather diverse. Much was done to improve the conditions for biodiversity research and use in several countries, primarily in those with a promising economic development. However, ASEAN as a whole still has further potential for more joint initiatives. Especially Indonesia has the highest biodiversity potential within the ASEAN and beyond, but likewise the highest risk of biodiversity loss.

We conclude that Indonesia has not taken full advantage of this potential yet. A growing national interest in local biodiversity as a natural resource is a welcome development on one hand, but the risk of too many restrictions for, e.g., the science community (high level of bureaucracy at all project stages from planning phase, visa procedures, field work permits, scientific exchange and project managment issues, governmental budget cuts for basic research and restricted access to international literature for Indonesian researchers) does significantly hamper the internationalization of biodiversity-related science. In the long run, Indonesia has to find a balance between protectionism and sensible access to its national biodiversity to tackle global challenges in biodiversity conservation, health issues, food security, and climate change.