Search Results (286)

Hymenoptera play important ecological roles in agroecosystems as parasitoids, predators, and pollinators. This study investigated the species composition and diversity of Hymenoptera in a conventionally managed pummelo (Citrus maxima (Burm.) Merr.) orchard in Xishuangbanna, Yunnan Province, China, from February 2025 to February 2026. A total of 8446 specimens were collected using Malaise traps and sweep netting, belonging to 11 superfamilies, 37 families, and 191 morphospecies. The community was dominated by parasitoids (140 morphospecies, 73.30%), followed by predators (30 morphospecies, 15.71%), pollinators (18 morphospecies, 9.42%), and phytophagous gall-inducers (3 morphospecies, 1.57%). Ichneumonoidea (42 morphospecies, 21.99%), Chalcidoidea (35 morphospecies, 18.32%), Vespoidea (30 morphospecies, 15.71%) and Apoidea (28 morphospecies, 14.66%) were the dominant superfamilies, collectively accounting for 70.68% of all morphospecies. At the family level, Ichneumonidae (25 morphospecies), Braconidae (17 morphospecies), Bethylidae (13 morphospecies), and Pompilidae and Scelionidae (11 morphospecies each) were the most morphospecies-rich families. Shannon–Wiener diversity was higher at the family level (H′ = 2.9340) than at the superfamily level (H′ = 2.0302), indicating greater heterogeneity at a finer taxonomic resolution. These results demonstrate that the surveyed pummelo orchard in Xishuangbanna harbors a species-rich and functionally diverse hymenopteran community with substantial potential for biological pest control and pollination services. Full article

Larval fish assemblages provide critical insights into reproductive dynamics, biodiversity baselines, and ecosystem resilience, yet remain poorly documented in the Colombian Pacific. This study analyzed ichthyoplankton diversity and spatial turnover across six neritic localities sampled between 2008 and 2022. Standardized plankton tows yielded 43,277 larvae representing 291 morphospecies, 150 genera, 66 families, and 38 orders. The richness observed accounts for ~34% of fish species listed for the Eastern Tropical Pacific and 15% of adult bony fishes reported for the Colombian Pacific, exceeding previous records. Diversity patterns revealed pronounced spatial heterogeneity: Cupica emerged as a biodiversity hotspot, Pizarro and Tortugas were dominated by few taxa, and Sanquianga exhibited high evenness despite moderate richness. Beta diversity analyses indicated turnover exceeding 60% and dissimilarity surpassing 70%, underscoring strong locality identity shaped by oceanographic gradients, geomorphology, and estuarine dynamics. Dominance patterns highlighted contrasting ecological strategies, with cosmopolitan taxa such as Cetengraulis mysticetus coexisting alongside habitat-restricted species of Labrisomus. These findings establish the Colombian Pacific neritic zone as a reservoir of genetic and functional diversity, with high richness and turnover reinforcing its role in sustaining ecosystem functioning and fisheries productivity. Methodological handicaps—including reliance on morphology-based identification, formalin preservation limiting molecular analyses, and uneven temporal coverage—constrain taxonomic resolution, yet the ecological patterns observed provide a robust foundation for conservation planning. Future research integrating molecular tools, trait-based approaches, and long-term monitoring will be essential to refine diversity estimates and strengthen adaptive management under scenarios of climate variability and increasing anthropogenic pressures in the Eastern Tropical Pacific. Full article

Alkaloid biosynthesis is a central topic in plant specialized metabolism because many alkaloids have ecological, pharmacological, and biotechnological relevance. Isoquinoline alkaloids (IAs) and Amaryllidaceae alkaloids (AAs) are both connected to aromatic amino acid metabolism, but they differ in taxonomic distribution, scaffold-forming chemistry, pathway resolution, and biotechnological development. This review compares the historical and methodological trajectories that have shaped IA and AA pathway elucidation, from compound isolation, radiotracer experiments, and biochemical inference to transcriptomics, metabolomics, functional enzymology, isotope-guided active-tissue identification, regulatory studies, and heterologous pathway reconstruction. In IAs, especially benzylisoquinoline alkaloids, broad genomic and transcriptomic resources have supported candidate gene discovery and functional characterization of several branches, including morphinan, protoberberine, benzophenanthridine, and aporphine-related pathways. In contrast, AA biosynthesis has advanced more recently through function-driven approaches that clarified key steps such as N4OMT-mediated 4′-O-methylation, NBS/NR-mediated norbelladine formation, CYP96T-dependent regioselective oxidative coupling, and transient reconstruction of major scaffold-forming branches. Remaining gaps include the unresolved enzymatic formation of 3,4-dihydroxybenzaldehyde in AAs and incomplete functional validation across less-studied IA scaffold classes. By integrating biochemical logic, omics-guided discovery, enzyme evolution, tissue specificity, regulation, and synthetic biology, this review identifies priorities for future alkaloid pathway discovery and sustainable production. Full article

The Greek seas have hosted a diversity of sharks and rays since antiquity, with Aristotle providing the earliest detailed descriptions in his History of Animals, while the first modern documented record dates back to 1858. Despite this long history of attention and the acceleration of research on elasmobranchs over the past two decades, information on their spatial distribution remains fragmented, with most studies focusing on biological and fisheries-related parameters at low taxonomic and/or spatial resolution. This is concerning given that over 50% of Mediterranean chondrichthyans are now threatened with extinction. The present study reconstructs the distribution of extant species in the Greek seas by integrating published literature, mass and social media, biodiversity platforms, citizen science programs, research projects, and national datasets. Although records were compiled from 1858 onwards, only those starting from 1942 contained sufficiently precise locality information to be georeferenced. The review yielded 5596 spatial presence records of initially 67 species; however, after data validation, 62 species were confirmed: 33 shark species, 28 batoid species, and 1 chimaera species, of which 54.8% were from research programs, 30.5% were from published research, and 14.4% were from citizen science and were previously unpublished. These records enrich knowledge of threatened and data-deficient taxa and may serve as a useful baseline for future analyses and distribution modeling, as well as for informing marine spatial planning and conservation prioritization efforts in the eastern Mediterranean. Full article

Blastus Lour. is a taxonomically complex genus of Sonerileae (Melastomataceae), with unresolved infrageneric relationships and controversial boundaries among several species and varieties. In this study, we integrated morphological evidence with a broadly sampled internal transcribed spacer (ITS) dataset, an expanded nuclear ribosomal DNA (nrDNA) dataset, plastome data, and genomic single-nucleotide polymorphism (SNP) data to evaluate the phylogenetic relationships and classification within Blastus. The broadly sampled ITS and expanded nrDNA analyses supported the monophyly of the sampled Blastus accessions but provided limited resolution of relationships among closely related taxa. The plastome analysis did not recover the sampled Blastus accessions as monophyletic and revealed marked cytonuclear phylogenetic incongruence. The genomic SNP analysis strongly supported the monophyly of the sampled Blastus accessions and recovered the sampled members of the terminal inflorescence group as a monophyletic clade. However, the sampled members of the traditional axillary inflorescence group were not monophyletic because Blastus borneensis was recovered as sister to the terminal inflorescence clade. Within the terminal inflorescence clade, the sampled members of the B. pauciflorus and B. cavaleriei groups formed two strongly supported sister lineages. Morphological comparisons showed that inflorescence position and architecture, the distribution of yellow glands on the abaxial leaf surfaces, and calyx lobe morphology generally corresponded to the principal lineages recovered in the SNP tree, whereas indumentum characters varied considerably among individuals and populations. We therefore recommend retaining the axillary and terminal inflorescence groups as descriptive morphological categories and treating the B. pauciflorus and B. cavaleriei groups as two informal working subdivisions within the terminal inflorescence group. The broad circumscription of B. pauciflorus adopted in the Flora of China requires reassessment, whereas the boundaries of B. longiflorus var. apricus and B. dunnianus require broader population sampling before formal taxonomic changes are proposed. Full article

Immune checkpoint inhibitors have improved outcomes in esophageal cancer across settings, yet clinical benefit remains heterogeneous, with current host-derived biomarkers incompletely predicting response. This mini review evaluates recent studies that integrate gut or intratumoral microbial features with host immune, molecular, or metabolic assessment in esophageal cancer. We classify the evidence using a four-level hierarchy of host-microbiome integration: ecological association, functional association, mechanistic integration, and clinical predictive integration. Tissue studies reveal compartment-specific relationships between microbial diversity or individual taxa and immune architecture, whereas treatment cohorts identify bacterial and fungal signatures associated with pathological or immunotherapy response. Mechanistic studies offer the strongest biological evidence, most notably the Lactobacillus salivarius-indole-3-lactic acid-AhR/NF-κB axis, which drives CD8-positive T-cell exhaustion and resistance to anti-PD-1 therapy. However, biological integration is substantially more advanced than clinical response prediction. Small cohorts, heterogeneous regimens, contamination of low-biomass samples, coarse taxonomic (rather than functional) resolution, confounding by histology, multi-omic layers measured in different patients, and lack of external validation currently jeopardize integration of microbiome to guide treatment. Future studies should use longitudinal, multicenter, compartment-matched sampling and test whether microbial genes or metabolites improve patient selection and predict clinical response beyond established clinical and host biomarkers. Full article

Reliable molecular identification of plants depends on reference libraries of DNA sequences, and complete plastid genomes (plastomes) used as super-barcodes are increasingly the reference of choice for taxonomically difficult groups. We assess how ready the flora of Poland is for plastome-based super-barcoding by combining national checklists of vascular plants, mosses, and liverworts with the current availability of complete plastomes in GenBank. For 3339 species we quantify coverage, its distribution across families and genera, the provenance of the sequenced material, and the gap between coverage and expected species-level resolution. A complete plastome was available for 54.4% of species, but coverage was uneven: liverworts (76.0%) and mosses (75.6%) were close to reference-complete, whereas the much larger vascular flora reached only 45.9%. Effective vascular coverage fell to roughly 39% once low-resolution genera were excluded, because many uncovered species belong to apomictic or hybridogenous complexes such as Taraxacum, Hieracium, and Alchemilla, where plastomes alone cannot resolve identity. Most sequenced material was of non-European origin, which weakens fine-scale identification of local populations. We identify 1011 high-value sequencing targets and recommend a tiered, marker-aware strategy combining the plastome with nuclear ribosomal DNA and, selectively, low-copy nuclear or mitochondrial markers. Defining readiness by the proportion of the flora that can actually be identified turns a static inventory into a prioritized roadmap transferable to other Central European floras. Full article

The Paleozoic–Modern Evolutionary Fauna transition is defined by the ecological replacement of brachiopods by bivalves. However, it remains debated whether post-Paleozoic brachiopods experienced a simple, continuous global decline or a complex macroevolutionary reorganization. Previous studies are often limited by ecological mismatches, uncorrected sampling biases, and single taxonomic scales. To resolve this, this study presents a high-resolution analysis of brachiopod evolution from the Triassic to the Quaternary. Using Paleobiology and Geobiodiversity Database records, I applied coverage-based standardization and, for guild-level comparisons, strict ecological filtering, comparing brachiopods only to ecologically equivalent bivalves and echinoderms. Results reveal three major patterns. First, regional and global diversity decoupled: global diversity showed Mesozoic diversification pulses, whereas the Chinese record exhibited a sustained post-Triassic collapse, showing global aggregates mask regional extirpations. Second, brachiopods displayed strong hierarchical resilience: environmental crises drastically pruned species richness (causing generic monotypy), yet family-level diversity remained remarkably stable. Third, brachiopods underwent a macroecological reorganization, retreating from carbonate reefs and shifting poleward to establish their modern anti-tropical distribution. Ultimately, the post-Paleozoic history of brachiopods is not a passive decline, but a multi-dimensional reorganization driven by regional habitat loss, geographic redistribution, and deep-lineage survival. Full article

The taxonomic status of Cipangopaludina chinensis and C. cathayensis remains controversial due to morphological overlap. We combined morphometrics (24 landmarks vs. 200 semilandmarks) with multi-locus phylogenetics (COI, 16S rRNA, H3, 28S rRNA) and haplotype networks on sympatric populations from Liuzhou and GenBank. Morphometrics completely separated C. chinensis_lz from C. cathayensis_lz in shell shape; key diagnostic traits include aperture size, spire height, and body whorl inflation. The high-density semilandmark method outperformed discrete landmarks in dimensionality reduction and fine-scale resolution, capturing subtle apex and lateral whorl variations. No sexual dimorphism occurred in C. cathayensis_lz, with only weak dimorphism in C. chinensis_lz. Molecular data were ambiguous: the species tree and mitochondrial gene tree recovered C. chinensis and C. cathayensis as monophyletic, but the nuclear gene tree showed mixing of C. chinensis_lz/C. cathayensis_lz with C. wisseli, C. chinensis, and C. cathayensis. Haplotype networks revealed haplotypes sharing between C. chinensis_lz and C. cathayensis_lz, yet neither population shared haplotype with GenBank sequences of the two nominal species. Morphology strongly supports C. chinensis_lz and C. cathayensis_lz as distinct species, whereas molecular evidence shows only low-level differentiation and discordant signals between mitochondrial and nuclear markers. We conclude they are likely valid species, yet mitonuclear discordance warrants further genomic investigation. Despite no evidence of microhabitat partitioning, the stable morphological divergence between these sympatric morphospecies supports separate management units to conserve phenotypic diversity and local adaptive potential. This study validates geometric morphometrics as an efficient frontline tool for biodiversity assessment in morphologically diverse yet genetically conserved freshwater snails, and reinforces the need for genome-wide data to resolve species boundaries within the Cipangopaludina complex. Full article

The northern margin of the East Asian tropics harbors exceptional endemism, yet its freshwater fish fauna remains poorly characterized. Tachysurus virgatus, long considered a single widespread species in this region, exemplifies this taxonomic gap. Through integrative taxonomic analyses combining morphological and molecular evidence, we uncovered remarkable cryptic diversity within this species. Phylogenetic reconstructions reveal that true T. virgatus is restricted to the Wanquan River basin on Hainan Island, whereas nine additional lineages from other drainages represent previously unrecognized species described in this study. Together with two known congeners (T. spilotus and T. kyphus), these form the monophyletic T. virgatus species group for which we provide morphological diagnoses. Pronounced incongruence between morphological and molecular divergence characterizes this group, underscoring the necessity of integrative approaches for species delimitation in morphologically conserved lineages. Moreover, distinct habitat specialization patterns were identified within the group, with species exhibiting adaptations to three ecological niches: mainstem river, montane streams, and generalist habitats occupying both. Correlations between habitat preferences and functional morphology were preliminarily discussed. Using our revised taxonomic framework, we evaluated the conservation status of all species under IUCN Red List criteria, with several newly described taxa warranting threatened status due to extremely limited distributions. This study highlights the pervasive cryptic diversity of freshwater fishes in the north margin of East Asian tropics and emphasizes the critical importance of rigorous taxonomic resolution to guide effective conservation in this biogeographically complex region. Full article

Biological research relies on the use of taxa, with species expressed in the form of a Latin binomial. Although taxa are commonly regarded as established entities, they actually represent hypotheses on the distribution of natural biological variation and may change their status as new systematic knowledge becomes available. A long-standing problem affecting systematics and taxonomy, with important consequences for other biological disciplines, is that a binomial itself conveys no information about the strength of the taxonomic hypothesis it represents. Here, we introduce the concept of a standardized heuristic index, named Turrill’s Omega Index (TOI), to estimate the degree of support for a taxonomic hypothesis. Turrill’s Omega Index is a single numerical value calculated by integrating four macro-categories of comparative data: Phenotype, Genealogy, Isolation, and Geography-Ecology. Turrill’s Omega Index provides a practical and reliable framework for quantifying the support for a taxonomic hypothesis, without requiring resolution of the long-standing debate surrounding species delimitation and species concepts. Accordingly, it has the potential to represent a valuable and transformative advance in systematics and taxonomy. In addition, TOI can support conservation decision-making by helping prioritize funding allocation among equally threatened taxa according to their degree of support. Full article

Accurate assessment of phylogenetic relationships is essential for understanding the evolution, taxonomy, and conservation of the carnivorous genus Nepenthes. In Thailand, species delimitation remains challenging because of extensive morphological variation and the occurrence of several closely related taxa. This study integrated genome-wide single nucleotide polymorphisms (SNPs) generated by Genotyping-by-Sequencing (GBS), chloroplast trnK intron sequences, nuclear ITS sequences, and AFLP markers to investigate phylogenetic relationships and genetic diversity among Thai Nepenthes taxa. Genome-wide SNP analysis recovered three principal clades, whereas trnK and ITS datasets provided complementary resolution at deeper and intermediate phylogenetic levels. The molecular datasets revealed broadly congruent phylogenetic patterns and improved resolution among several closely related Thai taxa. AFLP analysis of Nepenthes mirabilis populations revealed moderate polymorphism despite relatively high overall genetic similarity. Across all datasets, N. mirabilis var. globosa was consistently recovered within the broader N. mirabilis lineage and showed limited genetic differentiation from sampled N. mirabilis accessions. These findings provide an integrated molecular framework for understanding phylogenetic relationships among Thai Nepenthes and support future taxonomic, evolutionary, and conservation studies in the region. Full article

Microbial communities associated with fish mucosal tissues play important roles in host health and environmental adaptation. However, the effects of contrasting aquaculture conditions on the microorganisms of the large yellow croaker (Larimichthys crocea, L. crocea) remain poorly understood. In this study, 16S rRNA gene sequencing was used to compare the gut and gill microbiota of L. crocea cultured in a marine system and a saline–alkaline system, together with the corresponding surrounding water samples. The results showed that both host tissue type and rearing environment significantly influenced microbial community structure. Water samples generally exhibited higher alpha diversity than host-associated samples, whereas the gut and gill communities were clearly separated from the surrounding water microbial community. The intestine showed stronger culture system differentiation than the gill, suggesting greater niche selectivity, while the gill retained a closer association with the rearing water. Across multiple taxonomic levels, microbial composition differed markedly among water, gut, and gill samples, and the divergence between the marine culture and saline–alkaline culture system became more pronounced at finer taxonomic resolution. Differentially enriched taxa further revealed clear tissue- and habitat-associated microbial patterns. In addition, several dominant taxa were significantly correlated with environmental variables, especially salinity and nutrient-related factors, indicating that physicochemical heterogeneity contributed substantially to microbial community assembly. Overall, this study shows that host mucosal niche and rearing environment are associated with distinct gut and gill microbiota patterns in L. crocea and provides preliminary ecological information for future microbiome-informed aquaculture management, functional validation of candidate taxa, and the development of land-based culture systems for marine fish. Full article

Accurate species-level identification of Legionella during routine environmental surveillance remains challenging, as standard proteomic screening methods like MALDI-TOF MS often lack the resolution to distinguish closely related taxa. This study introduces a novel, cost-effective, and stepwise taxonomic framework that bridges routine environmental monitoring with multi-layered, genome-resolved analysis. We expanded upon our previous screening of four novel candidate lineages by focusing on the three remaining, uncharacterized environmental isolates, while using the recently validly described Legionella sheltonii (strain PATHC038) as a reference framework control. By applying nucleotide- and protein-based overall genomic relatedness indices (ANI, dDDH, AAI, and POCP) alongside core-genome phylogenomics, our framework independently confirmed the genomic distinctiveness of the three isolates, which exhibited AAI values of 94.3–96.6% and POCP values of 86.5–91.0%, with POCP values lying close to the proposed species delineation threshold. By defining clear criteria for escalating isolates from culture to targeted sequencing, this workflow prevents diagnostic misidentification during epidemiological outbreak investigations and provides public health agencies with a scalable tool to monitor hidden Legionella diversity, ultimately enhancing proactive water safety and risk assessment. Full article

The Caribbean is a recognized biodiversity hotspot; however, on islands such as Jamaica, many faunal groups of ecological and forensic importance, including flesh flies, remain poorly characterized, particularly at the genetic level. This study represents an initial step towards addressing that gap through DNA barcoding. Forty-four specimens from 16 species were analyzed through partial sequencing of the cytochrome c oxidase subunit I (COI) gene. Of the 44 sequences, 30% shared 97–100% similarity with reference sequences in GenBank and BOLD; however, taxonomic resolution varied between databases. The remaining sequences gave lower similarity matches (88–96%), with assignments restricted to the genus level or higher taxonomic ranks, or were discordant with morphology-based identifications. With one exception, pairwise intraspecific genetic distances were low (0.17%), whereas interspecific distances ranged from 5.68% to 12.83%. Neighbor-joining analysis showed that Jamaican taxa, including five endemic species and two new records, formed largely distinct monophyletic clades relative to sequences from North and South America, Europe and Oceania, with >70% bootstrap support. These findings demonstrate the utility of COI barcoding for species discrimination among Jamaican flesh flies and represent an important step towards establishing a regional DNA barcode library. Expanding Caribbean representation in global databases will be essential for improving the accuracy of molecular identification and resolving uncharacterized taxa. Full article