Mitochondrial COI Sequences Research Articles

A new species of genus Acrossus Mulsant, 1842 (Scarabaeidae, Aphodiinae, Aphodiini) from South Korea.

A new species of the genus Acrossus Mulsant, 1842, Acrossusbaei sp. nov. from South Korea, is described and illustrated on the basis of morphology and mitochondrial COI sequences. The species was compared with four related species; Acrossusatratus (Waterhouse, 1875), A.humerospinosus (Petrovitz, 1958), A.luridus (Fabricius, 1775), and A.superatratus (Nomura & Nakane, 1951). The taxonomic status and diagnostic characters of the new species are discussed. A key to species of the genus Acrossus in the Korean Peninsula is given.

Megachilid bees (Hymenoptera: Anthophila: Megachilidae) of Ladakh: A morphological and molecular approach

The megachilid bees of Ladakh are documented based on the collections deposited in the National Zoological Collection and the collections made from Leh district by S. Angmo during 2020–2023. Accounts of sixteen species known from this region belonging to three tribes viz., Anthidiini (03 species), Megachilini (09 species) and Osmiini (01 species) are provided. Thirteen species have been detected among which seven species, Stelis scutellaris Morawitz, Coelioxys conoideus (Illiger), Coelioxys rufescens Lepeletier and Serville, Megachile creutzburgi (Tkalců), Megachile leachella Curtis, Megachile lagopoda (Linnaeus) and Megachile maritima (Kirby) are new to India, while three among the remaining six species are new to Ladakh. Floral associations for the recently collected specimens are provided. The Mitochondrial COI sequences of 09 species are deposited in BOLD/NCBI among which sequences for 03 species are novel deposits. Based on the COI sequences already available in the database and the sequences deposited, a phylogenetic tree for the studied specimens has been included.

Genetic structure of a population of “peanutfish” (“dragonfish”) sea cucumbers using mitochondrial COI sequences in Marau, Guadalcanal, Solomon Islands

Genetic structure of a population of “peanutfish” (“dragonfish”) sea cucumbers using mitochondrial COI sequences in Marau, Guadalcanal, Solomon Islands

Two new species of the genus Sycanus Amyot & Serville (Insecta: Hemiptera: Reduviidae: Harpactorinae) from Vietnam

The genus Sycanus Amyot & Serville, 1843 includes seventy-two valid species distributed in African and Asian regions. Among those species, eight of them, Sycanus atrocoeruleus Signoret, 1862, S. bifidus (Fabricius, 1787), S. croceus Hsiao, 1979, S. falleni Stål, 1863, S. minor Hsiao, 1979, S. rubricatus Stål, 1874, S. sichuanensis Hsiao, 1979, and S. ventralis Distant, 1919, were described and recorded in Vietnam. In this study, we examined species of Sycanus collected from Vietnam based on external morphology, male genital morphology, and molecular phylogenetic analyses inferred from mitochondrial COI sequences. Consequently, two new species, Sycanus thuathienhuensis sp. nov. and Sycanus taynguyenensis sp. nov., were discovered, described, and illustrated here.

Climate change will lead to range shifts and genetic diversity losses of dung beetles in the Gobi Desert and Mongolian Steppe

Desertification is known to be a major threat to biodiversity, yet our understanding of the consequent decline in biodiversity remains insufficient. Here, we predicted climate change-induced range shifts and genetic diversity losses in three model dung beetles: Colobopterus erraticus, Cheironitis eumenes, and Gymnopleurus mopsus, distributed across the Gobi Desert and Mongolian Steppe, areas known for desertification. Phylogeographic analyses of mitochondrial COI sequences and species distribution modeling, based on extensive field investigations spanning 14 years, were performed. Species confined to a single biome were predicted to contract and shift their distribution in response to climate change, whereas widespread species was predicted to expand even if affected by range shifts. We indicated that all species are expected to experience significant haplotype losses, yet the presence of high singleton frequencies and low genetic divergence across geographic configurations and lineages mitigate loss of genetic diversity. Notably, Cheironitis eumenes, a desert species with low genetic diversity, appears to be the most vulnerable to climate change due to the extensive degradation in the Gobi Desert. This is the first study to predict the response of insects to desertification in the Gobi Desert. Our findings highlight that dung beetles in the Gobi Desert and Mongolian Steppe might experience high rates of occupancy turnover and genetic loss, which could reshuffle the species composition.

DNA barcoding is currently unreliable for species identification in most crayfishes.

DNA barcoding is commonly used for species identification. Despite this, there has not been a comprehensive assessment of the utility of DNA barcoding in crayfishes (Decapoda: Astacidea). Here we examined the extent to which local barcoding gaps (used for species identification) and global barcoding gaps (used for species discovery) exist among crayfishes, and whether global gaps met a previously suggested 10× threshold (mean interspecific difference being 10× larger than mean intra specific difference). We examined barcoding gaps using publicly available mitochondrial COI sequence data from the National Center for Biotechnology Information's nucleotide database. We created two versions of the COI datasets used for downstream analyses: one focused on the number of unique haplotypes (N H) per species, and another that focused on total number of sequences (N S; i.e., including redundant haplotypes) per species. A total of 81 species were included, with 58 species and five genera from the family Cambaridae and 23 species from three genera from the family Parastacidae. Local barcoding gaps were present in only 30 species (20 Cambaridae and 10 Parastacidae species). We detected global barcoding gaps in only four genera (Cambarus, Cherax, Euastacus, and Tenuibranchiurus), which were all below (4.2× to 5.2×) the previously suggested 10× threshold. We propose that a ~5× threshold would be a more appropriate working hypothesis for species discovery. While the N H and N S datasets yielded largely similar results, there were some discrepant inferences. To understand why some species lacked a local barcoding gap, we performed species delimitation analyses for each genus using the N H dataset. These results suggest that current taxonomy in crayfishes may be inadequate for the majority of examined species, and that even species with local barcoding gaps present may be in need of taxonomic revisions. Currently, the utility of DNA barcoding for species identification and discovery in crayfish is quite limited, and caution should be exercised when mitochondrial-based approaches are used in place of taxonomic expertise. Assessment of the evidence for local and global barcoding gaps is important for understanding the reliability of molecular species identification and discovery, but outcomes are dependent on the current state of taxonomy. As this improves (e.g., via resolving species complexes, possibly elevating some subspecies to the species-level status, and redressing specimen misidentifications in natural history and other collections), so too will the utility of DNA barcoding.

Phylogeography of the Intertidal Limpet Lottia dorsuosa (Mollusca: Gastropoda: Lottiidae).

We investigated geographic, genetic, and morphological variations in the intertidal limpet Lottia dorsuosa, a species with a broad distribution across Japan. A total of 98 specimens were obtained from 36 locations spanning the entire Japanese Archipelago, encompassing both the northern and southern regions. Examination of mitochondrial COI sequences revealed a distinct geographic genetic structure, delineating three prominent clades: (1) the Kuroshio Current, (2) the Tsushima Current, and (3) the Ryukyu-China groups. The observed geographical structuring between the Pacific and Sea of Japan side mirror patterns was noted in previously studied species, such as Turbo sazae and Batillaria attramentaria. Within L. dorsuosa, the Kuroshio Current group exhibited a substantial genetic distance, reaching a maximum of 12.35%, when compared to the more closely linked Tsushima Current and Ryukyu-China groups. Compared to other groups, the Ryukyu and China groups represented relatively recent differentiations, and the former group is currently facing a heightened risk of extinction owing to its sparse population density. The emergence of intraspecific geographic structures is likely attributable to the comparatively brief planktonic larval stage, which is a common characteristic of patellogastropod limpets.

Remarkable sexual dimorphism found in Nosophora insignis (Butler) (Lepidoptera, Crambidae, Spilomelinae)

An unidentified spilomeline moth, “Nosophora sp.” was first illustrated by Inoue (1982) from Japan. Since little is known about the immature stage of “Nosophora sp.”, we attempted to rear this species from eggs. As a result, we found that “Nosophora sp.” can be successfully reared on Quercus serrata Murray and Q. glauca Thunb. Surprisingly, of the adults that emerged, all females showed the “Nosophora sp.” phenotypes, while all males showed the N. insignis (Butler, 1881) phenotypes. We also found that the mitochondrial COI sequences of “Nosophora sp.” and N. insignis are completely identical. Based on these results, we concluded that “Nosophora sp.” and N. insignis represent the sexual dimorphisms of the same species, and redescribed N. insignis.

A review of Nearctic Lathrobium (Coleoptera, Staphylinidae), with revision and descriptions of new flightless species from the mountains of the southeastern U.S.

Species of the genus Lathrobium Gravenhorst (Coleoptera: Staphylinidae: Paederinae) from North America north of Mexico are reviewed and 41 species are recognized. Morphology and mitochondrial COI sequence data were used to guide species designations in three flightless lineages endemic to the southern Appalachian Mountains, a biologically diverse region known for cryptic diversity. Using a combination of phylogeny, algorithm-based species delimitation analyses, and genitalic morphology, five new cryptic species are described and possible biogeographic scenarios for their speciation hypothesized: L.balsamense Haberski & Caterino, sp. nov., L.camplyacra Haberski & Caterino, sp. nov., L.islae Haberski & Caterino, sp. nov., L.lividum Haberski & Caterino, sp. nov., L.smokiense Haberski & Caterino, sp. nov. Five additional species are described: L.absconditum Haberski & Caterino, sp. nov., L.hardeni Haberski & Caterino, sp. nov., L.lapidum Haberski & Caterino, sp. nov., L.solum Haberski & Caterino, sp. nov., and L.thompsonorum Haberski & Caterino, sp. nov. Two species are transferred from Lathrobium to Pseudolathra Casey: Pseudolathraparcum (LeConte, 1880), comb. nov. and Pseudolathratexana (Casey, 1905), comb. nov. Twenty-six names are reduced to synonymy. Lectotypes are designated for 47 species. Larvae are described where known, and characters of possible diagnostic value are summarized. Species diagnoses, distributions, illustrations of male and female genitalia, and a key to Lathrobium species known from the Nearctic region (including several introduced species) are provided.

DNA barcoding, life history and taxonomy of Lablab pod borer, Adisura atkinsoni Moore (Lepidoptera, Noctuidae)

DNA barcoding and morphological characters together with thorough bioecological investigations to diagnose field bean pod borer, Adisura atkinsoni Moore, 1881 an important pest was carried out. A. atkinsoni has a limited host range. The incidence of Adisura was higher on local varieties (photo sensitive) compared to HA4 hybrid (photo-insensitive). The field bean pod borer appeared during middle of October and continue to March. The undefined taxa were identified using both female and male genitalia. But since they could be differentiated from their morphologically closest relative, they were marked as sensu lato. While doing BLAST analysis, the mitochondrial COI Sequence of Adisura specimens collected from Bengaluru showed similarity to A. bella. In the phylogenetic tree, these two samples Sp1 and Sp2 separate new sub-clade which stands separately from the rest of the Adisura species. It was identified that the lepidopteran samples collected from Bengaluru are Adisura and the DNA sequences did not match with any of the existing species of Adisura. The shift in this pest’s prevalence has been discussed.

A new species of freshwater snail of Fenouilia (Gastropoda, Pomatiopsidae) from northern Guangxi, China, based on morphological and DNA evidence.

A new species of pomatiopsid freshwater snail, Fenouiliaundata Chen & He, sp. nov., is described from Guangxi, China, based on morphological and molecular evidence. The new species can be distinguished from its congeners by the following combination of characters: shell with low, prosocline, rounded axial ribs and fine spiral striae, broader than high; aperture broader than shell height; radula with lateral teeth have only two or three faint, wavy ridges on inner side. A molecular analysis of partial mitochondrial COI and 16S DNA sequences supports the systematic position of the new taxon.

Genetic and Distribution Data of the Bramble Shark Echinorhinus brucus (Bonnaterre, 1788) and the Prickly Shark Echinorhinus cookei Pietschmann, 1928 to Better Reconstruct Their Conservation Status.

Elasmobranch species show low resilience in relation to anthropogenic stressors such as fishing efforts, loss of habitats, and climate change. In this sense, the elasmobranch populations appear to be at risk of extinction in many cases. Despite conservation researchers making efforts to implement knowledge, the information on the biology, reproduction, distribution, or genetic structure of some species is still scattered, often caused by the occurrence of species in inaccessible habitats. Echinorhinus brucus is a deep benthic shark evaluated as "Endangered" on which little information is available, particularly about its geographical range and genetic structure, while E. cookei is listed as "Data Deficient". Echinorhinus brucus belongs to the Echinorhinidae family, and its unique congeneric species is E. cookei. The main morphological diagnostic characteristic of both species is the presence of denticles with different shapes and patterns on the derma. In the present paper, mitochondrial COI and NADH2 sequences were retrieved from both E. brucus and E. cookei species, and analyses were conducted by applying different models of phylogenetic inference. Sequences of E. brucus captured in the Indian Ocean (IOS) did not cluster with the Atlantic E. brucus counterparts (AOS) but instead with E. cookei sequences; the different models showed an overlapping tree topology. Concurrently, a review of the historical and recent captures of the two species was carried out. The worldwide distribution of E. brucus excludes the Pacific Ocean area, where E. cookei occurs, and is characterised by presumably current local extinctions in the North Sea and the western Mediterranean Sea. The dataset describes two definite areas of significantly high abundance of E. brucus located in the Atlantic Ocean (Brazil) and the Indian Ocean (India). These areas suggest zones for conservation plans, especially considering the two lineages identified through molecular approaches.

Morphological Ontogeny, Ecology, and Biogeography of Fuscozetes fuscipes (Acari, Oribatida, Ceratozetidae).

The systematic status of Fuscozetes Sellnick, 1928, is not clear in the literature. Therefore, the morphological ontogeny of F. fuscipes (C.L. Koch, 1844), the type species of this genus, was investigated and compared with its congeners in this study, and a new diagnosis of Fuscozetes is given. The juveniles of F. fuscipes are light brown, with a brown prodorsum, sclerites, epimeres, and legs. In all juveniles, a humeral organ and a humeral macrosclerite are present. The gastronotum of the larva has 12 pairs of setae (h3 is present), whereas the nymphs have 15 pairs. In the larva, the gastronotal shield is weakly developed, and most gastronotal setae are short except for a slightly longer h2. Most of the gastronotal setae are inserted on the microsclerites except for h3, and several other macrosclerites and many microsclerites are present on the hysterosoma. In the nymphs, the gastronotal shield is well developed, with 10 pairs of setae (d-, l-, and h-series, and p1), and setae p2 and p3 are located on a large posteroventral macrosclerite. In all the instars, femora I and II are oval in cross-section, without a large ventral carina. Mitochondrial COI sequence data revealed a deep split between the Nearctic and Palearctic populations of F. fuscipes, and a less, but significant, divergence within each continent. These strong geographical barriers were contrasted with multiple cases of shared haplotypes over long distances in the Palearctic, indicating high migration rates in modern times.

The Nanling Mountains of southern China played a variable role as a barrier and refuge for birds depending upon landscape structure and timing of events

The Nanling Mountains, an important mountain range and watershed in south China, harbor a wealth of relictual plant species, and are considered a ‘museum' of subtropical biodiversity. With respect to birds, however, the roles of the Nanling Mountains in impeding the dispersal of the subtropical birds and, as a result, shaping their population and community structures have received little consideration. To examine these roles, we compiled and analyzed two datasets. 1) To test the mountains' influence on gene flow, we undertook a comparative phylogeographic study comparing mitochondrial COI and Cytb DNA sequences of five sylvioid resident bird species of the mountains (Huet's fulvetta Alcippe hueti, red‐billed leiothrix Leiothrix lutea, greater necklaced laughingthrush Pterorhinus pectoralis, Indochinese yuhina Staphida torqueola and mountain bulbul Ixos mcclellandii). 2) To examine differential community development over the history of modern birds, we examined distributional data of all species of the Nanling region using public species occurrence records. For part 1), we sampled 327 individuals from 36 sites and conducted correlation analysis of genetic and geographic distances, taking into account the landscape of the mountains. We found that the mountains do not seriously impede gene flow among populations but influenced species differently. For part 2), comparative analysis of 446 species in 81 families indicated that family membership influenced the community composition of birds in Nanling region. Variation in family distributions is attributable to both environmental and evolutionary factors. Overall, we found that the Nanling Mountains are not currently a substantial barrier to gene flow among the species we studied but act as a corridor and refuge for these birds. However, analyses on higher ranked community data suggest the mountains acted as a barrier in older times, corresponding to the known diversification events in southeast Asian avifauna.

Untangling the taxonomic ambiguities of the spotted seerfish Scomberomorus guttatus with the description of a new species from India.

Scomberomorus guttatus has been subjected to a series of synonym assignations over the years. Its taxonomy has been mired with ambiguities due to the greater-than-average morphological variations observed in samples from different regions. An integrated taxonomic revision with molecular support indicated that the species that was thought to be a single entity, in reality, is a complex of three distinct species. They are morphologically distinct with respect to the body depth and elongation, cephalic morphometry, and meristic characteristics. Otolith morphometry and phylogenetic evidence further established the taxonomic divergence within the spotted seerfish complex. The phylogenetic characteristic as indicated by the mitochondrial Cytochrome c Oxidase subunit I (COI) sequence unveiled that S. guttatus had a high intraspecific divergence of 11.1% from its two identical congeners and a divergence of 2.34% between the congeners, indicating scope for categorizing them as separate species. Based on the morphological and molecular evidence, S. guttatus is redescribed; the senior synonym Scomberomorus leopardus is resurrected as a valid species; and a new species Scomberomorus avirostrus n. sp. is described with keys for species distinction.

Comparative ontogeny and phylogenetic relationships of eight lizardfish species (Synodontidae) from the Northwest Pacific, with a focus on Trachinocephalus monophyly.

Lizardfish (Aulopiforms: Synodontidae), distributed broadly in temperate to tropical waters, are represented globally by 83 species across four genera, with 10 species in Korea. Despite these numbers, few studies have been conducted on the early life history of lizardfishes compared to their adult counterparts. Thus, we conducted molecular identification of 123 Synodontidae larvae collected from the Northwest Pacific (Korea Strait, Yellow Sea, East China Sea, and East Sea) between June 2017 and July 2021, using mitochondrial DNA COI and 16S rRNA sequences. Significant morphological differences were observed in the larvae and juvenile, including variation in melanophore, count, morphometric characteristics, and body shape. The morphological traits of eight species (Harpadon nehereus, Saurida macrolepis, Saurida wanieso, Saurida sp., Synodus hoshinonis, Synodus kaianus, Synodus macrops, and Trachinocephalus trachinus) served as vital data for interpreting the phylogenetic relationships within the Northwest Pacific Synodontidae. Ultimately, the identification key revealed by this study will enable accurate identification of Synodontid larvae and juveniles, and further facilitate our understanding of the phylogenetic relationships within this family.

Clarification of the identity of deep-sea crab Tymolus uncifer (Ortmann, 1892) and validation of Tymolus melanommus (Doflein, 1904) (Decapoda: Brachyura: Cyclodorippidae).

Examination of material from Japanese waters has disclosed that two species have been confounded under Tymolus uncifer (Ortmann, 1892) (Decapoda: Brachyura: Cyclodorippidae) in previous literature. The identity of Tymolus uncifer sensu stricto is clarified in reference to the lectotype, and the second taxon is herein attributed to T. melanommus (Doflein, 1904), which was originally recognised as a forma of T. uncifer with one specimen from off Kenya and one specimen from Japan. A lectotype is herein selected for T. melanommus in the interest of nomenclatural stability. Differentiating characters between the two species are assessed in detail, and those two species are compared also with T. glaucommus (Alcock, 1894), T. similis (Grant, 1905), T. brucei Tavares, 1991, T. daviei Tavares, 1997, T. hirtipes Tan & Huang, 2000 and T. globosus Spiridonov & Trkay, 2007, all of them are considered as valid. Sexual dimorphism and ontogenetic variation are seen in the relative length and stoutness of the pereopods 2 and 3 in T. uncifer and T. melanommus, but the morphometric characters derived from the two pereopods are useful as diagnostic at comparison between same sex in adults. Comparison of partial fragments of the mitochondrial COI and 16S rRNA gene sequences strongly supports that the two taxa are distinct. Previous records of T. uncifer, including fossil records, are reviewed based on the present findings. Tymolus uncifer and T. melanommus are restricted to Japanese waters at present.

A possible circulation of a dominant Dibothriocephalus nihonkaiensis haplotype in Japan revealed by molecular analysis of clinical tapeworm samples.

Human diphyllobothriasis, caused by Dibothriocephalus nihonkaiensis, is prevalent globally, especially in regions where raw fish is consumed. Recent molecular diagnostic techniques have made species identification of tapeworm parasites and the determination of genetic variations among parasite populations possible. However, only a few studies done over a decade ago, have reported on the genetic variation among D. nihonkaiensis in Japan. The present study employed PCR-based mitochondrial DNA analysis to specifically detect D. nihonkaiensis from archived clinical samples, and to determine any genetic variation that may exist among the Japanese broad tapeworms from patients of Kanagawa Prefecture, Japan. Target genes were amplified from DNA extracted from the ethanol- or formaldehyde-fixed samples by PCR. Further sequencing and comparative phylogenetic analyses based on mitochondrial COI and ND1 sequences were also performed. In our results, all PCR-amplified and sequenced samples were identified as D. nihonkaiensis. Analysis of COI sequences revealed two haplotype lineages. However, clustering of almost all COI (and ND1) sample sequences into one of the two haplotype clades, together with reference sequences from different countries worldwide, revealed a common haplotype among D. nihonkaiensis samples in our study. Our results suggest a possible presence of a dominant D. nihonkaiensis haplotype, with a global distribution circulating in Japan. Results from this study have the potential to improve the management of clinical cases and establish robust control measures to reduce the burden of human diphyllobothriasis in Japan.

Mitochondrial phylogeny of fusilier fishes (family Caesionidae) from the Laccadive archipelago reveals a new species and two new records from the Central Indian Ocean.

Fusiliers of the family Caesionidae comprise a group of Indo-Pacific reef fishes important in the live bait and artisanal fisheries in many parts of its range, particularly in the Indian Ocean region. Using newly generated mitochondrial COI sequences of 10 species of caesionid fishes from the Laccadive archipelago, we carried out a molecular phylogenetic analysis, which has helped improve our understanding of the diversity, distribution, and systematics of this poorly known group of fishes. The two speciose genera within Caesionidae, Caesio and Pterocaesio, were revealed to be paraphyletic, and as a result, four names earlier considered as subgenera within Caesionidae (Flavicaesio, Odontonectes, Pisinnicaesio, and Squamosicaesio) were elevated to the status of distinct genera. We also discovered the presence of a new lineage in the Central Indian Ocean, sister to Caesio caerulaurea and Caesio xanthalytos, but distinct from both in several morphological characters and a genetic distance of between 2% and 3% in the mitochondrial COI gene. We describe this lineage as Caesio idreesi, a new species, with a distribution spanning the Laccadive Sea and the Bay of Bengal. Our genetic data also helped confirm the first confirmed records of two species, Pisinnicaesio digramma and Squamosicaesio randalli, from the Central Indian Ocean, and a new distribution record for C. xanthalytos in the Laccadive Sea. Combined, these results have helped bridge key biodiversity knowledge gaps of the family Caesionidae and form an excellent baseline for further investigations on their taxonomy, systematics, and life history.

Molecular and morphological evidence reveals a hidden new taxon in the endemic genus Pseudocuneopsis (Bivalvia, Unionidae) from China.

A new species of freshwater mussel belonging to the genus Pseudocuneopsis, namely Pseudocuneopsiswuanasp. nov., is diagnosed and described from Guangxi Province, China. This paper provides a detailed shell morphological description, soft-body anatomical characteristics, and partial sequences of mitochondrial COI as DNA barcode data for the novel species. The new species can be distinguished from its congeners (Pseudocuneopsissichuanensis, P.yangshuoensis, and P.capitata) by shell shape, beak position, and surface sculpture. Phylogenetic analyses based on the mitochondrial COI gene reveal that Pseudocuneopsiswuanasp. nov. forms a sister group with P.yangshuoensis and exhibits an interspecific genetic distance of 5.1%. Therefore, we provide robust morphological and molecular evidence to support the validity of this new species.