Search Results (1,309)

Evolutionary trees are of central importance in biology to develop explanatory frameworks for many kinds of studies, including studies of behaviour, ecology, and conservation. Since the last major estimate of evolutionary relationships among many bumblebee species two decades ago, there have been revisions to their taxonomy, descriptions of new species, and sequencing of many rarer species. By combining: (1) earlier data mostly from slow-evolving nuclear genes as a backbone tree; with (2) new data from fast-evolving mitochondrial COI barcodes to resolve more of the twigs on the tree, including sequences obtained from rare old specimens with ancient DNA techniques; as well as (3) the results from broader genomic data for resolving deep relationships, we make a Bayesian estimate of evolutionary relationships with BEAST 2 among all 289 published and accepted extant bumblebee species, an increase of more than 29% of the species on the previous largest tree. The new tree will serve as a framework for future comparative studies that should enable broader insights into the evolution and ecology of all bumblebees. We illustrate this with an analysis of the evolution of some male morphological characters related to male mate-searching behaviour. We also present a novel map of spatial variation in net diversification rates among bumblebee species world-wide, which indicates an especially rapid net diversification within the more recent Mesoamerican and South American faunas. Full article

Decomposing whale carcasses on the seabed (whale falls) are known to support distinct communities, with many taxa new to science. This paper describes a new polynoid species, Macellicephala irisae sp. nov., from a natural whale fall at 1240 m depth in Santa Catalina Basin off California, USA. The new species was associated with a cladorhizid sponge growing on a bone, transitioning from the sulphophilic to reef stage. We also highlight the biodiversity of exclusively deep-sea Macellicephalinae subfamily and its most species-rich genus Macellicephala. Morphological and molecular data support the description of the new species, which is also placed within a phylogenetic context using COI, 16S and 18S markers. The new species possesses distinctive filamentous notochaetae not previously reported in Macellicephala, and with the future increase in taxon coverage, an erection of new genus may be warranted. Full article

Jasmonate ZIM-domain (JAZ) proteins are pivotal repressors in the jasmonate (JA) signaling pathway, yet their specific roles in garlic (Allium sativum) remain largely unexplored. In this study, 28 AsJAZ genes were identified through a genome-wide analysis. The expansion of this family was primarily driven by whole-genome duplication events, with a significant majority (71.43%) of members belonging to a lineage-specific clade, Subfamily E. While AsJAZ proteins harbor conserved TIFY and Jas domains, they exhibit diverse gene structures and subcellular localization patterns. Notably, AsJAZ17 is strictly localized to the nucleus, whereas AsJAZ16 shows a nucleocytoplasmic distribution, suggesting potential functional compartmentalization within the family. Transcriptomic and qRT–PCR analyses revealed that most AsJAZ genes are responsive to heat, salt, and methyl jasmonate (MeJA) treatments. Protein–protein interaction (PPI) modeling and yeast two-hybrid (Y2H) assays confirmed that AsJAZ17 physically interacts with the MYC2 transcription factor, identifying it as a key regulator within the conserved COI1-JAZ-MYC2 signaling module. Functional validation demonstrated that overexpression of AsJAZ17 in Arabidopsis significantly enhances salt tolerance. This improvement is attributed to an optimized growth-defense trade-off and a reinforced antioxidant defense system, as evidenced by the increased activities of superoxide dismutase (SOD), peroxidase (POD), and catalase (CAT), which collectively maintain reactive oxygen species (ROS) homeostasis under stress. These findings provide comprehensive insights into the evolutionary and functional landscape of the garlic JAZ family and identify AsJAZ17 as a promising candidate gene for molecular breeding to improve abiotic stress resilience in Allium crops. Full article

Biological invasions by crop pests increasingly threaten global food security, yet the mechanisms underlying invasion success remain poorly understood, particularly within focal crop systems. Here, we examined how evolutionary history and species traits jointly shape rice pest invasions using a global dataset of 129 rice pests. We reconstructed a COI-based phylogeny, compiled ten functional traits, and analyzed invasion status using Bayesian phylogenetic and non-phylogenetic generalized linear mixed models. Invasive rice pests were non-randomly distributed across the phylogeny, with more than 50% of species in Aphididae, Gryllotalpidae, and Noctuidae being invasive. Most functional traits showed phylogenetic signal, whereas invasion status exhibited a weaker but still non-random phylogenetic pattern. Incorporating phylogeny improved model performance, with phylogenetic effects explaining more variation than measured traits alone. After accounting for phylogenetic dependence, fecundity remained the strongest positive predictor of invasion status, whereas host number, body length, and migration distance showed weaker directional trends. These findings show that rice pest invasions are jointly shaped by phylogenetic background and functional traits, and provide a basis for phylogeny-informed risk screening and biosecurity management. Full article

Poterioochromonas is a typical mixotrophic chrysophyte that plays an important ecological role in natural aquatic environments and has received particular attention from morphological and ecological perspectives over the last few decades because of its peculiar mode of feeding and relevance for practical applications. However, the taxonomic classification of this genus remains controversial, and the true extent of its diversity remains largely unknown. Here, we use a complementary approach of culturing, morphological and phylogenetic analyses, and sequence database mining to address this issue. We collected 16 cultures of Poterioochromonas to determine the essential morphological characteristics and clarify the taxonomy and phylogeny of the genus. Our results confirmed that all Poterioochromonas strains produce lorica, which is the diagnostic character for the genus. We suggest that the shape of the lorica cup and the morphology of the cyst could be used as diagnostic characteristics to differentiate different species within the genus. Molecular phylogenetic analysis based on the SSU rDNA and rbcL gene sequences confirmed the monophyly of Poterioochromonas, which is subdivided into heterotrophic and mixotrophic clades. Comparative analysis of six molecular markers revealed that the COI gene is the most sensitive for distinguishing both inter- and intraspecific relationships. An exhaustive screening of the NCBI GenBank database and publicly available amplicon sequencing datasets revealed 100 SSU rDNA gene sequences for Poterioochromonas. The results showed that many soil-derived environmental sequences grouped with heterotrophic Poterioochromonas and indicated that the heterotrophic representatives of the genus are abundant in the soil environment. The results also revealed that many environmental sequences did not group with any reference sequences of known species, indicating that the genus Poterioochromonas is much more diverse than previously thought. This study contributes to a clearer taxonomic and distributional framework for Poterioochromonas, thereby facilitating future basic and applied research on this genus and similar mixotrophic chrysophytes. Full article

Monacha cartusiana (O. F. Müller, 1774), native to the Mediterranean region and Europe, is a terrestrial gastropod recognized as a highly destructive agricultural pest that causes significant damage to crop plants, fruit trees, vegetables, ornamentals, and natural ecosystems. Despite its broad geographic distribution, the evolutionary history and phylogeographic relationships of M. cartusiana populations remain globally unexplored. This study reports the first molecularly confirmed record of M. cartusiana in Pakistan and investigates its genetic diversity and phylogeographic structure within a global context using mitochondrial markers. After morphological identification, genomic DNA was extracted from collected specimens using the CTAB method, followed by amplification and sequencing of the mitochondrial COI and 16S rRNA genes. The resulting sequences were subsequently analyzed using DnaSP and PopART software to estimate genetic diversity, perform neutrality tests, and construct haplotype networks. Published sequences of M. cartusiana retrieved from GenBank were incorporated to provide a global comparative framework. The COI dataset (555 bp) revealed 52 haplotypes, whereas the 16S rRNA dataset (269 bp) identified 14 haplotypes across global populations. High haplotype diversity (Hd = 0.946 for COI; Hd = 0.831 for 16S rRNA) and moderate nucleotide diversity (π = 0.010 for COI; π = 0.01253 for 16S rRNA) indicated substantial genetic variability within the species. Neutrality tests produced negative and insignificant values for Tajima’s D for COI and significant values for 16S rRNA (−1.428 for COI; −0.20586 for 16S rRNA) and Fu’s Fs (−29.776 for COI; −1.263 for 16S rRNA), suggesting historical population expansion. Phylogenetic reconstruction and haplotype network analyses identified two major clades (Clade A and Clade B), reflecting genetic relationships among populations from different geographic regions. AMOVA based on COI and 16S rRNA sequences revealed significant population structuring, with 29.98–51.30% of the total genetic variation occurring among populations and high fixation indices (FST = 0.299–0.51398, p = 0.001), indicating pronounced genetic differentiation and restricted gene flow. Pairwise FST analyses indicated that the Pakistani population is most closely related to populations from Italy and Central Europe, suggesting a closer genetic affinity with Southern or Central European populations. However, FST alone does not allow definitive inference of introduction directionality, and additional analyses would be required to robustly identify the source population. Overall, this study provides the first comprehensive molecular and phylogeographic assessment of the M. cartusiana species from Pakistan within a global context. These findings contribute important baseline data for understanding the evolutionary dynamics, dispersal history, and population connectivity of this economically important pest species. The pronounced genetic differentiation among populations and the suggested genetic affinity of the Pakistani population with European lineages have direct implications for biosecurity monitoring, invasion pathway tracing, and targeted pest management strategies. Future research integrating nuclear markers with the mitochondrial data presented here will be essential for a more complete understanding of gene flow and local adaptation in this species. Full article

Hypoderma diana Brauer, 1858, poses a significant threat to species of deer, yet records of this species in China remain fragmented and lack comprehensive documentation. Following high mortality in wapiti populations in Inner Mongolia during 2023–2024, surveys were conducted in the Gaogesitai Hanwula Nature Reserve in March 2025. Species identity was established through rigorous morphological analysis of third-instar larvae and an emerged adult female using light and scanning electron microscopy, supplemented by a 689 bp COI fragment. Results confirmed H. diana as the causative agent, with larvae localized along the host’s vertebral column. Comparative SEM analysis of the antennomaxillary sensory complex in H. diana, H. bovis (Linnaeus, 1758), and H. lineatum (Villers, 1789) revealed undifferentiated, volcano-like warts, contrasting sharply with the highly differentiated antennae and sensilla of Oestrus ovis Linnaeus, 1758. This study represents an inaugural record of H. diana in the Chifeng region and provides the first atlas of diagnostic features for both third-instar larvae and adults. These findings document H. diana as a critical agent of myiasis in the Manchurian wapiti, refining its known epidemiological profile in China and establishing an essential morphological reference for future wildlife health surveillance. Full article

The durian seed borer, Mudaria stahlgretschae, is a major economic pest that has significantly impacted durian cultivation in Southeast Asia; however, comprehensive biological and ecological data for this species remain limited. This study employs an integrative taxonomic approach, combining morphological examination with molecular validation of the mitochondrial cytochrome c oxidase subunit I (COI) gene. Phylogenetic analysis (Neighbor-Joining) confirmed that all collected specimens (n = 11) formed a distinct monophyletic clade within the genus Mudaria, showing a genetic identity of 95.75–96.85% with existing GenBank accessions, thereby confirming their identity as M. stahlgretschae. Systematic monitoring using light traps in Uttaradit Province revealed a clear seasonal phenology, with adult flight activity restricted to a five-month period from April to July 2025. Population density peaked in May (55.56%), synchronized with the mid-stages of durian fruit development. Furthermore, chemical profiling of female gland volatiles via GC-MS identified 40 compounds; among these, four putative sex pheromone candidates—1-Hexacosene, (Z)-7-Hexadecenal, 11-Octadecenal, and 2-Hexadecanol—were identified as key constituents based on their consistent detection across all replicates (n = 3), high relative abundance, and absence in male extracts or blank controls. These findings establish a critical foundation for developing synthetic pheromone lures and synchronized monitoring programs, offering a robust framework for the sustainable management of M. stahlgretschae in durian agroecosystems. Full article

The genus Hydrochara (Coleoptera: Hydrophilidae) comprises large-bodied water beetles associated with shallow, well-vegetated freshwater habitats and is characterised by considerable taxonomic complexity. While Hydrochara caraboides is relatively well studied in western and central Europe, lineage diversity and species boundaries within the genus remain poorly resolved in eastern and south-eastern Europe. This study uses an integrative approach combining mitochondrial DNA data, morphometric analyses, and male genital morphology to investigate Hydrochara populations in continental Croatia. Specimens were collected from floodplain and lowland aquatic habitats across major river basins, morphologically identified and verified using cytochrome oxidase subunit I (16S) sequences through comparison with reference data from public databases (GenBank and BOLD). Molecular analyses confirmed the presence of H. caraboides and Hydrochara flavipes in continental Croatia. A single specimen from the upper Drava River basin (CROH030-26) formed a distinct mitochondrial lineage positioned between H. caraboides and Hydrochara dichroma in the COI phylogeny. Morphometric analyses showed extensive overlap between this specimen and H. caraboides, indicating no clear differentiation in external body size. In contrast, examination of male genitalia revealed an intermediate aedeagus morphology with transitional characters between H. caraboides and H. dichroma. Haplotype network analysis revealed a star-like structure with a dominant central haplotype shared by most H. caraboides specimens and several low-frequency variants, while the divergent specimen occupies a peripheral position, separated from the main cluster by multiple mutational steps. These results indicate that H. caraboides is a genetically heterogeneous taxon comprising multiple divergent mitochondrial lineages, suggesting that lineage diversity within this species may be underestimated. By integrating molecular and morphological evidence, this study provides new insights into the lineage diversity of Hydrochara in floodplain ecosystems of south-eastern Europe and highlights the importance of integrative approaches for resolving species boundaries and informing freshwater biodiversity conservation. Full article

Lake Bacalar is an oligotrophic body of water considered an extreme environment due to its unusual chemistry, with many species yet to be discovered. Mysids were recently collected in this system using light traps. Most previous records of these organisms in the continental Yucatán Peninsula are from closed cenotes (sinkholes or dolines) and caves. We applied integrative taxonomy, considering morphological characters of mature males and females, their geographical distribution, and mitochondrial cytochrome C oxidase subunit I (COI) gene sequences to describe Mayamysis bacalarensis n. gen., n. sp. The morphological analyses included scanning electron microscopy (SEM) and bright-field microscopy observations. We found that M. bacalarensis n. gen., n. sp. has a unique combination of morphological characters within the tribe Gastrosaccini, such as the absence of rostrum, the terminal structure of the third pair of pleopods in males, which are highly developed and have a reduced endopod. Both sexes have a lamellar projection on the fifth abdominal segment and numerous setae (35–40) and spines (22) on the margins of the exopod and endopod of the uropods. In addition, the telson has a posterior cleft margin, bearing a total of 32 spines, the apical and lateral ones being the largest. Furthermore, the genetic sequences of these mysids indicate that the organisms from Bacalar are unique, showing an average of 15% genetic divergence from the closest relative, represented by Chlamydopleon dissimile, and over 20% to more than 50% divergence with other mysids sequenced from Mexico. The geographic range of M. bacalarensis n. gen., n. sp. includes the northern part of Chetumal Bay, a brackish oligotrophic lagoon, where organisms identical to those from Lake Bacalar were collected. This finding indicates a possible permanent connectivity through subterranean water flows. Based on the evidence, we conclude that this is a new genus and species, possibly microendemic to southeastern Quintana Roo, Mexico. Full article

Plant-parasitic reniform nematodes of the genus Rotylenchulus are semi-endoparasites of herbaceous and woody plants occurring in regions with Mediterranean, tropical, and subtropical climates. In the present study, the occurrence of reniform nematodes in the rhizosphere of three olive orchards in Central Italy and six in Sicily (Italy) was investigated. Two Rotylenchulus species were recovered in olive groves in Central Italy, and no Rotylenchulus species were found in Sicily. Using the integrative taxonomy approach, combining morphological, molecular and multivariate morphological analyses, the two species were identified as R. borealis and R. macrodoratus. The D2-D3 sequencing of four individual specimens of Italian R. macrodoratus revealed the occurrence of unique haplotypes differing in nucleotide composition each other. Interestingly, the sequencing of different ITS clones from an individual specimen of the Italian R. borealis showed two ITS paralogs differing in length and nucleotide sequence compared with those of other specimens from the same population and showing higher similarity with those from other populations. Phylogenetic analyses, based on D2-D3 expansion domains of the 28S rRNA gene, ITS, and mitochondrial COI, confirmed the high level of ribosomal variability in both species and the occurrence of new mitochondrial haplotypes for the COI. The present study confirms the occurrence of high variability in Rotylenchulus genus and the existence of variant gene copies in the same specimen that could contribute to the survival of these species in different environments. Full article

The distribution of medically significant ticks in Vietnam requires ongoing monitoring. This study presents data on tick distribution and molecular screening for Borrelia spp. and Coxiella burnetii DNA. Ticks were collected from domestic animals and vegetation in four provinces over the period of 2024–2025. Species identification was performed based on morphology and confirmed by sequencing mitochondrial COI and 16S rRNA genes. A total of 2347 ticks were collected, representing eight species from the genera Haemaphysalis, Rhipicephalus, and Amblyomma. The study provides new distribution records for H. bispinosa, H. cornigera, A. integrum, and several rarely reported species (H. lagrangei, H. hystricus, and H. wellingtoni). PCR screening revealed a relatively high detection rate of Borrelia DNA in H. cornigera from Cao Bang province. Sequencing identified the pathogen as B. theileri, the agent of bovine borreliosis. Borrelia theileri was also detected in R. microplus in other regions, indicating wider circulation. PCR screening for Coxiella burnetii was positive for 13 ticks from cattle in Cao Bang province. To rule out false-positive results due to detection of DNA from Coxiella-like endosymbionts, we sequenced a fragment of the IS1111 element for three positive samples. The sequences confirmed that the DNA belongs to bacteria of the genus Coxiella, but the data do not allow confident assignment to C. burnetii at the species level. These positive ticks originated from eight neighboring households, suggesting a potential localized focus that requires further assessment in livestock and humans to determine the epidemiological significance. This research enhances the understanding of Vietnam’s tick fauna and associated pathogens of medical and veterinary importance. Full article

This study presents the first comprehensive molecular assessment of the Lepidoptera fauna of Austria based on DNA barcodes (cytochrome c oxidase I, COI; 658 bp Folmer region). The barcode reference library comprises approximately 23,500 sequences, representing 3591 Linnaean species or about 85% of the known national species (ca. 4200 species). Congruence between morphological species identifications under the Linnaean system and barcode data was evaluated using the Barcode Index Number (BIN) system. A total of 244 species could not be unambiguously assigned, showing two to seven BINs that exhibit elevated genetic divergence and may partially represent cryptic diversity. These taxa, together with 40 currently unnamed lineages, require further integrative taxonomic assessment. The distinctiveness of the Austrian Lepidoptera fauna is discussed in the context of endemic genetic diversity. Finally, 17 new faunistic records for Austria are reported. Full article

Environmental DNA (eDNA) metabarcoding has emerged as a powerful tool for biodiversity monitoring, yet its accuracy is fundamentally constrained by the completeness and taxonomic reliability of reference sequence databases. For the Three Gorges Reservoir (TGR), no integrated multi-marker eDNA reference library exists, hampering standardized fish conservation monitoring under the Yangtze River Ten-Year Fishing Ban. Here, we constructed a comprehensive, multi-marker eDNA reference database for the fish fauna of the TGR, encompassing mitochondrial 12S rRNA, 16S rRNA, and cytochrome c oxidase subunit I (COI) gene sequences from 173 specimens (120 species) collected between 2021 and 2024. After integrating publicly available sequences, the final database comprised 161 species. Then, we quantitatively compared species annotation performance between this local database and public repositories. Results showed that while public databases achieved higher nominal species coverage (94.67%), they exhibited critical deficiencies in annotation accuracy, correctly annotating only 77.97% (12S rRNA), 75.00% (16S rRNA), and 38.14% (COI) of sequences from shared species under controlled conditions. In contrast, the local database exhibited 92.37%, 93.10% and 100% annotation accuracy for the respective markers. Optimal interspecific Kimura 2-parameter (K2P) thresholds for species delimitation were 0.00448 (12S rRNA), 0.00531 (16S rRNA), and 0.00734 (COI). In addition, 15, 0, and 4 species pairs exhibited zero interspecific distance for 12S rRNA, 16S rRNA, and COI, respectively. These limitations reinforce the need for cautious interpretation of eDNA metabarcoding results and the integration of multiple markers or complementary nuclear loci. This study provides preliminary evidence that regionally curated, multi-marker reference libraries could improve taxonomic assignment reliability in eDNA metabarcoding compared to uncurated public repositories, providing a foundational resource for biodiversity conservation. Full article

Ochetobibus elongatus (Kner) is a migratory fish found in the Yangtze River basin and areas south of it, and listed as a critically endangered (CR) fish on the China Red List of Vertebrates. To achieve group recovery and artificial breeding, this study investigated the dietary characteristics of O. elongatus based on high-throughput sequencing of its intestinal contents, and its digestive system morphology, and its histology. Results showed that the digestive system of O. elongatus lacked a stomach and mainly consisted of the oropharynx, pharyngeal teeth, esophagus, intestine, and anus. The gut index was 0.88, with clear segmentation of the foregut, midgut, and hindgut, and the visceral mass index was 7.35%. Histological analysis of the digestive system revealed the presence of keratinized dental plates or pharyngeal teeth in the pharynx, as well as a high density of taste bud cells in the soft palate of the oral cavity. The surface layer of the intestinal villi contained numerous mucous cells, with the average number of mucous cells per villus gradually increasing from the esophagus to the hindgut, and the foregut having the longest and most abundant mucosal folds. The esophagus exhibited well-developed circular and longitudinal muscle layers, while in the hindgut, both the circular and longitudinal muscle layers were slightly thicker than those in the midgut. High-throughput sequencing of the intestinal contents of O. elongatus revealed the following phyla based on 18S V4 meta-barcoding: Chlorophyta, Diatoms, Arthropoda, Basidiomycetes, and Ascomycetes, with the genus Hypophthalmichthys and algae being the main classifications. In contrast, based on COI meta-barcoding, the study newly identified the phyla Cnidaria and Mollusca, with the genera Chlorophyta, Scenedesmus, Pectinodesmus, and zooplankton such as Pseudodiaptomus. Metagenomic sequencing revealed that the gut microbiota at the phylum level was predominantly composed of Pseudomonadota, Ascomycota, Basidiomycota, Chytridiomycota, and Bacillota, with key genera including Cetobacter, Pseudomonas, Acinetobacter, Aeromonas, and Clostridium. This study indicates that O. elongatus is an omnivore with carnivorous tendencies. Basic biological research on O. elongatus is of great significance for the restoration of the population, artificial breeding, and the development of its artificially formulated feed. It also provides important data for the formulation of biodiversity conservation measures. Full article