Cytochrome C Oxidase Subunit I Research Articles

Molecular identification of billfish (Osteichthyes, families Xiphiidae and Istiophoridae) products in Costa Rica as a tool to reduce mislabeling and fraudulent sales of fish

Commercial billfish (Osteichthyes, families Xiphiidae and Istiophoridae) products are frequently misidentified by the fishing industry due to common practices conducted as part of the commercialization process (e.g. fin and head removal), resulting in mislabeling. Molecular tools have been proposed to properly identify the species at the market stage. This research aims to identify the billfishes commercialized in Costa Rican markets using DNA barcoding. Sequences of the cytochrome oxidase subunit I (COI) region from 178 tissue samples were analyzed from markets and fish stores located throughout the seven provinces of Costa Rica. Sequence analyses showed that samples sold as “sailfish” and “swordfish” had the highest percent of correct identification (93.44% and 96.43% respectively). On the other hand, fish sold as “white marlin”, and “pink marlin” showed the highest percentages of mislabeling (100% and 28.19% respectively). The main source of mislabeling is inconsistencies with the use of common names by local fishing authorities and fishermen when compared to common names used by other countries in the region. Overall, mislabeling occurred in 33.71% of the samples analyzed, which can have important impacts not only on consumer rights but also on fisheries statistics, management policies, and conservation.

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.

Authentication of Barbonymus spp. From Lake Singkarak Using DNA Barcoding

The local community distinguishes between Barbonymus belinka (Balingka) and Barbonymus schwanefeldii (Kapiek) in Lake Singkarak based on size due to the morphological similarities between the two species. From previous reports, B. belinka (Balingka) is a fish endemic to Lake Singkarak, West Sumatra, while B. schwanefeldii has a wider distribution, including Sumatra, Kalimantan, and Java. Consequently, molecular identification is necessary to discern between the species and to understand the DNA barcode characteristics of fish belonging to the genus Barbonymus in Lake Singkarak. One molecular technique utilized for species identification is DNA barcoding, which focuses on the COI (Cytochrome Oxidase Subunit I) gene. Liver tissue samples from Balingka and Kapiek fish from Lake Singkarak were used in the study. Based on 585 bp of COI gene sequences and 30 comparison sequences from BOLD system and GenBank NCBI, seven samples from Lake Singkarak show a genetic distance of 0–1.2% from B. schwanefeldii populations elsewhere, with 15 differing nucleotide bases. Moreover, samples from Lake Singkarak show a genetic distance of 7.7–8.2% from B. belinka in the BOLD system from Aceh, with 42 differing nucleotide bases. Furthermore, two specific bases are present in B. schwanefeldii from Lake Singkarak. Based on the results of this research, it is known that all samples from Lake Singkarak, including Balingka and Kapiek, belong to the same species, namely B. schwanefeldii.

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

Mitochondrial evidence on the phylogenetic position of the Southeast Asian catfish genus Encheloclarias Myers, 1937 (Actinopterygii: Siluriformes: Clariidae): Evolutionary and conservation implications

The phylogenetic position of the Southeast Asian catfish genus Encheloclarias Myers, 1937 within the family Clariidae is inferred herein using three mitochondrial nucleotide markers: cytochrome b, cytochrome oxidase subunit I, and 16S rRNA genes. We found that Encheloclarias is neither exclusively related to the African taxa having extended neural spines posterior to the dorsal fin (Encheloclarias shares with some of these taxa the presence of an adipose fin, as opposed to absent in all other clariid taxa) nor to the Asian species of the genus Clarias Scopoli, 1777. Encheloclarias is hypothesized to be the sister group of all other clariids, except Horaglanis Menon, 1951. The inferred position of Encheloclarias confirms that the adipose fin in this genus has an evolutionary origin independent to that of the adipose fin found in some African clariids. Encheloclarias is not only ecologically remarkable, being adapted to acidic peat swamps in Southeast Asia, but it is also an ancient lineage sheltering in these habitats. However, the precise timing of the colonization of peat swamps by Encheloclarias remains to be investigated. The phylogenetic position of Encheloclarias further underscores the importance of studying and protecting the remaining peat swamp habitats in Southeast Asia and their distinctive aquatic fauna.

Megaselia scalaris and Senotainia tricuspis Infesting Apis mellifera: Detection by Quantitative PCR, Genotyping, and Involvement in the Transmission of Microbial Pathogens.

The Megaselia scalaris and Senotainia tricuspis parasitoid flies of the honeybee Apis mellifera were found to infest apiaries of different European and Mediterranean countries but their prevalence and impact on apiary health are little known. Therefore, in this study, quantitative PCR (qPCR)-based methods were developed for their rapid detection directly in hive matrices. The newly developed qPCR assays were targeted at the mitochondrial cytochrome oxidase subunit I (COI) gene for the M. scalaris and the cytochrome B (cytB) gene for the S. tricuspis. The tests were preliminarily applied to 64 samples of adult honeybees and hive debris collected in the Abruzzo and Molise regions, Central Italy, and the Republic of Kosovo showing that both flies occur in the two countries and more frequently in Italy. The positive apiaries in Italy were re-sampled by capturing viable forager bees and isolating emerging flies to carry out the genotyping and analyses aimed at defining if these flies can transmit honeybee pathogens. Genotyping based on the COI and cytB gene sequencing for M. scalaris and S. tricuspis, respectively, identified one S. tricuspis genotype and diverse genotypes of M. scalaris highly similar to those from distant countries. Some fly isolates harbored the DNA or RNA of honeybee microbial pathogens Paenibacillus larvae, deformed wing viruses A and B (DWVA and B), black queen cell virus (BQCV), chronic paralysis virus (CBPV), and Nosema ceranae. The results indicated that these parasites should be efficiently controlled in apiaries by using rapid detection methods to facilitate the large screening studies and early detection.

Integrative morphological, cytogenetic and molecular characterization of the Andean climbing catfish Astroblepus mindoensis (Regan, 1916) (Siluriformes:Astroblepidae).

Astroblepus species, commonly known as Andean climbing catfish, exhibit a unique challenge in species delimitation, leading to ongoing taxonomic debates. Here we report data on Astroblepus mindoensis, a vulnerable species endemic to Ecuador, obtained by an integrative approach that includes cytogenetic analysis, molecular identification of the specimens, and recording of morphological and morphometric characters useful for species diagnosis. Thus, this study aimed to associate the karyotype data of the specimens analyzed with morphological and molecular characters, improving and expanding the existing taxonomic information, thus contributing to the systematics of the species. Our morphology results, unlike Regan's original description, which is brief and ambiguous, provide a more detailed morphometric and meristic description. Molecular phylogenetic reconstruction and genetic distance based on a fragment of the cytochrome c oxidase subunit I (COI) showed that our samples constitute a well-supported and monophyletic clade within the A. grixalvii species complex. The cytogenetic analysis identified distinct chromosomal markers, including a single cluster of major ribosomal genes (on chromosome pair 3) and of minor ribosomal genes (on chromosome pair 12) with their localization differing from those reported in other Astroblepus species analyzed. Additionally, the presence of a heteromorphic chromosome pair in males suggests the presence of an XX/XY sex-determination system that has not been identified in other congeneric species. Further investigation is necessary to determine if these chromosomes are associated with the accumulation of repeated sequences, as typically occurs with sex chromosomes, and to assess their presence in other species of the genus.

Morphological and molecular identification of freshwater eutardigrade Dactylobiotus parthenogeneticus (Bertolani, 1982) in the Greater Zab River of Kurdistan Region - Iraq.

Dactylobiotus parthenogeneticus is one of the widespread species of tardigrade all over the world. Tardigrades of this species were collected from the Greater Zab River in Erbil City-Iraq by filtering water of the river through a plankton net with a mesh of 45 µm pore. The samples were mounted on a slide with a cover slip and examined under the microscope to determine morphological characteristics and measurements. Based on these characters the species identified to be D. parthenogeneticus. To support this diagnosis, DNA barcoding techniques were applied to do molecular analysis and sequencing on the cytochrome oxidase subunit I (COI) gene. The sequence was subjected to the GenBank database of NCBI and recorded with the accession number PP140905. The result of the sequencing and molecular analysis of the cytochrome oxidase subunit I (COI) gene confirmed to be the same species diagnosed by relying upon morphological characters. This study represents one of the pioneer researches and documents on tardigrades and found D. parthenogeneticus for the first time in the Greater Zab River in Kurdistan, North of Iraq. Tardigrades play a magnificent role in different trophic levels and can be utilized as an indicator of ecosystem health.

Hidden species diversity in the Enteromius Cope, 1867 (Teleostei: Cyprinidae) from the Aruwimi basin (Middle Congo) in the Okapi Wildlife Reserve (Democratic Republic of the Congo).

Two new African minnow species, Enteromius cerinus sp. nov. and Enteromius ruforum sp. nov., are described for science from the Angadiko River, a left-bank sub-affluent of first order of the Nepoko River, draining the north-eastern part of the Okapi Wildlife Reserve (OWR). Both new species belong to the group of Enteromius for which the last unbranched dorsal-fin ray is flexible and underrated. Within this morphological group, both are most similar to Enteromius kamolondoensis, especially in life colour pattern characteristics. However, Enteromius cerinus sp. nov. differs from E. kamolondoensis by its low number of circumpeduncular scales, 10-11 (vs. 12), low maximum body depth, 22.8%-25.7% standard length (Ls) (vs. 26.1%-30.0%), and long anterior and posterior barbel lengths, 32.6%-35.3% head length (LH) (vs. 23.6%-27.2%) and 41.6%-43.9% LH (vs. 30.3%-34.9%), respectively. Further, E. ruforum sp. nov. is also easily distinguished from E. kamolondoensis by its high maximum body depth, 30.6%-33.3% Ls (vs. 26.1%-30.0%), and small, isometric, eye diameter, 26.2%-28.0% LH (vs. 29.1%-31.9%). A barcoding study (mtDNA, cytochrome oxidase subunit I [COI]) revealed that specimens of both new species form lineages well differentiated from those of other available species. As such, (i) E. cerinus sp. nov. diverges from E. kamolondoensis by a K2P genetic distance (GD) of 10.3% and (ii) E. ruforum sp. nov. by a K2P GD of 11.2%. To the present day, the fish fauna of the left-bank sub-affluents of the Nepoko River, in general, remains poorly known or undocumented. Unfortunately, at the same time, multiple anthropogenic impacts are affecting this fauna, such as (i) the destruction of habitats along the river banks for agriculture and fishing and (ii) the use of illegal fishing practices, such as fishing with plant-based ichthyotoxins during ecopage, which is combined with dam building. As a result of the demographic growth, this ecopage results in overfishing and thus is threatening both new species in particular, but all other co-occurring fish species as well. Both new species, E. cerinus sp. nov. and E. ruforum sp. nov., should thus be considered Vulnerable (VU) according to IUCN criterion D2. It is therefore hoped that their discovery highlights the urgent need for a better protection and further in situ exploration of the reserve's freshwater (fish) biodiversity, in general, and that of those small sub-affluents, in particular.

Phylogeography of the Sinica Group of Macaques in the Himalayas: Taxonomic and Evolutionary Implications.

Owing to the taxonomic incongruence between the morphological features and genetic relationships of the sinica group of macaques (genus Macaca), the taxonomy of this macaque group has remained inconclusive. We aimed to resolve the taxonomic quandary and improve our understanding of the historical biogeography of the group by including macaque DNA samples from previously unsampled areas in the Himalayas. We sequenced and analyzed three mitochondrial DNA loci [cytochrome b (CYTB), cytochrome oxidase subunit 1 (COI) and D-loop; 2898 bp] for sequence polymorphism, phylogenetics, species delimitation, and ancestral area reconstruction. We confirmed the occurrence of Arunachal macaque (Macaca munzala) on the southern slopes of the Eastern Himalayas in the Xizang Zizhiqu (Tibet Autonomous Region) of China. The results revealed that the sinica group of macaques is a parapatric species group composed of seven distinct species. Phylogenetic and species delimitation analyses revealed that the two previously considered subspecies of Assamese macaques (the eastern subspecies M. assamensis assamensis and the western subspecies M. a. pelops) are two distinct species. The eastern Assamese macaque is a sister species to the Tibetan macaque, whereas the western Assamese macaque and Arunachal macaque are the closest genetic sister species. The sinica group of macaques underwent five vicariance and seven dispersal radiations in the past, which mainly coincided with the Quaternary climatic oscillations between the late Pliocene and the late Pleistocene. By integrating our phylogenetic and ancestral area reconstruction results with findings from previous paleontological and molecular studies, we propose a robust hypothesis about the phylogeography of the sinica group of macaques.

Character-based Identification System (CBIS) for Authentication and Conservation of Fishes from the Thamirabarani River, Western Ghats of India

Background: Accurate identification of freshwater fish is essential to preserving freshwater fish diversity. BLOG uses a short DNA sequence taken from a portion of mitochondrial DNA called Cytochrome C Oxidase subunit I (COI), which varies by several percent, even between closely related species, so it can be used to identify the species of a particular individual. Methods: BLOG 2.0 is an advancement of logic data mining and can identify nucleotide positions that characterize DNA barcode sequences and classify species using logic formulas. This character-based identification method identifies specimens to species with the help of their logic rules and diagnostic nucleotides in the selected gene sequences. In this study, 30 species distributed in the Indian freshwater region were taken as the target group. A 30 -110 mtCOI sequences for each species were downloaded and modified. Results: With the help of BLOG.2.0 software, to identified specific diagnostic nucleotides for these freshwater species. Species-specific probes ranging from 18-22 base pairs were designed based on identified diagnostic nucleotide sites that could be useful in customized microarrays (DNA chips). This BLOG based CBIS will be a promising technique for obtaining quick, convenient, and extensive knowledge about the conservation of various freshwater fishes and their forensic applications.

DNA Barcoding using Cytochrome C Oxidase Subunit I (COI) Reveals Wildlife Consumption of Malayan Tapir (Tapirus indicus) and Dusky Leaf Monkey (Trachypithecus obscurus) by the Senoi (Semoq Beri) Tribe in Peninsular Malaysia

Abstract Malaysia, a culturally diverse nation, encompasses various ethnicities, including the Orang Asli, the region’s aboriginal people. Among the Orang Asli tribes in Peninsular Malaysia, the Senoi constitute the largest demographic, followed by the Proto-Malay and Negrito groups, each comprising six distinct subtribes. Traditional methods, such as surveys and interviews, have been instrumental in understanding wildlife consumption practices among indigenous communities like the Senoi. However, they may not always provide accurate and comprehensive data. The adoption of molecular techniques, such as DNA barcoding, presents a promising avenue for enhancing the accuracy and reliability of wildlife consumption studies. This study investigates wildlife consumption practices among the Senoi tribe, particularly the Semoq Beri subgroup in Maran, Pahang, using DNA barcoding that focuses on the Cytochrome C Oxidase Subunit I (COI) gene. Following the collection of biological samples with consent from Semoq Beri villagers, DNA extraction and PCR amplification were performed using established protocols. Subsequently, phylogenetic analysis was conducted to identify wildlife species consumed by the tribe. From the DNA barcoding analysis, two wildlife species were successfully detected: including the Malayan Tapir (Tapirus indicus) and the dusky leaf monkey (Trachypithecus obscurus), commonly consumed by the Semoq Beri tribe. Despite their status conservation, the findings suggest that the Semoq Beri tribe’s hunting practices are relatively sustainable, as they hunt only for subsistence purposes and in small quantities. The study emphasizes the significance of incorporating molecular techniques alongside conventional methods to accurately assess wildlife consumption patterns among indigenous communities. The findings highlight the necessity of collaborative approaches involving indigenous peoples, government agencies, and conservation organizations to preserve traditional knowledge, safeguard wildlife resources, and promote the sustainable coexistence of indigenous communities and biodiversity.