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Ants are often the most ubiquitous and ecologically influential components of terrestrial systems, exhibiting an exceptionally high level of endemic diversity. Simultaneously, exotic ants can be amongst the most environmentally and economically devastating biological invaders. Distinguishing between exotic and related natives is essential for early detection and to reduce the chance of establishment, but at the species-level there remains a great deal of uncertainty among several of the most diverse, widespread and ecologically dominant genera. This taxonomic impediment negatively impacts the use of molecular techniques relying on reference databases, due to the poor state of ant DNA sequences in publicly available repositories, with many species not represented at all and others incorrectly identified. As a result, biosecurity screening for targeted exotic ants and assigning ant species-level identifications for biodiversity remain two separate areas of focus in Australia. Here we propose a workflow for the identification of ants that enables simultaneous processing of large numbers of “bulk” ant samples each containing many individuals, increasing resolution for taxonomic assignment, and generating a curated database linked to voucher specimens. We use a non-destructive DNA extraction method and compare two high throughput sequencing (HTS) metabarcoding platforms – MiSeq (Illumina) and MinION (Oxford Nanopore Technologies) – processing up to 180 bulk mixed ant samples per run. This approach allowed for the acquisition of curated DNA sequences from voucher specimens morphologically examined by expert taxonomists. This work highlights the advantages and current limitations of DNA-based identifications, the needs for standardisation, as well as the importance of a taxonomy-based curation of DNA database for both biodiversity and biosecurity.

Abstract Diaphorina citri Kuwayama, also known as the Asian citrus psyllid (ACP), can vector the bacterium Candidatus Liberibacter asiaticus (CLas), agent of Huanglongbing (HLB): an incurable disease affecting citrus trees worldwide. In citrus growing regions where ACP and HLB are absent, such as Australia, the risk of an incursion and consequent economic damage to citrus industries make this psyllid one of the top-priority pests. Due to ACP’s small dimensions and the generally poorly studied native psylloid fauna worldwide, morphological identification of this insect to distinguish it from harmless species is challenging, especially in the field, and with immature, partial or damaged specimens. To allow rapid and efficient detection of ACP in the field, we designed and optimised a new Loop-mediated isothermal amplification (LAMP) assay for the detection of D. citri based on the mitochondrial 16S locus. The optimised ACP 16S LAMP assay produced amplification from D. citri samples within 13.3 ± 3.6 min, with an anneal derivative of ~ 78.5 °C. A synthetic gBlock gene fragment was also developed to be used as positive control for the new LAMP assay with a different anneal derivative of ~ 83 °C. An existing commercially available LAMP assay for detection of the bacterium CLas was also tested in this study on ACP DNA. The ACP 16S LAMP assay we developed and tested here provides a valuable new in-field compatible tool that can allow early detections of ACP, enabling a quick biosecurity response, and could potentially be adopted by a wide range of users, from farmers to agronomists and from researchers to industry.

Abstract Recent advances in the field of environmental DNA (eDNA) metabarcoding have produced a promising platform for early detection and broad‐spectrum monitoring of plant pests and pathogens. To date, the majority of fungal metabarcoding assays have relied upon universal primers amplifying segments of the ribosomal DNA, to ensure broad taxonomic coverage while studying changes in community composition, or more recently, to screen for presence/absence of target species. In a diagnostics framework however, single, universal molecular barcodes do not discriminate accurately enough for many groups of important fungal phytopathogens at the required species level. Here, a modular, multi‐barcode amplicon sequencing pipeline was established to provide rapid and reliable diagnostics targeting the Ophiostomatales, an order containing economically important phytopathogens vectored by bark and ambrosia beetles (Curculionidae). Using compositionally varied mock communities, we evaluated five barcoding loci: ITS1, ITS2, the large ribosomal sub‐unit (LSU), translation elongation factor 1‐alpha (TEF1α) and calmodulin (CAL), for their ability to provide species‐level resolution. The sensitivity and detection limit of the assay was established by spiking genomic DNA of the exotic Dutch elm disease pathogen, Ophiostoma novo‐ulmi Brasier, into both the controlled mock communities and eDNA sampled from Ips grandicollis (Eichhoff) beetles collected in New South Wales, Australia. The TEF1α barcode successfully detected the Dutch elm pathogen DNA with 100% accuracy down to approx. 5 pg/μl, while the ITS1 barcode had a 100% accuracy down to approx. 0.4 pg/μl within a given sample. Our results demonstrate that a dual‐barcode approach targeting the ITS1 and TEF1α regions simultaneously is sufficient for accurate species level detection and characterisation of the Ophiostomatales and offers confident detection of low‐abundance taxa (relative read abundances of 0.1%–0.01%). Multi‐barcode metabarcoding provides a framework which can quickly and efficiently be adapted to new targets when establishing high throughput diagnostics for post‐border biosecurity surveillance of fungal phytopathogens.

Surveillance and long-term monitoring of insect pest populations are of paramount importance to limit dispersal and inform pest management. Molecular methods have been employed in diagnostics, surveillance and monitoring for the past few decades, often paired with more traditional techniques relying on morphological examinations. Within this context, the ‘iMapPESTS: Sentinel Surveillance for Agriculture’ project was conceptualised to enhance on-farm pest management decision-making via development and deployment of smart traps, able to collect insects, as well as recording associated environmental data. Here, we compared an iMapPESTS ‘Sentinel’ smart trap to an alternative suction trap over a 10-week period. We used a non-destructive insect metabarcoding approach complemented by insect morphological diagnostics to assess and compare aphid species presence and diversity across trap samples and time. Furthermore, we paired this with environmental data recorded throughout the sampling period. This methodology recorded a total of 497 different taxa from 70 traps over a 10-week period in the grain-growing region in western Victoria. This included not only the 14 aphid target species, but an additional 12 aphid species, including a new record for Victoria. Ultimately, with more than 450 bycatch species detected, this highlighted the value of insect metabarcoding, not only for pest surveillance, but also at a broader ecosystem level, with potential applications in integrated pest management and biocontrol.

Background The Australian citrus industry remains one of the few in the world to be unaffected by the African and the Asian citrus psyllids, Trioza erytreae Del Guercio and Diaphorina citri Kuwayama, respectively, and the diseases their vectored bacteria can cause. Surveillance, early detection, and strict quarantine measures are therefore fundamental to safeguard Australian citrus. However, long-term targeted surveillance for exotic citrus pests can be a time-consuming and expensive activity, often relying on manually screening large numbers of trap samples and morphological identification of specimens, which requires a high level of taxonomic knowledge. Methods Here we evaluated the use of non-destructive insect metabarcoding for exotic pest surveillance in citrus orchards. We conducted an 11-week field trial, between the months of December and February, at a horticultural research farm (SuniTAFE Smart Farm) in the Northwest of Victoria, Australia, and processed more than 250 samples collected from three types of invertebrate traps across four sites. Results The whole-community metabarcoding data enabled comparisons between different trapping methods, demonstrated the spatial variation of insect diversity across the same orchard, and highlighted how comprehensive assessment of insect biodiversity requires use of multiple complimentary trapping methods. In addition to revealing the diversity of native psyllid species in citrus orchards, the non-targeted metabarcoding approach identified a diversity of other pest and beneficial insects and arachnids within the trap bycatch, and recorded the presence of the triozid Casuarinicola cf warrigalensis for the first time in Victoria. Ultimately, this work highlights how a non-targeted surveillance approach for insect monitoring coupled with non-destructive DNA metabarcoding can provide accurate and high-throughput species identification for biosecurity and biodiversity monitoring.

Post-border surveillance for forestry’s high priority pests and pathogens is conducted routinely through established programs focused on the main points-of-entry and across the major plantation growing regions. Currently, most diagnostic protocols used to identify fungal phytopathogens sampled during these surveys rely on traditional methods, such as morphological examination and DNA barcoding techniques. This stepwise process from isolation to species identification is often regarded as slow, expensive, and limited due to the need for disease manifestation and/or comprehensive expertise for rapid and accurate detection. In this study, we applied a recently validated high-throughput, dual-marker amplicon sequencing approach on insect surveillance traps from across Australia to assess its performance for the targeted surveillance of the Ophiostomatales, an order of fungi comprising notable phytopathogens which are vectored by bark beetles. By using a recently validated assay we were able to confidently characterize a range of Ophiostomatalean taxa known to be present in Australia, while reporting eight first detections from environmental DNA. Our study demonstrates the value of targeted multi-barcode amplicon sequencing for high-throughput screening of fungi caught in post-border surveillance traps, in addition to emphasizing research priorities that require further investigation before such methods can be implemented routinely for biosecurity.

The bacterial microbiome of psyllids has been studied for decades, with a strong focus on the primary and secondary endosymbionts capable of providing essential amino acids for the insects' diet and therefore playing a key role in the insects' ability to radiate on novel plant hosts. Here, we combine metabarcoding analysis of the bacterial communities hosted by psyllids with a multi-gene phylogenetic analysis of the insect hosts to determine what factors influence the bacterial diversity of the psyllids' microbiomes, especially in the context of the dispersal and evolutionary radiation of these insects in Aotearoa New Zealand. Using multi-gene phylogenetics with COI, 18S and EF-1α sequences from 102 psyllid species, we confirmed for the first time monophyly for all the six genera of native/endemic Aotearoa New Zealand psyllids, with indications that they derive from at least six dispersal events to the country. This also revealed that, after its ancestral arrival, the genus Powellia has radiated onto a larger and more diverse range of plants than either Psylla or Ctenarytaina, which is uncommon amongst monophyletic psyllids globally. DNA metabarcoding of the bacterial 16S gene here represents the largest dataset analysed to date from psyllids, including 246 individuals from 73 species. This provides novel evidence that bacterial diversity across psyllid species is strongly associated with psyllid phylogenetic structure, and to a lesser degree to their host plant association and geographic distribution. Furthermore, while the strongest co-phylogenetic signals were derived from the primary and secondary symbionts, a signal of phylosymbiosis was still retained among the remaining taxa of the bacterial microbiome, suggesting potential vertical transmission of bacterial lineages previously unknown to have symbiotic roles.

A fast and reliable method for obtaining a species-level identification is a fundamental requirement for a wide range of activities, from plant protection and invasive species management to biodiversity assessments and ecological studies. For insects, novel molecular techniques such as DNA metabarcoding have emerged as a rapid alternative to traditional morphological identification, reducing the dependence on limited taxonomic experts. Until recently, molecular techniques have required a destructive DNA extraction, precluding the possibility of preserving voucher specimens for future studies, or species descriptions. Here we paired insect metabarcoding with two recent non-destructive DNA extraction protocols, to obtain a rapid and high-throughput taxonomic identification of diverse insect taxa while retaining a physical voucher specimen. The aim of this work was to explore how non-destructive extraction protocols impact the semi-quantitative nature of metabarcoding, which alongside species presence/absence also provides a quantitative, but biased, representation of their relative abundances. By using a series of mock communities representing each stage of a typical metabarcoding workflow we were able to determine how different morphological (i.e., insect biomass and exoskeleton hardness) and molecular traits (i.e., primer mismatch and amplicon GC%), interact with different protocol steps to introduce quantitative bias into non-destructive metabarcoding results. We discuss the relevance of taxonomic bias to metabarcoding identification of insects and potential approaches to account for it.

Psyllids, also known as jumping plant lice, are phloem feeding Hemiptera that often show a strict species-specific relationship with their host plants. When psyllid-plant associations involve economically important crops, this may lead to the recognition of a psyllid species as an agricultural or horticultural pest. The Australian endemic tea tree, Melaleuca alternifolia (Maiden & Betche) Cheel., has been used for more than a century to extract essential oils and, long before that, as a traditional medicine by Indigenous Australian people. Recently, a triozid species has been found to damage the new growth of tea trees both in Queensland and New South Wales, raising interest around this previously undocumented pest. Furthermore, adults of the same species were also collected from Citrus plantations, leading to potential false-positive records of the exotic pest Trioza erytreae (Del Guercio 1918), the African Citrus psyllid. Here we describe for the first time Trioza melaleucae Martoni sp. nov. providing information on its distribution, host plant associations and phylogenetic relationships to other Trioza species. This work enables both morphological and molecular identification of this new species, allowing it to be recognized and distinguished for the first time from exotic pests as well as other Australian native psyllids. Furthermore, the haplotype network analysis presented here suggests a close relationship between Trioza melaleucae and the other Myrtaceae-feeding Trioza spp. from Australia, New Zealand, and Taiwan.

An annotated checklist of the psyllids of the Cook Islands is presented. The presence of Syntomoza tahuata (Klyver, 1932) and Trioza alifumosa Klyver, 1932 in the archipelago, based on new material collected, is reported for the first time. This is the first record from these islands of the genus Syntomoza and the family Liviidae. An identification key to the psyllid species known from the Cook Islands is provided, and their origin and provenance are discussed in relation to their biogeographic implications.

Despite being classified as critically endangered, little work has been done on leopard protection in Pakistan. Once widely present throughout this region, leopards are now sparsely distributed, and possibly extinct from much of their previously recorded habitat. While leopards show morphological and genetic variation across their species range worldwide, resulting in the classification of nine different subspecies, the leopard genetic structure across Pakistan is unknown, with previous studies including only a very limited sampling. To clarify the genetic status of leopards in Pakistan we investigated the sequence variation in the subunit 5 of the mitochondrial gene NADH from 43 tissue samples and compared it with 238 sequences available from online databases. Phylogenetic analysis clearly separates the Pakistani leopards from the African and Arabian clades, confirming that leopards from Pakistan are members of the Asian clade. Furthermore, we identified two separate subspecies haplotypes within our dataset: P. p. fusca (N = 23) and P. p. saxicolor (N = 12).

A recent molecular-based assessment of the psyllid fauna of New Zealand reported two genetically distinct, undescribed psyllid taxa on host plants not native to that country. Here, a morphological examination confirmed species-level variation that resulted in the description of two new psyllid species: Acizzia errabunda sp. nov. (Hemiptera: Psyllidae) from Acacia baileyana F. Muell and Ctenarytaina insularis sp. nov. (Hemiptera: Aphalaridae) from Syzygium smithii (Poir.) Nied. Furthermore, the examination of specimens from entomological collections and from observations recorded on an online database enabled a better understanding of the distribution and host plant associations of these psyllid species. The description of A. errabunda is based on material collected in both New Zealand and Australia from the same plant species, A. baileyana, whereas the psyllid C. insularis has been found to be present in Brunei and New Zealand on S. smithii and in New Caledonia on Melaleuca quinquenervia (Cav.) S. T. Blake.

A recent DNA-based assessment of the psyllid fauna of New Zealand recorded high genetic variation between populations that were expected to belong to the same psyllid species. Among these, a number of populations of the kōwhai psyllid Psylla apicalis (Ferris & Klyver, 1932), from a kōwhai species, Sophora microphylla Aiton (Fabaceae), presented high genetic variability. This gave new endorsement of an 87-year-old observation made by the entomologists Ferris and Klyver who, when describing the kōwhai psyllid, from Sophora tetraptera J.S. Muell., suggested that morphological variations could support more than one species. Accordingly, the morphological assessment conducted here, together with the genetic information now available, resulted in the description of Psylla frodobagginsi sp. nov. as a second New Zealand endemic psyllid species hosted by S. microphylla.

Plant bio-protection and biosecurity programs worldwide use trap-based surveillance for the early detection of agricultural pests and pathogens to contain their incursions and spread. This task is reliant on effective preservation in insect traps, which is required to maintain specimen quality for extended periods under variable environmental conditions. Furthermore, with traditional morphological examinations now increasingly paired with modern molecular diagnostic techniques, insect traps are required to preserve both the specimens’ morphology and the DNA of insects and vectored bacterial pathogens. Here, we used psyllids (Hemiptera) and their hosted bacteria as a model to test the preservative ability of propylene glycol (PG): a non-flammable, easily transportable preservative agent that could be used in pitfall, suction or malaise traps. We tested preservation using various PG concentrations, at different temperatures and for multiple time periods, paired with non-destructive DNA extraction methods, which allow isolation of both insect and arbobacterial DNA while retaining a morphological voucher of the insect host specimens. PG concentrations between 40% and 100% performed best for both insect and bacterial DNA preservation up to 28 days. Ultimately, given the viscous nature of PG at high concentrations, we recommend using it at a concentration between 40% and 60% to enable insects to sink into the solution, thus enhancing DNA preservation.

The superfamily Psylloidea includes numerous species which play a key role in Australian ecology and biodiversity, as well as pests and biological control agents, and sometimes threatened species of conservation concern. Different psyllid sampling and collection techniques are usually performed depending on the nature and aim of the study: from the beating and sweeping of psyllid host plants for conservation and biodiversity assessment, to suction and sticky traps in agriculture. Due to a general lack of information on its efficacy for psyllids, however, light trapping has not usually been employed. Here we present the results obtained trapping psyllids using different light sources and we discuss the strengths and weaknesses of this technique to assess psyllid biodiversity. In particular, we highlight the strength of using this methodology paired with DNA barcoding, to cast some light on psyllid biodiversity. The results obtained here suggest that the psyllid fauna of Australia is heavily understudied and the number of undescribed species might be many times higher than previously expected. Additionally, we report, for the first time, the species Trioza adventicia Tuthill 1952, and Cryptoneossa triangula Taylor 1990 in the state of Queensland.

The insect superfamily Psylloidea (Hemiptera) includes economically important biocontrol agents, pests and plant pathogen vectors, for which a rapid and accurate identification is fundamental for international biosecurity. Australasia is a hot spot for psyllid diversity, but previous species assessments in the region were largely based on morphology and host plant association. Morphological identification of psyllids remains challenging for a wide number of species and for juvenile insects, while a robust molecular framework for identification is not available. Consequently, knowledge of psyllid biology is compromised. Here, incorporating morphological evidence and host plant associations, insects collected from almost 600 primarily New Zealand locations were linked to 67 previously described species. By applying species delimitation methods including GYMC (General Mixed Yule–Coalescent method), PTP (Poisson Tree Processes), mPTP (multi–rate Poisson Tree Processes) and ABGD (Automatic Barcode Gap Discovery) to a dataset composed of 425 cytochrome oxidase I (COI) DNA barcode sequences, further cryptic diversity was revealed among the psyllid collection; more than 20 undescribed taxa are reported here for the first time, resulting in a total of 90 taxa across 21 genera and six families included in this study. Our improved understanding of psyllid diversity in New Zealand revealed new plant host-psyllid associations and geographical variation. The DNA barcode resource will enable future studies of psyllid ecology and more accurate, rapid identifications of psyllids that pose biosecurity threats to Australasia.

R2 is an extensively investigated non-LTR retrotransposon that specifically inserts into the 28S rRNA gene sequences of a wide range of metazoans, disrupting its functionality. During R2 integration, first strand synthesis can be incomplete so that 5' end deleted copies are occasionally inserted. While active R2 copies repopulate the locus by retrotransposing, the non-functional truncated elements should frequently be eliminated by molecular drive processes leading to the concerted evolution of the rDNA array(s). Although, multiple R2 lineages have been discovered in the genome of many animals, the rDNA of the stick insect Bacillus rossius exhibits a peculiar situation: it harbors both a canonical, functional R2 element (R2Brfun) as well as a full-length but degenerate element (R2Brdeg). An intensive sequencing survey in the present study reveals that all truncated variants in stick insects are present in multiple copies suggesting they were duplicated by unequal recombination. Sequencing results also demonstrate that all R2Brdeg copies are full-length, i. e. they have no associated 5' end deletions, and functional assays indicate they have lost the active ribozyme necessary for R2 RNA maturation. Although it cannot be completely ruled out, it seems unlikely that the degenerate elements replicate via reverse transcription, exploiting the R2Brfun element enzymatic machinery, but rather via genomic amplification of inserted 28S by unequal recombination. That inactive copies (both R2Brdeg or 5'-truncated elements) are not eliminated in a short term in stick insects contrasts with findings for the Drosophila R2, suggesting a widely different management of rDNA loci and a lower efficiency of the molecular drive while achieving the concerted evolution.