Search Results (993)

Hydropower plants have significant impacts on aquatic biodiversity, particularly on migratory fish species. Effectively managing these impacts requires a comprehensive understanding of fish reproduction and recruitment within altered river systems, which can be assessed through ichthyoplankton studies. However, traditional morphological methods for identifying fish eggs and larvae present considerable challenges due to morphological ambiguity and developmental constraints. In this study, we applied DNA barcoding to characterize the ichthyoplankton community within a relictual lotic stretch downstream of the Capivara Dam, located on the Paranapanema River in Southern Brazil. Cytochrome oxidase I (COI) gene sequences from 79 samples were compared against the Barcode of Life Data System (BOLD) and GenBank databases, resulting in successful species-level identification for all samples, each exhibiting around 99.8% similarity. The identified specimens comprised eight species, six genera, four families, and two orders. Species from the order Siluriformes accounted for 60.5% of the total abundance, predominantly including migratory species such as Pimelodus ornatus, Pimelodus maculatus, Leporinus friderici, and Pinirampus pirinampu, the latter a species rarely observed in the basin. These findings highlight the importance of lotic stretches as spawning grounds and emphasize the need for their conservation. DNA barcoding proved to be an efficient method for species identification, providing essential data for environmental assessments and conservation strategies targeting local fish populations. Full article

Agarwood, valued for its resin, has long been used in perfumery, incense, and traditional medicine. Its resin is primarily derived from species of Aquilaria and is produced through a still-unknown process in response to biotic or abiotic stress. Concerns regarding agarwood’s sustainability and conservation have emerged because of the substantial loss of natural resources due to overharvesting and illegal trade. To address these concerns, artificial techniques are being used to produce agarwood. The mechanism underlying agarwood production must be elucidated to enhance yield. The authentication of agarwood species is challenging because of morphological similarities between pure and hybrid Aquilaria species. Techniques such as DNA barcoding, molecular marker assessment, and metabolomics can ensure accurate identification, facilitating conservation. Artificial intelligence and machine learning can support this process by enabling rapid, automated identification on the basis of genetic and phytochemical data. Advances in resin induction methods (e.g., fungal inoculation) and chemical induction treatments are improving yield and quality. Endophytic fungi and bacteria promote resin production at minimal harm to the tree. Agarwood’s pharmacological potential—antimicrobial, anti-inflammatory, and anticancer effects—has driven research into bioactive compounds such as sesquiterpenes and flavonoids for the development of novel drugs. This systematic review synthesized current evidence on species authentication, induction techniques, and pharmacological properties. The findings may guide future research aimed at ensuring sustainable use and enhancing the medicinal value of agarwood. Full article

Indocalamus Nakai, a genus within the tribe Arundinarieae, has significant horticultural and economic value. However, its classification has long been challenging, and due to limited sampling, both intra- and intergeneric phylogenetic relationships, as well as its evolutionary history, remain unclear. In this study, extensive field surveys and comprehensive sample collection were conducted to address these challenges. A total of 31 complete plastomes of Indocalamus species were assembled. All plastomes exhibit a typical quadripartite structure, ranging in length from 139,555 bp to 139,791 bp, and contain 137 genes, including 90 protein-coding genes, 39 tRNA genes, and 8 rRNA genes. Phylogenetic analyses indicate that Indocalamus is polyphyletic and divided into three distinct clades (IV, V, and X). Based on integrated phylogenomic and morphological evidence, we propose a revised classification of Indocalamus into three major sections. Fossil-calibrated divergence estimates reveal that the major clades of Indocalamus are not monophyletic, highlighting a complex reticulate evolutionary history exemplifying the widespread rapid radiation observed in temperate woody bamboos. The intensification of the East Asian monsoon is likely to have played a key role in driving the rapid radiation of these lineages. Additionally, several clade-specific DNA barcodes (trnT-trnE, petN-trnC, petA-psbJ, and petD-rpoA) were identified, which will enhance the identification of Indocalamus and its closely related genera. This study, through extensive sampling and integration of morphological and molecular phylogenetic evidence, provides a preliminary delimitation of the genus Indocalamus, elucidates its complex evolutionary history, and lays a solid foundation for future systematic research and horticultural applications. Full article

Background/Objectives: Pothos chinensis is commonly used as traditional medicine in China and India. Codon usage analysis is a good way to understand plants’ evolution. However, there is no report about the codon usage bias of chloroplast genomes in P. chinensis. Methods: In this study, the chloroplast genome of the medicinal plant P. chinensis was newly obtained. Comparative analyses, DNA barcoding investigation, codon usage bias, and phylogenetic reconstruction were conducted to reveal the chloroplast genome characteristics of P. chinensis. Results: The length of the chloroplast genome of P. chinensis was 165,165 bp. A total of 134 genes were annotated, i.e., 90 protein-coding genes, 36 transfer RNA genes, and eight ribosomal RNA genes. Compared to its sister group Anthurium andraeanum, the length of the large single-copy region (LSC) had been expanded, while the small single-copy region (SSC) had been contracted. Within P. chinensis and P. scandens there were no obvious differences in the length of LSC, SSC, and two inverted repeat regions. Based on Pi values, seven hypervariable regions of whole plastomes were identified. The analysis of codons showed that an average frequency of the 50 candidate genes was 35.30%, and these genes preferred A/U-ending codons. The average effective number of codon (ENC) value was 45.49, which indicated weak codon usage bias. ENCs had a highly significant positive correlation with GC3. Fourteen optimal codons had been identified, 11 of which ended with A/U. The results of the neutrality plot, ENC-plot, and PR2-plot analysis indicated that natural selection might have a significant impact on codon usage patterns. Conclusions: Taken together, our study unraveled the codon usage patterns in P. chinensis and provided valuable genetic information for the genus Pothos. Full article

We developed and validated a rapid, cost-effective multiplex PCR assay targeting mitochondrial cytochrome c oxidase subunit I (COX1) to discriminate three commercially important sea-squirt species, Halocynthia roretzi, H. aurantium and H. hilgendorfi ritteri. Species-specific forward primers were designed from interspecific single-nucleotide polymorphisms within the barcode region and combined with a common reverse primer in a single reaction. Specificity was confirmed in all tested individuals (n = 7 per species) without cross-amplification. Sensitivity tests demonstrated consistent amplification down to 0.1 ng of template DNA, matching or surpassing detection limits reported for other food-authentication markers. Because the entire reaction including DNA extraction can be completed within three hours and requires only basic laboratory equipment, the method is well suited for quality control laboratories, border inspections and routine monitoring of processed products. The COX1 multiplex PCR set proposed here provides a reliable tool to enhance traceability, protect consumer choice, and support regulatory enforcement in the sea-squirt supply chain. Full article

In the context of the progressive tendency to perceive a degraded environmental state as normal, due to the loss of memory of past ecological conditions (i.e., the Shifting Baseline Syndrome), natural history museum collections represent invaluable resources for studying long-term biodiversity shifts. This study deals with the taxonomic validation of the chondrichthyan species from the historical ichthyological collection assembled by Pietro Doderlein from 1863 to 1922 at the Museum of Zoology of the University of Palermo. The chondrichthyan specimens were digitally catalogued to meet current standards of museum documental identification. Biometric measurements were taken for each specimen, and an integrated analytical approach—combining morphology and ancient DNA analysis—was applied to assign species identities. The collection comprises 342 specimens associated with 76 valid codes. Of these, 288 specimens were identified to species level by morphology, revealing 58 discrepancies with the historical identifications. Sixteen specimens that could not be morphologically assigned were analyzed by DNA barcoding, resulting in eight additional species-level identifications. In total, 62 valid species belonging to 27 families were digitally catalogued according to ministerial guidelines. This taxonomic validation and cataloguing of the “P. Doderlein” chondrichthyan collection represent the first successful effort to bridge the gap in available data and tissue resources from Italian historical natural museums. Full article

The genus Sargassum is taxonomically complex and poorly studied in the Eastern Tropical Pacific. We analyzed specimens collected along the Pacific coast of Central America and compared them with historical records and herbarium material to clarify species identities. Using detailed morphological analyses with molecular phylogenetic reconstruction based on concatenated ITS2 (Internal Transcribed Spacer 2) and COX3 (Cytochrome Oxidase Subunit 3) sequences, we identify two distinct morphotypes corresponding to two well-supported clades. One clade matches the morphology and molecular profile of Sargassum liebmannii. We provide the most comprehensive description of this species to date, including the first published ITS2 and COX3 sequences. Since Taylor’s 1945 work on the tropical Pacific of the Americas, S. liebmannii has been widely reported and considered the predominant species. It forms a genetic clade with other species from the Gulf of California; therefore, we propose a new section, Herporhizum/Sinicola. The second clade represents a previously unrecognized taxon from Central America, which we describe as a new species: Sargassum lacrucense, within the subgenus Sargassum, section Sargassum. Contrary to previous reports, Sargassum brandegeei—now recognized as Sargassum herporhizum—was not found in the region. This study underscores the importance of integrating morphological and molecular data to resolve Sargassum taxonomy in Central America. Full article

The genus Raiamas currently comprises 18 valid species, only 2 of which occur in Asia; the remaining 16 are endemic to Africa. Raiamas harmandi was originally described by Sauvage in 1880 as Bola harmandi, which is distributed in the Great Lakes, Cambodia, the Mekong River Basin. It was considered a synonym of R. guttatus by later researchers. In this study, we examined 49 Raiamas individuals from the Mekong, Irrawaddy, and Salween river basins, recording both meristic counts and morphometric measurements. Based on the morphological evidence, we revised the taxonomy of Raiamas in the Mekong River Basin, confirming R. harmandi as a valid species and providing a comprehensive redescription. Raiamas harmandi can be distinguished from R. guttatus mainly by having more predorsal scales (25–28 vs. 21–23) and a different color pattern on the lateral body. Utilizing a total of 44 aligned COI and Cyt b sequences—including eight newly sequenced individuals of Raiamas from three river basins—we reconstructed its phylogenetic relationships. The analysis strongly supported four R. harmandi individuals from the Mekong River Basin forming a distinct clade, which was the sister to the clade comprising five R. guttatus individuals from the Irrawaddy and Salween river basins. Genetic distances between R. harmandi and R. guttatus ranged from 14.0 to 14.9% for COI and 16.1 to 17.0% for Cyt b. Distributionally, R. harmandi occurs throughout the Mekong River Basin, as evidenced by combined voucher specimens and molecular sequence data. Full article

Although 5–20% of global crop production is lost to arthropod damage, current biomonitoring programs are extremely limited. This study evaluates the feasibility of using metabarcoding to assess overall insect diversity and detect pest species in agricultural settings. It introduces a curated DNA barcode reference library for Canadian insects that are agricultural pests and applies it to metabarcoding data from the analysis of Malaise trap samples from two experimental farms in Southern Ontario. A total of 7707 arthropod species were collected across the two farms, and projections indicate that another 4000 await detection. These taxa included 231 registered pest species. The composition of the overall arthropod community composition was more heavily influenced by site location than crop type, but pest species composition was influenced by the crop. This study confirms that metabarcoding enables the evaluation of the species composition of arthropod communities in agroecosystems, allowing pest species to be tracked. Full article

The Yuanjiang River, situated in the upper reaches of the Red River, is a crucial component of a biodiversity hotspot in the mountains of southwestern China, supporting a high diversity of fish species. Nevertheless, systematic research on fish diversity in the Yuanjiang River is scarce, scattered, and outdated. In our study, we produced 764 DNA barcodes belonging to 64 fish morphospecies to evaluate fish diversity in the Yuanjiang River. Barcoding gap analysis and DNA-based delimitation approaches achieved a high identification success rate (>93%), indicating that DNA barcoding is a practical approach for delimiting fish in the Yuanjiang River. However, four species were characterized by high levels of intraspecific divergence, generating multiple clades and/or molecular operational taxonomic units (MOTUs), suggesting that these species might comprise undetected species. Meanwhile, two closely related species within the genus Schistura, i.e., S. callichroma and S. caudofurca, cannot be delimited by the DNA barcoding technique, which is indicative of recent speciation. In summary, this study established a reliable DNA barcode reference library for fish species in the Yuanjiang River and revealed previously unknown fish diversity. Full article

The genus Discobola Osten Sacken, 1865 from China is taxonomically reviewed using an integrative approach that combines detailed morphological examination and molecular analysis. Discobola parvispinula (Alexander, 1947), a species widely distributed across the Palaearctic region, is newly recorded from China. Updated distributional data are presented for species known from China: D. annulata (Linnaeus, 1758), D. armorica (Alexander, 1942), D. margarita Alexander, 1924, and D. taivanella (Alexander, 1930). Detailed redescriptions and illustrations, including intraspecific morphological variation, are provided for these species. An identification key to Chinese Discobola species is also presented. Geographical analysis reveals a higher species richness in southern China and the Qinghai–Tibet region, with a progressive decline toward northern and northwestern China. The first DNA barcode reference library for Chinese Discobola is established, comprising 15 mt COI sequences from five species. These sequences, analyzed alongside an additional 101 mt COI sequences from Discobola species in other countries, show that intraspecific divergence within the genus remains below 7.4%, while interspecific divergence ranges from 7.6% to 17.7%. These findings provide important insights into the taxonomy, species delimitation, and biogeography of Discobola in China, contributing to a more comprehensive understanding of Discobola diversity across the region. Full article

Abrus bottae belongs to the subfamily Papilionoideae DC. and the family Fabaceae Lind., endemic to the Arabian Peninsula. This genus encounters numerous taxonomic issues concerning both the quantity of species within the genus and the systematic relationships among its species. Notably, there is a complete absence of sequence data in the GenBank database for this species. A molecular and phylogenetic study of the chloroplast genome of the species A. bottae was performed in this work. The chloroplast genome is 152,540 bp in size and exhibits a typical quadripartite structure, consisting of a substantial single-copy region of 83,507 bp, a small single-copy region of 17,681 bp, and a pair of inverted repeat regions of 25,676 bp each. The chloroplast genome of Abrus bottae encompasses 130 genes. An analysis of nucleoside diversity revealed 26 nucleotide polymorphism sites with Pi values (a measure of genetic variation within species) ≥ 0.04, serving as hotspots of variation. This work represents the first molecular phylogenetic study on the endemic species Abrus bottae and presents a comparative and phylogenetic analysis of the cp genomes of related taxa within the tribe Abreae. These outcomes can be used to develop DNA barcodes to study variation among the Abrus species. Full article

Polyphagous fruit fly (Diptera: Tephritidae) pests from the Pacific Islands pose a biosecurity risk to New Zealand, a country free from pest fruit flies. Among them, Bactrocera facialis, B. passiflorae, B. kirki, and B. distincta are sympatric species commonly intercepted at immature stages at the border. However, current mitochondrial cytochrome oxidase I (COI) barcode data lack sufficient variation for a confident identification of the above four species. To address this, we generated COI barcode data for 403 fruit fly individuals including these four species and an additional 17 related fruit fly species. A phylogenetic analysis of the COI sequences of B. facialis revealed two genetically distinct populations, one closely related to B. passiflorae. Complete mitochondrial genomes were explored, identifying minor fixed differences in Cytochrome b (CYTB), NADH dehydrogenase 2 (ND2), and ATP synthase membrane subunit 6 (ATP6) genes. Based on sequence data for COI, ND2, and ATP6 genes, a multiplex real-time PCR assay has been developed and validated for the four target species. Each assay demonstrated high specificity, with no cross-reactions, and sensitivity as low as 10 copies/μL of the target DNA. This study shows that the developed assays enable the rapid and reliable identification of the target fruit fly species, supporting global biosecurity efforts. Full article

Mosquito blood meals provide a biological sample of host blood which can then be used in downstream applications including host–pathogen detection. We conducted DNA barcoding to identify the host species of blood meals from 4557 blood engorged mosquitoes collected in south central Florida, USA. We identified 314 blood meals from invasive wild pigs, 219 wild turkey blood meals, and 1046 white-tailed deer blood meals. From a subset of these host blood meals, we used molecular assays to detect the nucleic acids of Torque teno sus virus 1 (TTSuV1) in wild pig blood meals, Lymphoproliferative virus (LPDV) in wild turkey blood meals, and bluetongue virus (BTV) in white-tailed deer blood meals. None of these wildlife pathogens are transmitted by mosquitoes, but viral nucleic acids circulate in the peripheral blood of host species during or post infection. Prevalence of TTSuV1 in wild pig blood meals was 34%; in wild turkey blood meals the prevalence of LPDV was 2.7%, and BTV prevalence in blood meals of white-tailed deer was 3.6%. These prevalence values were similar to estimates obtained from peripheral blood collected directly from these hosts in Florida. Our analysis suggests that mosquito blood meals are a valuable sampling tool for the detection of wildlife pathogens. We suggest that this type of exogenous xenosurveillance, using mosquitoes to infer information about the vertebrate host, is distinct from endogenous xenosurveillance in which the goal is to understand the role of the arthropod in vectoring a pathogen. Full article

Plant genetics and chemotaxonomic analysis are considered key parameters in understanding evolution, plant diversity and adaptation. Korean Peninsula has a unique biogeographical landscape that supports various aromatic plant species, each with considerable ecological, ethnobotanical, and pharmacological significance. This review aims to provide a comprehensive overview of the chemotaxonomic traits, biological activities, phylogenetic relationships and potential applications of Korean aromatic plants, highlighting their significance in more accurate identification. Chemotaxonomic investigations employing techniques such as gas chromatography mass spectrometry, high-performance liquid chromatography, and nuclear magnetic resonance spectroscopy have enabled the identification of essential oils and specialized metabolites that serve as valuable taxonomic and diagnostic markers. These chemical traits play essential roles in species delimitation and in clarifying interspecific variation. The biological activities of selected taxa are reviewed, with emphasis on antimicrobial, antioxidant, anti-inflammatory, and cytotoxic effects, supported by bioassay-guided fractionation and compound isolation. In parallel, recent advances in phylogenetic reconstruction employing DNA barcoding, internal transcribed spacer regions, and chloroplast genes such as rbcL and matK are examined for their role in clarifying taxonomic uncertainties and inferring evolutionary lineages. Overall, the search period was from year 2001 to 2025 and total of 268 records were included in the study. By integrating phytochemical profiling, pharmacological evidence, and molecular systematics, this review highlights the multifaceted significance of Korean endemic aromatic plants. The conclusion highlights the importance of multidisciplinary approaches including metabolomics and phylogenomics in advancing our understanding of species diversity, evolutionary adaptation, and potential applications. Future research directions are proposed to support conservation efforts. Full article