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This project aims to mitigate the critical decline in bee populations, essential for crop pollination and food security. With a shortage of taxonomic specialists to identify the vast array of bee species, the project's goal is to enhance the monitoring of population changes through an automated classification system. Utilizing a dataset of bee wing images, the project aims to develop a computational pipeline to identify species based on their unique wing vein patterns. This approach not only supports bee conservation efforts but also expands our understanding of complex geometric variations in nature, offering wider applications in biological research. This poster was presented at the UCSB Data Science Capstone showcase in 2024.

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. [ABSTRACT FROM AUTHOR]

Background: Malaria is the parasitic disease with the highest morbimortality worldwide. The World Health Organization (WHO) estimates that there were approximately 249 million cases in 2022, of which 3.4% were in Angola. Diagnosis is based on parasite identification by microscopy examination, antigen detection, and/or molecular tests, such as polymerase chain reaction (PCR). This study aimed to evaluate the usefulness of real-time PCR as a diagnostic method for malaria in an endemic area (Cubal, Angola). Methods: A cross-sectional study was carried out at the Hospital Nossa Senhora da Paz in Cubal, Angola, including 200 patients who consulted for febrile syndrome between May and July 2022. From each patient, a capillary blood sample was obtained by finger prick for malaria field diagnosis [microscopy and rapid diagnostic test (RDT)] and venous blood sample for real-time PCR performed at the Hospital Universitario Vall d'Hebron in Barcelona, Spain. Any participant with a positive result from at least one of these three methods was diagnosed with malaria. Results: Of the 200 participants included, 54% were female and the median age was 7 years. Malaria was diagnosed by at least one of the three techniques (microscopy, RDT, and/or real-time PCR) in 58% of the participants, with RDT having the highest percentage of positivity (49%), followed by real-time PCR (39.5%) and microscopy (33.5%). Of the 61 discordant samples, 4 were only positive by microscopy, 13 by real-time PCR, and 26 by RDT. Plasmodium falciparum was the most frequent species detected (90.63%), followed by P. malariae (17.19%) and P. ovale (9.38%). Coinfections were detected in ten participants (15.63%): six (60%) were caused by P. falciparum and P. malariae, three (30%) by P. falciparum and P. ovale, and one (10%) triple infection with these three species. In addition, it was observed that P. falciparum and P. malariae coinfection significantly increased the parasite density of the latter. Conclusions: RDT was the technique with the highest positivity rate, followed by real-time PCR and microscopy. The results of the real-time PCR may have been underestimated due to suboptimal storage conditions during the transportation of the DNA eluates. However, real-time PCR techniques have an important role in the surveillance of circulating Plasmodium species, given the epidemiological importance of the increase in non-falciparum species in the country, and can provide an estimate of the intensity of infection. [ABSTRACT FROM AUTHOR]

• South Africa ranks third in global flowering plant barcode data. • The country has submitted more than 12,000 DNA barcode records to BOLD. • Endemic families and taxa are underrepresented, leaving significant data gaps. • Underutilised resources and funding constraints hinder data growth in the region. • Urgent need for collaboration, targeted sampling, and database harmonisation. South Africa, a global biodiversity hotspot, faces escalating threats to its rich plant diversity, including habitat loss, climate change, invasive species, and illegal harvesting. These threats are further exacerbated by the country's taxonomic impediment, which hinders both conservation and sustainable development efforts. This paper assesses the efficiency of DNA barcoding as a tool for species identification and biodiversity conservation within the South African context. While DNA barcoding offers promising applications in conservation, significant gaps and challenges persist. We provide a comprehensive overview of plant barcoding initiatives in South Africa – by querying the public data portal for plant barcoding records, 12,456 published specimen records encompassing 159 families and ca. 3,449 species were returned. These numbers highlight historical progress, database contributions, technological advancements, and taxonomic coverage. Despite South Africa contributing the third-highest number of Magnoliophyta records to the Barcode of Life Data System (BOLD), significant gaps in endemic families and geographic regions highlight the urgent need for targeted DNA barcoding initiatives and increased collaboration, as only ca. 16 % of the known flora has been barcoded. The underutilisation of BOLD and financial constraints pose significant barriers to expanding plant barcoding records. However, advancements in sequencing technologies offer cost-effective solutions. We advocate for concerted efforts to enhance DNA barcoding utilisation, harmonise databases, and prioritise sampling of underrepresented taxa to effectively preserve South Africa's diverse plant life. [ABSTRACT FROM AUTHOR]

For plant identification in school biology, many digital and analogue identification methods have been developed to make this demanding and little motivating process more student-orientated. In this experimental field study, we examine two empirically developed tools: the digital identification app "ID-Logics' and the paper-based key, generated by the online platform 'Eikes Baumschule'. In line with Self-Determination Theory (SDT), an evaluation study with 251 students was conducted to investigate the effect of both tools on students' intrinsic motivation. The results of the study were unexpected, as the different media regarding the SDT did not present themselves as projected: While both tools influence students' intrinsic motivation positively, each displays specific effects regarding enjoyment, perceived competence, and perceived autonomy. Taking these effects into account, each tool under investigation offers different advantages and disadvantages for plant identification in the field. The resulting opportunities and challenges, for plant identification, of both tools are discussed critically against the background of SDT, and future directions for research on intrinsic motivation in the context of species identification are mapped. Furthermore, this study shed light on the process of species identification and thus indicates recommendations for practical use in biology lessons. [ABSTRACT FROM AUTHOR]

The genus Amomum includes over 111 species, 6 of which are widely utilized as medicinal plants and have already undergone taxonomic revision. Due to their morphological similarities, the presence of counterfeit and substandard products remains a challenge. Accurate plant identification is, therefore, essential to address these issues. This study utilized 11 newly sequenced samples and extensive NCBI data to perform molecular identification of the six medicinal "Doukou" species. The plastomes of these species exhibited a typical quadripartite structure with a conserved gene content. However, independent variation shifts of the SC/IR boundaries existed between and within species. The comprehensive set of genetic sequences, including ITS, ITS1, ITS2, complete plastomes, matK, rbcL, psbA-trnH, and ycf1, showed varying discrimination of the six "Doukou" species based on both distance and phylogenetic tree methods. Among these, the ITS, ITS1, and complete plastome sequences demonstrated the highest identification success rate (3/6), followed by ycf1 (2/6), and then ITS2, matK, and psbA-trnH (1/6). In contrast, rbcL failed to identify any species. This research established a basis for a reliable molecular identification method for medicinal "Doukou" plants to protect wild plant resources, promote the sustainable use of medicinal plants, and restrict the exploitation of these resources. [ABSTRACT FROM AUTHOR]

Snow Lotus Seed (SLS), esteemed for its nutritional and market value, faces challenges of authentication due to the absence of appropriate testing standards and methods. This results in frequent adulteration of SLS sourced from Gleditsia sinensis (G. sinensis) with other plant seeds endosperm. Traditional chloroplast DNA barcoding methods are inadequate for species identification due to the absence of chloroplasts in G. sinensis seeds endosperm. In this study, the homology of 11 ITS genes among 6 common Gleditsia species was analyzed. Universal primers suitable for these species were designed and screened. A DNA barcoding method for distinguishing SLS species was developed using Sanger sequencing technology, leveraging existing GenBank and Barcode of Life Data System (BOLD) databases. Optimized sample pretreatment facilitated effective DNA extraction from phytopolysaccharide-rich SLS. Through testing of commercial SLS products, the species origin has been successfully identified. Additionally, a novel instance of food fraud was uncovered, where the Caesalpinia spinosa endosperm was used to counterfeit SLS for the first time. The study established that the developed DNA barcoding method is effective for authenticating SLS species. It is of great significance for combating food fraud related to SLS, ensuring food safety, and promoting the healthy development of the SLS industry. [ABSTRACT FROM AUTHOR]

This study aimed to investigate the performance and factors affecting the species classification of convolutional neural network (CNN) architecture using whole-part and earlywood-part cross-sectional datasets of six Korean Quercus species. The accuracy of species classification for each condition was analyzed using the datasets, data augmentation, and optimizers—stochastic gradient descent (SGD), adaptive moment estimation (Adam), and root mean square propagation (RMSProp)—based on a CNN architecture with three to four convolutional layers. The model trained with the augmented dataset yielded significantly superior results in terms of classification accuracy compared to the model trained with the non-augmented dataset. The augmented dataset was the only factor affecting classification accuracy in the final five epochs. In contrast, four factors in the entire epoch, such as the Adam and SGD optimizers and the earlywood-part and whole-part datasets, affected species classification. The arrangement of earlywood vessels, broad rays, and axial parenchyma was identified as a major influential factor in the CNN species classification using gradient-weighted class activation mapping (Grad-CAM) analysis. The augmented whole-part dataset with the Adam optimizer achieved the highest classification accuracy of 85.7% during the final five epochs of the test phase. [ABSTRACT FROM AUTHOR]

Wild boletus mushrooms, which are macrofungi of the phylum Basidiomycetes, are a nutritious and unique natural food that is widely enjoyed. Since boletus are consumed with problems of indistinguishable toxic and non‐toxic species and heavy metal enrichment, their species identification and traceability are crucial in ensuring quality and safety of consumption. In this study, the attenuated total reflection Fourier transform infrared (ATR‐FTIR) spectroscopy technique combined with three feature variable extraction methods, manual selection method, semi‐manual selection method, and algorithm method, were used to improve the accuracy and computational speed of the model identification, and the models were established for the identification of boletus species with an accuracy of up to 100% as well as for the identification of boletus origin with an accuracy of 86.36%. It was found that the best methods to improve the accuracy of the models were semi‐manual selection, manual selection and algorithmic selection in that order. This study can provide rapid and accurate species identification and origin traceability of wild boletus, and provide theoretical basis for the rational use of feature variable selection methods. [ABSTRACT FROM AUTHOR]

In the realm of biological image analysis, deep learning (DL) has become a core toolkit, for example for segmentation and classification. However, conventional DL methods are challenged by large biodiversity datasets characterized by unbalanced classes and hard‐to‐distinguish phenotypic differences between them. Here we present BioEncoder, a user‐friendly toolkit for metric learning, which overcomes these challenges by focussing on learning relationships between individual data points rather than on the separability of classes. BioEncoder is released as a Python package, created for ease of use and flexibility across diverse datasets. It features taxon‐agnostic data loaders, custom augmentation options, and simple hyperparameter adjustments through text‐based configuration files. The toolkit's significance lies in its potential to unlock new research avenues in biological image analysis while democratizing access to advanced deep metric learning techniques. BioEncoder focuses on the urgent need for toolkits bridging the gap between complex DL pipelines and practical applications in biological research. [ABSTRACT FROM AUTHOR]

Simple Summary: In forensic entomology, insects are used to estimate the time since death and to answer other investigative questions, such as determining if the body was moved postmortem or identifying the season of death. In funerary archeoentomology, insects provide information related to the season of death, body transfer, and funerary practices. To obtain this information, the correct identification of specimens collected from the scene is fundamental. In old cases and archeological contexts, the majority of entomological evidence samples found are fly puparia, barrel-like structures formed from the third-instar larval cuticle where metamorphosis takes place. Despite recent publications of identification keys for certain fly larvae and adults, there is still a lack of tools for puparium identification. This problem is exacerbated by the scarcity of diagnostic features present on the puparia. This paper critically reviews the techniques available for puparium identification in addition to traditional morphological analysis. It describes DNA-based approaches and chemical analyses of cuticular lipids and hydrocarbons, highlighting the importance of using non-invasive methods to guarantee the repeatability of the analysis—a key element in forensic science—or to preserve precious and unique specimens from museum collections. Diptera identification is fundamental in forensic entomology as well as in funerary archeoentomology, where the challenge is exacerbated by the presence of immature stages such as larvae and puparia. In these two developmental stages, specimens possess a very limited number of diagnostic features, and for puparia, there is also a lack of identification tools such as descriptions and identification keys. Morphological analysis, DNA-based techniques, and cuticular chemical analyses all show good potential for species identification; however, they also have some limitations. DNA-based identification is primarily hindered by the incompleteness of genetic databases and the presence of PCR inhibitors often co-extracted from the puparial cuticle. Chemical analysis of the cuticle is showing promising results, but this approach is also limited by the insufficient profile database and requires specific, expensive equipment, as well as trained personnel. Additionally, to ensure the repeatability of the analysis—a critical aspect in forensic investigations—and to preserve precious and unique specimens from museum collections, non-invasive protocols and techniques must be prioritized for species identification. [ABSTRACT FROM AUTHOR]

The inconsistency between traditional morphological taxonomy and molecular phylogenetic data is a major issue that puzzles the study of fish classification and evolution. Although mitochondrial genes are commonly used in phylogenetic analyses to compare fish species, the mitochondrial evolution and diversity of Schistura are still not well understood. To better understand the evolution of Schistura, we sequenced the mitochondrial genome of Schistura fasciolata and compared it with other species of Schistura. A 16,588 bp circular mitochondrial genome of S. fasciolata was obtained and it contains 13 protein-coding, 22 transfer RNA, and two ribosomal RNA genes, and a non-coding control region. The gene arrangement in the mitochondrial genomes of all Schistura species was consistent. However, we also found that S. fasciolata was not monophyletic. Although mitochondrial genes can be effectively used for Schistura species identification, they may not be suitable for inferring the evolutionary process of Schistura species. These results provide support for the use of mitochondrial genes in identifying Schistura species, and also serve as a warning against mistakenly using them to evaluate the evolution process of Schistura species. [ABSTRACT FROM AUTHOR]

Terrestrial orchids are a group of genetically understudied, yet culturally and economically important plants. The Orchidinae tribe contains many species that produce edible tubers that are used for the production of traditional delicacies collectively called 'salep'. Overexploitation of wild orchids in the Eastern Mediterranean and Western Asia threatens to drive many of these species to extinction, but cost‐effective tools for monitoring their trade are currently lacking. Here we present a custom bait kit for target enrichment and sequencing of 205 novel genetic markers that are tailored to phylogenomic applications in Orchidinae s.l. A subset of 31 markers capture genes putatively involved in the production of glucomannan, a water‐soluble polysaccharide that gives salep its distinctive properties. We tested the kit on 73 taxa native to the area, demonstrating universally high locus recovery irrespective of species identity, that exceeds the total sequence length obtained with alternative kits currently available. Phylogenetic inference with concatenation and coalescent approaches was robust and showed high levels of support for most clades, including some which were previously unresolved. Resolution for hybridizing and recently radiated lineages remains difficult, but could be further improved by analysing multiple haplotypes and the non‐exonic sequences captured by our kit, with the promise to shed new light on the evolution of enigmatic taxa with a complex speciation history. Offering a step‐up from traditional barcoding and universal markers, the genome‐wide custom loci targeted by Orchidinae‐205 are a valuable new resource to study the evolution, systematics and trade of terrestrial orchids. [ABSTRACT FROM AUTHOR]

We developed phyloBARCODER (https://github.com/jun-inoue/phyloBARCODER), a new web tool that can identify short DNA sequences to the species level using metabarcoding. phyloBARCODER estimates phylogenetic trees based on the uploaded anonymous DNA sequences and reference sequences from databases. Without such phylogenetic contexts, alternative, similarity-based methods independently identify species names and anonymous sequences of the same group by pairwise comparisons between queries and database sequences, with the caveat that they must match exactly or very closely. By putting metabarcoding sequences into a phylogenetic context, phyloBARCODER accurately identifies (i) species or classification of query sequences and (ii) anonymous sequences associated with the same species or even with populations of query sequences, with clear and accurate explanations. Version 1 of phyloBARCODER stores a database comprising all eukaryotic mitochondrial gene sequences. Moreover, by uploading their own databases, phyloBARCODER users can conduct species identification specialized for sequences obtained from a local geographic region or those of nonmitochondrial genes, e.g. ITS or rbcL. [ABSTRACT FROM AUTHOR]

The Croaking Gourami Trichopsis vittata (Cuvier, 1831) is a native fish to southeastern Asia and Sundaland, with introduction reports from the USA, Philippines, and many other countries including India. In India, this species was first reported from Chembarampakkam Lake situated in Chennai during the year 2015. This study reports the presence of this fish for the first time in the Magra Beel, a wetland in the district of Nadia, West Bengal, in 2021, 2022, 2023. The laboratory evaluated the fish samples taken from the marsh to determine their fin ray counts and morphometric data. The results identified the species as T. vittata and supported previous research. [ABSTRACT FROM AUTHOR]

Melon (Cucumis melo L.) is one of the most extensively grown horticulture crops of the world. Based on the morphological characters, melon was formerly divided into two subspecies, Cucumis melo ssp. melo and C. melo ssp. agrestis. However, the present methods are still inadequate to distinguish between them. The phylogenetic analysis based on chloroplast genome sequences could provide essential evidence for the classification of melon varieties. We sequenced the chloroplast genomes of nine different melon varieties by the Illumina Hiseq and performed bioinformatic analyses including repeat element analysis, genome comparison and phylogenetic analysis. The results showed that the melon chloroplast genome has a typical quadripartite structure that was conserved across the analyzed sequences. Its length ranges between 155, 558 and 156, 569 bp, with a total GC content varying from 36.7% to 37%. We found 127-132 genes in melon chloroplast genomes, including 85-87 protein-coding regions, 34-37 tRNA and 6-8 rRNA genes. The molecular structure, gene order, content, codon usage, long repeats, and simple sequence repeats (SSRs) were mostly conserved among the nine sequenced genomes. Phylogenetic analysis showed that the chloroplast genome could clearly distinguish between C. melo ssp. melo and C. melo ssp. agrestis. This study not only provides valuable knowledge on melon chloroplasts, but also offers a theoretical basis and technical support for the genetic breeding of melons. [ABSTRACT FROM AUTHOR]

Despite the critical role of mitochondrial genomes (mitogenomes) in species identification and evolutionary studies in the genus Parupeneus, current resources are inadequate, given the species richness. Although previous studies have suggested a complex evolutionary history, the detailed mitogenomic variations and their implications remain largely unexplored. Therefore, we sequenced and assembled the mitogenomes of P. barberinoides, P. barberinus, P. biaculeatus, P. crassilabris, P. cyclostomus, P. heptacanthus, P. multifasciatus, and P. chrysopleuron, to enrich the molecular data and provide novel insights into the genetic diversity, evolutionary dynamics and phylogenetics of the family Mullidae. Our analysis revealed a novel gene rearrangement in P. chrysopleuron, Cytb-T-P-CR-Q-I-F-12S-V-16S-ND1-M-ND2, which differed from the conventional sequence of Cytb-TP-CR-F-12S-V-16S-ND1-I-Q-M-ND2 observed in other species. In the novel rearrangement, four non-coding regions are inserted between ND1 and M, Q and I, I and yM (tRNA-Met pseudogene), yM and F. We assume that two tandem duplication/random loss events occur in the CR and IQM, making the entire sequence longer than that in other Parupeneus species. The phylogenetic results indicated that Mullidae formed a sister group relationship with the family Dactylopteridae, contradicting previous studies that identified a sister group relationship between Mullidae and Callionymoidei. The genera Parupeneus and Mullus formed a sister group, and discrepancies were found in the topological structure of the interspecies relationships within the genus Parupeneus compared with those reported by previous studies. Through combined phylogenetic and mitochondrial structural analysis, we found that phylogenetic topology is closely related to mitochondrial structural abnormalities. This study not only expands the mitogenomic dataset available for Mullidae but also underscores the importance of mitochondrial DNA studies in resolving taxonomic ambiguities and understanding the evolutionary history of marine fishes. Our study contributes to the ongoing research on marine fish taxonomy, mitogenomics, and evolutionary biology by providing new insights into the genetic diversity of marine ecosystems. [ABSTRACT FROM AUTHOR]

DNA barcoding is commonly used for species identification. Despite this, there has not been a comprehensive assessment of the utility of DNA barcoding in crayfishes (Decapoda: Astacidea). Here we examined the extent to which local barcoding gaps (used for species identification) and global barcoding gaps (used for species discovery) exist among crayfishes, and whether global gaps met a previously suggested 10× threshold (mean interspecific difference being 10× larger than mean intra specific difference). We examined barcoding gaps using publicly available mitochondrial COI sequence data from the National Center for Biotechnology Information's nucleotide database. We created two versions of the COI datasets used for downstream analyses: one focused on the number of unique haplotypes (NH) per species, and another that focused on total number of sequences (NS; i.e., including redundant haplotypes) per species. A total of 81 species were included, with 58 species and five genera from the family Cambaridae and 23 species from three genera from the family Parastacidae. Local barcoding gaps were present in only 30 species (20 Cambaridae and 10 Parastacidae species). We detected global barcoding gaps in only four genera (Cambarus, Cherax, Euastacus, and Tenuibranchiurus), which were all below (4.2× to 5.2×) the previously suggested 10× threshold. We propose that a ~5× threshold would be a more appropriate working hypothesis for species discovery. While the NH and NS datasets yielded largely similar results, there were some discrepant inferences. To understand why some species lacked a local barcoding gap, we performed species delimitation analyses for each genus using the NH dataset. These results suggest that current taxonomy in crayfishes may be inadequate for the majority of examined species, and that even species with local barcoding gaps present may be in need of taxonomic revisions. Currently, the utility of DNA barcoding for species identification and discovery in crayfish is quite limited, and caution should be exercised when mitochondrial‐based approaches are used in place of taxonomic expertise. Assessment of the evidence for local and global barcoding gaps is important for understanding the reliability of molecular species identification and discovery, but outcomes are dependent on the current state of taxonomy. As this improves (e.g., via resolving species complexes, possibly elevating some subspecies to the species‐level status, and redressing specimen misidentifications in natural history and other collections), so too will the utility of DNA barcoding. [ABSTRACT FROM AUTHOR]

Aims Urinary tract infections are the most common hospital-acquired infection, 80% of which are associated with catheterization. Diagnostic methods may influence the reported identities of these pathogens, and phenotypic testing under laboratory conditions may not reflect infection phenotypes. This study aimed to evaluate the efficacy of diagnostic methods and whether medium composition alters phenotypes by characterizing catheter-associated urinary tract infection isolates from a UK hospital. Methods and results We compared five bacterial identification methods, including biochemical testing, matrix-assisted laser desorption/ionization biotyping, and genome sequencing, finding differences in genus- or species-level identifications. Antibiotic susceptibility comparisons between phenotypic assays and genomic predictions showed high agreement only in multidrug-resistant strains. To determine whether growth rate and biofilm formation were affected by medium composition, strains were grown in both planktonic and biofilm states. Low planktonic growth and significant biofilm formation were observed in artificial urine compared to rich laboratory media, underscoring the importance of assay design. Conclusions This study highlights the risks of relying on a single diagnostic method for species identification, advocating for whole-genome sequencing for accuracy. It emphasizes the continued importance of phenotypic methods in understanding antibiotic resistance in clinical settings and the need for characterization conditions that mirror those encountered by pathogens in the body. [ABSTRACT FROM AUTHOR]

Meretrix, a popular marine bivalve, features several species with significant ecological and commercial value, distributed in various marine habitats worldwide. Despite their importance, accurate global population estimates of these species are hindered by inadequate classification frameworks that often rely on external shell characteristics, which are susceptible to environmental influences. This limitation underscores the necessity for comprehensive research into the physiological and molecular attributes of these species for accurate identification. This study focused on identifying the local Meretrix species from Tarakan Island by analyzing their COI nucleotide sequences and comparing them with reference sequences in the BOLD and GenBank databases. The results demonstrate that the 14 specimens obtained with diverse morphological variations were found only within two major groups: Meretrix meretrix and Meretrix lusoria. These findings validate the efficacy of DNA barcoding as a tool for classifying marine bivalves, offering a robust framework for identifying unknown species, particularly in the Asian marine ecosystems. The study's approach and findings have broader implications for enhancing global marine biodiversity research and conservation strategies. [ABSTRACT FROM AUTHOR]

Mitragyna speciosa, commonly known as kratom, is a narcotic plant that is used for its unique mood‐enhancing and pain‐relieving effects. It is marketed throughout the United States as a 'legal high' and has gained popularity as an alternative to opioids. However, kratom's increasing involvement in accidental overdoses, especially among polydrug users, has prompted warnings from the Drug Enforcement Agency (DEA) and the Food and Drug Administration (FDA). Despite these warnings, kratom remains legal federally, although it is banned in six states. This legal disparity complicates monitoring and enforcement efforts in states where kratom is illegal. Common forensic techniques using morphology or chemical analysis are beneficial in some instances but are not useful in source attribution because most seized kratom is powdered and the alkaloid content of samples can vary within products, making sourcing unreliable. This study focused on developing a DNA barcoding method to access sequence variation in commercial kratom products. It evaluated the utility of one nuclear barcode region (ITS) and three chloroplast barcode regions (matK, rbcL, and trnH‐psbA) in assessing sequence variation across commercially available kratom products. Novel polymorphisms were discovered, and the ITS region showed the greatest variation between samples. Among the 15 kratom products tested, only two haplotypes were identified across the four barcoding regions. The findings highlight the potential of DNA barcoding as a forensic tool in the traceability and enforcement against illegal kratom distribution. Nonetheless, the limited haplotypic diversity points to a need for further development and expansion of the M. speciosa DNA sequence database. [ABSTRACT FROM AUTHOR]

Baijiu is an ancient, distilled spirit with a complicated brewing process, unique taste, and rich trace components. These trace components play a decisive role in the aroma, taste, and espe‑ cially the quality of baijiu. In this paper, the redox reaction between the Fenton reagent and four reducing agents, including o‑phenylenediamine (OPD), p‑phenylenediamine (PPD), 4‑aminophenol (PAP), and 2‑aminophenol (OAP), was adopted to construct a four‑channel visual sensor array for the rapid detection of nine kinds of common organic acids in baijiu and the identification of baijiu and its adulteration. By exploiting the color‑changing fingerprint response brought by organic acids, each organic acid could be analyzed accurately when combined with an optimized variable‑weighted least‑squares support vector machine based on a particle swarm optimization (PSO‑VWLS‑SVM) model. What is more, this novel sensor also could achieve accurate semi‑quantitative analysis of the mixed organic acid samples via partial least squares discriminant analysis (PLSDA). Most impor‑ tantly, the sensor array could be further used for the identification of baijiu with different species through the PLSDA model and the adulteration assessment with the one‑class partial least squares (OCPLS) model simultaneously. [ABSTRACT FROM AUTHOR]

The herpetofauna diversity of Pakistan is underestimated due to the country's lack of molecularbased identification. Field surveys were conducted from August 2018 through July 2022 to collect as many as possible specimens from Punjab, Pakistan. A total of 21 species were collected and initially identified by morphological characteristics. The three gene fragments in four amphibian species and seven reptile species were successfully amplified and sequenced. A total of 18 DNA sequences of 11 species representing nine genera and five families were deposited in GenBank, and accession numbers were obtained. Furthermore, phylogenetic analysis was performed through the Neighbor-joining method using 100 bootstrap pseudo-replicates in MEGA X. Closely related toad species, namely Duttaphrynus melanostictus and Duttaphrynus stomatitis, were clearly separated in the tree inferred from Cytb gene sequences. Similarly, conspecific sequences were analyzed for multiple individuals of Platyceps rhodorachis clustered together in the tree inferred from COI gene sequences. In our findings, 16S rRNA appears to be more reliable in identifying amphibian species, while COI has a better success rate in reptile species identification. In our recommendations, molecular-based identification of herpetofauna is necessary nationwide to document any new subspecies. [ABSTRACT FROM AUTHOR]

Abstract Background Malaria is the parasitic disease with the highest morbimortality worldwide. The World Health Organization (WHO) estimates that there were approximately 249 million cases in 2022, of which 3.4% were in Angola. Diagnosis is based on parasite identification by microscopy examination, antigen detection, and/or molecular tests, such as polymerase chain reaction (PCR). This study aimed to evaluate the usefulness of real-time PCR as a diagnostic method for malaria in an endemic area (Cubal, Angola). Methods A cross-sectional study was carried out at the Hospital Nossa Senhora da Paz in Cubal, Angola, including 200 patients who consulted for febrile syndrome between May and July 2022. From each patient, a capillary blood sample was obtained by finger prick for malaria field diagnosis [microscopy and rapid diagnostic test (RDT)] and venous blood sample for real-time PCR performed at the Hospital Universitario Vall d’Hebron in Barcelona, Spain. Any participant with a positive result from at least one of these three methods was diagnosed with malaria. Results Of the 200 participants included, 54% were female and the median age was 7 years. Malaria was diagnosed by at least one of the three techniques (microscopy, RDT, and/or real-time PCR) in 58% of the participants, with RDT having the highest percentage of positivity (49%), followed by real-time PCR (39.5%) and microscopy (33.5%). Of the 61 discordant samples, 4 were only positive by microscopy, 13 by real-time PCR, and 26 by RDT. Plasmodium falciparum was the most frequent species detected (90.63%), followed by P. malariae (17.19%) and P. ovale (9.38%). Coinfections were detected in ten participants (15.63%): six (60%) were caused by P. falciparum and P. malariae, three (30%) by P. falciparum and P. ovale, and one (10%) triple infection with these three species. In addition, it was observed that P. falciparum and P. malariae coinfection significantly increased the parasite density of the latter. Conclusions RDT was the technique with the highest positivity rate, followed by real-time PCR and microscopy. The results of the real-time PCR may have been underestimated due to suboptimal storage conditions during the transportation of the DNA eluates. However, real-time PCR techniques have an important role in the surveillance of circulating Plasmodium species, given the epidemiological importance of the increase in non-falciparum species in the country, and can provide an estimate of the intensity of infection. Graphical abstract

Spread of the Anopheles stephensi mosquito, an invasive malaria vector, threatens to put an additional 126 million persons per year in Africa at risk for malaria. To accelerate the early detection and rapid response to this mosquito species, confirming its presence and geographic extent is critical. However, existing molecular species assays require specialized laboratory equipment, interpretation, and sequencing confirmation. We developed and optimized a colorimetric rapid loop-mediated isothermal amplification assay for molecular An. stephensi species identification. The assay requires only a heat source and reagents and can be used with or without DNA extraction, resulting in positive color change in 30–35 minutes. We validated the assay against existing PCR techniques and found 100% specificity and analytical sensitivity down to 0.0003 ng of genomic DNA. The assay can successfully amplify single mosquito legs. Initial testing on samples from Marsabit, Kenya, illustrate its potential as an early vector detection and malaria mitigation tool.

Abstract This study aimed to investigate the performance and factors affecting the species classification of convolutional neural network (CNN) architecture using whole-part and earlywood-part cross-sectional datasets of six Korean Quercus species. The accuracy of species classification for each condition was analyzed using the datasets, data augmentation, and optimizers—stochastic gradient descent (SGD), adaptive moment estimation (Adam), and root mean square propagation (RMSProp)—based on a CNN architecture with three to four convolutional layers. The model trained with the augmented dataset yielded significantly superior results in terms of classification accuracy compared to the model trained with the non-augmented dataset. The augmented dataset was the only factor affecting classification accuracy in the final five epochs. In contrast, four factors in the entire epoch, such as the Adam and SGD optimizers and the earlywood-part and whole-part datasets, affected species classification. The arrangement of earlywood vessels, broad rays, and axial parenchyma was identified as a major influential factor in the CNN species classification using gradient-weighted class activation mapping (Grad-CAM) analysis. The augmented whole-part dataset with the Adam optimizer achieved the highest classification accuracy of 85.7% during the final five epochs of the test phase.

In order to understand the types, biological characteristics, and metabolites types of pathogenic fungi in carambola, the typical diseased parts of carambola fruit were collected for fungal isolation by tissue isolation methods. The fungi were identified by morphological and molecular identification methods based on ITS sequencing analysis. The biological characteristics of pathogenic fungi were explored, and metabolites were isolated and purified using liquid chromatography. Their structures were established on the basis of 1H NMR and 13C NMR. The results were as follows: The four strains were identified as Fusarium equiseti, Neopestalotiopsis sp., Schizophyllum commune and Cladosporium cladosporioides. All four strains could cause disease in carambola fruit. The fermentation products of Fusarium equiseti were chemically investigated, leading to the discovery of four compounds, 3,7,9-trihydroxy-1-methyl-6H-dibenzo[b,d]pyran-6-on, 1,4,7-trihydroxy-3,9-dimethoxy-6H-benzo[c]chromen-6-one, lecanoric acid and 7-hydroxy-4-methyl-1(3H)-isobenzofuranone. The results of biological characteristics indicated that the optimal growth temperature for the four pathogenic fungi was 25~28 ℃, and they could all grow within the pH range of 4~10.

Abstract [Objective] Most species of Phoebe are similar in morphology and the boundaries among species are blurring, making the identification and recognition of species difficult, particularly in the period without flowers and fruits. Micromorphological characteristics of leaves are valuable for the interspecific identification of plants, but studies on Phoebe in this aspect are still scarce. [Methods] In this study, authors observed leaf morphology and micromorphology of eight species and one variant of Phoebe in Hubei Province using stereo microscope and light microscope. For all species, authors measured and analyzed both the quality and quantity properties of stomata and trichomes. The purpose was to provide the basis for the identification and classification of Phoebe. [Results] Four types of leaf shapes were characterized, including large, medium, small, and irregular leaves of Phoebe plants. Trichomes were grouped into thin pubescent, thick pubescent, villous, and mixed pubescent and villous (villous trichomes are mainly found on leaf veins). The trichoid density of P . hunanensis (200 mm-2) differed significantly from P . bournei, P . chekiangensis, and P . sheareri (under 100 mm-2). Shapes of epidermis cells were polygon or irregular, and the anticlinal wall in epidermis cells was classified into straight-curved, sinuolate or undulated. The shape of stomata was wide oval or nearly round. Density of stomatal apparatus was the highest in P . sheareri and the lowest in P . chinensis and P . hunanensis (less than 500/mm2). In addition, there was a significant negative correlation between density and aspect ratio of stoma, as well as density and length of trichome. [Conclusion] The combination of morphological and micromorphological characteristics of leaves not only provided basis for identification and differentiation of the nine species but also provided references for interspecific identification of Phoebe.

The taxonomic status of × Bolboschoenoplectus mariqueter (Tang & F. T. Wang) Tatanov is still up for debate. To clarify this status and explore its genetic relationship with closely related species, the candidate DNA barcode sequences of one nuclear gene (ITS) and five chloroplast genes (matK, ndhF, rbcL, trnL and trnL-trnF) were used for PCR amplification and sequencing of 21 individuals from four species, including × Bolboschoenoplectus mariqueter and its related species. The basic local alignment search tool was then applied to evaluate the identification efficiency of the screened barcode sequences and sequence combinations. Finally, species identification analyses were performed by constructing a phylogenetic tree using the Bayesian inference method. The results were as follows: (1) The ITS + matK sequence combination showed the highest species-resolving degree of 71.4%, which could achieve interspecific differentiation and identification of × Bolboschoenoplectus mariqueter and its closely related species. (2) According to the phylogenetic tree based on ITS + matK sequence combination, samples of the same species showed better aggregation and were mostly monophyletic, with × Bolboschoenoplectus mariqueter clustered together with all Bolboschoenus (Asch.) Palla individuals, rather than Schoenoplectus (Rchb.) Palla species. All × Bolboschoenoplectus mariqueter and Bolboschoenus maritimus (Linnaeus) Palla samples formed a monophyletic clade. In conclusion, ITS + matK sequence combination appears to be the best barcode sequence for interspecific identification of × Bolboschoenoplectus mariqueter and its related species. Furthermore, × Bolboschoenoplectus mariqueter could be a synonym of Bolboschoenus maritimus rather than a natural hybrid. This study establishes a theoretical foundation for the taxonomic research on × Bolboschoenoplectus mariqueter and its closely related species.

Abstract Background The genus Caragana encompasses multiple plant species that possess medicinal and ecological value. However, some species of Caragana are quite similar in morphology, so identifying species in this genus based on their morphological characteristics is considerably complex. In our research, illumina paired-end sequencing was employed to investigate the genetic organization and structure of Caragana tibetica and Caragana turkestanica, including the previously published chloroplast genome sequence of 7 Caragana plants. Results The lengths of C. tibetica and C. turkestanica chloroplast genomes were 128,433 bp and 129,453 bp, respectively. The absence of inverted repeat sequences in these two species categorizes them under the inverted repeat loss clade (IRLC). They encode 110 and 111 genes (4 /4 rRNA genes, 30 /31tRNA genes, and 76 /76 protein-coding genes), respectively. Comparison of the chloroplast genomes of C. tibetica and C. turkestanica with 7 other Caragana species revealed a high overall sequence similarity. However, some divergence was observed between certain intergenic regions (matK-rbcL, psbD-psbM, atpA-psbI, and etc.). Nucleotide diversity (π) analysis revealed the detection of five highly likely variable regions, namely rps2-atpI, accD-psaI-ycf4, cemA-petA, psbN-psbH and rpoA-rps11. Phylogenetic analysis revealed that C. tibetica’s sister species is Caragana jubata, whereas C. turkestanica’s closest relative is Caragana arborescens. Conclusions The present study provides worthwhile information about the chloroplast genomes of C. tibetica and C. turkestanica, which aids in the identification and classification of Caragana species.

Identification of Helicotylenchus species is very challenging due to phenotypic plasticity and existence of cryptic species complexes. Recently, the use of rDNA barcodes has proven to be useful for identification of Helicotylenchus. Molecular markers are a quick diagnostic tool and are crucial for discriminating related species and resolving cryptic species complexes within this speciose genus. However, DNA barcoding is not an error-free approach. The public databases appear to be marred by incorrect sequences, arising from sequencing errors, mislabeling, and misidentifications. Herein, we provide a comprehensive analysis of the newly obtained, and published DNA sequences of Helicotylenchus, revealing the potential faults in the available DNA barcodes. A total of 97 sequences (25 nearly full-length 18S-rRNA, 12 partial 28S-rRNA, 16 partial internal transcribed spacer [ITS]-rRNA, and 44 partial cytochrome c oxidase subunit I [COI] gene sequences) were newly obtained in the present study. Phylogenetic relationships between species are given as inferred from the analyses of 103 sequences of 18S-rRNA, 469 sequences of 28S-rRNA, 183 sequences of ITS-rRNA, and 63 sequences of COI. Remarks on suggested corrections of published accessions in GenBank database are given. Additionally, COI gene sequences of H. dihystera, H. asiaticus and the contentious H. microlobus are provided herein for the first time. Similar to rDNA gene analyses, the COI sequences support the genetic distinctness and validity of H. microlobus. DNA barcodes from type material are needed for resolving the taxonomic status of the unresolved taxonomic groups within the genus.

Abstract Background Rapid identification and classification of bats are critical for practical applications. However, species identification of bats is a typically detrimental and time-consuming manual task that depends on taxonomists and well-trained experts. Deep Convolutional Neural Networks (DCNNs) provide a practical approach for the extraction of the visual features and classification of objects, with potential application for bat classification. Results In this study, we investigated the capability of deep learning models to classify 7 horseshoe bat taxa (CHIROPTERA: Rhinolophus) from Southern China. We constructed an image dataset of 879 front, oblique, and lateral targeted facial images of live individuals collected during surveys between 2012 and 2021. All images were taken using a standard photograph protocol and setting aimed at enhancing the effectiveness of the DCNNs classification. The results demonstrated that our customized VGG16-CBAM model achieved up to 92.15% classification accuracy with better performance than other mainstream models. Furthermore, the Grad-CAM visualization reveals that the model pays more attention to the taxonomic key regions in the decision-making process, and these regions are often preferred by bat taxonomists for the classification of horseshoe bats, corroborating the validity of our methods. Conclusion Our finding will inspire further research on image-based automatic classification of chiropteran species for early detection and potential application in taxonomy.

Mushroom poisoning contributes significantly to global foodborne diseases and related fatalities. Amanita mushrooms frequently cause such poisonings; however, identifying these toxic species is challenging due to the unavailability of fresh and intact samples. It is often necessary to analyze residues, vomitus, or stomach extracts to obtain DNA sequences for the identification of species responsible for causing food poisoning. This usually proves challenging to obtain usable DNA sequences that can be analyzed using conventional molecular biology techniques. Therefore, this study aimed to develop a DNA mini-barcoding method for the identification of Amanita species. Following the evaluation and optimization of universal primers for DNA mini-barcoding in Amanita mushrooms, we found that the internal transcribed spacer (ITS) gene sequence primer ITS-a was the most suitable DNA barcode primer for identifying Amanita species. Forty-three Amanita samples were subsequently amplified and sequenced. The sequences obtained were analyzed for intra- and inter-species genetic distances, and a phylogenetic tree was constructed. The findings indicated that the designed primers had strong universality among the Amanita samples and could accurately identify the target gene fragment with a length of 290 bp. Notably, the DNA mini-barcode accurately identified the 43 Amanita samples, demonstrating high consistency with the conventional DNA barcode. Furthermore, it effectively identified DNA from digested samples. In summary, this DNA mini-barcode is a promising tool for detecting accidental ingestion of toxic Amanita mushrooms. It may be used as an optimal barcode for species identification and traceability in events of Amanita-induced mushroom poisoning. Key points: • Development of a DNA mini-barcoding method for Amanita species identification without fresh samples. • The ITS-a primer set was optimized for robust universality in Amanita samples. • The mini-barcode is suitable for screening toxic mushroom species in mushroom poisoning cases. [ABSTRACT FROM AUTHOR]

The article discusses a scientific study that misidentified a species of hydrothermal vent barnacle, which has implications for the interpretation of the data. The study compared the genetic makeup of two barnacle species and concluded that one had adapted to the deep-sea environment. However, it was later discovered that the barnacle used in the study was actually a different species. The article also mentions the diversity patterns of hydrothermal vent barnacles in the Pacific and Indian Oceans, supporting a hypothesis about their dispersal. The authors stress the importance of correctly identifying species in scientific research. [Extracted from the article]

Sheep and goat may become carriers of some zoonotic diseases. They are important livestock and experimental model animals for human beings. The fast and accurate identification of genetic materials originating from sheep and goat can prevent and inhibit the spread of some zoonotic diseases, monitor market product quality, and maintain the stability of animal husbandry and food industries. This study proposed a methodology for identifying sheep and goat common specific sites from a genome-wide perspective. A total of 150 specific sites were selected from three data sources, including the coding sequences of single copy genes from nine species (sheep, goat, cow, pig, dog, horse, human, mouse, and chicken), the dbSNPs for these species, and human 100-way alignment data. These 150 sites exhibited low intraspecific heterogeneity in the resequencing data of 1450 samples from five species (sheep, goat, cow, pig, and chicken) and high interspecific divergence in the human 100-way alignment data after quality control. The results were proven to be reliable at the data level. Using the process proposed in this study, specific sites of other species can be screened, and genome-level species identification can be performed using the screened sites. [ABSTRACT FROM AUTHOR]

The present study provides the morphotaxonomic-based identification of the world species of the subgenus Oligonychus (Oligonychus) Berlese. In this lieu, five diagnostic keys were erected to identify Oligonychus (O.) species belonging to five subgroups; smithi, peruvianus, subnudus, aceris, and coffeae. In addition, taxonomic notes on some Oligonychus (O.) species, either briefly described or closely related, were provided, and intraspecific variations were highlighted. [ABSTRACT FROM AUTHOR]

This electron microscope study investigated the micromorphological characteristics of the leaf epidermis of 5 species (10 populations) of Ribes (Grossulariaceae) in Iran: R. biebersteinii, R. uva‐crispa, R. orientale, R. aureum, and R. khorasanicum. Samples were collected and identified, and the similarities between the species were evaluated using information from micromorphological traits of leaf epidermis and multivariate analysis (cluster analysis and principal component analysis). The traits useful for discriminating the species were presence or absence of hairs and glandular trichomes, presence or absence of granular with verrucae on hair surface, position of hairs on epidermal surface, hair location on the leaf (lamina, leaf margin, midrib), stomata shape, wax distribution on stomata, prominence and shape of anticlinal walls and outer periclinal layer, and epicuticular wax sculpturing. An identification key based on these leaf micromorphological characters is provided for Ribes species in Iran. The multivariate analysis of micromorphological traits was efficient for inter‐ and intra‐specific delimitation. The present findings correspond to a large extent with existing classifications. [ABSTRACT FROM AUTHOR]

The Cosmonaut Sea is one of the least accessed regions in the Southern Ocean, and our knowledge about the fish biodiversity in the region is sparse. In this study, we provided a description of demersal fish diversity in the Cosmonaut Sea by analysing cytochrome oxidase I (COI) barcodes of 98 fish samples that were hauled by trawling during the 37th and 38th Chinese National Antarctic Research Expedition (CHINARE) cruises. Twenty-four species representing 19 genera and 11 families, namely, Artedidraconidae, Bathydraconidae, Bathylagidae, Channichthyidae, Liparidae, Macrouridae, Muraenolepididae, Myctophidae, Nototheniidae, Paralepididae and Zoarcidae, were discriminated and identified, which were largely identical to local fish occurrence records and the general pattern of demersal fish communities at high Antarctic shelf areas. The validity of a barcoding gap failed to be detected and confirmed across all species due to the indicative signals of two potential cryptic species. Nevertheless, DNA barcoding still demonstrated to be a very efficient and sound method for the discrimination and classification of Antarctic fishes. In the future, various sampling strategies that cover all geographic sections and depth strata of the Cosmonaut Sea are encouraged to enhance our understanding of local fish communities, within which DNA barcoding can play an important role in either molecular taxonomy or the establishment of a dedicated local reference database for eDNA metabarcoding analyses. [ABSTRACT FROM AUTHOR]

Here, we characterise the standard “Folmer region” of the mitochondrial cytochrome c oxidase subunit 1 (CO1) marker and a fragment of nuclear 28S marker in four species of the Jaera albifrons complex. Jaera albifrons (Leach, 1814), Jaera ischiosetosa Forsman, 1949, Jaera praehirsuta Forsman, 1949, and Jaera forsmani Bocquet, 1950 were collected from localities on the Norwegian coast and identified with morphological characters. We compared DNA sequences with sequences available in GenBank and BOLDsystems and calculated haplotype networks and interspecific versus intraspecific genetic distances. These analyses revealed low interspecific genetic distance (CO1 0.00–1.57%, 28S 0.00–0.39%) and extensive haplotype sharing between J. albifrons group species and specimens from both sides of the North Atlantic for both CO1 and 28S. Genetic distances between J. albifrons group species and other Jaera species, however, exceeded 29% for both CO1 and 28S, with no haplotype sharing. These assessments, together with taxonomically unconstrained analyses with software ABGD and ASAP, show that these markers are unable to distinguish between the J. albifrons group of morphospecies. The sequences do, however, clearly identify J. albifrons species complex from other Jaera species. Thus, a likely hypothesis is that taxa in this complex represent a single species. Our results corroborate previous finds where discordance between mitochondrial gene clusters, AFLP, and other data highlights the potential conflict between different “species criteria” and the well-established distinction between gene trees and species trees. In operational terms, common protocols for metabarcoding will potentially underestimate sympatric species diversity with cases like the J. albifrons complex, if the members of this complex indeed represent different species. [ABSTRACT FROM AUTHOR]

Introduction: The COVID‐19 pandemic was associated with an increased global use of traditional medicines, including Ayurvedic herbal preparations. Due to their growing demand, their processed nature, and the complexity of the global supply chain, there is an increased risk of adulteration in these products. Objectives: The objective of this study was to assess the use of DNA barcoding for species identification in herbal supplements on the US market associated with the Ayurvedic treatment of respiratory symptoms. Methods: A total of 54 commercial products containing Ayurvedic herbs were tested with four DNA barcoding regions (i.e., rbcL, matK, ITS2, and mini‐ITS2) using two composite samples per product. Nine categories of herbs were targeted: amla, ashwagandha, cinnamon, ginger, guduchi, tribulus, tulsi, turmeric, and vacha. Results: At least one species was identified in 64.8% of products and the expected species was detected in 38.9% of products. Undeclared plant species, including other Ayurvedic herbs, rice, and pepper, were detected in 19 products, and fungal species were identified in 12 products. The presence of undeclared plant species may be a result of intentional substitution or contamination during harvest or processing, while fungal DNA was likely associated with the plant material or the growing environment. The greatest sequencing success (42.6–46.3%) was obtained with the matK and rbcL primers. Conclusion: The results of this study indicate that a combination of genetic loci should be used for DNA barcoding of herbal supplements. Due to the limitations of DNA barcoding in identification of these products, future research should incorporate chemical characterization techniques. This study assessed the use of DNA barcoding for species identification in herbal supplements associated with the Ayurvedic treatment of respiratory symptoms. A total of 54 commercial herbal products were tested with four DNA barcoding regions. The expected species was detected in 21 of the 54 products; undeclared plant species were detected in 19 products; and fungal species were identified in 12 products. The results reveal that a combination of genetic loci allows for increased sequencing success in herbal products. [ABSTRACT FROM AUTHOR]

Copyright of Chinese Journal of Inorganic Analytical Chemistry / Zhongguo Wuji Fenxi Huaxue is the property of Beijing Research Institute of Mining & Metallurgy Technology Group and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

In order to understand the types, biological characteristics, and metabolites types of pathogenic fungi in carambola, the typical diseased parts of carambola fruit were collected for fungal isolation by tissue isolation methods. The fungi were identified by morphological and molecular identification methods based on ITS sequencing analysis. The biological characteristics of pathogenic fungi were explored, and metabolites were isolated and purified using liquid chromatography. Their structures were established on the basis of 1H NMR and 13C NMR. The results were as follows: The four strains were identified as Fusarium equiseti, Neopestalotiopsis sp., Schizophyllum commune and Cladosporium cladosporioides. All four strains could cause disease in carambola fruit. The fermentation products of Fusarium equiseti were chemically investigated, leading to the discovery of four compounds, 3,7,9-trihydroxy-1-methyl-6H-dibenzo[b,d] pyran-6-on, 1,4,7-trihydroxy-3,9-dimethoxy-6H-benzo[c]chromen-6-one, lecanoric acid and 7-hydroxy-4-methyl-1(3H)-isobenzofuranone. The results of biological characteristics indicated that the optimal growth temperature for the four pathogenic fungi was 25~28 °C, and they could all grow within the pH range of 4~10. [ABSTRACT FROM AUTHOR]

Copyright of Journal of Forensic Medicine / Fayixue Zazhi is the property of Journal of Forensic Medicine Editorial Office and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

Because of the detrimental effects of terrestrial invasive plant species (TIPS) on native species, ecosystems, public health, and the economy, many countries have been actively looking for strategies to prevent the introduction and minimize the spread of TIPS. Fast and accurate detection of TIPS is essential to achieving these goals. Conventionally, invasive species monitoring has relied on morphological attributes. Recently, DNA‐based species identification (i.e., DNA barcoding) has become more attractive. To investigate whether DNA barcoding can aid in the detection and management of TIPS, we visited multiple nature areas in Southwest Michigan and collected a small piece of leaf tissue from 91 representative terrestrial plant species, most of which are invasive. We extracted DNA from the leaf samples, amplified four genomic loci (ITS, rbcL, matK, and trnH‐psbA) with PCR, and then purified and sequenced the PCR products. After careful examination of the sequencing data, we were able to identify reliable DNA barcode regions for most species and had an average PCR‐and‐sequencing success rate of 87.9%. We found that the species discrimination rate of a DNA barcode region is inversely related to the ease of PCR amplification and sequencing. Compared with rbcL and matK, ITS and trnH‐psbA have better species discrimination rates (80.6% and 63.2%, respectively). When ITS and trnH‐psbA are simultaneously used, the species discrimination rate increases to 97.1%. The high species/genus/family discrimination rates of DNA barcoding indicate that DNA barcoding can be successfully employed in TIPS identification. Further increases in the number of DNA barcode regions show little or no additional increases in the species discrimination rate, suggesting that dual‐barcode approaches (e.g., ITS + trnH‐psbA) might be the efficient and cost‐effective method in DNA‐based TIPS identification. Close inspection of nucleotide sequences at the four DNA barcode regions among related species demonstrates that DNA barcoding is especially useful in identifying TIPS that are morphologically similar to other species. [ABSTRACT FROM AUTHOR]

Comprehensive vegetation surveys are crucial for species selection and layout during the restoration of degraded island ecosystems. However, due to the poor accessibility of uninhabited islands, traditional quadrat surveys are time-consuming and labor-intensive, and it is challenging to fully identify the specific species and their spatial distributions. With miniaturized sensors and strong accessibility, high spatial and temporal resolution, Unmanned Aerial Vehicles (UAVs) have been extensively implemented for vegetation surveys. By collecting UAVs multispectral images and conducting field quadrat surveys on Anyu Island, we employ four machine learning models, namely Gradient Boosting Decision Tree (GBDT), Support Vector Machine (SVM), Random Forest (RF) and Multiple Classifier Systems (MCS). We aim to identify the dominant species and analyze their spatial distributions according to spectral characteristics, vegetation index, topographic factors, texture features, and canopy heights. The results indicate that SVM model achieves the highest (88.55%) overall accuracy (OA) (kappa coefficient = 0.87), while MCS model does not significantly improve it as expected. Acacia confusa has the highest OA among 7 dominant species, reaching 97.67%. Besides the spectral characteristics, the inclusion of topographic factors and texture features in the SVM model can significantly improve the OA of dominant species. By contrast, the vegetation index, particularly the canopy height even reduces it. The dominant species exhibit significant zonal distributions with distance from the coastline on the Anyu Island (p < 0.001). Our study provides an effective and universal path to identify and map the dominant species and is helpful to manage and restore the degraded vegetation on uninhabited islands. [ABSTRACT FROM AUTHOR]

This paper discusses the development of rapid, reliable, and accurate polymerase chain reaction (PCR) assays for detecting opium poppy (Papaver somniferum L.) in food. Endpoint, quantitative, and digital PCRs were compared based on the amplification of a newly developed DNA marker targeting the NADPH-dependent codeinone reductase (COR) gene. Designed assays were shown to be highly specific and sensitive in discriminating opium poppy from other plant species, even in heat-treated and food samples. Digital PCR was the most sensitive, with a detection limit of up to 5 copies, i.e., approximately 14 pg of target DNA per reaction. Quantitative and digital PCR further allowed the quantification of opium poppy in up to 1.5 ng and 42 pg (15 copies) of target DNA in a sample, respectively. In addition, two duplex PCRs have been developed for the simultaneous detection of opium poppy DNA and representatives of (i) the Papaveraceae family or (ii) the Plantae kingdom. Finally, all designed assays were successfully applied for analysis of 15 commercial foodstuffs; two were suspected of being adulterated. The study results have an important impact on addressing food fraud and ensuring the safety and authenticity of food products. Beyond food adulteration, the study may also have significant implications for forensics and law enforcement. [ABSTRACT FROM AUTHOR]

The commercially important species Lutjanus campechanus (Northern/Gulf red snapper) and Lutjanus purpureus (Southern/Caribbean red snapper) are the protagonists of a decade's long taxonomic debate over their species delimitation, due in part to partial habitat overlap, extensive morphological similarity, and the lack of resolution when applying canonically reliable DNA barcoding approaches. In this study, we leveraged publicly available RAD-Seq data for L. campechanus and L. purpureus to identify species-informative singlenucleotide polymorphisms (SNPs) at the genome scale that were successful in distinguishing the Northern and Southern red snappers, while also detecting individuals exhibiting introgression. This 4-step empirical approach demonstrates the value of applying novel bioinformatics pipelines to existing genome-scale data to maximize the distillation of informative subsets. Our results facilitate economically relevant species identification in addition to confirming or challenging species identifications for specimens with data in public databases. These findings and their applications will benefit future sustainability strategies and broader research questions surrounding these overfished and evolutionarily entangled snapper species. [ABSTRACT FROM AUTHOR]

SM, Binashikhbubkr K, Setyawan AD, Md Naim D. 2024. Geometric morphometric divergence of five populations of Pampus argenteus (Euphrasen, 1788) from Malaysian waters. Nusantara Bioscience 16: 1-12. Phenotypic variation in fish may indicate different environmental conditions that affect species' growth and maturation rates and result from genetic factors that allow fish to adapt to different environments. Understanding population structure and dynamics is extremely important for establishing sustainable fisheries. Silver pomfret, Pampus argenteus (Euphrasen, 1788), is an economically important fish species with extensive geographical distribution from the East China Sea to Southeast Asia, Indian Ocean, Arabian Gulf, and the North Sea. It may represent morphologically distinct populations across their range. The main aim of this study is to use geometric morphometric analysis based on physical characteristics to look into the phenotypic diversity of the species across five different populations in Malaysia. Digital images of 260 mature specimens were captured for further analysis. Principle Component Analysis (PCA) and Multivariate analysis (MANOVA) were used in the intra-population analysis based on the transformed distance. At the same time, the Canonical Variance Analysis (CVA) and the Procrustes ANOVA were utilized to determine the inter-population analysis of P. argenteus. The Unweighted Pair Group with Arithmetic Mean (UPGMA) method used to support the analysis has shown that the population is clearly grouped according to homologous body shape. The results show that South, West, and North Coast specimens were grouped while the East Coast and Borneo Island shared in another group. The variations in the body shape of P. argenteus occurred in body depth, caudal region, and head orientation. The findings separated the populations into two main groups representing the marine region to which they belong. This present study is the first report on phenotypic variations of P. argenteus from Malaysian waters utilizing the geometric morphometric method. [ABSTRACT FROM AUTHOR]

Our research has developed a highly sensitive and simple assay to detect small amounts of animal and human biological material in less than 40 min. The handheld SaLux19 device developed at the Max Planck Institute of Experimental Medicine in Göttingen, Germany, was used to validate our concept. The proposed system uses isothermal amplification of DNA in a rapid assay format. Our results show that the assay can detect Sus scrofa nucleic acids with very high sensitivity and specificity. This detection system has potential for forensic scenarios. [ABSTRACT FROM AUTHOR]