Cytochrome Oxidase I Research Articles

Investigating the Phylogenetic Relationships of the Iranian Honey Bee with Other Bee Breeds Worldwide Using the Cytochrome Oxidase I Region

Background: Honey bees, classified within the insect class and widely distributed globally, consist of 26 identified subspecies across five evolutionary lines. Among these, the Iranian honey bee (Apis mellifera meda) is notable for its presence in Iran and neighboring regions. This subspecies exhibits unique biological traits, including a high reproductive capacity and effective propolis collection, distinguishing it from other local bee populations. Understanding genetic diversity within these populations is crucial for conservation and breeding efforts. Objectives: The aim of this study is to determine the phylogenetic relationships and natural variations of the Iranian honey bee in comparison to other bee breeds worldwide using the cytochrome oxidase I (COI) region. Methods: The study focuses on the identification of COI gene sequences in honeybees. The mitochondrial COI gene sequences related to the Iranian honey bee and eight populations of other honey bee breeds from around the world (24 ecotypes) were extracted and aligned from the genome database (NCBI). BLAST was used for sequence retrieval, and Clustal W was employed for alignment among species. Phylogenetic analysis was performed using MEGA software, applying the Neighbor Joining method to construct a phylogenetic tree based on the edited sequences. The percentage of nucleotide substitutions and replacements was calculated using the maximum likelihood method. Additionally, molecular diversity indices were computed using DnaSP software to assess genetic variation and conservation parameters among populations. Results: The bioinformatics analysis of biological data revealed that transfer substitution occurred more frequently than crossover substitution. Additionally, the percentage of substitution in pyrimidine bases was higher than in purine bases. The dN/dS substitution ratio in the gene locus sequence across the examined ecotypes was estimated at 0.08, indicating purifying selection during the evolution of this gene locus. Furthermore, examination of the COI region of the mitochondrial genome identified a total of 4 haplotypes, 20 mutations, and 195 polymorphic loci within the entire studied population. The neutrality values, based on Tajima's test, indicated effects related to genetic drift, genetic bottlenecks, or balancing selection during the evolutionary history of the studied population. Phylogenetic analysis revealed nine distinct categories of evolutionary paths for the COI gene in the studied ecotypes. In the phylogenetic tree, the Iranian honey bee was placed in a separate cluster, exhibiting the highest and lowest phylogenetic distances relative to Apis koschevnikovi and Apis mellifera, respectively. Conclusions: This research indicates that the conserved region of the mitochondrial cytochrome oxidase gene among various bee species is minimal, highlighting significant polymorphism and susceptibility to mutations. A total of 20 mutations and 195 polymorphic sites were identified, suggesting purifying selection processes that contribute to the gene's biological functions. The study also demonstrates that the COI region can effectively differentiate Iranian honey bee populations from others globally. Overall, these findings enhance our understanding of genetic diversity and evolutionary relationships within bee species, underscoring the importance of continued research for conservation efforts.

First detection of Culex tritaeniorhynchus in Western Australia using molecular diagnostics and morphological identification

BackgroundCulex tritaeniorhynchus has long been considered the primary vector of Japanese encephalitis virus (JEV), but until recently, it was considered exotic to Australia. When the species was detected in the country’s Northern Territory (NT) for the first time, the Western Australia (WA) Department of Health was cognisant of the risk it posed to the State because of the shared border and continuous mosquito habitat adjoining the two jurisdictions. The aim of this study was to undertake intensive mosquito surveillance in the Kimberley region to ascertain whether Cx. tritaeniorhynchus was present in WA, define the extent of its distribution and undertake phylogenetic analysis of select specimens to support hypothesized routes of entry into the state.MethodsCarbon dioxide (CO2)-baited encephalitis virus surveillance (EVS) mosquito traps were deployed at various sites throughout the Kimberley region by surveillance officers within the Medical Entomology unit of the Western Australia (WA) Department of Health. Mosquitoes were then morphologically identified, and a subset of four specimens were confirmed as Cx. tritaeniorhynchus by molecular identification using Cytochrome Oxidase I (COI) DNA data and phylogenetic analysis.ResultsFrom 31 March 2021 to 30 May 2024, a total of 211 female Cx. tritaeniorhynchus specimens were collected from 21 unique trap sites in the Kimberley’s Shire of Wyndham-East Kimberley (SWEK). Four COI DNA barcode regions were amplified and successfully sequenced for analysis. These sequences fell within a clade recognised as Cx. tritaeniorhynchus and specifically all sequences were in a clade with other specimens from the NT and Timor-Leste.ConclusionsThis study represents the first detection of Cx. tritaeniorhynchus in WA. Given the widespread nature of trap sites that yielded the species and consecutive seasons over which it was observed, the authors surmise that Cx. tritaeniorhynchus is now established within the northeast Kimberley region. The findings are significant given the detection of the species coincides with the first significant outbreak of JEV activity on mainland Australia involving an estimated 45 human cases of Japanese encephalitis, 80 impacted commercial piggeries and widespread feral pig activity. Although the role that Cx. tritaeniorhynchus may play in JEV transmission into the future is not yet understood, it presents a potential risk to public health in the region.Graphical abstract

First Report of the cyst nematode Heterodera koreana parasitizing bamboo (Phyllostachys reticulata) in Georgia, USA.

Soil and root samples were collected from two plots (5.5 x 6 m) cultivated with bamboo Phyllostachys reticulata (syn. P. bambusoides) at the USDA Southeastern Fruit and Tree Nut Research Station in Byron, Georgia, USA, in November 2021, December 2022, and December 2023. Each soil sample consisted of five randomly collected subsamples, which were analyzed for the presence of plant-parasitic nematodes as part of regular monitoring. No aboveground symptoms were seen in the field plots, but roots showed discoloration and stunted growth (Fig. 1A). An average population density of 160, 36, and 188 second-stage juveniles (J2) of cyst nematodes (Heterodera spp.) per 100 cm3 of soil was detected in 2021, 2022, and 2023, respectively. To confirm the cyst nematode parasitism, three healthy P. reticulata plants were transplanted into 10 cm diameter pots filled with nematode-infested soil and grown in a greenhouse at 25-28°C. After three months, young cysts containing eggs protruding from the bamboo roots were seen, confirming nematode parasitism (Fig. 1B and C). Morphological and molecular analyses were conducted to identify the nematode species. The J2 body shape was cylindrical with three incisures in lateral field and well-developed rounded stylet knobs. Measurements of J2 (n = 10) included the length (range = 406.0-518.1 μm, mean = 458.2 ± 16.1 μm) and width (16.0-17.2 μm, 16.6 ± 0.5 μm) of body, labial region height (3.0-3.6 μm, 3.2 ± 0.2 μm), stylet (17.2-18.9 μm, 18.02 ± 0.6 μm), tail (61.1-65.9 μm, 63.1 ± 5.8 μm), body width at anus (9.7-12.4 μm, 10.8 ± 0.3 μm), and hyaline tail terminus (35.4-53.0 μm, 44.0 ± 3.8 μm). The cysts (n = 5) were relatively lemon-shaped, light to dark brown in color with projected neck and vulval cone that lacked fenestration, bullae, and underbridge. Morphometrics were body length including neck (420.5-745.0 μm, 550.4 ± 72 μm), body width (345.0-544.1 μm, 430.1 ± 59 μm), and L/W ratio (1.0-1.4 μm, 1.1 ± 0.1 μm). The morphometric of vulval cone included fenestral length (48 to 69 µm, 60.2 ± 4.0 µm), fenestral width (43 to 51 µm, 48.9 ± 4.0 µm) and vulval slit (47 to 58 µm, 49.1 ± 2.6 µm). Morphology and morphometric measurements of the cysts and J2 (Fig. 2A-C) were comparable to previous reports of Korean cyst nematode, H. koreana from other Asian countries (Mundo-Ocampo et al., 2008; Wang et al., 2012; Tanha Maafi and Taheri, 2015; Sekimoto et al., 2017). For molecular diagnosis, DNA was extracted from single cysts (n= 3) using DNeasy Blood and Tissue Kit, and 28S rRNA and partial cytochrome oxidase I (COI) gene fragments were amplified using D2A/D3B and Het-coxiF/Het-coxiR primer sets, respectively according to Subbotin et al. (2015) and Hajihassani et al. (2018). PCR products were then purified by a DNA Clean & Concentrator kit (Zymo Research, CA, USA) and sequenced at Genewiz (South Plainfield, NJ, USA). The resulting sequences were deposited into the GenBank database and subjected to BLASTn searches. Sequence analysis of the 28S rRNA gene (GenBank accession number OL812726) showed that the H. koreana isolate from Georgia was 100% identical (692/692 bp) with H. koreana populations from Japan and South Korea. Analysis of the H. koreana isolate from Georgia based on the COI sequence (OL813218 and OL813219) revealed 100% similarity (421/422 bp) with a population of H. koreana from Japan and 98% similarity (409/409 bp) with a population from South Korea. To our knowledge, this is the first report of H. koreana parasitizing P. reticulata in Georgia as the second state in the USA. This nematode was first reported in Florida infecting fish pole bamboo (P. aurea) propagated from plant material from the Far East (Inserra et al. 1999). This report expands the information on the geographical distribution of H. koreana. Given the significant potential for damage to bamboo, precautions should be taken to prevent the nematode's spread to unaffected regions.

First molecular evidence of Penthaleus major (Dugés) (Penthaleidae) in Brazil

Penthaleus major (Dugés) (Penthaleidae) is an invasive pest in Brazil, first detected in 2009, attacking oat plants in Rio Grande do Sul, southern Brazil. This pest went unnoticed for almost 12 years until 2020 when suspected specimens of a blue mite were collected on oat plants in the municipalities of André da Rocha and Cachoeira do Sul, Rio Grande do Sul state, Brazil. Genomic DNA was extracted from these specimens and used for PCR amplification of a region of the mitochondrial gene Cytochrome Oxidase I (COI). The amplified fragments were sequenced, and the genetic sequences obtained were compared with those in GenBank. The results confirm, for the first time, the presence of the species P. major in Brazil using DNA barcoding. Further analysis revealed the presence of a single and specific haplotype in the country, suggesting either a single invasion or multiple invasions with the same maternal lineage.

On some new and poorly-known Chrysillini from arid western South Africa (Araneae, Salticidae)

Following a rapid biodiversity assessment of spiders in the arid western interior of South Africa, we report on the occurrence of some poorly known and new species of chrysilline jumping spiders. Helafricanus patellaris (Simon, 1901), Heliocapensis capensis (Wesołowska, 1986), H. mirabilis (Wesołowska, 1986) and Menemerus lesserti Lawrence, 1927 are recorded from the Northern Cape Province for the first time, and Heliocapensis maluti (Wesołowska & Haddad, 2014) (Lesotho) and Heliophanus deformis Wesołowska, 1986 (Angola) are recorded from South Africa for the first time, both also from the Northern Cape. The hitherto unknown females of Heliocapensis mirabilis (Wesołowska, 1986) and Icius pulchellus Haddad & Wesołowska, 2011 and the male of M. lesserti are described for the first time. Three new species are described: Icius jacksonisp. nov. (♂), Menemerus foordisp. nov. (♂) and Natta triguttatasp. nov. (♂♀). One new combination, Afraflacilla matabelensis (Wesołowska, 2011), comb. nov. (ex Pseudicius Simon, 1885), is proposed. We present the first comprehensive molecular analysis of South Africa Chrysillini jumping spiders, based on the cytochrome oxidase I (COI) gene, which supports the monophyly of all but two genera (Helafricanus Wesołowska, 1986 and Heliophanus C.L. Koch, 1833), which we briefly discuss.

Global Invasion of Thrips parvispinus (Karny) (Thysanoptera: Thripidae) Across Three Continents Associated With Its One Haplotype

ABSTRACTThrips parvispinus (Karny) is an exotic pest that has invaded many regions around the world in the last three decades. It was first detected in Florida in 2020 on ornamental plants (Hoya and Anthurium) in greenhouses and subsequently on ornamental plants in residential landscapes (Gardenia) in 2021. However, its first report on open vegetable field crops (Capsicum) in Florida was in 2022. We conducted field surveys and genetic analysis to answer three questions: (1) Is the population of T. parvispinus that invaded Florida the same as the one that has spread globally in the last few decades? (2) Is the host expansion to Capsicum in Florida a new population or the extension of the existing population reported on ornamental plants? and (3) What are the native and invaded distribution ranges of T. parvispinus? We analysed the genetic variation in the mitochondrial gene cytochrome oxidase I (COI) to address these questions. The global genetic diversity analysis of T. parvispinus revealed 18 haplotypes (populations) worldwide based on available data, but only one population (Hap1) invaded three continents: Africa, Europe, and North America. Based on available data, the highest haplotype diversity was observed in India, suggesting India may be part of the presumed native range (South and Southeast Asian countries) of T. parvispinus. Our survey of retail plant stores across 10 Florida counties indicated that plant trade is the source of T. parvispinus in open vegetable field crops and ornamental landscape plants. The outcome of this study will assist with regulatory and management decisions of T. parvispinus in Florida and elsewhere.

Phylogeography of Microphis retzii (Bleeker, 1856) and Microphis brachyurus (Bleeker, 1854) in the Pacific.

Syngnathidae are a charismatic family of teleost fishes, represented by seahorses, seadragons, and pipefishes. Syngnathidae are mainly composed of marine species, but about 30 species of pipefishes inhabit freshwater insular environments of the Indo-Pacific realm. Recent research has shown that some freshwater pipefish species are amphidromous and exhibit high intraspecific divergences across their distribution range, like Microphis brachyurus (Bleeker, 1854) distributed from Sri Lanka to French Polynesia and Microphis retzii (Bleeker, 1856) distributed from Taiwan to Indonesia. In this study, we used the mitochondrial cytochrome oxidase I (COI) partial gene of 91 specimens of M. brachyurus and 30 specimens of M. retzii from localities representative of their respective distribution area to improve knowledge on the population structure of these two widespread species. Genetic species delimitation and phylogeographic analyses were combined to explore spatial patterns of genetic diversity across the distribution ranges of the two species. We have highlighted deep genetic structuring within the two species and relate these results to various biotic and abiotic factors. For M. brachyurus, the population in Polynesia is distinct from those in the West Pacific, suggesting its distinctiveness and recognition as an evolutionary significant unit (ESU). For M. retzii, three lineages are delimited in its range distribution, suggesting the existence of two distinct species in Southeast Asia (Bali/Java/Lombok and China/Taiwan). Pipefish species are particularly vulnerable to anthropogenic pressures (inherent to Syngnathidae and insular environments). The present results, revising species delimitation and geographic distribution, will help implement effective conservation and management measures.

DNA Barcoding for the Identification of Adult Mosquitoes (Diptera: Culicidae) in Western Australia.

Precise mosquito identification is integral to effective arbovirus surveillance. Nonetheless, the conventional morphological approach to identifying mosquito species is laborious, demands expertise and presents challenges when specimens are damaged. DNA barcoding offers a promising alternative, surmounting challenges inherent in morphological identification. To integrate DNA barcoding into arbovirus surveillance effectively, a robust dataset of mosquito barcode sequences is required. This study established a comprehensive repository of Cytochrome Oxidase I (COI) barcodes, encompassing 177 samples representing 45 mosquito species from southern and northern Western Australia (WA), including 16 species which have not been previously barcoded. The average intraspecific and interspecific genetic distances were 1% and 6.8%, respectively. Anopheles annulipes sensu lato had the highest intraspecific distance at 9.1%, signifying a genetically diverse species. While validating the potential of COI barcodes to accurately differentiate mosquito species, we identified that some species pairs have low COI divergence. This includes Aedes clelandi and Ae. hesperonotius, Tripteroides atripes and Tp. punctolaeralis and Ae. turneri and Ae. stricklandi. In addition, we observed ambiguity in identification of the members of Culex sitiens subgroup (Cx. annulirostris, Cx. palpalis and Cx. sitiens) and three members of Cx. pipiens complex (Cx. australicus, Cx. globocoxitus, Cx. quinquefasciatus). In summary, despite presenting challenges in the identification of some mosquito species, the COI barcode accurately identified most of the species and generated a valuable resource that will support the WA arbovirus surveillance program and enhance public health intervention strategies for mosquito-borne disease control.

Description of a new species of Anomala Samouelle, 1819 (Coleoptera: Scarabaeidae: Rutelinae) from the Nanling Mountains (China) and remarks on three related species.

Anomala calceuiformis Huang & Lu, sp. nov. is described as a new species based on specimens collected from Mangshan National Nature Reserve, Hunan Province, China. Anomala calceuiformis sp. nov., which has an elongate, red-brown body, a strongly reflected clypeus, and convex elytral intervals, is similar to Anomala fukiensis Machatschke, 1955, Anomala longicarcarata Lin, 2002, and Anomala spatuliformis Lin, 2002. Here we provide a key to these species, describe and diagnose each of them, and compile a distribution map. In addition, the Cytochrome oxidase I (COI) DNA sequence of Anomala calceuiformis sp. nov. is provided. The morphological features that distinguish Anomala calceuiformis sp. nov. from related species are discussed.

Revealing the Genetic Differentiation of Rattus norvegicus (Berkenhout 1769) Populations by Analyzing Two Mitochondrial Markers

Rattus norvegicus (Brown rat) has a great importance for public health and economy because it lives in close association with human populations. However, molecular systematic studies on global populations of R. norvegicus are very few. In this study, sequences obtained from Europe, Asia, Africa, and America regions were analyzed using mitochondrial Cytochrome-b and Cytochrome oxidase-I gene regions and genetic differentiation levels between these populations were revealed. Accordingly, samples belonging to the studied populations did not split in Bayesian Inference trees and Median-joining networks; these samples also formed common haplotypes, and mean genetic distance and fixation index values were generally low. The results of the study showed that gene flow between these populations may be continuing due to the transportation activity by humans.

Molecular identification of ecologically relevant hoverflies (Diptera, Syrphidae) from eastern India

Syrphid identification keys that cover all life cycle stages of the taxonomy are insufficient, and there are problems with the morphological identification of these flies. Cytochrome oxidase I (COI) is widely used for molecular identification and phylogenetic reconstruction. The study examined the effectiveness of COI in identifying 18 specimens containing 13 agriculturally important species of syrphids collected from different geo-climatic regions of West Bengal. Phylogenetic analysis was performed using Maximum Likelihood (ML) and Bayesian (BA) trees, which were almost congruent. Barcodes were generated for Dasysyrphus orsua and Eristalinus polychromata for the first time. This is the first study to use the COI for barcoding ecologically and agriculturally relevant syrphid flies from eastern India and their phylogeny. The findings contribute to the basic understanding of the diversity of syrphids across West Bengal and the molecular characterization of hoverflies, promoting their conservation and thus leading to the augmentation of crops.

Is the mantid Brunneria borealis (Mantodea: Coptopterygidae) really a native North American, or actually a South American colonist?

Abstract The common grass mantid, Brunneria borealis Scudder, is well known as perhaps the only completely parthenogenetic species among the more than 2,400 named mantid species. An abundant mantid within its broad geographic range, it has long been considered a native North American endemic; however, all other known species in the genus Brunneria (and in its family, Coptopterygidae) are South American. We were able, for the first time, to perform a genetic comparison between B. borealis and a congeneric South American species, B. subaptera. We sequenced a standard segment of the mitochondrial cytochrome oxidase I (COI) gene for which there is no variation among different populations among localities throughout the range of B. borealis, and compared this sequence with haplotypes from different South American populations of B. subaptera. The single B. borealis haplotype falls within the genetic variation of populations of B. subaptera, suggesting that the North American mantid is really a colonist from this South American species.

Barcode Reveals Hidden Diversity and Cryptic Speciation among Butterfly Rays Distributed in the Americas

The taxonomic status of butterfly rays within the genus Gymnura remains a subject of ongoing debate among researchers. Some authors recognize up to five valid species for the Americas, while others considered several to be synonyms, which has posed a persistent challenge. We aimed to shed light on this complexity by employing molecular operational taxonomic units (MOTUs) based on the mitochondrial gene cytochrome oxidase I (COI). Genetic sequences were obtained from fresh muscle tissue collected in the marine ecoregions corresponding to the type locality from all the nominal butterfly ray species distributed along the Eastern Tropical Pacific (ETP). Our results unveiled compelling findings; all the species delimitation models used consistently identified seven MOTUs for the American continent and an extra G. altavela MOTU restricted to Africa. In addition, our results and models exceeded the worldwide accepted interspecific threshold of 2.0%. Remarkably, our results support the taxonomic reinstatement of Gymnura afuerae (Hildebrand, 1946) as a valid species, with a range expanding into the ETP in the Southern Hemisphere. Similarly, our data support the recent suggestion of resurrecting Gymnura valenciennii (Duméril, 1865) as a valid species in the western Atlantic. These findings urge a reassessment of the conservation status and a comprehensive taxonomic revision of American butterfly rays.

Comparative phylogeography and genetic diversity of two co-occurring anti-tropical krill species Hansarsia megalops and Thysanoessa gregaria in the Atlantic Ocean

Abstract Hansarsia megalops and Thysanoessa gregaria are two abundant krill species in the warm-temperate belts in the North and South Atlantic. This pattern of disjunct distribution, often referred to as anti-tropical (or bipolar), is a regular phenomenon among marine organisms that can appear at different taxonomic levels. Analysis of spatial genetic diversity based on variation of the mitochondrial cytochrome oxidase I (COI) gene was carried out to understand whether these broadly sympatric krill species have similar patterns in population structure and demographic history. The results suggested that the anti-tropical distribution of both species was driven by trans-equatorial migrations during different historical periods. We observed contrasting differences in genetic diversity between species coupled with similar patterns of genetic diversity and structure in disjunct populations on both sides of the equator. We also found additional genetically distinctive populations of T. gregaria in the South Atlantic in Subantarctic waters and showed that the Southern Subtropical Frontal Zone acts as a strong boundary between two genetically distinctive populations of T. gregaria. The results suggest that both species-specific habitat preferences and interactions between closely related species (congeners) may shape differences in population genetic diversity and structure among species.

High-resolution melting analysis to authenticate deer-derived materials in processed products in China using a cytochrome oxidase I mini-barcode.

Deer-derived materials (antler, venison, fetus, penis, bone, tail, and others) are some of the most valuable traditional animal-based medicinal and food materials in China. In production, processing, and trade, the quality of deer products varies. The market is confusing, and counterfeit and shoddy products are common. There is an urgent need to establish an accurate identification method. Two pairs of primers suitable for identifying deer-derived medicinal materials were obtained by screening the cytochrome oxidase I (COI) sequences of 18 species from nine genera of the deer family. The two primers were used to identify the species and adulteration of 22 batches of commercially available deer-derived products with a mini-barcode combining high-resolution melting (HRM) technology and methodical investigation. Deer-derived materials (sika and red deer) were correctly identified by species using varying DNA amounts (1 to 500 ng). The two pairs of primers COI-1FR and COI-2FR yielded melting temperatures (Tm) of 80.55 to 81.00 °C and 82.00 to 82.50 °C for sika deer, and 81.00 to 82.00 °C and 81.40 to 82.00 °C for red deer. Twenty-two batches of commercially available samples were analyzed by HRM analysis and conventional amplification sequencing, and it was found that the species samples had an error rate of species labeling of 31.8%. Four batches of samples were identified as mixed (adulterated) in the HRM analysis. The combination of DNA mini-barcode with HRM analysis facilitated the accurate identification of species of deer-derived materials, especially the identification of samples in an adulterated mixed state. © 2024 Society of Chemical Industry.

Applicability and perspectives for DNA barcoding of soil invertebrates

Belowground invertebrate communities are dominated by species-rich and very small microarthropods that require long handling times and high taxonomic expertise for species determination. Molecular based methods like metabarcoding circumvent the morphological determination process by assigning taxa bioinformatically based on sequence information. The potential to analyse diverse and cryptic communities in short time at high taxonomic resolution is promising. However, metabarcoding studies revealed that taxonomic assignment below family-level in Collembola (Hexapoda) and Oribatida (Acariformes) is difficult and often fails. These are the most abundant and species-rich soil-living microarthropods, and the application of molecular-based, automated species determination would be most beneficial in these taxa. In this study, we analysed the presence of a barcoding gap in the standard barcoding gene cytochrome oxidase I (COI) in Collembola and Oribatida. The barcoding gap describes a significant difference between intra- and interspecific genetic distances among taxa and is essential for bioinformatic taxa assignment. We collected COI sequences of Collembola and Oribatida from BOLD and NCBI and focused on species with a wide geographic sampling to capture the range of their intraspecific variance. Our results show that intra- and interspecific genetic distances in COI overlapped in most species, impeding accurate assignment. When a barcoding gap was present, it exceeded the standard threshold of 3% intraspecific distances and also differed between species. Automatic specimen assignments also showed that most species comprised of multiple genetic lineages that caused ambiguous taxon assignments in distance-based methods. Character-based taxonomic assignment using phylogenetic trees and monophyletic clades as criteria worked for some species of Oribatida but failed completely for Collembola. Notably, parthenogenetic species showed lower genetic variance in COI and more accurate species assignment than sexual species. The different patterns in genetic diversity among species suggest that the different degrees of genetic variance result from deep evolutionary distances. This indicates that a single genetic threshold, or a single standard gene, will probably not be sufficient for the molecular species identification of many Collembola and Oribatida taxa. Our results also show that haplotype diversity in some of the investigated taxa was not even nearly covered, but coverage was better for Collembola than for Oribatida. Additional use of secondary barcoding genes and long-read sequencing of marker genes can improve metabarcoding studies. We also recommend the construction of pan-genomes and pan-barcodes of species lacking a barcoding gap. This will allow both to identify species boundaries, and to cover the full range of variability in the marker genes, making molecular identification also possible for species with highly diverse barcode sequences.

Shallow-water Trapezioidea (Decapoda: Brachyura) from the South China Sea, including two new records, and notes on Tetralia glaberrima Herbst, 1790.

A collection of coral symbiotic crabs (Trapezioidea) from the South China Sea reports a total of 24 species, including 12 species of Trapeziidae (including one new record: Trapezia plana Ward, 1941), four species of Domeciidae, and eight species of Tetraliidae (including one new record: Tetralia brengelae Trautwein, 2007). Live color and mitochondrial cytochrome oxidase I (COI) sequence data of all species are provided.

Comparative Study of Two Himalayan Snow Trouts, Schizothorax esocinus and Schizothorax curvifrons Within the Schizothoracinae and Other Nearest Relatives of Cyprinidae, Inferred from Mitochondrial Sequences of Cytochrome b (Cyt-b) and Cytochrome Oxidase I (Co-I) Gene.

The Himalayan region encompasses varied aquatic ecosystems, characterized by the presence of diverse ichthyofauna, particularly represented by members of the Schizothorax genus, commonly referred to as snow trout. The primary objective of this work was to examine the molecular phylogeny of Schizothoracinae, specifically focusing on the two species, Schizothorax esocinus and Schizothorax curvifrons, which are known to inhabit the northern and north-eastern regions of the Himalayas. This investigation was conducted by analyzing the entire mitochondrial Cyt-b and Co-I gene sequences. The aligned Cyt-b and Co-I sequences for S. esocinus, S. curvifrons, and related members within the subfamily Schizothoracinae, spanned 1130 to 1141 and 1536 to 1551 base pairs, respectively. Using these gene, phylogenetic trees were created to compare Schizothoracinae species to other subfamilies of the family Cyprinidae (Barbinae, Alburninae, Leuciscinae, Xenocyprinae, Cyprininae, and Cultrinae). Genetic distances for Cyt-b and Co-I sequence at three hierarchical levels shows significant disparities in their average score. For Cyt-b, average p-distances for intraspecies, intragenus, and intrafamily were 2.13%, 4.1%, and 15.23%, respectively. Similarly, for Co-I, average p-distances were 1.19%, 3.6%, and 13.8% for intraspecies, intragenus, and intrafamily, respectively. Total number of haplotypes (h) based on Cyt-b and Co-I gene were 6 and 12 within the target Schizothorax spp. In the present study, the observed range of haplotype diversity (hd) for the Cyt-b gene varied from 0.00 to 0.847, with an average haplotype diversity of 0.847 ± 0.034. Similarly, for the Co-I gene, the observed haplotype diversity ranged from 0.00 to 0.931, with an average value of haplotype diversity estimated to be 0.931 ± 0.024. The results of the present study clearly shows that the representative species exhibited close affinities with members of Barbinae and Cyprininae, while other subfamilies formed distinct groups. The findings of the study also indicated that the Cyt-b and Co-I gene exhibits polymorphism and has the potential to serve as a marker for identifying genetic differentiation among populations based on ecological habitats. Mitochondrial Cyt-b and Co-I have been established as a universally accepted and validated genetic marker within a comprehensive bio-identification system at the species level.

In Silico Analysis of Cytochrome Oxidase-I Gene Variation in the Genus Ceratitis1

In Silico Analysis of Cytochrome Oxidase-I Gene Variation in the Genus Ceratitis1

Biodiversity of Demersal Fish Communities in the Cosmonaut Sea Revealed by DNA Barcoding Analyses.

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