Biological identifications through DNA barcodes

Classification, identification, and DNA barcoding study for common cockroach species (Dictyoptera: Blattaria) from China

Cockroaches are well-known pests and quarantined organisms worldwide. Due to morphological diversity and a lack of molecular data, their classification and identification are facing challenges. This study performed classification, identification, and DNA barcoding for cockroaches collected from China. Seventy-six samples were morphologically identified as seven species of two superfamilies that included Blattella germanica, Eublaberus posticus and Blaptica dubia belonging to the superfamily Blaberoidea, and Periplaneta americana, Periplaneta lateralis, Periplaneta fuliginosa and Periplaneta australasiae belonging to the superfamily Blattoidea. Based on sequence alignments of nine ribosomal and mitochondrial genes across the order Blattaria retrieved from GenBank, rDNA ITS2-517 bp and mtDNA 16S-327 bp were screened as candidates for molecular identification. Universal primers were designed for PCR amplification, cloning, and sequencing of the 37 representative samples. Sequence alignments and phylogeny analysis showed that both ITS2 and 16S confirmed samples 1-9, 20-24, and 25-29 as B. germanica, P. americana, and P. lateralis, respectively; only 16S (not ITS2) confirmed samples 10-14, 15-19, 30-34, and 35-37 as E. posticus, Blap. dubia, P. fuliginosa, and P. australasiae, respectively, indicating that 16S was a better target than ITS2 for molecular identification of cockroaches. Conservative motif and divergence analysis further revealed that ITS2 sequences vary significantly among different taxa, whereas 16S sequences are relatively conserved. There is an obvious barcoding gap between maximum intraspecific divergence and minimum interspecific divergence (2.57 % vs. 5.62 %) for ITS2, but not for 16S (6.15 % vs. 2.63 %). Therefore, it was confirmed that ITS2 is an ideal DNA barcode for molecular identification of cockroaches at lower category.

Morpometric and molecular characterization of Surguli goat through CO1 gene in district Kohat

The present study was designed with the aim to study morphometric characterization as well as phylogeny and diversity of the local Surguli goat at their breeding tract district Kohat through mitochondrial DNA region, i.e., Cytochrome C Oxidase Subunit One (CO1) gene. Morphometric data and blood samples were collected from thirty (30) pure goats. Morphometric analysis showed that sex had significant effect (p < 0.05) on body weight, body length, hearth girth and horn length while no significant effect (p > 0.05) was observed for other characteristics. The results also indicated that age had significant effect (p < 0.05) on height at rump, ear length, horn length and tail length while no significant effect (p > 0.05) was observed for other characteristics. The phylogenetic analysis through CO1 nucleotide sequences within nucleotide range 1-767 showed nine polymorphic sites segregating into eight haplotypes. The mean intraspecific diversity and mean interspecific diversity were calculated as 0.23 and 2.36%, respectively. Phylogenetic tree revealed that Capra Ibex and native Surguli goat have common ancestors. The morphometric and molecular results obtained from the present study can be exploited as a selection tool for breeding and overall improvement.

MycoAI: Fast and accurate taxonomic classification for fungal ITS sequences

Efficient and accurate classification of DNA barcode data is crucial for large-scale fungal biodiversity studies. However, existing methods are either computationally expensive or lack accuracy. Previous research has demonstrated the potential of deep learning in this domain, successfully training neural networks for biological sequence classification. We introduce the MycoAI Python package, featuring various deep learning models such as BERT and CNN tailored for fungal Internal Transcribed Spacer (ITS) sequences. We explore different neural architecture designs and encoding methods to identify optimal models. By employing a multi-head output architecture and multi-level hierarchical label smoothing, MycoAI effectively generalizes across the taxonomic hierarchy. Using over 5 million labelled sequences from the UNITE database, we develop two models: MycoAI-BERT and MycoAI-CNN. While we emphasize the necessity of verifying classification results by AI models due to insufficient reference data, MycoAI still exhibits substantial potential. When benchmarked against existing classifiers such as DNABarcoder and RDP on two independent test sets with labels present in the training dataset, MycoAI models demonstrate high accuracy at the genus and higher taxonomic levels, with MycoAI-CNN being the fastest and most accurate. In terms of efficiency, MycoAI models can classify over 300,000 sequences within 5 min. We publicly release the MycoAI models, enabling mycologists to classify their ITS barcode data efficiently. Additionally, MycoAI serves as a platform for developing further deep learning-based classification methods. The source code for MycoAI is available under the MIT Licence at https://github.com/MycoAI/MycoAI.

Forensic species identification: practical guide for animal and plant DNA analysis

The importance of non-human DNA in the forensic field has increased greatly in recent years, together with the type of applications. The molecular species identification of animal and botanical material may be crucial both for wildlife trafficking and crime scene investigation. However, especially for forensic botany, several challenges slow down the implementation of the discipline in the routine.Although the importance of molecular analysis of animal origin samples is widely recognized and the same value is acknowledged to the botanical counterpart, the latter does not find the same degree of application.The availability of molecular methods, especially useful in cases where the material is fragmented, scarce or spoiled preventing the morphological identification, is not well known. This work is intended to reaffirm the relevance of non-human forensic genetics (NHFG), highlighting differences, benefits and pitfalls of the current most common molecular analysis workflow for animal and botanical samples, giving a practical guide. A flowchart describing the analysis paths, divided in three major working areas (inspection and sampling, molecular analysis, data processing and interpretation), is provided. More real casework examples of the utility of non-human evidence in forensic investigations should be shared by the scientific community, especially for plants. Moreover, concrete efforts to encourage initiatives in order to promote quality and standardization in the NHFG field are also needed.

Performance of DNA metabarcoding, standard barcoding and morphological approaches in the identification of insect biodiversity

For two decades, DNA barcoding and, more recently, DNA metabarcoding have been used for molecular species identification and estimating biodiversity. Despite their growing use, few studies have systematically evaluated these methods. This study aims to evaluate the efficacy of barcoding methods in identifying species and estimating biodiversity, by assessing their consistency with traditional morphological identification and evaluating how assignment consistency is influenced by taxonomic group, sequence similarity thresholds and geographic distance. We first analysed 951 insect specimens across three taxonomic groups: butterflies, bumblebees and parasitic wasps, using both morphological taxonomy and single-specimen COI DNA barcoding. An additional 25,047 butterfly specimens were identified by COI DNA metabarcoding. Finally, we performed a systematic review of 99 studies to assess average consistency between insect species identity assigned via morphology and COI barcoding and to examine the distribution of research effort. Species assignment consistency was influenced by taxonomic group, sequence similarity thresholds and geographic distance. An average assignment consistency of 49% was found across taxonomic groups, with parasitic wasps displaying lower consistency due to taxonomic impediment. The number of missing matches doubled with a 100% sequence similarity threshold and COI intraspecific variation increased with geographic distance. Metabarcoding results aligned well with morphological biodiversity estimates and a strong positive correlation between sequence reads and species abundance was found. The systematic review revealed an 89% average consistency and also indicated taxonomic and geographic biases in research effort. Together, our findings demonstrate that while problems persist, barcoding approaches offer robust alternatives to traditional taxonomy for biodiversity assessment.

COI DNA barcoding to differentiate Haemagogus janthinomys and Haemagogus capricornii (Diptera: Culicidae) mosquitoes

The genus Haemagogus (Diptera: Culicidae) includes species that are important vectors of pathogens such as the yellow fever virus. The accurate identification of these species is essential for the control of zoonoses. Females of Hg. capricornii and Hg. janthinomys are morphologically indistinguishable, which makes the use of alternative identification techniques desirable. This study aimed to obtain sequences of the mitochondrial cytochrome c oxidase I (COI) gene, in the region widely used for DNA barcoding, of Haemagogus specimens from the state of São Paulo, Brazil, to evaluate the effectiveness of these sequences in the molecular identification of the species. A total of 37 female and 2 male mosquitoes were collected in various locations in the state of São Paulo, using methods such as hand-nets, Shannon traps, CDC light traps with CO2 bait and Nasci aspirators. The sequences of a 710 bp fragment of the COI gene were amplified by PCR and sequenced. A phylogenetic tree reconstruction was conducted using the Bayesian approach implemented in MrBayes v3.2.2, providing support values for taxa where genetic clusters may indicate the presence of new or cryptic species. We obtained 39 COI sequences representing three species: Haemagogus capricornii, Haemagogus leucocelaenus, and Haemagogus janthinomys. Bayesian analysis of the sequences produced clades that corroborate the morphological identification of the species. The separation of Hg. capricornii and Hg. janthinomys received 100 % statistical support and the Hg. capricornii was very well supported (91 %). The two sequences from male specimens, morphologically identified as Hg. capricornii, were grouped in the same clade, a sister clade of Hg. janthinomys. It is important to highlight that the Hg. janthinomys were positioned in several subclades, showing a polymorphism of this species within the state, a situation not observed for Hg. capricornii. For the first time, sequences of the mtCOI gene from Hg. capricornii were obtained and related to morphologically identified specimens. COI sequences proved effective in the molecular identification of Haemagogus species. This study contributes to the expansion of the GenBank database, providing the first sequences of Hg. capricornii and new sequences for Hg. janthinomys and Hg. leucocelaenus.

Evolutionary History and Ecology of Andrena (Foveoandrena) androfovea: A New Nearctic Mining Bee (Hymenoptera, Andrenidae) Species and Subgenus

With about 1700 described species, the mining bee genus Andrena is a rapidly diversifying lineage and one of the most species-rich groups of bees. Recent phylogenomic advances have greatly improved our understanding of the phylogeny of the genus, yet many species still await description, subgeneric assignments that are in line with their evolutionary history, as well as study of their morphology and behavior. Here we provide a comprehensive account of a newly discovered species, Andrena androfovea n. sp. We sequence the genome of the new species and include it in the presently most comprehensive phylogenomic analysis of Andrena using ultraconserved element (UCE) sequence data, comprising 264 samples and 249 species. Given the recovered phylogenetic position of the new species, we establish a new subgenus, Foveoandrena, provide a detailed morphological description, and discuss the antiquity and historical biogeography of the lineage in light of molecular divergence time estimates. Lastly, we study and document the foraging behavior of the new species with photos and video footage, and discuss the species' unusual host plant associations with Chamaesaracha and Quincula, both Solanaceae. Being likely oligolectic on these plants, we present the first documented case of an Andrena species being narrowly associated with members of this plant family. By integrating multiple lines of documentation, our study provides a particularly detailed account of species discovery and description.

Enhancing RNA-lipid nanoparticle delivery: Organ- and cell-specificity and barcoding strategies

Recent advancements in RNA therapeutics highlight the critical need for precision gene delivery systems that target specific organs and cells. Lipid nanoparticles (LNPs) have emerged as key vectors in delivering mRNA and siRNA, offering protection against enzymatic degradation, enabling targeted delivery and cellular uptake, and facilitating RNA cargo release into the cytosol. This review discusses the development and optimization of organ- and cell-specific LNPs, focusing on their design, mechanisms of action, and therapeutic applications. We explore innovations such as DNA/RNA barcoding, which facilitates high-throughput screening and precise adjustments in formulations. We address major challenges, including improving endosomal escape, minimizing off-target effects, and enhancing delivery efficiencies. Notable clinical trials and recent FDA approvals illustrate the practical applications and future potential of LNP-based RNA therapies. Our findings suggest that while considerable progress has been made, continued research is essential to resolve existing limitations and bridge the gap between preclinical and clinical evaluation of the safety and efficacy of RNA therapeutics. This review highlights the dynamic progress in LNP research. It outlines a roadmap for future advancements in RNA-based precision medicine.

Rapid expansion and ecosystem health risk of invasive biopollutants dispersed by maritime traffic in French Polynesia

The introduction of biopollutant species challenge ecosystem health and economy in remote islands. Here we checked the advance of invasive fouling species in five French Polynesian islands. Expansion of invasive species (Acantophora spicifera, Bugula neritina, Chthamalus proteus, Dendostrea frons) was detected using individual barcoding (COI for animals, RBLC for algae), and metabarcoding on biofouling (COI and 18S sequences). They were especially abundant in Port Phaeton (Tahiti), Bora Bora and Rangiroa atoll. Chthamalus proteus is a vector of bacterial diseases and may harm native French Polynesian mollusks. Dendostrea frons is a vector of Perkinsus, a parasite to which black pearl oysters, the mainstay of the Polynesian economy, are susceptible. High ecological and epidemiological risks were estimated for C. proteus and D. frons, and ecological risks also for A. spicifera and especially for B. neritina. Strengthening marine biosecurity measures is highly recommended to conserve these unique ecosystems and their associated services.

Under the Sea: Investigation of Telson Morphology and Cryptic Diversity within Eucopia sculpticauda, a Deep-Sea Lophogastrid from the Gulf of Mexico (Peracarida: Lophogastrida)

The field of phylogenetics employs a variety of methods and techniques to study the evolution of life across the planet. Understanding evolutionary relationships is crucial to enriching our understanding of how genes and organisms have evolved throughout time and how they could possibly evolve in the future. Eucopia sculpticauda Faxon, 1893 is a deep-water peracarid in the order Lophogastrida Boas, 1883, which can often be found in high abundances in pelagic trawls. The species can be found along the Mariana Trench, in the Mid-Atlantic Ridge, west Atlantic and east Pacific Oceans, and in the Gulf of Mexico and as deep as 7526 m. Recent collections of E. sculpticauda in the Gulf of Mexico have revealed putative cryptic diversity within the species based on both molecular and morphological evidence. Previous studies have documented two different morphotypes of the telson: the terminal part of the pleon (abdomen) and part of the tail fan. In adults, the morphotypes can be distinguished by lateral constrictions in the telson. This evidence, combined with a previous barcoding study, led to the speculation that telson morphology may be a distinguishing character useful to define cryptic diversity within E. sculpticauda. This study presents additional molecular data from the mitochondrial genes cytochrome c oxidase subunit I, and the large ribosomal subunit (16S), and the nuclear histone 3 gene (H3) to investigate telson morphotypes in relation to evolutionary history within this species. Molecular data identified two strongly supported clades, lending support for potential cryptic diversification within the Gulf of Mexico. Investigations into telson morphology suggest that this character may be informative, but the morphotypes were sometimes ambiguous and additional characters could not be found that discriminate clades. At present, our data suggest early evidence for cryptic diversification within Gulf of Mexico populations, but additional morphological characters and geographic sampling are needed before a new species can be described.

DNA barcode reference library of the fish larvae and eggs of the South China Sea: taxonomic effectiveness and geographic structure

Fish early-stages constitute useful indicators of the states of marine ecosystems, as well as important fishery resources. Given the spectacular phenotypic changes during ontogeny, and the paucity of diagnostic morphological characters at the species level, the identification of fish early-stages is a challenging task. DNA barcoding, the use of the mitochondrial gene of the cytochrome c oxidase subunit I (COI) as an internal species tag, opened new perspectives for the identifications of both larval fish and fish eggs. However, the accuracy of the identifications assisted by DNA barcoding are dependent of the completeness of the DNA barcode reference libraries used to assigned unknown sequences to known species. Here, we built a DNA barcode reference library for 113 species of larval fish and 85 species of fish eggs involving the production of 741 newly generated DNA barcodes from South China Sea (63 localities). Together with 514 DNA barcodes mined from Genbank for 116 species from the South China Sea regions, a reference library including 1255 DNA barcodes for 308 species (248 locations) was assembled. The present study emphasizes the importance of integrating DNA barcoding to large scale inventories of early stages, as DNA-based species delimitation analyses delimited 305 molecular operational taxonomic units (MOTUs) and multiple cases of discordance with morphological identifications were detected. Cryptic diversity is detected with 14 species displaying two MOTUs and a total of 23 species were lumped into 11 MOTUs due to low interspecific divergence and/or mixed lineages.

Sympatric diversity pattern driven by the secondary contact of two deeply divergent lineages of the soybean pod borer Leguminivora glycinivorella

The soybean pod borer, Leguminivora glycinivorella (Matsumura), is an important tortricid pest species widely distributed in most parts of China and its adjacent regions. Here, we analyzed the genetic diversity and population differentiation of L. glycinivorella using diverse genetic information including the standard cox1 barcode sequences, mitochondrial genomes (mitogenomes), and single-nucleotide polymorphisms (SNPs) from genotyping-by-sequencing. Based on a comprehensive sampling (including adults or larvae of L. glycinivorella newly collected at 22 of the total 30 localities examined) that covers most of the known distribution range of this pest, analyses of 543 cox1 barcode sequences and 60 mitogenomes revealed that the traditionally recognized and widely distributed L. glycinivorella contains two sympatric and widely distributed genetic lineages (A and B) that were estimated to have diverged ∼1.14 million years ago during the middle Pleistocene. Moreover, low but statistically significant correlations were recognized between genetic differentiation and geographic or environmental distances, indicating the existence of local adaptation to some extent. Based on SNPs, phylogenetic inference, principal component analysis, fixation index, and admixture analysis all confirm the two divergent sympatric lineages. Compared with the stable demographic history of Lineage B, the expansion of Lineage A had possibly made the secondary contact of the two lineages probable, and this process may be driven by the climate fluctuation during the late Pleistocene as revealed by ecological niche modeling.

Genomic and transcriptomic perspectives on the origin and evolution of NUMTs in Orthoptera

Nuclear mitochondrial pseudogenes (NUMTs) result from the transfer of mitochondrial DNA (mtDNA) to the nuclear genome. NUMTs, as "frozen" snapshots of mitochondria, can provide insights into diversification patterns. In this study, we analyzed the origins and insertion frequency of NUMTs using genome assembly data from ten species in Orthoptera. We found divergences between NUMTs and contemporary mtDNA in Orthoptera ranging from 0 % to 23.78 %. The results showed that the number of NUMT insertions was significantly positively correlated with the content of transposable elements in the genome. We found that 39.09 %-68.65 % of the NUMTs flanking regions (2,000 bp) contained retrotransposons, and more NUMTs originated from mitochondrial rDNA regions. Based on the analysis of the mitochondrial transcriptome, we found a potential mechanism of NUMT integration: mitochondrial transcripts are reverse transcribed into double-stranded DNA and then integrated into the genome. The probability of this mechanism occurring accounts for 0.30 %-1.02 % of total mitochondrial nuclear transfer events. Finally, based on the phylogenetic tree constructed using NUMTs and contemporary mtDNA, we provide insights into ancient evolutionary events such as species-specific "autaponumts" and "synaponumts" shared among different species, as well as post-integration duplication events.

Massive citizen science sampling and integrated taxonomic approach unravel Danish cryptogam-dwelling tardigrade fauna

Tardigrade diversity and distribution are enigmatic in most parts of the globe, and only some European countries can boast of a relatively well-studied water bear fauna. However, even these suffer from the lack of genetic data, which would substantiate faunistic data and make biogeographic comparisons easier. Denmark has never been intensively and systematically researched in this regard, thus a citizen science sampling of cryptogams (mosses, liverworts, and lichens) was launched in spring 2023, aiming at a comprehensive biodiversity survey across this insular country. Nearly 700 samples were selected out of 8.000 sent to NHMD, based on the quality of samples, representativeness of various regions of Denmark, and the type of substrate to allow unravelling of potential ecological associations between tardigrades and cryptogams. Importantly, a large fraction of morphological identifications was backed up by DNA barcode data based on ITS-2 (1001 sequences), and in some cases also on COI (93 sequences) and ITS-1 (22 sequences) molecular markers, which are recognised DNA fragments used in species delimitation. We quadruple the number of known Danish limno-terrestrial tardigrade species (55 spp. reported in this paper vs. 14 spp. reported in literature so far, most of which were contentious due to the insufficient knowledge on tardigrade taxonomy), demonstrating the power of integrative taxonomy. No fewer than nine spp. are new to science. This is the first case where tardigrade fauna of an entire country is examined both from morphological and DNA barcoding data perspective.

Cascading impacts of nitrogen deposition on soil microbiome and herbivore communities in desert steppes

Human activities in the last century have intensified global nitrogen deposition, resulting in the degradation of ecosystem function and loss of biodiversity worldwide. Nitrogen addition is a crucial method for examining the effects of atmospheric nitrogen deposition on species composition and structure of soil microbiome and biotic community, as exogenous nitrogen inputs can trigger cascading effects on ecosystem functions. In a 6-year experiment, we evaluated the impact of nitrogen addition on soil microbial-plant-insect systems in desert steppes. Our results show that nitrogen addition significantly altered soil microbial composition and ecological function, leading to a decrease in nitrogen-fixing bacteria and an increase in saprophytic fungi. High levels of nitrogen addition increased total plant biomass while decreasing species diversity. Additionally, high nitrogen addition levels suppressed below-ground biomass of gramineae and legumes compared to low nitrogen addition. Nitrogen addition also increased herbivore abundance by altering insect community structure, particularly benefiting chewing pests over sucking pests, thus heightening the risk of biological disasters through trophic cascading effects. Consequently, excessive nitrogen addition may destabilize desert steppe ecosystems by disturbing soil microbial-plant-insect interactions, hindering the maintenance of biotic community diversity and steppe productivity.

Detection Methods for Pine Wilt Disease: A Comprehensive Review

Pine wilt disease (PWD), caused by the nematode Bursaphelenchus xylophilus, is a highly destructive forest disease that necessitates rapid and precise identification for effective management and control. This study evaluates various detection methods for PWD, including morphological diagnosis, molecular techniques, and remote sensing. While traditional methods are economical, they are limited by their inability to detect subtle or early changes and require considerable time and expertise. To overcome these challenges, this study emphasizes advanced molecular approaches such as real-time polymerase chain reaction (RT-PCR), droplet digital PCR (ddPCR), and loop-mediated isothermal amplification (LAMP) coupled with CRISPR/Cas12a, which offer fast and accurate pathogen detection. Additionally, DNA barcoding and microarrays facilitate species identification, and proteomics can provide insights into infection-specific protein signatures. The study also highlights remote sensing technologies, including satellite imagery and unmanned aerial vehicle (UAV)-based hyperspectral analysis, for their capability to monitor PWD by detecting asymptomatic diseases through changes in the spectral signatures of trees. Future research should focus on combining traditional and innovative techniques, refining visual inspection processes, developing rapid and portable diagnostic tools for field application, and exploring the potential of volatile organic compound analysis and machine learning algorithms for early disease detection. Integrating diverse methods and adopting innovative technologies are crucial to effectively control this lethal forest disease.

Intraspecific diversity of Myrmecophilus acervorum (Orthoptera: Myrmecophilidae) indicating an ongoing cryptic speciation

Myrmecophilus acervorum, previously considered a parthenogenetic species widely-distributed in Europe, has been observed to have both sexes in populations inhabiting the central part of the distribution range. Specimens from those heterosexual populations have been found being infected with Wolbachia. New mitochondrial data (COI and 16S markers) revealed the well-supported differentiation of M. acervorum populations inhabiting western Polesie (Poland) and southern Europe. In turn, analyses of EF1α marker support the hypothesis on the unfinished lineage sorting at the nuclear DNA level. Interestingly, we found that parthenogenetic populations inhabiting western Polesie are infected with Wolbachia belonging to supergroup A, while endosymbionts occurring in sexual populations of M. acervorum observed in Romania belong to supergroup B. Furthermore, new and potentially diagnostic characteristics in the external structures of the eyes of M. acervorum were identified. The surface of ommatidia in specimens occurring in southern Europe was smooth. In contrast, the ommatidia surface of individuals collected in Poland was visibly sculptured. To sum up, the significant genetic variability found in the present case, and the differentiating morphological character, are almost certainly effects of cryptic species being present within M. acervorum. This is indicative of ongoing speciation within the populations of this insect, and of simultaneous unfinished lineage sorting at the nuclear DNA level.

Wireworm species associated with corn and soybean agroecosystems in Ontario, Canada

Wireworms, the larvae of click beetles (Coleoptera: Elateridae), are often the target of insecticide seed treatments commonly used in corn (Zea mays L.) and soybean (Glycine max (L.) Merr.) production in North America. Nevertheless, there is a lack of knowledge of the species, life history, and economic impact of wireworms present in these agroecosystems. An extensive survey of wireworms was conducted in corn and soybean fields in Ontario, Canada, from 2014 to 2017 to document species distribution and co-occurrence and to identify risk factors related to their abundance. In total, 4,332 specimens were collected from 1,245 different sampling records. The dominant species collected was Limonius agonus (Say) (Coleoptera: Elateridae) comprising 71.5% of the specimens. The remaining wireworm specimens were identified as Hypnoidus abbreviatus (Say), Melanotus similis (Kirby), M. cribulosus (LeConte), M. depressus (Melsheimer), M. communis (Gyllenhal), Agriotes mancus (Say), Aeolus mellillus (Say), and Hemicrepidius spp (Germar). Multiple wireworm species were found to commonly occur within the same field and the same sample. Path analysis was conducted to investigate whether site, soil, and agronomic characteristics influenced wireworm distribution and abundance. Several significant relationships were found between wireworm species and geographic factors, soil texture, and agronomic practices. The results of this survey provide critical information that can be used to improve integrated pest management of the major wireworm genera found in corn and soybean agroecosystems in Ontario.

Diversity and composition of the bacterial communities associated with the Australian spittlebugs Bathyllus albicinctus and Philagra parva (Hemiptera: Aphrophoridae)

Spittlebugs and froghoppers (Hemiptera: Cercopoidea) are insects feeding on xylem, which potentially can cause significant economic damage worldwide by transmitting plant pathogenic bacteria such as Xylella fastidiosa. Australia and New Zealand are currently free from X. fastidiosa, but they are home to at least 45 native spittlebug species. Among these, the Australian natives Bathyllus albicinctus (Erichson, 1842) and Philagra parva (Donovan, 1805) are particularly widespread and can be found across southern and eastern Australia, with B. albicinctus also in New Zealand. The potential that both species might be capable of vectoring Xylella fastidiosa poses a substantial biosecurity risk if the bacterium were to invade these regions. In this study, we examined 87 spittlebug nymphs collected across 12 different host plant species, in five locations in Victoria, Australia. Our objective was to explore the factors influencing bacterial communities within and between these widespread spittlebug species, considering geographic location, insect phylogenetics, and host plant associations. We employed COI barcoding to assess insect genetic variation and 16S high throughput sequencing (HTS) metabarcoding to analyse bacterial microbiome diversity across various host plants. Our findings revealed minimal genetic divergence among spittlebug individuals in the same species, highlighting conspecificity despite conspicuous morphological divergences. On the other hand, we recorded significant variation in bacterial communities harboured by Bathyllus albicinctus nymphs feeding on different plants, even when these were collected within close proximity to each other. Therefore, host plant association appeared to shape the bacterial communities of spittlebugs more than insect genetic divergence or geographical location. These diverse bacterial communities could potentially facilitate transmission of plant pathogenic bacteria, underscoring the risk of widespread transmission among numerous plant hosts through insect-plant interactions. This study emphasizes the critical need to understand these complex interactions, particularly in the context of biosecurity.

Barcode 100K Specimens: In a Single Nanopore Run

It is a global priority to better manage the biosphere, but action must be informed by comprehensive data on the abundance and distribution of species. The acquisition of such information is currently constrained by high costs. DNA barcoding can speed the registration of unknown animal species, the most diverse kingdom of eukaryotes, as the BIN system automates their recognition. However, inexpensive sequencing protocols are critical as the census of all animal species is likely to require the analysis of a billion or more specimens. Barcoding involves DNA extraction followed by PCR and sequencing with the last step dominating costs until 2017. By enabling the sequencing of highly multiplexed samples, the Sequel platforms from Pacific BioSciences slashed costs by 90%, but these instruments are only deployed in core facilities because of their expense. Sequencers from Oxford Nanopore Technologies provide an escape from high capital and service costs, but their low sequence fidelity has, until recently, constrained adoption. However, the improved performance of its latest flow cells (R10.4.1) erases this barrier. This study demonstrates that a MinION flow cell can characterise an amplicon pool derived from 100,000 specimens while a Flongle flow cell can process one derived from several thousand. At $0.01 per specimen, DNA sequencing is now the least expensive step in the barcode workflow.

Integrative morphological, cytogenetic and molecular characterization of the Andean climbing catfish Astroblepus mindoensis (Regan, 1916) (Siluriformes:Astroblepidae)

Astroblepus species, commonly known as Andean climbing catfish, exhibit a unique challenge in species delimitation, leading to ongoing taxonomic debates. Here we report data on Astroblepus mindoensis, a vulnerable species endemic to Ecuador, obtained by an integrative approach that includes cytogenetic analysis, molecular identification of the specimens, and recording of morphological and morphometric characters useful for species diagnosis. Thus, this study aimed to associate the karyotype data of the specimens analyzed with morphological and molecular characters, improving and expanding the existing taxonomic information, thus contributing to the systematics of the species. Our morphology results, unlike Regan's original description, which is brief and ambiguous, provide a more detailed morphometric and meristic description. Molecular phylogenetic reconstruction and genetic distance based on a fragment of the cytochrome c oxidase subunit I (COI) showed that our samples constitute a well-supported and monophyletic clade within the A. grixalvii species complex. The cytogenetic analysis identified distinct chromosomal markers, including a single cluster of major ribosomal genes (on chromosome pair 3) and of minor ribosomal genes (on chromosome pair 12) with their localization differing from those reported in other Astroblepus species analyzed. Additionally, the presence of a heteromorphic chromosome pair in males suggests the presence of an XX/XY sex-determination system that has not been identified in other congeneric species. Further investigation is necessary to determine if these chromosomes are associated with the accumulation of repeated sequences, as typically occurs with sex chromosomes, and to assess their presence in other species of the genus.

Comparative Study of Potential Habitats for Two Endemic Grassland Caterpillars on the Qinghai-Tibet Plateau Based on BIOMOD2 and Land Use Data

This study has systematically investigated and compared the geographical distribution patterns and population density of G. menyuanensis (Gm) and G. qinghaiensis (Gq), which are endemic to the QTP region and inflict severe damage. Using a method combining the BIOMOD2 integration model (incorporating nine ecological niche models) and current species distribution data, this study has compared changes in potential habitats and distribution centers of these two species during ancient, present, and future climate periods and conducted a correlation test on the prediction results with land use types. The study results indicate that there are differences in geographical distribution patterns, distribution elevations, and population density of these two species. Compared with single models, the integration model exhibits prominent accuracy and stability with higher KAPPA, TSS, and AUC values. The distribution of suitable habitats for these two species is significantly affected by climatic temperature and precipitation. There is a significant difference between the potential habitats of these two species. Gm and Gq are distributed in the northeastern boundary area and the central and eastern areas of the QTP, respectively. The areas of their suitable habitats are significantly and positively correlated with the area of grassland among all land use types of QTP, with no correlations with the areas of other land use types of QTP. The potential habitats of both species during the paleoclimate period were located in the eastern and southeastern boundary areas of the QTP. During the paleoclimate period, their potential habitats expanded towards the Hengduan Mountains (low-latitude regions) in the south compared with their current suitable habitats. With the subsequent temperature rising, their distribution centers shifted towards the northeast (high-latitude) regions, which could validate the hypothesis that the Hengduan Mountains were refuges for these species during the glacial period. In the future, there will be more potential suitable habitats for these two species in the QTP. This study elucidates the ecological factors affecting the current distribution of these grass caterpillars, provides an important reference for designating the prevention and control areas for Gm and Gq, and helps protect the alpine meadow ecosystem in the region.

Discovery of a new gall-inducing species, Aciurinaluminaria (Insecta, Diptera, Tephritidae) via multi-trait integrative taxonomy

Integrative taxonomic practices that combine multiple lines of evidence for species delimitation greatly improve our understanding of intra- and inter-species variation and biodiversity. However, extended phenotypes remain underutilized despite their potential as a species-specific set of extracorporeal morphological and life history traits. Primarily relying on variations in wing patterns has caused taxonomic confusion in the genus Aciurina, which are gall-inducing flies on Asteraceae plants in western North America. However, species display distinct gall morphologies that can be crucial for species identification. Here we investigate a unique gall morphotype in New Mexico and Colorado that was previously described as a variant of that induced by Aciurinabigeloviae (Cockerell, 1890). Our analysis has discovered several consistent features that distinguish it from galls of A.bigeloviae. A comprehensive description of Aciurinaluminaria Baine, sp. nov. and its gall is provided through integrative taxonomic study of gall morphology, host plant ecology, wing morphometrics, and reduced-representation genome sequencing.

Phylogenetics and species delimitation of the recluse spider, Loxosceles rufescens (Araneae: Sicariidae) populations invading Bangkok, Thailand

The Mediterranean recluse spider, Loxosceles rufescens, has been discovered for the first time inhabiting human dwellings in Bangkok, Thailand. Expeditions across 39 localities revealed five establishments with L. rufescens populations. The highest density was recorded in a storage house on Yaowarat Road, located in the heart of Bangkok's Chinatown, where 315 individuals were found, including adults, juveniles, and spiderlings. This medically significant spider's presence in such a densely populated urban area raises concerns about potential envenomation risks. Thirteen specimens of L. rufescens were extracted for DNA and sequenced for molecular phylogenetic analyses. COI and ITS2 markers were used to investigate relationships within L. rufescens and across available Loxosceles species sequences. Results indicate COI is superior for resolving species-level genetic clusters compared to ITS2. Surprisingly, L. rufescens individuals from the same house were found in significantly distant COI lineages, suggesting mtDNA may not be suitable for studying intra-specific phylogeography in this case. Species delimitation methods ABGD and ASAP demonstrated promising results for both COI and ITS2, while bPTP and GMYC tended to overestimate species numbers. ITS2 exhibited high sequence similarity in L. rufescens, suggesting potential utility as a barcoding marker for identification of this globally distributed species. Genetic distance analyses revealed a potential barcoding gap (K2P) of 8-9 % for COI and <2 % for ITS2 in Loxosceles. This study contributes valuable sequence data for the medically important genus Loxosceles and highlights the need for integrative approaches in understanding its evolution and spread. The findings have important implications for pest management strategies and public health in urban environments.

Species traits, landscape quality and floral resource overlap with honeybees determine virus transmission in plant-pollinator networks

Emerging infectious diseases pose a threat to pollinators. Virus transmission among pollinators via flowers may be reinforced by anthropogenic land-use change and concomitant alteration of plant-pollinator interactions. Here, we examine how species' traits and roles in flower-visitation networks and landscape-scale factors drive key honeybee viruses-black queen cell virus (BQCV) and deformed wing virus-in 19 wild bee and hoverfly species, across 12 landscapes varying in pollinator-friendly (flower-rich) habitat. Viral loads were on average more than ten times higher in managed honeybees than in wild pollinators. Viral loads in wild pollinators were higher when floral resource use overlapped with honeybees, suggesting these as reservoir hosts, and increased with pollinator abundance and viral loads in honeybees. Viral prevalence decreased with the amount of pollinator-friendly habitat in a landscape, which was partly driven by reduced floral resource overlap with honeybees. Black queen cell virus loads decreased with a wild pollinator's centrality in the network and the proportion of visited dish-shaped flowers. Our findings highlight the complex interplay of resource overlap with honeybees, species traits and roles in flower-visitation networks and flower-rich pollinator habitat shaping virus transmission.

A multiscale analysis of coralline algae Lithophylloideae (Corallinophycidae, Rhodophyta) shedding new light on understanding cryptic diversity

Cryptic diversity abounds in many biological species, posing challenges to our understanding of biological diversity, conservation and management. Taking the common coralline algae, the subfamily Lithophylloideae as an illustration, this study delved into the implications of cryptic diversity through global-level phylogenetic and geographical analysis based upon Lithophylloideae molecular data worldwide, as well as a multi-locus time-calibrated phylogeny to elucidate their possible evolutionary process. The multiscale analysis revealed the polyphyly in current concept of the genus Lithophyllum. Geographic isolation resulting from the Tethys terminal event (TTE) has led to two distinct distribution regions for this so-called cosmopolitan genus: one regionally distributed along European coasts/Mediterranean that should include the taxonomical Lithophyllum; others widely distributed, particularly among pan-tropic waters, suggesting at least five groups to be rediscovered within the subfamily Lithophylloideae. Meanwhile, the cryptic genus Titanoderma, lacking morphological identification features with Lithophyllum, exhibited differences in distribution and evolutionary patterns consistent with their ecological habits, thus supporting their separation. This study provided useful hints for cryptic diversity, which advocated an integrative thinking to investigating global cryptic diversity and exploring the broad linkages between phylogenetic relationships and evolutionary origin, biogeography, morphological and ecological traits to achieve a more comprehensive understanding of biodiversity.

DNA barcoding and cryptic diversity in fishes from the Ili River Valley in China, Xinjiang

The Ili River Valley, located in the northwest of China, serves as a vital repository for fish genetic resources. Its extensive water network and diverse climate have given rise to a unique fish composition and endemic species. In this study, we collected the cytochrome c oxidase subunit I (COI) sequences from 660 fish specimens in the Ili River Valley. The effectiveness of DNA barcoding in identifying fish species in the area was assessed by examining genetic distances, constructing phylogenetic trees, and performing ABGD (Automatic Barcode Gap Discovery) analyses, among other methods. In total, 20 species were identified, including one unidentified species (Silurus sp.). Except for Silurus asotus and Hypophthalmichthys molitrix (only one sample), the maximum intraspecific genetic distance among the remaining species was smaller than the minimum interspecific distance, which proves that the species exhibit obvious barcode gaps. In the Neighbor-Joining trees, 20 species formed separate monophyletic branches. According to ABGD analysis, 660 sequences were categorized into 19 Operational Taxonomic Units, with Silurus sp. and S. asotus grouped into a single OTU. The Silurus in this study exhibits shared haplotypes and significant genetic divergence, suggesting the potential presence of cryptic species. Furthermore, the nucleotide diversity across all species fell below the threshold level, indicating that the local fish population is gradually declining. In conclusion, this study has demonstrated the effectiveness of DNA barcoding in identifying fish species in the Ili River Valley, providing valuable data to support the conservation of local fish resources.

Detection Limits of Insect Fragments in Spiked Whole Wheat Flour Using Multiplex Polymerase Chain Reaction (PCR)

The need for a sensitive molecular method to detect specific species of insect contaminants in food products remains a significant challenge in the food industry. This study evaluated the detection limit of a multiplex end-point PCR assay for detecting insects in food. The assay amplifies two fragments of the cytochrome oxidase subunit I gene (COI-Fa and COI-Fb) and one fragment of the protein-coding wingless (wg) gene found in insects. Five insect species, comprising three vectors of foodborne pathogens (the housefly, Musca domestica, the American cockroach, Periplaneta americana, and the pharaoh ant, Monomorium pharaonis) and two storage insect pests (the red flour beetle, Tribolium castaneum and the Indian meal moth, Plodia interpunctella), were spiked separately and in combination at levels of 1, 0.1, 0.01, and 0.001% in whole wheat flour. At spike levels greater than 0.01%, amplicon bands of expected sizes were seen in 100% of samples containing fragments from distinct insect species. At least 25% of spiked samples at the lowest spike level had amplicon bands, except for samples spiked with M. domestica. Results showed an 18.9% probability (with 11.3% and 30% lower and upper confidence limits, respectively) of detecting insect fragments at the lowest spike level (0.001%, corresponding to 3-22 fragments), which is far below the FDA's regulatory level of less than 75 fragments per 50 g of wheat flour. The intensity of amplicon bands in the gel images was higher at higher spike levels. However, this method is not quantitative enough to extrapolate the intensity of the amplicon bands to the number of insect fragments present in a sample. This multiplex assay was also evaluated in a variety of market food samples derived from plants and animals, showing its potential use in various food types. Overall, the sensitivity and specificity of this molecular approach suggest that it could be used in the future as a screening tool for detecting insect contaminants in food.

Enhancing metabarcoding efficiency and ecological insights through integrated taxonomy and DNA reference barcoding: A case study on beach meiofauna

Molecular techniques like metabarcoding, while promising for exploring diversity of communities, are often impeded by the lack of reference DNA sequences available for taxonomic annotation. Our study explores the benefits of combining targeted DNA barcoding and morphological taxonomy to improve metabarcoding efficiency, using beach meiofauna as a case study. Beaches are globally important ecosystems and are inhabited by meiofauna, microscopic animals living in the interstitial space between the sand grains, which play a key role in coastal biodiversity and ecosystem dynamics. However, research on meiofauna faces challenges due to limited taxonomic expertise and sparse sampling. We generated 775 new cytochrome c oxidase I DNA barcodes from meiofauna specimens collected along the Netherlands' west coast and combined them with the NCBI GenBank database. We analysed alpha and beta diversity in 561 metabarcoding samples from 24 North Sea beaches, a region extensively studied for meiofauna, using both the enriched reference database and the NCBI database without the additional reference barcodes. Our results show a 2.5-fold increase in sequence annotation and a doubling of species-level Operational Taxonomic Units (OTUs) identification when annotating the metabarcoding data with the enhanced database. Additionally, our analyses revealed a bell-shaped curve of OTU richness across the intertidal zone, aligning more closely with morphological analysis patterns, and more defined community dissimilarity patterns between supralittoral and intertidal sites. Our research highlights the importance of expanding molecular reference databases and combining morphological taxonomy with molecular techniques for biodiversity assessments, ultimately improving our understanding of coastal ecosystems.

DNA barcoding of southern African mammal species and construction of a reference library for forensic application

Combating wildlife crimes in South Africa requires accurate identification of traded species and their products. Diagnostic morphological characteristics needed to identify species are often lost when specimens are processed and customs officials lack the expertise to identify species. As a potential solution, DNA barcoding can be used to identify morphologically indistinguishable specimens in forensic cases. However, barcoding is hindered by the reliance on comprehensive, validated DNA barcode reference databases, which are currently limited. To overcome this limitation, we constructed a barcode library of cytochrome c oxidase subunit 1 and cytochrome b sequences for threatened and protected mammals exploited in southern Africa. Additionally, we included closely related or morphologically similar species and assessed the database's ability to identify species accurately. Published southern African sequences were incorporated to estimate intraspecific and interspecific variation. Neighbor-joining trees successfully discriminated 94%-95% of the taxa. However, some widespread species exhibited high intraspecific distances (>2%), suggesting geographic sub-structuring or cryptic speciation. Lack of reliable published data prevented the unambiguous discrimination of certain species. This study highlights the efficacy of DNA barcoding in species identification, particularly for forensic applications. It also highlights the need for a taxonomic re-evaluation of certain widespread species and challenging genera.

Molecular identification and genetic variation of forensically important fly species (Order: Diptera) in Thailand using DNA barcoding

Forensic entomology plays a crucial role in criminal investigations by providing vital insights into minimum postmortem interval (PMImin) and corpse relocation by identifying insect species that colonize in decomposing remains. This study aimed to identify and analyze the genetic variation of forensically significant fly species in Thailand, using DNA barcoding of the mitochondrial cytochrome c oxidase subunit I COI gene. A total of 3,220 fly specimens were collected from 18 provinces across six regions of Thailand from October 2017 to September 2022. These specimens were classified by morphological identification into 21 species among three Dipteran families: Calliphoridae, Muscidae, and Sarcophagidae, with Chrysomya megacephala Diptera: Calliphoridae being the most abundant species. DNA barcoding confirmed the morphological identifications with 100 % accuracy, showing low intraspecific K2P distances0.0 to 1.1 %) and significant interspecific K2P distances 2.5 % to 17.2 %. A Neighbour-Joining (NJ) analysis was conducted to assess the molecular identification capabilities of the barcoding region. This analysis successfully recovered nearly all species as distinct monophyletic groups. The species groupings obtained were generally consistent with both morphological and molecular identifications. These findings underscore the effectiveness of DNA barcoding for precise species identification and contribute to a comprehensive database of forensically important flies in Thailand, thus facilitating improved forensic investigations and biodiversity studies.

Most soil and litter arthropods are unidentifiable based on current DNA barcode reference libraries

We are far from knowing all species living on the planet. Understanding biodiversity is demanding and requires time and expertise. Most groups are understudied given problems of identifying and delimiting species. DNA barcoding emerged to overcome some of the difficulties in identifying species. Its limitations derive from incomplete taxonomic knowledge and the lack of comprehensive DNA barcode libraries for so many taxonomic groups. Here, we evaluate how useful barcoding is for identifying arthropods from highly diverse leaf litter communities in the southern Appalachian Mountains (USA). We used 3 reference databases and several automated classification methods on a data set including several arthropod groups. Acari, Araneae, Collembola, Coleoptera, Diptera, and Hymenoptera were well represented, showing different performances across methods and databases. Spiders performed the best, with correct identification rates to species and genus levels of ~50% across databases. Springtails performed poorly, no barcodes were identified to species or genus. Other groups showed poor to mediocre performance, from around 3% (mites) to 20% (beetles) correctly identified barcodes to species, but also with some false identifications. In general, BOLD-based identification offered the best identification results but, in all cases except spiders, performance is poor, with less than a fifth of specimens correctly identified to genus or species. Our results indicate that the soil arthropod fauna is still insufficiently documented, with many species unrepresented in DNA barcode libraries. More effort toward integrative taxonomic characterization is needed to complete our reference libraries before we can rely on DNA barcoding as a universally applicable identification method.

Mitogenomic recognition of incognito lineages in the mud spiny lobster Panulirus polyphagus (Herbst, 1793): A tale of unique genetic structuring and diversification

This study provides the first documentation of three deep conspecific lineages within Panulirus polyphagus in the Indian Ocean, bridging the gap in genetic research. Comparative mitogenomics between lineages (L) at both species and family levels, evolutionary relationships and heterogeneity of sequence divergence within Decapoda, and divergence time estimation were performed. The characterized mitogenomes ranged from 15,685-15,705 bp in size and exhibited a typical pancrustacean pattern. Among the three lineages, L1 predominated the Bay of Bengal, L2 the Arabian Sea, and L2.a, a less common lineage genetically closer to L2, was restricted to the latter region. A minor lineage L1.a, was observed in the Coral Triangle area. All PCGs displayed evidence of purifying selection across species and family levels. The largest genetic distance (K2P) between lineages was 9 %, notably between L1.a and L2.a. The phylogenetic tree subdivided the Achelates into Palinuridae and Scyllaridae, and the topology demonstrated a distinct pattern of lineage diversification within P. polyphagus. AliGROOVE analysis revealed no discernible divergence in Decapoda. The diversification of P. polyphagus appears to have occurred during Miocene, with further diversification in Pliocene. Furthermore, genetic stocks and population connectivity recognized here will provide valuable insight for spatial management planning of this dwindling resource.

Unique among high passes: Insights into the genetic uniqueness among butterflies of Ladakh Trans-Himalaya through DNA barcoding

BACKGROUND

The butterfly assemblage of Ladakh Trans-Himalaya demands a thorough analysis of their population genetic structure owing to their typical biogeographic affinity and their adaptability to extreme cold-desert climates. No such effort has been taken till date, and in this backdrop, we created a COI barcode reference library of 60 specimens representing 23 species.

METHODS AND RESULTS

Barcodes were generated from freshly collected leg samples using the Sanger sequencing method, followed by phylogenetic clade analyses and divergence calculation. Our data represents 22% of Ladakh's Rhopaloceran fauna with the novel barcode submission for six species, including one Schedule II species, Paralasa mani. Contrary to the 3% threshold rule, the interspecific divergence between two species pairs of typical mountain genus Hyponephele and Karanasa was found to be 2.3% and 2.2%, respectively. The addition of conspecific global barcodes revealed that most species showed little increase in divergence value, while a two-fold increase was noted in a few species. Bayesian clade clustering outcomes largely aligned with current morphological classifications, forming monophyletic clades of conspecific barcodes, with only minor exceptions observed for the taxonomically complicated genus Polyommatus and misidentified records of Aulocera in the database. We also observed variations within the same phylogenetic clades forming nested lineages, which may be attributed to the taxonomic intricacies present at the subspecies level globally, mostly among Eurasian species.

CONCLUSIONS

Overall, our effort not only substantiated the effectiveness of DNA Barcoding for the identification and conservation of this climatically vulnerable assemblage but also highlighted the significance of deciphering the unique genetic composition among this geographically isolated population of Ladakh butterflies.

Morphological and molecular characterisation of Mordellistenapeloponnesensis Batten, 1980 (Coleoptera, Mordellidae), with first records from Italy and Turkey

Mordellistenapeloponnesensis Batten, 1980, previously known from Cyprus and Greece, is reported from Italy and Turkey for the first time. The species is redescribed based on type specimens and additional material from its entire known distributional range. Eighteen DNA barcoding sequences of M.peloponnesensis from Greece, Cyprus, and Italy were generated, and genetic variability across the sampling localities was examined. Three mitochondrial haplotypes were detected within M.peloponnesensis. Specimens from mainland Italy share the same haplotype as those from Rhodes and Cyprus, whereas Sardinian specimens exhibit a distinct haplotype. The third haplotype is represented by one specimen from Cyprus. The DNA barcoding sequences of M.peloponnesensis were compared with those of the morphologically allied M.gemellata Schilsky, 1898, and M.pyrenaea Ermisch, 1966, to reveal the phylogenetic relationships between the species.

Elevational shifts in reproductive ecology indicate the climate response of a model chasmophyte, Rainer's bellflower (Campanula raineri)

BACKGROUND AND AIMS

Elevation gradients provide 'natural experiments' for investigating plant climate change responses, advantageous for the study of protected species and life forms for which transplantation experiments are illegal or unfeasible, such as chasmophytes with perennial rhizomes pervading rock fissures. Elevational climatic differences impact mountain plant reproductive traits (pollen and seed quality, sexual vs. vegetative investment) and pollinator community composition; we investigated the reproductive ecology of a model chasmophyte, Campanula raineri Perp. (Campanulaceae), throughout its current elevational/climatic range to understand where sub-optimal conditions jeopardise survival. We hypothesised that: 1) reproductive fitness measures are positively correlated with elevation, indicative of the relationship between fitness and climate; 2) C. raineri, like other campanulas, is pollinated mainly by Hymenoptera; 3) potential pollinators shift with elevation.

METHODS

We measured pollen and seed quality, seed production, the relative investment in sexual vs. vegetative structures and vegetative (Grime's CSR) strategies at different elevations. Potential pollinators were assessed by combining molecular and morphological identification.

KEY RESULTS

Whereas CSR strategies were not linked to elevation, pollen and seed quality were positively correlated, as was seed production per fruit (Hypothesis 1 is supported). The main pollinators of C. raineri were Apidae, Andrenidae, Halictidae (Hymenoptera) and Syrphidae (Diptera), probably complemented by a range of occasional pollinators and visitors (Hypothesis 2 partially supported). Potential pollinator communities showed a taxonomic shift towards Diptera with elevation (particularly Anthomyiidae and Muscidae) and away from Hymenoptera (Hypothesis 3 was supported).

CONCLUSIONS

Pollinator availability is maintained at all elevations by taxon replacement. However, reduced pollen quality and seed production at lower elevations suggest an impact of climate change on reproduction (especially <1200 m a.s.l., where seed germination was limited). Aside from guiding targeted conservation actions for C. raineri, our results highlight problems that may be common to mountain chasmophytes worldwide.

Wolbachia Natural Infection of Mosquitoes in French Guiana: Prevalence, Distribution, and Genotyping

Wolbachia are the most spread bacterial endosymbionts in the world. These bacteria can manipulate host reproduction or block virus transmission in mosquitoes. For this reason, Wolbachia-based strategies for vector control are seriously considered or have already been applied in several countries around the world. In South America, Wolbachia have been studied in human pathogen vectors such as sand flies and mosquitoes. In French Guiana, the diversity and distribution of Wolbachia are not well known in mosquitoes. In this study, we screened for Wolbachia natural infection in mosquitoes in French Guiana by using 16S rRNA, Wolbachia surface protein (WSP), and multi-locus sequence typing (MLST) molecular assays. A total of 29 out of 44 (65.9%) mosquito species were positive for natural Wolbachia infection according to the PCR results, and two Wolbachia strains co-infected three specimens of Mansonia titillans. Then, we analyzed the phylogenetic relationships among the Wolbachia detected. All of the tested specimens of Aedes aegypti, the major dengue vector of French Guiana, were negative. These results regarding Wolbachia strain, distribution, and prevalence in mosquitoes from French Guiana highlight Wolbachia-mosquito associations and pave the way for a future Wolbachia-based strategy for vector control in this Amazonian territory.

Barcoding of Italian mosquitoes (BITMO): generation and validation of DNA barcoding reference libraries for native and alien species of Culicidae

BACKGROUND

Mosquitoes (Culicidae), as disease vectors, represent a risk for human health worldwide. Repeated introductions of alien mosquito species and the spread of invasive species have been recorded in different countries. Traditionally, identification of mosquitoes relies on morphological observation. However, morphology-based identification is associated with a number of potential disadvantages, such as the high level of specialisation of the operator and its limited applicability to damaged samples. In these cases, species identification is achieved through molecular methods based on DNA amplification. Molecular-based taxonomy has also enabled the development of techniques for the study of environmental DNA (eDNA). Previous studies indicated the 16S mitochondrial ribosomal RNA (rRNA) gene as a promising target for this application; however, 16S rRNA sequences are available for only a limited number of mosquito species. In addition, although primers for the 16S rRNA gene were designed years ago, they are based on limited numbers of mosquito sequences. Thus, the aims of this study were to: (i) design pan-mosquito 16S rRNA gene primers; (ii) using these primers, generate a 16S rRNA gene mosquito reference library (with a focus on mosquitoes present in Italy); and (iii) compare the discriminatory power of the 16S rRNA gene with two widely used molecular markers, cytochrome c oxidase subunit 1 mitochondrial gene (COI) and internal transcribed spacer 2 (ITS2).

METHODS

A total of six mosquito genera (28 mosquito species) were included in this study: Aedes (n = 16 species), Anopheles (5 species), Coquillettidia (1 species), Culex (3 species), Culiseta (2 species) and Uranotaenia (1 species). DNA was extracted from the whole mosquito body, and more than one specimen for each species was included in the analysis. Sanger sequencing was used to generate DNA sequences that were then analysed through the Barcode of Life Data Systems (BOLD). Phylogenetic analyses were also performed.

RESULTS

Novel 16S rDNA gene, COI and ITS2 sequences were generated. The 16S rRNA gene was shown to possess sufficient informativeness for the identification of mosquito species, with a discriminatory power equivalent to that of COI.

CONCLUSIONS

This study contributes to the generation of DNA barcode libraries, focussed on Italian mosquitoes, with a significant increase in the number of 16S rRNA gene sequences. We hope that these novel sequences will provide a resource for studies on the biodiversity, monitoring and metabarcoding of mosquitoes, including eDNA-based approaches.

Molecular Markers for Analyses of Genetic Diversity within the Anastrepha fraterculus Complex with Emphasis on Argentine Populations

The South American fruit fly Anastrepha fraterculus (Wiedmann) has a vast range extending from northern Mexico, through Central America, to South America where it is an extremely polyphagous pest of wild and cultivated fruits. It is a complex of cryptic species currently composed of eight recognised morphotypes: "Mexican", "Venezuelan", "Andean", "Peruvian", "Ecuadorian", and the three Brazilian morphotypes "Brazilian-1", "Brazilian-2", and "Brazilian-3". Molecular markers that can identify the member species of the complex are crucial for the implementation of effective pest control measures, such as the sterile insect technique. The object of this study was to evaluate the use of the internal transcribed spacer 2 (ITS2) sequence for discriminating several members of the A. fraterculus cryptic species complex (Mexican, Peruvian, and Brazilian-1) and a related species, Anastrepha schultzi Blanchard. The analysis highlighted significant genetic differentiation between the evaluated morphotypes, allowed their discrimination within the A. fraterculus cryptic species complex, and provided new insights into their genetic relationships. The ITS2 marker provides a basis for the development of taxonomic keys for the discrimination of the cryptic taxa within the A. fraterculus cryptic species complex. ITS2 also represents an important marker for the poorly studied species A. schultzi.

Herbgenomics meets Papaveraceae: a promising -omics perspective on medicinal plant research

Herbal medicines were widely used in ancient and modern societies as remedies for human ailments. Notably, the Papaveraceae family includes well-known species, such as Papaver somniferum and Chelidonium majus, which possess medicinal properties due to their latex content. Latex-bearing plants are a rich source of diverse bioactive compounds, with applications ranging from narcotics to analgesics and relaxants. With the advent of high-throughput technologies and advancements in sequencing tools, an opportunity exists to bridge the knowledge gap between the genetic information of herbs and the regulatory networks underlying their medicinal activities. This emerging discipline, known as herbgenomics, combines genomic information with other -omics studies to unravel the genetic foundations, including essential gene functions and secondary metabolite biosynthesis pathways. Furthermore, exploring the genomes of various medicinal plants enables the utilization of modern genetic manipulation techniques, such as Clustered Regularly-Interspaced Short Palindromic Repeats (CRISPR/Cas9) or RNA interference. This technological revolution has facilitated systematic studies of model herbs, targeted breeding of medicinal plants, the establishment of gene banks and the adoption of synthetic biology approaches. In this article, we provide a comprehensive overview of the recent advances in genomic, transcriptomic, proteomic and metabolomic research on species within the Papaveraceae family. Additionally, it briefly explores the potential applications and key opportunities offered by the -omics perspective in the pharmaceutical industry and the agrobiotechnology field.

Advances in bioinformatic approaches to tardigrade phylogeny

The quest to discover the evolutionary relationships of organisms is an evolving, long-time topic of research. Such research gave rise to many different taxonomic databases and various definitions of systematic groups. One such group is the phylum Tardigrada. Tardigrades are an important field of study because of their biotechnological potential as well as their complex biological processes, which have the potential to answer questions about animal evolution. The evolutionary relationships within the phyla are subject to rigorous research, and new data is added to the literature constantly. For these studies, a widespread technique is the use of bioinformatic approaches in order to put forward concrete phylogenetic evidence. Bioinformatics is a field of computational biology that interprets large amounts of data in order to compute and demonstrate results. It is widely used not only for phylogeny but also for various different types of analyses and has been growing as a field since its foundation. This review discusses the different aspects, advantages, and methods of the use of bioinformatics in tardigrade phylogeny. It aims to put forward a defining picture of how the bioinformatic methods prove useful for providing phylogenetic results and elaborate on future perspectives.

Identification of non-model mammal species using the MinION DNA sequencer from Oxford Nanopore

Background

The Neotropics harbors the largest species richness of the planet; however, even in well-studied groups, there are potentially hundreds of species that lack a formal description, and likewise, many already described taxa are difficult to identify using morphology. Specifically in small mammals, complex morphological diagnoses have been facilitated by the use of molecular data, particularly from mitochondrial sequences, to obtain accurate species identifications. Obtaining mitochondrial markers implies the use of PCR and specific primers, which are largely absent for non-model organisms. Oxford Nanopore Technologies (ONT) is a new alternative for sequencing the entire mitochondrial genome without the need for specific primers. Only a limited number of studies have employed exclusively ONT long-reads to assemble mitochondrial genomes, and few studies have yet evaluated the usefulness of such reads in multiple non-model organisms.

Methods

We implemented fieldwork to collect small mammals, including rodents, bats, and marsupials, in five localities in the northern extreme of the Cordillera Central of Colombia. DNA samples were sequenced using the MinION device and Flongle flow cells. Shotgun-sequenced data was used to reconstruct the mitochondrial genome of all the samples. In parallel, using a customized computational pipeline, species-level identifications were obtained based on sequencing raw reads (Whole Genome Sequencing). ONT-based identifications were corroborated using traditional morphological characters and phylogenetic analyses.

Results

A total of 24 individuals from 18 species were collected, morphologically identified, and deposited in the biological collection of Universidad EAFIT. Our different computational pipelines were able to reconstruct mitochondrial genomes from exclusively ONT reads. We obtained three new mitochondrial genomes and eight new molecular mitochondrial sequences for six species. Our species identification pipeline was able to obtain accurate species identifications for up to 75% of the individuals in as little as 5 s. Finally, our phylogenetic analyses corroborated the identifications from our automated species identification pipeline and revealed important contributions to the knowledge of the diversity of Neotropical small mammals.

Discussion

This study was able to evaluate different pipelines to reconstruct mitochondrial genomes from non-model organisms, using exclusively ONT reads, benchmarking these protocols on a multi-species dataset. The proposed methodology can be applied by non-expert taxonomists and has the potential to be implemented in real-time, without the need to euthanize the organisms and under field conditions. Therefore, it stands as a relevant tool to help increase the available data for non-model organisms, and the rate at which researchers can characterize life specially in highly biodiverse places as the Neotropics.

A DNA barcode reference library for the Tipulidae (Insecta, Diptera) of Germany

Tipulidae, commonly known as true crane flies, represent one of the most species-rich dipteran families, boasting approximately 4,500 known species globally. Their larvae serve as vital decomposers across diverse ecosystems, prompting their frequent and close observation in biomonitoring programs. However, traditional morphological identification methods are laborious and time-consuming, underscoring the need for a comprehensive DNA barcode reference library to speed up species determination. In this study, we present the outcomes of the German Barcode of Life initiative focused on Tipulidae. Our DNA barcode library comprises 824 high-quality cytochrome c oxidase I (COI) barcodes encompassing 76 crane fly species, counting for ca. 54% of the German tipulid fauna. Our results significantly increased the number of European tipulid species available in the Barcode of Life Data System (BOLD) by 14%. Additionally, the number of barcodes from European tipulid specimens more than doubled, with an increase of 118%, bolstering the DNA resource for future identification inquiries. Employing diverse species delimitation algorithms - including the multi-rate Poisson tree processes model (mPTP), Barcode Index Number assignments (BIN), Assemble Species by Automatic Partitioning (ASAP), and the TaxCI R-script - we successfully match 76-86% of the morphologically identified species. Further validation through neighbor-joining tree topology analysis and comparison with 712 additional European tipulid barcodes yield a remarkable 89% success rate for the species identification of German tipulids based on COI barcodes. This comprehensive DNA barcode dataset not only enhances species identification accuracy but also serves as a pivotal resource for ecological and biomonitoring studies, fostering a deeper understanding of crane fly diversity and distribution across terrestrial landscapes.

Alobophora sandrae n. gen. n. sp. (Digenea: Caballerotrematidae) infecting Arapaima gigas sensu lato (Osteoglossiformes: Arapaimidae) with a revision of Caballerotrema, key to Caballerotrematidae, and updated phylogeny

We propose and describe Alobophora sandrae Cajiao-Mora & Bullard n. gen., n. sp. (Digenea: Caballerotrematidae) for specimens we collected from arapaima, Arapaima gigas sensu lato (Osteoglossiformes: Arapaimidae) in the Amazon River near Leticia, Colombia. Alobophora differs from Caballerotrema Prudhoe, 1960 by lacking head collar projections and by having clustered corner spines and a narrow head collar (4-5× wider than pharynx), whereas Caballerotrema has head collar projections, lacks clustered corner spines, and has a broad head collar (7-8× wider than pharynx). We reassign Caballerotrema annulatum (Diesing, 1850) Ostrowski de Núñez & Sattmann, 2002 to the new genus, as Alobophora annulata (Diesing, 1850) Cajiao-Mora and Bullard n. comb., and provide a supplemental description of Caballerotrema brasiliense Prudhoe, 1960 based on specimens we collected from arapaima. We also examined the holotype and a paratype of Caballerotrema piscicola (Stunkard, 1960) Kostadinova & Gibson, 2001 and concluded that C. piscicola is a junior subjective synonym of C. brasiliense. Our 28S phylogeny recovered A. sandrae sister to A. annulata, with that clade sister to a clade comprising C. brasiliense and an innominate species of Caballerotrema. Caballerotrematidae was recovered sister to Echinostomatidae. We also provide a dichotomous key to caballerotrematids based on head collar projections, corner spine arrangement, proportional pharynx and head collar breadth, testes shape and arrangement, body surface spine shape and distribution, vitellarium distribution, and abundance of prostatic cells.

Molecular identification of whales remains from the Keller Peninsula, Admiralty Bay, King George Island, Antarctica

At the beginning of the 20th century, intense whaling activity took place in the South Shetland Islands, which is represented today in the form of ruins and numerous whale bones scattered along several Antarctic beaches. Despite being exposed to a harsh environment throughout the last decades, the present manuscript tried to answer if these bone remains still have viable DNA to allow species' identification using molecular methods. Several individuals were collected from the shores of Keller Peninsula, Admiralty Bay, Antarctica, and submitted to DNA extraction, amplification and Sanger sequencing. The challenging identification of these bone fragments proved to be still feasible. Mitochondrial DNA was successfully extracted, amplified and sequenced. A database with 43 sequences including previously published and newly determined sequences were built and enabled the precise identification to species level for some of the collected samples, therefore shedding light on the whales species that inhabited the region and how their overexploitation seems to have affected modern day presence of these species within the study area.

Identifying Key Genes as Progression Indicators of Prostate Cancer with Castration Resistance Based on Dynamic Network Biomarker Algorithm and Weighted Gene Correlation Network Analysis

Background: Androgen deprivation therapy (ADT) is the mainstay of treatment for prostate cancer, yet dynamic molecular changes from hormone-sensitive to castration-resistant states in patients treated with ADT remain unclear. Methods: In this study, we combined the dynamic network biomarker (DNB) method and the weighted gene co-expression network analysis (WGCNA) to identify key genes associated with the progression to a castration-resistant state in prostate cancer via the integration of single-cell and bulk RNA sequencing data. Based on the gene expression profiles of CRPC in the GEO dataset, the DNB method was used to clarify the condition of epithelial cells and find out the most significant transition signal DNB modules and genes included. Then, we calculated gene modules associated with the clinical phenotype stage based on the WGCNA. IHC was conducted to validate the expression of the key genes in CRPC and primary PCa patients Results:Nomograms, calibration plots, and ROC curves were applied to evaluate the good prognostic accuracy of the risk prediction model. Results: By combining single-cell RNA sequence data and bulk RNA sequence data, we identified a set of DNBs, whose roles involved in androgen-associated activities indicated the signals of a prostate cancer cell transition from an androgen-dependent state to a castration-resistant state. In addition, a risk prediction model including the risk score of four key genes (SCD, NARS2, ALDH1A1, and NFXL1) and other clinical-pathological characteristics was constructed and verified to be able to reasonably predict the prognosis of patients receiving ADT. Conclusions: In summary, four key genes from DNBs were identified as potential diagnostic markers for patients treated with ADT and a risk score-based nomogram will facilitate precise prognosis prediction and individualized therapeutic interventions of CRPC.

Biodiversity of microorganisms in the Baltic Sea: the power of novel methods in the identification of marine microbes

Until recently, the data on the diversity of the entire microbial community from the Baltic Sea were relatively rare and very scarce. However, modern molecular methods have provided new insights into this field with interesting results. They can be summarized as follows. (i) Although low salinity causes a reduction in the biodiversity of multicellular species relative to the populations of the North-East Atlantic, no such reduction occurs in bacterial diversity. (ii) Among cyanobacteria, the picocyanobacterial group dominates when considering gene abundance, while filamentous cyanobacteria dominate in means of biomass. (iii) The diversity of diatoms and dinoflagellates is significantly larger than described a few decades ago; however, molecular studies on these groups are still scarce. (iv) Knowledge gaps in other protistan communities are evident. (v) Salinity is the main limiting parameter of pelagic fungal community composition, while the benthic fungal diversity is shaped by water depth, salinity, and sediment C and N availability. (vi) Bacteriophages are the predominant group of viruses, while among viruses infecting eukaryotic hosts, Phycodnaviridae are the most abundant; the Baltic Sea virome is contaminated with viruses originating from urban and/or industrial habitats. These features make the Baltic Sea microbiome specific and unique among other marine environments.

Molecular characterization of anopheline species diversity in the Andaman and Nicobar archipelago, with a particular emphasis on Anopheles barbirostris

This study investigates anopheline species diversity in the Andaman and Nicobar Islands, employing morphological and molecular methods, focusing on the D3 domain of 28S rRNA (D3) and second internal spacer (ITS2). Ten Anopheline species were identified morphologically and confirmed with molecular markers. While the D3 region demonstrated low level of inter- and intra-specific genetic distance in all the species, ITS2 revealed clear barcoding gap. Among the ten species, A. barbirostris exhibited significant diversity when compared with the sequences from other countries available in GenBank. Further analyses of additional samples of A. barbirostris were carried out using ITS2 and cytochrome oxidase I (COI) markers. Limited variations among the sequences from the islands were observed, suggesting a prevalent single molecular form. However, when compared with the GenBank sequences, our samples formed a separate cluster closely related to the A3 species. The genetic distance between our samples and the A3 cluster was 0.02 for COI but very high (0.104) for ITS2, suggesting a potentially new molecular form or species in the island region. This warrants a more comprehensive and detailed analysis of A. barbirostris in these islands at both genetic and morphometric levels. Overall, these observations added-up the new knowledge in the understanding of anopheline diversity in the Andaman and Nicobar archipelago and highlight the necessity for continuous molecular investigations to unravel complexities within mosquito population dynamics.

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

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

Syntormon Loew (Diptera, Dolichopodidae) from Inner Mongolia, China, with the description of a new species

Previously, no records of Syntormon Loew, 1857 species were known from Inner Mongolia (China). The genus is reported here from Inner Mongolia for the first time, with the description of a new species, S.sinicum sp. nov., along with two previously described species, S.dukha Hollis, 1964 and S.henanense Yang & Saigusa, 2000. Syntormonsinicum sp. nov. and S.dukha Hollis, 1964 are barcoded for the first time to support the species delimitation. A key to Syntormon species in China is provided.