Mitochondrial COI Research Articles

A DNA barcode reference library of Croatian mosquitoes (Diptera: Culicidae): implications for identification and delimitation of species, with notes on the distribution of potential vector species

BackgroundMosquitoes pose a risk to human health worldwide, and correct species identification and detection of cryptic species are the most important keys for surveillance and control of mosquito vectors. In addition to traditional identification based on morphology, DNA barcoding has recently been widely used as a complementary tool for reliable identification of mosquito species. The main objective of this study was to create a reference DNA barcode library for the Croatian mosquito fauna, which should contribute to more accurate and faster identification of species, including cryptic species, and recognition of relevant vector species.MethodsSampling was carried out in three biogeographical regions of Croatia over six years (2017–2022). The mosquitoes were morphologically identified; molecular identification was based on the standard barcoding region of the mitochondrial COI gene and the nuclear ITS2 region, the latter to identify species within the Anopheles maculipennis complex. The BIN-RESL algorithm assigned the COI sequences to the corresponding BINs (Barcode Index Number clusters) in BOLD, i.e. to putative MOTUs (Molecular Operational Taxonomic Units). The bPTP and ASAP species delimitation methods were applied to the genus datasets in order to verify/confirm the assignment of specimens to specific MOTUs.ResultsA total of 405 mosquito specimens belonging to six genera and 30 morphospecies were collected and processed. Species delimitation methods assigned the samples to 31 (BIN-RESL), 30 (bPTP) and 28 (ASAP) MOTUs, with most delimited MOTUs matching the morphological identification. Some species of the genera Culex, Aedes and Anopheles were assigned to the same MOTUs, especially species that are difficult to distinguish morphologically and/or represent species complexes. In total, COI barcode sequences for 34 mosquito species and ITS2 sequences for three species of the genus Anopheles were added to the mosquito sequence database for Croatia, including one individual from the Intrudens Group, which represents a new record for the Croatian mosquito fauna.ConclusionWe present the results of the first comprehensive study combining morphological and molecular identification of most mosquito species present in Croatia, including several invasive and vector species. With the exception of some closely related species, this study confirmed that DNA barcoding based on COI provides a reliable basis for the identification of mosquito species in Croatia.Graphical

Distribution and genetic diversity of cobitid species in Iran (Teleostei: Cobitidae)

Several species of Cobitis have been reported within Iran, but only four are recognized as valid. The geographical distribution and genetic diversity of these species are not well-known. Two new populations of C. saniae and C. avicennae were reported herein based on their morphological and phylogenetic characters from the Mahabad River, a tributary of the Urmia Lake basin, and the Razavar River, a tributary of the Karkheh drainage, respectively. The genetic diversity and genetic structure of populations of C. saniae, C. avicennae, and C. faridpaki were analysed using the DNA sequences of the mitochondrial COI gene. COI sequences from various watersheds in Iran, Azerbaijan, and Georgia were used. A moderate to high level haplotype diversity and low nucleotide diversity were found in most of the populations of all three species. The AMOVA test and pairwise FST comparison revealed significant genetic structure and genetic distance between the Urmia Lake basin and other C. saniae populations. The results highlight the importance of conserving these species and their habitats, particularly in the Urmia Lake basin, where significant genetic differentiation was observed.

Taxonomic notes on the genus Baetiella Uéno, 1931 (Ephemeroptera, Baetidae), with description of three new species from Thailand

Based on material recently collected in northern Thailand, the present study provides an updated of the genus Baetiella, including Gratia. It comprises six species in Thailand, three of them being new species: Baetiella (Gratia) narumonae, Baetiella (Gratia) sororculaenadinae, Baetiella (Baetiella) bispinosa, Baetiella (Baetiella) baeisp. nov., Baetiella (Baetiella) lannaensissp. nov. and Baetiella (Baetiella) bibranchiasp. nov.Baetiella (Baetiella) baeisp. nov. can be distinguished from other species by the reduction of the posteromedian protuberances on abdominal tergites I–III, the asymmetrical coniform terminal segment of labial palp, the distal margin of abdominal sternites VII–X each with a row of long, spatulate setae, the dorsal margin of femur with two long, robust setae distally. Baetiella (Baetiella) lannaensissp. nov. is diagnosed by the posteromedian protuberances present on tergites I–VIII, dorsal margin of femur with a regular row of long, rounded, ciliated setae and body surface covered with numerous, dense, rounded scale-like setae. Baetiella (Baetiella) bibranchiasp. nov. can be separated from other species by coxal gills present at the base of forelegs and midlegs. The molecular study based on the mitochondrial gene COI and a larval key to species of Thai Baetiella are also provided.

Genetic Profile of Greek Indigenous Honey Bee Populations, Local Extinctions, Geographical Distinction, and Patterns, by Using mtDNA COI and Nuclear CSD Gene Analysis Markers

Evaluation and conservation of local genetic resources of the domestic honey bee populations is important, especially in regions with high diversity levels as well as high honey bee colony density. Greece is rich in honey bee biodiversity, hosting several subspecies, with the status of them being, though, doubtful. The purpose of the present study was to investigate the genetic relationships of both stationary and movable honey bee populations, originating from many location throughout Greece. Two molecular markers were utilized, namely, the conserved mitochondrial COI gene and the highly variable complementary sex determination (CSD) gene. Samples were collected from nine distant populations: eight populations from colonies that followed the traditional stationary beekeeping model and one following the modern migratory beekeeping model type, where the hives are transferred from place to place according to the season. Regardless the beekeeping model, all populations were characterized by sufficient genetic diversity indicating no signs of inbreeding or any bottleneck effects. Nevertheless, genetic differentiation and phylogenetic analysis in comparison with haplotypes obtained from GenBank revealed a genetic admixture pattern suggesting that movement causes genetic homogeneity, occasionally in the stable reared populations as well. Interestingly, two populations, namely, Kastoria and Protokklisi, belonging to A. m. macedonica population, were significantly differentiated, supporting the maintenance of their genetic integrity. Unfortunately, on the other hand, genetic structure of the populations from Crete (Sasalos population) provided evidence that the indigenous breed from the island, A. m. adami, has probably gone extinct. Future management strategies should focus on the conservation of the local genetic resources in which distinct genetic identity has been sustained.

A new genus and one new species of the family Uristidae Hurley, 1963 (Amphipoda, Lysianassoidea) described from hydrothermal vent of the Okinawa Trough, NW pacific

A new genus of the family Uristidae Hurley, 1963 is proposed, Liuiuristis gen. nov., with new species L. thermalis sp. nov. as the type species based on specimens collected by the expedition to hydrothermal vents on the Okinawa Trough. The new genus is characterized by the shape of accessory flagellum liking cap, the outer plate of the maxilla 1 having 11 setal-teeth, the gnathopod 1 parachelate in female and subchelate in male, the rami of the uropod 3 without plumose setae and the telson not cleft. K2P divergences of the mitochondrial COI gene in taxa attributed to Liuiuristis gen. nov. is presented.

Bat diversity in the Cuc Phuong National Park, Vietnam - Results from VIETBIO field training and annotated species list.

Biodiversity surveys are essential for both academic research and conservation. Integrative approaches that combine morphological, genetic and acoustic aspects for species identification can provide reliable information in taxonomy and evolution. This is especially relevant for those groups with a high degree of cryptic diversity such as bats. Here, we present the results from a field survey carried out in the Cuc Phuong National Park (CPNP) during 2019 as part of the VIETBIO project and from the examination of specimen collections preserved at the museums of CPNP and the Institute of Ecology and Biological Resources (IEBR). In addition, we include an annotated species list, based on this survey and a literature review. We here confirm that CPNP is home to at least 47 bat species belonging to 23 genera and seven families. We recorded ten of these bat species during our field survey. Obtained data in genetics (sequencing a fragment of the mitochondrial gene COI) supported the morphological identification of the recorded species for which we were able to produce these data. In addition, we include echolocation recordings obtained during our field training with the hope that they may contribute valuable insights to future work concerning the surveyed species. Results from the field survey represent a relevant contribution to biodiversity assessment efforts and, thus, support conservation and management efforts to maintain bat diversity in Vietnam.

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.

First Report on Banana Weevil, Cosmopolites sordidus (Germar 1823) (Coleoptera: Curculionidae), an Exotic Economically Important Pest from Saudi Arabia.

We report the first record of the occurrence of the banana weevil, Cosmopolites sordidus (Germar, 1823) (Coleoptera: Curculionidae), an economically important pest of bananas (Musa spp.), from Fifa Mountains in Saudi Arabia. Moreover, we recorded the first observation of damage caused to bananas by C. sordidus in a banana farm in Jazan Province, southwestern Saudi Arabia, in March 2022. Molecular characterization using DNA sequences of the mitochondrial COI gene confirmed the morphological identification of C. sordidus. This discovery is considered a warning notice to prevent the potential establishment and spread of this dangerous pest in the banana cultivation regions in Saudi Arabia. Therefore, it is recommended that detection and monitoring of banana weevil should be undertaken in Saudi banana farms in order to restrict the dissemination of this weevil to other banana cultivation areas.

A new chemosymbiotic bivalve species of the genus Acharax Dall, 1908 (Bivalvia, Solemyida, Solemyidae) from the Haima cold seep of the South China Sea.

Solemyidae is an ancient group of protobranch bivalves that typically inhabit unusual environments, such as deep-sea chemosynthetic environments, and are symbiotic with chemoautotrophic and gill-hosted bacteria. In May 2018, a living solemyid bivalve was collected using a remotely operated vehicle at a depth of 1,390 m from the Haima cold seep in the northwestern slope of the South China Sea. Through a comprehensive taxonomic approach combining morphological observations and molecular phylogeny reconstruction of concatenated mitochondrial COI,16S rRNA and 18S rRNA gene sequences, a new species, Acharaxhaimaensissp. nov. is identified and described. The discovery of this new species contributes to the diversity of known solemyids in deep-sea chemosynthetic environments.

Melanella martarum sp. nov. (Gastropoda: Eulimidae): the first parasitic deep-sea snail reported for the Salas & Gomez Ridge.

Eulimidae is a highly diverse family of gastropods that are often parasites of echinoderms. They are cosmopolitan and live from the intertidal to great depths. Despite its wide geographic and bathymetric distribution, no species of Eulimidae have been reported for the Salas & Gómez Ridge to date. In this study, we describe Melanella martarum sp. nov., which was collected during the EPIC oceanographic cruise onboard RV Mirai (JAMSTEC, Japan) in 2019. Seven specimens were collected with a modified Agassiz trawl on the summit of seamount "Pearl" (Zhemchuznaya) in the Salas & Gómez Ridge (25.59°S, 89.13°W) at 545 m depth. The morphology of M. martarum sp. nov. was compared with other Melanella species reported for the area, including Chile and Rapa Nui. DNA was extracted and partial sequences of the mitochondrial genes Cytochrome Oxidase 1 (COI) and 16S rDNA, and the nuclear gene Histone 3 (H3) were sequenced. Melanella martarum sp. nov. has morphological characteristics that separate it from other species of Melanella, such as the thickness and color of the shell, and the shape of the protoconch. In addition, M. martarum sp. nov. was genetically differentiated from other Melanella spp. sequences (uncorrected p distances from 18,1-8.6% in mitochondrial COI and 16S rDNA to 3% in nuclear H3 sequences). Although there is not much molecular data available for Eulimidae, the phylogenetic analysis confirms the results obtained by morphology, placing the species found on the Salas & Gómez Ridge within the genus Melanella. The current study advances the understanding of the poorly known benthic fauna found on seamounts in the easternmost part of the Sala & Gómez ridge, a location distinguished by a high level of endemism.

Description of a new species of the genus Cultellus Schumacher, 1817 (Bivalvia, Pharidae) from the South China Sea, based on integrative taxonomy

The present study describes a new species within the genus Cultellus Schumacher, 1817 collected from the South China Sea. An integrative taxonomic approach incorporating morphological comparisons, geometric morphometrics and genetic analyses was used to identify and differentiate the new species. Cultellus exilissp. nov. is distinguished from its congeners by its slender, fragile and translucent valves, curved posteroventral margins and relatively large protractor scars. The geometric morphometric analyses, based on outlines data, indicated that samples of Cultellus exilissp. nov. clustered together and were distinctly separated from other species. Multiple species delimitation results, based on the mitochondrial COI gene, support the separation of Cultellus exilissp. nov. from its related congeners. Phylogenetic analyses of a nuclear (28S rRNA) and two mitochondrial (COI, 16S rRNA) genes using Maximum Likelihood and Bayesian Inference methods revealed that the species belongs to the genus Cultellus. The superfamily Solenoidea Lamarck, 1809, which includes the families Solenidae Lamarck, 1809 and Pharidae H. Adams & A. Adams, 1856, exhibits closer affinity to the family Hiatellidae Gray, 1824 than to Solecurtidae d’Orbigny, 1846. Furthermore, we found that the genus Siliqua was clustered alongside the genera Ensiculus and Phaxas as a sister clade, which contradicts the current systematics of the subfamily within the family Pharidae. This work highlights the utility of integrative taxonomy for species identification, recognition and phylogenetic investigation.

Morphological description and DNA barcoding of Ceratophysella gracilimucronata sp. nov. (Collembola: Hypogastruridae) from China, with a key to species of the C. armata group of the Sino–Japanese Region

A new species, Ceratophysella gracilimucronata sp. nov. from Nan Ling Mountains (Guangdong Province, China), is described. It resembles C. ainu (Yosii, 1972), C. glancei Hammer, 1953 and C. falcifer Cassagnau, 1959 due to the B type chaeotataxy and short and slender mucro. Mitochondrial COI gene sequence of C. gracilimucronata sp. nov. is provided. A key to species of the C. armata group of the Sino–Japanese Region is given.

The unseen invaders: Tracking phylogeographic dynamics and genetic diversity of cryptic Pomacea canaliculata and P.maculata (Golden apple snails) across Taiwan.

The cryptic invasion of golden apple snails (Pomacea canaliculata and P. maculata) in Taiwan has caused significant ecological and economical damage over the last few decades, however, their management remains difficult due to inadequate taxonomic identification, complex phylogeny, and limited population genetic information. We aim to understand the current distribution, putative population of origin, genetic diversity, and potential path of cryptic invasion of Pomacea canaliculata and P. maculata across Taiwan to aid in improved mitigation approaches. The present investigation conducted a nationwide survey with 254 samples collected from 41 locations in 14 counties or cities across Taiwan. We identified P. canaliculata and P. maculata based on mitochondrial COI and compared their genetic diversity across Taiwan, as well as other introduced and native countries (based on publicly available COI data) to understand the possible paths of invasion to Taiwan. Based on mitochondrial COI barcoding, sympatric and heterogeneous distributions of invasive P. canaliculata and P. maculata were noted. Our haplotype analysis and mismatch distribution results suggested multiple introductions of P. canaliculata in Taiwan was likely originated directly from Argentina, whereas P. maculata was probably introduced from a single, or a few, introduction event(s) from Argentina and Brazil. Our population genetic data further demonstrated a higher haplotype and genetic diversity for P. canaliculata and P. maculata in Taiwan compared to other introduced regions. Based on our current understanding, the establishment of P. canaliculata and P. maculata is alarming and widespread beyond geopolitical borders, requiring a concerted and expedited national and international invasive species mitigation program.

Molecular identification and genetic diversity of ten Pierid butterflies based on mitochondrial COI gene

The IUCN Bangladesh has documented a total of 31 species belonging to the Pieridae family in Bangladesh. There is currently limited knowledge regarding the genetic diversity and molecular relationships among these butterflies. The present investigation involved the generation of mitochondrial COI (mtCOI) gene sequences for ten species of butterflies belonging to the Pierid family. After that, BLAST analysis showed 96% to 100% similarity, and then the sequences were submitted to NCBI’s GenBank. MEGA10 and BioEdit were used to identify a 584 bp COI gene fragment with 179 variable sites and 128 parsimony-informative sites. The COI sequences' average base compositions were 38.56% T, 17.12% C, 30.18% A, and 14.12% G. While a significant AT bias (68.74%) existed among the Pierid species. The genetic distance between ten Pierid species was assessed using the Kimura 2-Parameter (K2P) algorithm, and the nucleotide differences ranged from 0.00172% to 0.24261%. Afterwards, the Maximum Likelihood (ML) method was used to construct a phylogenetic tree using ten sequences of Pierid species. These species belongs to two subfamilies, Pierinae and Coliadinae in Bangladesh. On the tree, the Pierinae subfamily of Pieridae formed a paraphyletic arrangement whereas the Coliadinae subfamily was shown to be monophyletic. The data analyses support the following relationships between the two subfamilies as follows: [(Appias + Leptosia) + (Pieris + Appias) + (Delias) + (Eurema + Catopsilia) + (Pareronia)]. This supported the theory that Pierinae and Coliadinae are sister taxa. Nonetheless, Pareronia hippia remains outside the main Pierinae group, requiring further study to resolve this issue. Finally, these studies generated ten mtCOI gene sequences that have the potential to serve as valuable references for the accurate identification of Pierid species. In addition, this result could be used in the future to reveal the subfamily relationships within the Pieridae taxonomic classification. Bangladesh J. Zool. 51(3): 289-299, 2023  

Phylogeography and population structure of Lagocephalus spadiceus (Richardson, 1845) (Tetraodontiformes, Tetraodontidae) in the South China Sea.

The climate fluctuations during the Late Pleistocene significantly influenced the phylogeographic structure and historical dynamics of marine fishes in the marginal seas of the western Pacific Ocean. The puffer fish, Lagocephalus spadiceus, holds substantial nutritional and economic value in the South China Sea. To investigate the demographic history and population structure of the L. spadiceus, the mitochondrial DNA COI and Cyt b gene datasets from 300 individuals across eight populations in the South China Sea were sequenced. Our findings revealed high haplotype diversity (0.874 ± 0.013) and low nucleotide diversity (0.00075 ± 0.00058). The phylogenetic tree and haplotype networks revealed no significant genetic differentiation along the northern coast of South China Sea. Neutrality tests, mismatch distribution analyses, and Bayesian skyline plots suggested that L. spadiceus underwent population expansion during the Late Pleistocene. Both ocean currents and climate change significantly influenced the geographical distribution and genetic population structure of L. spadiceus.

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.

Molecular Identification of the Diversity of Insects, Spiders, Lizards, Birds and Mammals of Tuensang District, Nagaland, India

ABSTRACT: DNA barcoding is a method of species identification that revolutionized the way we study and understand biodiversity. With advancements in molecular genetics and DNA sequence archives, it has become possible to use short DNA sequences to identify species, even when the specimens are difficult to distinguish by traditional morphological methods. In this article, we explore the utility of DNA barcoding in the Tuensang ecosystem of Nagaland, India and evaluate its effectiveness for species identification, informing ongoing conservation of populations and species. A total of 62 species, which included insects, spiders, lizards, birds and mammals, were collected from Tuensang areas of northeast India and identified using DNA barcodes. DNA was extracted from muscle tissue and PCR was done with two pairs of primers targeting the mitochondrial COI gene. Sanger sequencing was employed and the obtained sequences were analysed to identify the species and reconstruct the evolutionary relationships amongst them. Our results provided molecular characterization of species from Tuensang areas of Nagaland for the first time.

A new species of the genus Sinomytilus (Bivalvia: Mytilidae) from Lake Fuxian, Yunnan Province, China

Based on specimens collected from Lake Fuxian in Yuxi City, Yunnan Province, China, we describe a new species of the genus Sinomytilus, Sinomytilus liuliwanqing sp. nov., all type specimens are deposited at Nanjing Normal University in Jiangsu Province, China. We provide a detailed morphological description of the species and molecular analysis based on partial mitochondrial COI supports its systematic position as a new taxon.

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.