Search Results (301)

Fruit flies that belong to the genus Zeugodacus (Diptera: Tephritidae) pose significant threats as invasive pests of agricultural crops in Asia and sub-Saharan Africa. The intensification of transboundary trade in fresh horticultural produce has increased the risk of introducing invasive species such as fruit flies, more so through the inadvertent transport of their immature developmental stages. Such immature stages of fruit flies belonging to the Tephritidae family are frequently intercepted at the international borders worldwide and are unable to be identified to the species level using morphological characteristics. Molecular identification using mitochondrial Cytochrome Oxidase I (COI) gene has proven to be quite useful, as they are not constrained by developmental stages, sex, or colour morphs of the pest species in question. Also, real-time PCR-based species-specific assays offer quicker turnaround time since they do not require any post-PCR procedures. This study evaluated the utility of a real-time PCR assay based on the COI gene region to identify Zeugodacus cucurbitae from other Tephritid species. The developed real-time PCR assay provides a swift and precise way of discriminating between these highly invasive pest species during an interception event for rapid decision making. High specificity, having no cross-reactions with closely related Tephritids, and sensitivity of the developed assay will be extremely useful in discriminating Z. cucurbitae from other closely related fruit fly species. Z. cucurbitae-specific real-time PCR developed in this study is appropriate for organizations that carry out routine diagnostics to facilitate fresh produce imports and exports. Our assay is fully optimized for rapid deployment at international borders, offering reliable detection of the target species regardless of developmental stage, sex, or geographic origins. Full article

Hainania Koller (Teleostei, Cypriniformes, Xenocyprididae) is known as a monotypic genus of sharpbelly fish that is endemic to Hainan Island, China. We describe Ha. minzhengi sp. nov., the second species of Hainania collected from Guangdong, based on morphology and molecular evidence. Phylogenetic relationships were inferred based on the mitochondrial cytochrome b (Cyt b) gene and cytochrome oxidase subunit 1 (COI) gene, by maximum likelihood and Bayesian methods and different partitioning schemes. Our result supports the sister group relationship between Ha. serrata and Ha. minzhengi sp. nov., but the monophyly of Pseudohemiculter or Hemiculterella was not recovered. A diagnostic key to Chinese species of Hainania and Pseudohemiculter is provided. Full article

In this study, the association between Neosilba batesi (Diptera: Lonchaeidae) and avocado fruits (Persea americana L.) was investigated. Fruits showing signs of rot and infested with Diptera larvae were collected from commercial orchards in the states of Michoacán and Jalisco, Mexico. N. batesi was identified in association with fruits from both trees and the ground at all sampling sites. Furthermore, a phylogenetic analysis based on the mitochondrial cytochrome c oxidase subunit I (COI) gene supported the morphological identification, showing >99% identity with records from Veracruz, and revealed distinct genetic lineages within the Neosilba genus. In a study within one Michoacán orchard, infested tree-borne fruits averaged 5.40 cm in length and 3.90 cm in width, with a mean of 9.61 larvae emerging per fruit. Females were observed to lay eggs in openings between the pedicel and the fruit, never piercing the exocarp. In contrast, on fallen fruit, they utilized existing wounds with exposed pulp. Infested avocados exhibit characteristic spots indicating the presence of internal larvae and generally detach from the tree. Larvae can feed on avocados in various stages of decomposition and may either emerge through wounds or pupate within the fruit. These findings support the opportunistic and saprophagous behavior associated with this fly species. Full article

Due to the potential role of Auchenorrhyncha in the transmission of the bacterium Xylella fastidiosa in a wide variety of cultivations, during recent years in Europe, many studies have focused on species composition, abundance and seasonal appearance of Auchenorrhyncha. However, females and nymphs are difficult to identify, as species-level identification relies primarily on male genitalia morphology. Sampling was conducted over four years in olive fields in Lesvos Island, in the Northeast Aegean, Greece, using sweep nets and Malaise traps. Both adults and nymphs were collected, with males identified to species level, while females and nymphs were separated on different morphotypes. Representatives from each morphotype and identified adults were sequenced using the mitochondrial cytochrome oxidase subunit I (COI) gene. Using a classical morphological approach, 58 species were identified to species level, and using DNA barcoding, nymph morphotypes and females were successfully identified within the families Cicadellidae, Aphrophoridae, Delphacidae and Issidae. A phylogenetic tree was generated, clustering nymphs together with the corresponding adults. Our results demonstrate the utility of combining morphological and molecular methods for accurate species identification and highlight the importance of enriching online databases with additional species records. Full article

Madagascar harbors a rich marine biodiversity, yet detailed knowledge of its fish species remains limited. Of the 1689 species listed in 2018, only 22% had accessible cytochrome oxidase I (COI) sequences in public databases. In response to growing pressure on fishery resources, this study aims to strengthen biodiversity monitoring tools. Its objectives were to enrich the COI database for Malagasy marine fishes, create the first 12S reference library, and evaluate the taxonomic resolution of different 12S metabarcodes for eDNA analysis, namely MiFish, Teleo1, AcMDB, Ac12S, and 12SF1/R1. An integrated approach combining morphological, molecular, and phylogenetic analyses was applied for specimen identification of fish captured using various types of fishing gear in Toliara and Ranobe Bays from 2018 to 2023. The Malagasy COI database now includes 2146 sequences grouped into 502 Barcode Index Numbers (BINs) from 82 families, with 14 BINs newly added to BOLD (The Barcode of Life Data Systems), and 133 cryptic species. The 12S library comprises 524 sequences representing 446 species from 78 families. Together, the genetic datasets cover 514 species from 84 families, with the most diverse being Labridae, Apogonidae, Gobiidae, Pomacentridae, and Carangidae. However, the two markers show variable taxonomic resolution: 67 species belonging to 35 families were represented solely in the COI dataset, while 10 species from nine families were identified exclusively in the 12S dataset. For 319 species with complete 12S gene sequences associated with COI BINs (Barcode Index Numbers), 12S primer sets were used to evaluate the taxonomic resolution of five 12S metabarcodes. The MiFish marker proved to be the most effective, with an optimal similarity threshold of 98.5%. This study represents a major step forward in documenting and monitoring Madagascar’s marine biodiversity and provides a valuable genetic reference for future environmental DNA (eDNA) applications. Full article

Accurate species identification of small aquatic insects remains challenging due to their morphological similarities. This study addresses this issue by developing a DNA barcode reference library for the globally distributed Brillia (Diptera: Chironomidae). We analyzed cytochrome c oxidase subunit I (COI) sequences of 241 specimens belonging to 13 Brillia species from 18 countries, including 56 newly generated and 185 publicly available COI barcodes. Our integrated approach included genetic distance analysis, haplotype network construction, and ecological niche modeling. The results revealed remarkable cryptic diversity, with sequences clustering into 30 Barcode Index Numbers and 158 unique haplotypes, most being region-specific. Notably, East Asian and North American populations showed complete genetic distinctness, suggesting long-term isolation. Environmental factors, particularly temperature and precipitation gradients, were identified as key drivers of this diversification. The study also corrected several misidentifications in existing databases. These findings significantly advance our understanding of Brillia diversity and provide a reliable molecular tool for freshwater ecosystem monitoring, with important implications for biodiversity conservation and environmental assessment. Full article

Dioryctria Zeller, 1846 (Lepidoptera: Pyralidae) is a significant genus whose species primarily infest coniferous trees and are predominantly distributed across the Northern Hemisphere. To date, 17 species within this genus have been recorded in China. This study reports the discovery of Dioryctria simplicella (Heinemann, 1863) in China. During field surveys in forests of Heilongjiang Province, D. simplicella was observed infesting the cones and trunks of Pinus sylvestris var. mongolica Litv. as larvae. Comprehensive morphological descriptions and diagnostic characteristics of the adult, larva, pupa, and egg stages of D. simplicella are provided herein to facilitate accurate species identification within the genus. Molecular phylogenetic analysis based on mitochondrial cytochrome c oxidase subunit I (COI) DNA barcoding sequences was conducted to assess the phylogenetic position of D. simplicella within Dioryctria. These results strongly support its species identity and clarify its phylogenetic relationships with congeners. This discovery not only expands the known diversity of Lepidoptera in China but also provides new data supporting taxonomic and phylogenetic studies of the genus Dioryctria. Full article

Kempnyia Klapálek, 1914 (Plecoptera: Perlidae) is the only genus within its family endemic to Brazil, being present in the Atlantic Forest and sections of the Cerrado. Taxonomic knowledge of the genus is incomplete, especially for nymphs. An integrative approach to the description of species and semaphoronts is essential for further studies. We describe a new species of Kempnyia based on morphological and molecular data, associate and describe the nymphs of both the new species and Kempnyia umbrina Froehlich, 1988, as well as expand its distribution and correct past mistakes in identification of K. umbrina. Specimens were identified morphologically and sequenced for the barcode region of the cytochrome oxidase subunit I (COI) mitochondrial gene, resulting in eight new sequences for three species of the genus. Both morphological and molecular analyses revealed a new species, Kempnyia krenaki sp. nov. Its nymph and that of K. umbrina are also described. With our additions, the number of known Kempnyia species rises to 41, of which 26 have COI sequences available in GenBank. Although only 11 nymphs have been associated and described for the genus so far, as the Kempnyia sequence database continues to grow, studies associating and describing nymphs will become more common, gradually reducing the Haeckelian deficit. Full article

This study analyses for the first time the genetic diversity, connectivity, and evolutionary dynamics of the small red scorpionfish (Scorpaena notata) in the Balearic Islands, using two mitochondrial DNA markers: Cytochrome c oxidase subunit I (COI) and the Control Region (CR). Nucleotide diversity of the COI gene was found to be low compared to other commercial fish species, suggesting that fishing may be impacting the population despite being a by-catch species. In contrast, the CR showed higher genetic variability. Demographic history analyses suggest that S. notata underwent a population expansion during the Pleistocene, possibly driven by sea-level changes. Genetic structure analyses (F_st and AMOVA) indicated genetic homogeneity and high connectivity among the Balearic Islands’ population, likely facilitated by its passive dispersion via pelagic eggs and larvae and the oceanographic conditions of the region. Our results suggest that the entire Balearic Islands could be considered as a unique Management Unit, although its potential relation to other nearby areas, such as the Iberian Peninsula, along with the analysis of additional genetic markers, should be addressed in future studies. Full article

Madhya Pradesh, a biodiversity-rich state in central India, reports sporadic non-indigenous leishmaniasis cases. Systematic entomological surveillance as part of molecular xenomonitoring in sand flies led to the discovery of a new species, Sergentomyia (Neophlebotomus) pradeepii n. sp. (Diptera: Psychodidae), from Johariya village in Sagar district, Madhya Pradesh, India. A systematic cross-sectional survey of sand flies was conducted in Bhopal, Sagar, and Hoshangabad districts of Madhya Pradesh. Standard collection methods were employed for two months, i.e., from July to August 2023. DNA barcoding targeting the mitochondrial Cytochrome c oxidase subunit I (COI) gene was performed, and the generated sequences were phylogenetically analyzed. Se. (Neo.) pradeepii, a newly recorded sand fly species, is reported in this study. Its taxonomic relationship to other congeners of subgenus Neophlebotomus is discussed. COI barcoding and phylogenetic analysis established that the specimens fit into the same taxonomic group, exhibiting negligible gene flow within the population, while a 13.4% genetic distance from congeners establishes it as a separate species. Madhya Pradesh, with its rich biodiversity and favorable conditions for sand fly proliferation, lacks systematic entomological surveillance. This study enhances the knowledge of the state’s sand fly fauna by reporting and providing a detailed morphological and molecular description of the new species. Full article

Giant clams are ecologically important coral reef animals, with many species facing imminent local extinction. While many regions have undertaken recent assessments of their biodiversity assets, persistent gaps remain even in otherwise well-surveyed areas. This study sought to understand the geographic distribution of smaller-bodied and morphologically similar giant clams, specifically Tridacna maxima and T. noae, in the eastern Indian Ocean. Due to the difficulties in reliably identifying these species using morphological characters, we confirmed species identity and investigated intraspecific variation using sequence data from the mitochondrial cytochrome C oxidase subunit I gene (COI). Seventy whole animal vouchers were newly sampled from a 1500 km span of remote northwestern Australian coastline over a decade, as part of an ongoing coral reef survey expedition of the Western Australian Museum and partners. Tridacna maxima had a limited distribution and was only genotyped from offshore oceanic reefs in the Rowley Shoals and Cocos Keeling Islands. In contrast, T. noae was well established beyond Ningaloo Reef, and was abundant at inshore sites throughout the Pilbara and Kimberley, and even offshore to Ashmore Reef. Phylogeographically, T. maxima did not group with conspecifics from the Western Pacific Ocean, including the east coast of Australia, but instead clustered with individuals from Malaysia, China, Taiwan, and Indonesia; T. noae exhibited a similar pattern. The affinity of Western Australian individuals with representatives from the Indo-Malay region and not eastern Australia will be an important consideration for these commercially important species. Novel haplotypes in both tested species occur in Western Australia. Continued sampling of eastern and central Indian Ocean giant clams, especially to continue to document the range of T. noae, is encouraged to understand connectivity in this basin. Together, these findings contribute to an improved baseline for conservation initiatives of these iconic coral reef animals in Western Australia. Full article

Biting midges, Culicoides spp. (Diptera: Ceratopogonidae), are significant vectors capable of transmitting arboviruses, such as bluetongue virus, to livestock. New Zealand is free of Culicoides, and a national surveillance programme is in place for the early detection of an incursion. Traditionally, insect trap samples from the surveillance programme are analyzed using morphology-based diagnostics under microscopes, which is time-consuming and relies on specialized taxonomic expertise. Here, we assessed the effectiveness of DNA metabarcoding using insect bulk samples and environmental DNA (eDNA) from liquid samples collected in surveillance traps. Two Cytochrome oxidase I (COI) barcoding primer sets were employed to study biodiversity and detect exotic species. The results indicated that DNA metabarcoding with homogenized insect bulk samples had a higher overall detection accuracy rate (over 81% for both primer pairs) compared to ethanol fluid-derived eDNA samples from traps (68.42% and 55.26% for the primer sets LCO1490/HCO2198 and mlCOIintF/jgHCO2198, respectively) based on congruence with morphological identification. Detection failures were likely due to eDNA extraction issues or low target species abundance. Both approaches showed similar insect community composition and diversity in the surveillance trap samples, suggesting the potential of DNA metabarcoding for biosecurity surveillance and biodiversity assessments. Overall, DNA metabarcoding using bulk insect samples could enhance the efficiency of Culicoides surveillance, reducing workload and screening time. Full article

India and Sri Lanka are known to exhibit high levels of biological diversity with many endemic taxa, such as the enigmatic scorpion genus Charmus Karsch, 1879. Members of this genus are rarely encountered in the field and are also known to be morphologically very similar, which impedes their systematic assessment. Our dedicated efforts towards sampling the members of the genus resulted in the collection of important material, which allowed us to carry out a thorough systematic revision of the genus using an integrated taxonomic approach. We propose several taxonomic changes based on the results of a detailed morphological study supported by molecular data. Charmus indicus Hirst, 1915 is synonymized with Charmus laneus Karsch, 1879, owing to the lack of morphological differences and low genetic divergence between the two taxa. We designate a neotype for Charmus sinhagadensis Tikader and Bastawade, 1983, and describe a new species from Sirumalai (Tamil Nadu, India). Moreover, we provide the first molecular phylogeny of Charmus based on Cytochrome c Oxidase subunit I (COI), 16S rRNA (16S) and 28S rRNA (28S) genes. The phylogenetic position of the genus within the family Buthidae C. L. Koch, 1837 is also tested using an independent genome-wide dataset (Ultraconserved Elements). Topological congruence and discrepancies between the phylogenies generated with Sanger sequences and the Ultraconserved Elements are commented on, and the reliability of these datasets when evaluating phylogenetic relationships at different hierarchical levels is further discussed. Full article

Species of the widespread Obsoletus Complex (Culicoides subgenus Avarita Fox, 1955) have been implicated as potential key vectors during the bluetongue and Schmallenberg epidemics in Central Europe in 2006 and 2012. Although extensive efforts have been made to clarify vector–pathogen relationships, one of the most important steps in this process—correct species identification—remains difficult, due to the presence of isomorphic species within the Obsoletus Group. To overcome the difficulties in morphological species identification, several PCR tests were developed. With the aim of developing a high-throughput PCR, capable of differentiating all putative vector species and newly described haplotypes of the subgenus Avaritia present in Europe, a dataset of 4407 published sequences of the mitochondrial (mt) cytochrome c oxidase subunit I (COI) was used to develop specific primers and probes, which can either be applied in a singleplex PCR or in different multiplex PCR approaches. The real-time PCR achieved very high diagnostic sensitivity (100%) and specificity (91.7%) and reliably detected the three clades of C. obsoletus sensu stricto (s.s.) in a pool of specimens. Thus, the new real-time PCR approach will provide an excellent tool for large-scale monitoring, which could improve the understanding of the biology, geographical distribution, and habitat preference of European biting midge species involved in the transmission of bluetongue, Schmallenberg, and epizootic hemorrhagic disease viruses. Full article

Background: Ptinidae, within the infraorder Bostrichiformia, are a cosmopolitan, ecologically diverse but poorly known group. The phylogeny within Bostrichiformia and the monophyly of Ptinidae and its phylogenetic placement in Bostrichiformia remain contentious. Methods: In this research, we determined the entire mitochondrial genome (mitogenome) of Gibbium aequinoctiale, the first representative mitogenome of the subfamily Ptininae, and reconstructed the phylogenetic relationships for Bostrichiformia based on four mitochondrial datasets using maximum likelihood (ML) and Bayesian inference (BI) methods. Results: The mitogenome of G. aequinoctiale is a circular molecule spanning 17,020 bp and harbors 37 mitochondrial genes and a presumed control region (CR). The mitogenome exhibited a marked preference for the utilization of A and T bases, which was also observed in three kinds of genes and CR. AAT was inferred as the putative candidate initiation codon for cytochrome oxidase subunits 1 (COI). The control region contains three tandem repeats (TDRs) and one poly-thymine stretch (Poly-T) in both coding strands. The phylogenetic results appeared to support the monophyly of four families, Nosodendridae, Derodontidae, Dermestidae, and Bostrichidae, and the basal position of the latter two families within Bostrichiformia. However, the family Ptinidae was not verified as monophyly because of one species diverging from the main lineage. Three families, Dermestidae, Bostrichidae, and Ptinidae, clustered as the major clade in Bostrichiformia, among which Bostrichidae and Ptinidae grouped together as sister groups. Conclusions: The present study provides valuable mitochondrial information for Ptinidae and provides novel perspectives on the inner phylogeny within the infraorder Bostrichiformia. Full article