Cytochrome C Oxidase Subunit I Research Articles

Hidden diversity in anthropophilic sand flies of the Monticola Series (Diptera, Psychodidae)

The Monticola series comprises two anthropophilic and widely distributed species in Brazil: Pintomyia (Pifanomyia) monticola (Costa Lima, 1932) and Pintomyia (Pifanomyia) misionensis (Castro, 1959). They mainly occur in the Atlantic Rainforest, and it is known that Pi. monticola comprises at least two well-structured genetic lineages regarding a fragment of the cytochrome c oxidase subunit I (COI) gene. Here, we aim to elucidate the taxonomic status of this group using integrative taxonomy tools. Collections were performed in nine localities of four Brazilian states, and COI fragments were sequenced and merged with publicly available data. Several single-locus species delimitation algorithms, genetic distance metrics, phylogenetic trees, and haplotype networks were used to uncover cryptic diversity and population structure within Pi. monticola and Pi. misionensis. The resulting genetic clusters were then tested for morphological differences through linear and geometric morphometry of several characters. We analyzed 152 COI sequences, comprising 48 haplotypes. The maximum intraspecific p distances were 8.21% (mean 4.17%) and 9.12% (mean 4.4%) for Pi. monticola and Pi. misionensis, respectively, while interspecific ones ranged from 10.94 to 14.09% (mean 12.33%). Phylogenetic gene trees showed well-supported clades for both species, with clear structuring patterns within them. Species-delimitation algorithms split our dataset into at least three putative species for each taxon. Moreover, population structure analysis showed a strong correlation between Atlantic Forest areas of endemism as sources of molecular variation in Pi. monticola. Morphometric analyses were significant for wing shape variation and some linear measurements (mainly of the head) when comparing specimens of different genetic clusters for both taxa. These results indicate strong genetic structuring of Monticola series species, confirmed by morphometry, indicating two possible cryptic species complexes.

The Mosquitoes (Diptera: Culicidae) of Sonora: Distribution, Ecology, and the First Records of Aedes deserticola Zavortink and Toxorhynchites septentrionalis (Dyar and Knab) in México

The diversity and distribution of mosquitoes from Sonora, Mexico, was documented through entomologic surveys conducted in the four physiographic regions and sub-regions of Sonora: the Sonoran Plain, the Sierra Madre Occidental, the Northern Mountains and Plains, and the Pacific Coastal Plain. Immature stages were collected from aquatic habitats, while adult mosquitoes were collected using Shannon traps, resting in vegetation, and by human landing collections. Overall, 11,316 specimens, which comprised 493 larvae, 224 larval exuviae, 400 pupal exuviae, 33 pupae, 4552 females, 5607 males, and seven male genitalia, were identified. Two subfamilies: Anophelinae and Culicinae, seven tribes, 10 genera, 23 subgenera, and 56 species are reported below. Of these, one tribe, one genus, five subgenera, and 15 species were recorded for the first time in Sonora. Two species, Aedes deserticola Zavortink and Toxorhynchites septentrionalis (Dyar and Knab), are the first recordings of their kind nationwide. Toxorhynchites septentrionalis was also barcoded with the cytochrome oxidase subunit 1 (COI) gene. The presence of Psorophora columbiae (Dyar and Knab) is confirmed in Mexico. Taxonomic notes, new geographic distribution limits of mosquitoes in Sonora, and information regarding their importance as disease vectors are provided. By adding Ae. deserticola and Tx. septentrionalis and confirming Ps. columbiae in Mexico, there are currently 251 mosquito species in the Country.

Cutaneous myiasis by Calliphoridae dipterans in dogs from Chad

Cutaneous myiasis caused by various Calliphoridae dipteran species is prevalent worldwide and is of particular veterinary and public health concern. Recently, in a scientific exploration of the Guinea Worm Eradication Program to Chad, Africa, we observed that dogs with mutilated ears, based on local awareness, were caused by cutaneous myiasis. In this study, we analyzed epidemiological, morphological, and molecular data on cutaneous myiasis in dogs from Chad. From September to October 2022, dogs (n = 1,562) from 56 villages situated along the Chari River were physically inspected for cutaneous myiasis. All larvae were collected and identified morphologically and by molecular analysis of the partial cytochrome oxidase c subunit I (COI) mitochondrial gene. The prevalence of myiasis infestation along with 95% confidence intervals (95% CI) was determined using the modified Wilson method. Myiasis was detected in dogs from 21 villages (37.5%; 95% CI 26 - 50%), predominating in the southernmost region. Of 1,562 dogs, 66 (4.22%; 95% CI 3.34 - 5.34%) were infested by calliphorid larvae, with a mean infestation of 2.28 larvae per animal (range = 1 to 24). Specimens were morphologically identified as Cordylobia anthropophaga (n = 94), Chrysomya bezziana (n = 54), and Chrysomya sp. (n = 3), which were detected in 57, eight and one dog, respectively. No co-infestations were observed. The molecular analyses confirmed the morphological identification and revealed the presence of 17 haplotypes for C. anthropophaga, 2 for C. bezziana, and one for Chrysomya sp. Our study emphasizes the veterinary importance of myiasis in dogs in Africa and proposes measures to assure their health and well-being.

Molecular phylogeny of Boninia (Platyhelminthes: Polycladida), with description of a new species from the Pacific coasts of Panama.

Mesopsammic polyclad members in the family Boniniidae have attracted attention in terms of their evolutionary shifts of microhabitat and their unique morphology such as a pair of pointed tentacles extending from the anterolateral margins and prostatoid organs harbouring stylets. Here, we establish a new species of this family as Boninia panamensis sp. nov. from the Pacific coasts of Panama, based on its morphological characteristics of (i) four cerebral and 61-80 marginal eyespots, (ii) two prostatoid organs located anterior and posterior to the penis papilla, and (iii) two uterine canals departing from the anterior part of the Lang's vesicle. We also report Boninia cf. uru from Hawai'i, USA, based on its morphological identity with B. uru from Okinawa, Japan, along with their genetic distances for the partial cytochrome c oxidase subunit I (COI ) sequences, which were beyond the range of intraspecific differences observed in congeners in this study. Boninia oaxaquensis is also reported from Panama as a new locality for the species. Involving the above-mentioned three species sequenced herein, we reconstructed molecular phylogenetic trees of Boninia based on the four gene markers (18S rDNA, 28S rDNA, 16S rDNA and COI ). Our phylogenetic trees indicated the synapomorphy within the genus Boninia of the small numbers of stylets (2-4) and the connection route of the uterine canals to the Lang's vesicle. The results also showed a characteristic distribution pattern in which pairs of species in distinct lineages occurred sympatrically with different microhabitats, as observed in Boninia uru and Boninia yambarensis in Okinawa and B. panamensis sp. nov. and B. oaxaquensis in Panama. In addition, we discuss possible speciation pathways in this genus based on the tree topology. ZooBank: urn:lsid:zoobank.org:pub:D414BACD-C14A-4B34-8AF9-7ACBA28F46D0.

First Record of Aphelenchoides oryzae on Foxtail Millet (Setaria italica (L.) P. Beauv.) in Jilin Province of China.

Aphelenchoides oryzae Yokoo caused a large reduction in rice yields in Japan (1948). It was later synonymised with A. besseyi by Allen (1952), but Subbotin et al. (2021) considered it a valid species. In the main foxtail millet (Setaria italica (L.) P. Beauv.) production area of western Jilin Province, China, many plants were stunted, with thin spikes and open, smooth, shiny glumes. Severely affected spikes were noticeably shorter, fluffy at the top, and erect. In August 2023, 10 foxtail millet samples were collected and nematodes were isolated from 9 of them. A population from Songyuan City, Jilin Province (E:123.64, N:44.86) was studied. The average number of nematodes isolated per gram of ear was 510.7 ± 15.17. Female body slender, lip region rounded, lateral fields with 4 or 6 incisures, vulva located at 71.6% of the body length, post vulvar uterine sac (PUS) 3.7 times anal body width long but less than quarter distance from vulva to anus (VA), tail conical with 3 or 4 terminal spikes. The body length (L), maximum body width (W) and tail length of the female (mean, n=25) were 648 μm, 15.9 μm and 36.7 μm, respectively. PUS length / (VA)% = 23.5, L/W = 41.1, L/ tail length = 17.8. Male body tail curves like a sickle, lacks bursa and shows three pairs of copulatory papillae. Spicules typical of the genus except that the proximal end lacks a dorsal process and has only a moderately developed rostrum. Male measured (mean, n = 25): L = 525.8 μm, W = 14.8 μm, tail length = 34.0 ± 0.7 μm, spicule length = 16.4 μm; L/W = 35.6; L/tail length = 15.6 μm. Amplification of the D2-D3 expansion segments of the 28S ribosomal RNA and the cytochrome oxidase subunit I (COI) gene of mitochondrial DNA (mtDNA) with primers the forward D2A (5'-ACAAGTACCGTGAGGGAAAGTTG-3') and the reverse D3B (5'-TCGGAAGGAACCAGCTACTA-3') (Subbotin et al. 2006), and forward COI-F1 (5'-CCTACTATGATTGGTGGTTTTGGTAATTG-3') and the reverse COI-R2 (5'-GTAGCAGCAGTAAAATAAGCACG-3') (Kanzaki and Futai 2002). PCR conditions were as described by Ye et al. (2007). The sequences of 28S D2-D3 region (726 bp, PP573753- PP573761) of rDNA were 100% identical to A. oryzae (KY123700, KY123694) and COI region (698-700 bp, PP733171-PP733179), were 98.88% identical to A. oryzae (GU367867). Bayesian inference was used to construct phylogenetic tree of 28S D2-D3 region and COI gene, which showed that the Jilin populations clustered together with A. oryzae, which was a sister branch of A. besseyi. Pathogenicity was established via the infection of foxtail millet (cv. Jiyou 2). The germinated foxtail millet seeds were planted in pots containing 350 ml of sterile soil mixture. On the 15th day, every 10 seedlings were inoculated with 100 A. oryzae at the leaf sheet wounds and 3 plants were noninoculated as control. Three independent replicates were performed on different dates. Forty days post-inoculation, an average of 88.3 ± 2.26 A. oryzae were extracted from each nematode-inoculated plant, and the plants were yellowed and necrotic, uninoculated plants grew normally. The molecular and morphological identification of the nematodes obtained by re-isolation from the plants was identical to that of A. oryzae. Our findings clarify the pathogen species, which can be targeted to develop prevention and control strategies, which are important for ensuring safe grain production and helping promote sustainable local agricultural production. To our knowledge, this is the first record of A. oryzae on foxtail millet in Jilin, China.

Survey of sand fly fauna in six provinces of Southern Vietnam with species identification using DNA barcoding

BackgroundSand flies, belonging to the Psychodidae family, represent small, hairy insects that serve as significant vectors in various important medical and veterinary diseases. Despite being recognized by the World Health Organization as an endemic area for leishmaniasis, Southeast Asia lacks comprehensive information on the species composition and biology of sand flies. To address this, the current study aimed to survey sand fly biodiversity.MethodsSand flies from six provinces in Southern Vietnam were collected using CDC light traps. Sand flies were subsequently identified morphologically and confirmed molecularly using mitochondrial cytochrome oxidase c subunit I (COI) and cytochrome b (cytb) sequences. BLASTN searches were conducted, and the species identity of sand flies was further confirmed through a Barcode of Life Database (BOLD) search utilizing COI sequences. Subsequently, nucleotide sequences were subjected to a panel of analyses including intraspecific variation, phylogenetic relationships and haplotype network. The average densities of collected sand flies (sand flies/trap/night) and species richness were also recorded.ResultsA total of 753 sand flies were collected. After excluding damaged specimens, six sand fly species, namely Phlebotomus stantoni, Sergentomyia khawi, Se. silvatica, Se. barraudi, Se. bailyi and Grassomyia indica, were identified. All conspecific sand fly sequences, including Ph. stantoni, Se. barraudi, Gr. indica, Se. bailyi, Se. khawi and Se. silvatica, clustered with their reference sequences, corroborating the results of morphology-based identification, BLASTN analysis and BOLD search. For intraspecific variation of sand flies obtained from the current study, COI diversity indices were consistently higher than those of cytb.ConclusionsThis study provides the first updates on morphological and molecular characterization of sand flies in Southern Vietnam. This acquired knowledge on sand fly species composition is essential for controlling sand fly-borne diseases in this potentially endemic region.Graphical

DNA barcode reference library of the fish larvae and eggs of the South China Sea: taxonomic effectiveness and geographic structure

Fish early-stages constitute useful indicators of the states of marine ecosystems, as well as important fishery resources. Given the spectacular phenotypic changes during ontogeny, and the paucity of diagnostic morphological characters at the species level, the identification of fish early-stages is a challenging task. DNA barcoding, the use of the mitochondrial gene of the cytochrome c oxidase subunit I (COI) as an internal species tag, opened new perspectives for the identifications of both larval fish and fish eggs. However, the accuracy of the identifications assisted by DNA barcoding are dependent of the completeness of the DNA barcode reference libraries used to assigned unknown sequences to known species. Here, we built a DNA barcode reference library for 113 species of larval fish and 85 species of fish eggs involving the production of 741 newly generated DNA barcodes from South China Sea (63 localities). Together with 514 DNA barcodes mined from Genbank for 116 species from the South China Sea regions, a reference library including 1255 DNA barcodes for 308 species (248 locations) was assembled. The present study emphasizes the importance of integrating DNA barcoding to large scale inventories of early stages, as DNA-based species delimitation analyses delimited 305 molecular operational taxonomic units (MOTUs) and multiple cases of discordance with morphological identifications were detected. Cryptic diversity is detected with 14 species displaying two MOTUs and a total of 23 species were lumped into 11 MOTUs due to low interspecific divergence and/or mixed lineages.

DNA barcode identification of a tropical liver fluke (Fasciola gigantica) in cattle from Oyo, southwestern Nigeria

BackgroundFascioliasis is a major parasite illness that affects ruminants, both domesticated and free, and has an impact on public health and animals’ productivity. The genetic diversity of Fasciola species in cattle from Oyo, Oyo State, Nigeria is yet not well understood. In this study, the genetic diversity of Fasciola gigantica in slaughtered cattle in Oyo was examined using a molecular-based approach targeting the mitochondrial cytochrome C oxidase subunit I (COI) gene region.ResultsOne hundred flukes were gathered from slaughtered cattle, and their COI gene sequences were analyzed using maximum likelihood methods. The results of phylogenetic analysis showed genetic similarities between Nigerian F. gigantica and isolates from Algeria, Egypt, Iran, Sudan, China, Japan and Nigeria. The predominant DNA substitution was the A to T transversion, while the least common substitution was the G to A transition.ConclusionOur results show how useful the COI gene region is for examining intraspecific differences between F. gigantica isolates. The genetic similarity observed among the sampled F. gigantica populations suggests the value of mitochondrial DNA sequences as a marker for the accurate identification and characterization of Fasciola species across different ruminants.

A novel m.5906G > a variant in MT-CO1 causes MELAS/Leigh overlap syndrome.

The MELAS/Leigh overlap syndrome manifests with a blend of clinical and radiographic traits from both MELAS and LS. However, the association of MELAS/Leigh overlap syndrome with MT-CO1 gene variants has not been previously reported. In this study, we report a patient diagnosed with MELAS/Leigh overlap syndrome harboring the m.5906G > A variant in MT-CO1, with biochemical evidence supporting the pathogenicity of the variant. The variant m.5906G > A that led to a synonymous variant in the start codon of MT-CO1 was filtered as the candidate disease-causing variant of the patient. Patient-derived fibroblasts were used to generate a series of monoclonal cells carrying different m.5906G > A variant loads for further functional assays. The oxygen consumption rate, ATP production, mitochondrial membrane potential and lactate assay indicated an impairment of cellular bioenergetics due to the m.5906G > A variant. Blue native PAGE analysis revealed that the m.5906G > A variant caused a deficiency in the content of mitochondrial oxidative phosphorylation complexes. Furthermore, molecular biology assays performed for the pathogenesis, mtDNA copy number, mtDNA-encoded subunits, and recovery capacity of mtDNA were all deficient due to the m.5906G > A variant, which might be caused by mtDNA replication deficiency. Overall, our findings demonstrated the pathogenicity of m.5906G > A variant and proposed a potential pathogenic mechanism, thereby expanding the genetic spectrum of MELAS/Leigh overlap syndrome.

Morpho-molecular characterization and phylogenetic relationships of Encotyllabe percussa n. sp. (Monogenea: Capsalidae) from the spangled emperor Lethrinus nebulosus (Teleostei, Lethrinidae).

Encotyllabe percussa n. sp. is proposed based on morphology and DNA sequences analysis of ribosomal (18S, 28S) and mitochondrial (COI) gene fragments. Encotyllabe percussa n. sp. was found infecting the spangled emperor Lethrinus nebulosus (n = 75) with higher prevalence from Dibba, Musandam (Gulf of Oman) than in Dhofar Salalah (Indian Ocean), Oman (p = 0.03). The general morphology of E. percussa n. sp. resembles E. caballeroi, E. chironemi and E. spari, which exhibit pre-equatorial testes. However, E. percussa n. sp. shows unique morphological characteristics distinguishing from congeneric species: the large hamuli bear notch allocated externally between the first half proximal of the root, and the small hamuli exhibit semicircular shape with undivided roots. Phylogenetic relationships within the Encotyllabe genus remain unresolved. However, the tree topology with the 28S showed overall consistency with the principal component analysis arrangement (PCA) derived from the morphological analysis. Which showed that the large and small hamuli, marginal hooks, ovary, testes (length and width) and peduncle are currently the most important morphological traits within the genus. Cytochrome c oxidase subunit I (COI) gene fragment showed high interspecific genetic divergence adding unambiguous resolution to discriminate/designate species identity. Interrelations within the genus support the identity of Encotyllabe percussa as a new species. This is the first species characterized with three gene fragments, the second congeneric species described in L. nebulosus and the first recorded in Oman.

Gene Sequencing Study of Mitochondrial Cytochrome Oxidase Subunit I (COI) in Aedes aegypti Mosquito

Aedes aegypti is an important vector from the public health point of view. It transmits pathogens of Dengue and various other diseases. Controlling vector populations is key to reducing disease transmission and it is possible by understanding the taxonomic characteristics of the vectors and their genetic analysis helps in the identification of the genetic variations in species of different geographical areas. The main aim of the present study is the screening of the Aedes mosquito genome of local species as genetic studies give some insights into the vaccine for the treatment of the diseases caused by mosquito species. In the present study, the adult Ae. aegypti collected from Suryapet town where Dengue fever is endemic, used for the mitochondrial Cytochrome Oxidase subunit I (COI) gene sequencing using the techniques of polymerase chain reaction, Electrophoretic separation, spectrophotometric analysis, and BLAST. The mitochondrial COI sequence of 583 bps is published in the National Centre for Biotechnology Information (NCBI) with accession number ON413769. The sequence data was matched with the database available in the NCBI to identify variation in the gene as this gene keeps changing in the organisms and may contribute to the species establishing itself in a particular region due to congenial environmental conditions. One match with the protein called haem copper oxidase subunit I. The transmission of different pathogens in different areas can be ascertained by comparing similar sequence studies documented. Genomic studies involving genetic markers are of immense help in developing the vaccine. The mitochondrial COI gene is the marker often used for evolutionary research. The single nucleotide polymorphisms (SNP) or Restricted fragment length polymorphisms (RFLPs) that occur in DNA also contribute to the vector's adaptability to the different geographical areas and also the survival benefit which are the basis for understanding the vectors thoroughly and their role in disease transmission.

Genetic Variation in the Invaded Population of the Fall Armyworm, Spodoptera frugiperda (J. E. Smith) (Lepidoptera: Noctuidae), in India

The fall armyworm, Spodoptera frugiperda, an invasive, polyphagous pest, causes significant damage to corn. The majority of insects rely on a broad range of digestive enzymes and an intricate detoxifying mechanism to consume chemically diverse host plants. The genetic variation in S. frugiperda was analyzed using cytochrome oxidase subunit I (COI) and triose phosphate isomerase (Tpi). In addition, a new attempt was made to determine the variation with respect to two detoxifying genes, viz., carboxylesterase and glutathione S-transferase. The highest genetic variation (3.03%) was found between the S. frugiperda populations of Tirupati and Delhi with respect to the Tpi gene and between the populations of Punjab and Hosur regarding COI (3.30%). The results for various genes revealed that populations of the fall armyworm were homogeneous, showing low genetic distance using COI, ranging from 0.40 to 3.30%, and, using Tpi, ranging from 0.43 to 3.03%. The variation in carboxylesterase and glutathione S-transferase ranged from 0.04 to 0.15% and from 0.01 to 0.02, respectively. Amino acid sequences were also produced using DNA sequences from several fall armyworm populations. Populations in Tirupati, Solapur, and Hyderabad shared 98.7% of their sequence with that in Delhi. Fall armyworm amino acid sequences showed 79.7 to 82.0% identity with S. exigua and 69.6 to 73.0% identity with S. litura. Our study provides vital information for understanding the genetic variation in the fall armyworm following its invasion of India.

A new species of Buresilia (Opiliones, Phalangiidae) from Turkey

A new harvestman species, Buresilia gumushanensis sp. nov. (Opiliones: Phalangiidae), is described based on male specimens collected from Gümüşhane province, Turkey. Detailed descriptions, diagnostic features and pictures of the new species are provided, together with mitochondrial cytochrome c oxidase subunit I (COI) sequences. The phylogenetic tree constructed using the COI gene region revealed the phylogenetic position of the genus Buresilia within the family Phalangiidae. In addition, the new species is compared with known species of the genus Buresilia.

A new species of Thoracophelia (Annelida, Opheliidae) from the Yellow Sea of South Korea.

Thoracophelia Ehlers, 1897 is a genus of Opheliidae characterised by the body divided into three distinct regions, modified parapodia in chaetiger 10 and a ventral groove restricted to the posterior half of the body. To date, 18 species have been described in the genus. Amongst them, six species have been recorded in northeast Asia. A new species, Thoracopheliafoliformis sp. nov., was discovered in the intertidal zone of the Yellow Sea, South Korea. This is the first Thoracophelia species report from the Yellow Sea. This new species is closely related to T.dillonensis (Hartman, 1938) from California and T.ezoensis Okuda, 1936 from Japan in having pectinate branchiae. However, the new species can be distinguished from the two species by the unique combination of the following characteristics: 15 pairs of wrinkled pectinate branchiae with 12-15 filaments at best development and a foliaceous mid-ventral plate in the pygidium instead of one or two thick ventral cirri. Detailed descriptions and illustrations of T.foliformis sp. nov. are provided. Sequences of the mitochondrial cytochrome c oxidase subunit I (COI), nuclear 18S ribosomal DNA (rDNA) and 28S rDNA of the new species were determined and analysed.

A new species of the pill millipede genus Rhopalomeris Verhoeff, 1906 (Diplopoda, Glomerida, Glomeridae) from Myanmar, and notes on Rhopalomeriscarnifex (Pocock, 1889).

The taxonomy of the pill millipede genus Rhopalomeris Verhoeff, 1906, which is restricted to Indochina and currently comprises six described species, is refined and updated. An integrative taxonomic approach was employed that combines morphological examination with DNA barcoding using the cytochrome c oxidase subunit I (COI) gene for species identification and delineation. The first objective was to confirm the identity of Rhopalomeriscarnifex (Pocock, 1889), a charismatic species known as the "candy pill millipede" due to its vivid coloration, based on specimens collected near the type locality in Myanmar. The second objective was to describe a new species, Rhopalomerisnigroflava Likhitrakarn, sp. nov., discovered in Linno Gu, Kayin State, Myanmar. This new species is distinguished by its small body size (5.1-9.7 mm long) and yellow body with contrasting brown to blackish markings on certain terga. In addition, the position of the telopod syncoxital lobe relative to the lateral syncoxite horns separates it from other Rhopalomeris species. The interspecific divergence between R.nigroflava Likhitrakarn, sp. nov. and other congeners ranges from 10.85% to 16.13%, based on uncorrected COI p-distances, while the intraspecific divergence was 0%-7.44%. A distribution map of and a revised identification key to all known species of Rhopalomeris are also provided.

Nasopharyngeal Botflies Oestrus ovis and Cephenemyia stimulator in Roe Deer (Capreolus capreolus) from Northern Spain.

Two of 19 roe deer (Capreolus capreolus) in northern Spain were infested with Cephenemyia stimulator and one individual with Oestrus ovis. Three larvae of O. ovis were recovered from the nasopharynx of an adult female deer examined in February 2017, during the hunting season in the province of Burgos. The larvae were identified by morphology, and DNA sequencing from cytochrome oxidase subunit I and 28S rDNA confirmed the identification of both species of larvae. The possibility of O. ovis parasitizing roe deer should be considered in the diagnosis of nasal bots in cervids.

Genetic diversity and species prevalence revealed by Mitochondrial COI- DNA sequence of thrips population in cotton

Aim: To elucidate the population genetic diversity and species prevalence of thrips on cotton. Methodology: Thrips species were identified utilizing both mitochondrial cytochrome oxidase subunit I (COI) sequence analysis and morphology-based keys. Results: Thrips palmi Karny, Thrips hawaiiensis (Morgan), Ayyaria chaetophora Karny, Scirtothrips dorsalis Hood and Rhipiphorothrips cruentatus Hood identified from collected samples. The distribution analysis revealed that T. palmi stands out as the most abundant and prevalent species, constituting a substantial majority (74%) and occupying a pervasive presence across most cotton-growing locations. The phylogenetic analysis, relying on COI sequences, clearly categorized these five species into four distinct major clades. T. hawaiiensis and R. cruentatus were placed within the first clade, while the second clade featured Scirtothrips dorsalis. The third clade comprised the abundant T. palmi, and the fourth clade accommodated A. chaetophora. Interpretation: The study highlighted genetic diversity of five species of thrips, accentuating the emergence of T. palmi as a dominant pest in cotton, an observation not previously reported. Key words: Cotton thrips, Genetic diversity, MtCOI, Phylogenetic analysis, Species prevalence

A new species of the thorid shrimp genus Lebbeus White, 1847 (Decapoda: Caridea) from the Amami Rift hydrothermal vent field in the Ryukyu region, Japan

A new species of the thorid shrimp genus Lebbeus White, 1847, is described and illustrated on the basis of two specimens collected from the recently discovered Amami Rift hot vent field in the Ryukyu region in southwestern Japan, at a depth of 628 m. Lebbeus parvirostris sp. nov. is morphologically similar to L. microceros (Krøyer, 1841), L. mundus Jensen, 2006, L. saldanhae (Barnard, 1947), L. schrencki (Bražnikov, 1907), L. spongiaris Komai, 2001, and L. tosaensis Hanamura & Abe, 2003, but differs from all of them in the lack of a pterygostomial tooth on the carapace in the female. Other diagnostic characters useful in differentiating the new species from the aforementioned close relatives are also discussed. Genetic analyses using sequences of two mitochondrial markers, including cytochrome c oxidase subunit I (COI) and 16S rRNA, are also presented to provide preliminary support for the status of the new species. Lebbeus parvirostris sp. nov. is the second representative of Lebbeus known from active hydrothermal vents in the Ryukyu region.

Characterizing spatial patterns among freshwater fishes and shrimps of the Poso River (Sulawesi, Indonesia) using DNA barcoding

Fish biodiversity assessments are vital for understanding threats and aquatic ecosystem health. In the Poso River, Central Sulawesi, changes in biodiversity are influenced by habitat alteration, non-native species, and overfishing. This study evaluates fish and crustacean biodiversity in the Poso River system to address these challenges for improving fisheries management, conservation, and fish passage integration into hydropower development. The present biodiversity study utilized a comprehensive methodology that encompassed both traditional taxonomic approaches and DNA barcoding, specifically targeting the mitochondrial cytochrome c oxidase subunit-1 (COI) gene for accurate species identification and spatial boundary validation. The survey was conducted in the upstream, hydropower area and downstream areas of the river. We found 27 species of fish in the Poso River, including both native (e.g., Anguilla celebesensis, Oryzias nebulosus, Rhyacichthys aspro) and non-native species (e.g., Melanochromis auratus, Amphilophus trimaculatus, Oreochromis niloticus). Two International Union for Conservation of Nature (IUCN) red listed endangered species were also observed (e.g., Adrianichthys poptae and Mugilogobius sarasinorum). DNA barcoding was performed to examine species spatial boundaries. The fish population in the Poso River was dominated by non-native species, accounting for 85.70% of the total population. The upstream reaches had the highest fish abundance and diversity, while the downstream reaches had the lowest. There was, however, no significant difference in species richness and diversity across different locations and seasons. The dominance of non-native species in the Poso River necessitates the improvement of existing fishways within the hydropower dams potentially through the development of selective technology that can block the distribution of these non-native species. This research highlights the critical issue of non-native species proliferation and the potential threat they pose to native fish populations, providing valuable insights for conservation and management efforts in Indonesia and similar ecosystems worldwide.

Morphometric trait normalization, cluster analysis and molecular phylogenetic analysis in delimiting sympatric Neolissochilus hexastichus and N. hexagonolepis in Umngi River, Meghalaya (India)

Aim: To assess the ability of an integrative approach comprising multivariate morphometric data analysis and mitochondrial cytochrome oxidase subunit I (CO I) sequence divergence analysis in delimiting sympatric Neolissochilus hexastichus (McClleland, 1839) and N. hexagonolepis (McClleland, 1839) mahseer populations in River Umngi, Meghalaya. Methodology: Authoritative descriptions of mahseers were referred during the sampling of 40 individuals from River Umngi, Meghalaya. Multivariate morphometric data were normalized with respect to standard length. The normalization procedure maintained the particular shape factor for each sample. Normalised data were subjected to hierarchical clustering on principal components Analysis (HCPC) for grouping samples according to morphometric features. Genetic affinities based on CO I sequence divergence were assessed by Bayesian Inference (BI) and Automatic Barcode Gap Discovery (ABGD) protocols. Results: The normalization protocols removed the variations in traits due to body size effects and facilitated the identification of allometric traits. HCPC analysis revealed morphometric features that had a significant impact on clustering. Nine N. hexagonolepis and 13 N. hexastichus individuals were identified by integrative morphological and molecular phylogenetic approach. The remaining 18 individuals had incongruence in their memberships in the morphometric and phylogenetic clusters. Interpretation: The integrative approach, apart from delineating N. hexagonolepis and N. hexastichus congeners, highlighted the need to include nuclear genetic markers in future studies for confirming the presence of natural hybrids in sympatric populations of Neolissochilus mahseers. Key words: Cluster, Morphometric, Neolissochilus, Normalization, Phylogenetics