DNA barcoding to fishes: current status and future directions

High Genetic Differentiation and Genetic Diversity in Endangered Mahseer Tor khudree (Sykes, 1839) as Revealed from Concatenated ATPase 6/8 and Cyt b Mitochondrial Genes

The Deccan mahseer, Tor khudree (Sykes 1839), belonging to family Cyprinidae is an important food and a game fish distributed in peninsular India. Due to overfishing and habitat destruction, the species is declared endangered and placed on the IUCN red list. Therefore, a well-designed conservation program may be essential to get this species protected in its natural habitat. We used a total of 152 samples from four rivers of peninsular India to assess the genetic diversity and structure of the mahseer using concatenated sequences of two mitochondrial genes, ATPase 6/8 (790 bp) and Cyt b (1000 bp). High haplotypic diversity was seen with 44 haplotypes. Individual gene wise haplotypes included 10 and 21 haplotypes for ATPase6/8 and Cyt b, respectively. AMOVA revealed most of the genetic variations (71.02%) to be within the populations. Significant genetic differentiation was observed between all population pairs, with FST values ranging from 0.121 to 0.372, with minimum between Tunga and Tungabhadra population and maximum between Tunga and Periyar population. Haplotype network showed one ancestral haplotype (TKACH04). Significant negative Fu's F and unimodal mismatch distribution suggested recent demographic expansion. The results of the present study would serve as a useful resource for further research on population genetics and conservation programs of the species.

New records of native and introduced fish species in a river basin of Western Ecuador, the Chocó-Darien Ecoregion, using DNA barcoding

DNA barcoding, based on mitochondrial markers, is widely applied in species identification and biodiversity studies. The aim of this study was to establish a barcoding reference database of fishes inhabiting the Cube River from Western Ecuador in the Chocó-Darien Global Ecoregion (CGE), a threatened ecoregion with high diversity and endemism, and evaluate the applicability of using barcoding for the identification of fish species. Barcode sequences were obtained from seven orders, 17 families, 23 genera and 26 species, which were validated through phylogenetic analysis, morphological measurements, and literature review. Our results showed that 43% of fish species in this region are endemic, confirmed the presence of known species in the area, and included the addition of three new records of native (Hoplias microlepis, Rhamdia guatemalensis and Sicydium salvini) and an introduced species (Xiphophorus maculatus) to Ecuador. In addition, eight species were barcoded for the first time. Species identification based on barcoding and morphology showed discrepancy with species lists from previous studies in the CGE, suggesting that the current baseline of western fishes of Ecuador is still incomplete. Because this study analyzed fishes from a relatively small basin (165 km2), more molecular-based studies focusing on fish are needed to achieve a robust sequence reference library of species inhabiting Western Ecuador. The new sequences of this study will be useful for future comparisons and biodiversity monitoring, supporting the application of barcoding tools for studying fish diversity in genetically unexplored regions and to develop well-informed conservation programs.

A comprehensive DNA barcoding of Indian freshwater fishes of the Indus River system, Beas

The Beas River is one of the important rivers of the Indus River system located in Himachal Pradesh, India, that harbors a diverse range of freshwater fish species. The present study employed COI gene to investigate the ichthyofaunal diversity of river Beas. Through the sequencing of 203 specimens from Beas River, we identified 43 species, belonging to 31 genera, 16 families, and 10 orders. To analyze the genetic divergence and phylogeny of identified species, 485 sequences of Indian origin were retrieved from BOLD, resulting in a dataset of 688 sequences. Our findings consistently revealed a hierarchical increase in the mean K2P genetic divergence within species (0.80%), genus (9.06%), and families (15.35%). Automated Barcode Gap discovery, Neighbour Joining, and Bayesian inference consensus tree methodologies were employed to determine the putative species and their phylogeny, successfully delimiting most of the species with only a few exceptions. The results unveiled six species exhibiting high intra-species divergence (> 2%), suggesting the presence of sibling species and falsely identified sequences on online databases. The present study established the first DNA barcoding-based inventory of freshwater fish species in the Beas River providing comprehensive insights into economically exploited endangered and vulnerable species. In order to ensure the sustainable use of aquatic resources in the Beas River, we recommend the implementation of species measures to protect biodiversity and genetic resources.

Blood meal identification reveals extremely broad host range and host-bias in a temporary ectoparasite of coral reef fishes

Appreciation for the role of cryptofauna in ecological systems has increased dramatically over the past decade. The impacts blood-feeding arthropods, such as ticks and mosquitos, have on terrestrial communities are the subject of hundreds of papers annually. However, blood-feeding arthropods have been largely ignored in marine environments. Gnathiid isopods, often referred to as "ticks of the sea", are temporary external parasites of fishes. They are found in all marine environments and have many consequential impacts on host fitness. Because they are highly mobile and only associated with their hosts while obtaining a blood meal, their broader trophic connections are difficult to discern. Conventional methods rely heavily on detecting gnathiids on wild-caught fishes. However, this approach typically yields few gnathiids and does not account for hosts that avoid capture. To overcome this limitation, we sequenced blood meals of free-living gnathiids collected in light traps to assess the host range and community-dependent exploitation of Caribbean gnathiid isopods. Using fish-specific COI (cox1) primers, sequencing individual blood meals from 1060 gnathiids resulted in the identification of 70 host fish species from 27 families. Comparisons of fish assemblages to blood meal identification frequencies at four collection sites indicated that fishes within the families Haemulidae (grunts) and Lutjanidae (snappers) were exploited more frequently than expected based on their biomass, and Labrid parrotfishes were exploited less frequently than expected. The broad host range along with the biased exploitation of diel-migratory species has important implications for the role gnathiid isopods play in Caribbean coral reef communities.

Revisiting the species list of freshwater fish in Israel based on DNA barcoding

Israel's region forms a continental bridge; hence, the freshwater fish fauna in Israel consists of unique populations of species that originated from Africa, Asia, or Europe and are often endemic or at the edge of their distribution range. Worldwide, fish biodiversity suffers significantly from pressures and disturbances of freshwater habitats, especially in arid regions, such as in parts of Israel. Biodiversity conservation requires efficient tools for monitoring changes in populations. DNA barcoding, by complementing and enhancing species identification, provides such monitoring tools. In this study, over 200 specimens representing over 28 species were DNA barcoded and together with previously available records, a DNA barcoding database for freshwater fish of Israel was established. Of the 71 distinct barcodes generated, 37% were new, attesting to the uniqueness of fish populations in Israel. For most species, morphological and molecular species identifications agreed. However, discrepancies were found for five genera. Based on DNA barcoding, we propose Acanthobrama telavivensis as a junior synonym for Acanthobrama lissneri. In Garra spp., we propose splitting Garra nana into two species and assigning Garra rufa in the region to Garra jordanica, or possibly to two species. Israeli Pseudophoxinus kervillei is not the same species as in Syria and Lebanon. However, Pseudophoxinus syriacus might not be endangered since it is genetically very similar to Pseudophoxinus drusensis. In Israel, instead of five reported Oxynoemacheilus species, combining DNA barcoding with morphology suggests only three. Genetic and geographic separation suggested that Aphanius mento is likely a species complex. The study provides a thorough barcoding database, suggests significant species reconsiderations in the region, and highlights the Sea of Galilee and the Beit She'an valley streams as biodiversity "hotspots." This study will therefore promote further studying of the fish species in the region and their ecology, as well as the monitoring and conservation of freshwater fish biodiversity in Israel and the region.

Mitochondrial Analysis of Sparidae Species to Detect a New DNA Barcoding Marker for Dentex gibbosus to Utilize against Fraud

Dentex gibbosus (Pink dentex) is a fish species of increasing economic interest in the Mediterranean Sea that is consumed both whole and processed. The growing value of this sparid in European markets is responsible for its substitution with fraudulent species. The distinctive morphologic feature of D. gibbosus is the conspicuous hump on the forehead in the older and larger specimens. However, the head is regularly convex in young individuals, requiring high skills and competencies for correct identification. Authentication becomes even more challenging in the case of prepared and processed products. Therefore, the molecular characterization of Pink dentex plays a crucial role in preventing commercial fraud with species substitution. This paper proposes a comparative mitogenome analysis between 19 sparid species of commercial interest as a tool to accurately design species-specific primers targeting a fragment of the NAD2 gene for the identification of D. gibbosus. We successfully detected Pink dentex DNA both using endpoint and real-time PCR. The findings showed the high specificity of the designed primers, demonstrating this a suitable, fast, and cost-effective method that could be used for the unambiguous identification of Pink dentex. This innovative approach for sparid authentication is expected to contribute to seafood traceability, public health assurance, integrity, and the credibility of the seafood industry.

DNA-based species identification of shark fins traded in thai markets

Shark fins are among the most highly prized seafood products in the world with massive consumption in Asia over the past several decades. The demand for shark fins is a major driver of the enormous population declines of elasmobranchs that are generally vulnerable to overexploitation. This study aims to better understand the species composition of shark fin products in Thailand and their conservation statuses by using DNA-based species identification. Various types and sizes of shark fins were collected from 4 locations in Thailand. DNA barcoding method based on a fragment of the cytochrome c oxidase subunit I (COI) gene was applied to species identification. Fins from at least 15 shark species were found from Thailand's markets. The spottail shark (Carcharhinus sorrah) and the night shark (Carcharhinus signatus) were the two dominant species presented in this study. 34% of identifiable samples are the species that have not been record in this region. 62% of species detected from the fin samples are categorized under the threatened categories of IUCN Red List. Species composition reported in shark fin products potentially helps indicate the appropriate conservation action and increases awareness from monitoring the trade in elasmobranch products.

Supplementary Information

The online version contains supplementary material available at 10.1007/s10592-023-01519-0.

Mitochondrial DNA barcoding of mosquito species (Diptera: Culicidae) in Thailand

The correct identification of mosquito species is important for effective mosquito vector control. However, the standard morphological identification of mosquito species based on the available keys is not easy with specimens in the field due to missing or damaged morphological features during mosquito collections, often leading to the misidentification of morphologically indistinguishable. To resolve this problem, we collected mosquito species across Thailand to gather genetic information, and evaluated the DNA barcoding efficacy for mosquito species identification in Thailand. A total of 310 mosquito samples, representing 73 mosquito species, were amplified using mitochondrial cytochrome c oxidase subunit I (COI) primers. The average maximum intraspecific genetic variation of the 73 mosquito species was 1% ranged from 0–5.7%. While, average minimum interspecific genetic variation (the distance to the nearest neighbour) of the 73 mosquito species was 7% ranged from 0.3–12.9%. The identification of success rates based on the “Best Match,” “Best Close Match,” and “All Species Barcodes” methods were 97.7%, 91.6%, and 81%, respectively. Phylogenetic analyses of Anopheles COI sequences demonstrated a clear separation between almost all species (except for those between An. baimaii and An. dirus), with high bootstrap support values (97%–99%). Furthermore, phylogenetic analyses revealed potential sibling species of An. annularis, An. tessellatus, and An. subpictus in Thailand. Our results indicated that DNA barcoding is an effective molecular approach for the accurate identification of mosquitoes in Thailand.

Aquatic food animals in the United States: Status quo and challenges

This review summarizes (1) the U.S. status quo for aquatic food animal production and marketing; (2) major food safety and quality issues/concerns for aquatic food animals in the United States, including fish misbranding, finfish/shellfish allergies, pathogens, toxins and harmful residues, microplastics, and genetically engineered salmon; and (3) various U.S. regulations, guidances, and detection methods for the surveillance of fishery products. Overall, fish misbranding is the biggest challenge in the United States due to the relatively low inspection rate. In addition, due to the regulatory differences among countries, illegal animal drugs and/or pesticide residues might also be identified in imported aquatic food animals. Future regulatory and research directions could focus on further strengthening international cooperation, enhancing aquatic food animal inspection, and developing reliable, sensitive, and highly efficient detection methods.

Stock Structure Analysis of the Endangered Queen Loach, Botia dario (Hamilton 1822) from Five Rivers of Northern Bangladesh by Using Morphometrics: Implications for Conservation

Identifying stock is key to sustainable fisheries management and conservation. Using traditional morphometrics (TMR) and image-based truss network analysis (ITNA), we evaluated the stock structure of the endangered queen loach, Botia dario. The study was carried out in the following five stocks in Bangladesh’s northern rivers: the Atrai, Dhorala, Danu, Jamuna, and Padma. The inventory regarding stock structure was investigated using a total of nine traditional morphometrics, 11 ratios, and 23 truss measurements for each individual. To generate 23 ITNA, 12 landmarks were used. To assess variations among the stocks, a principal component analysis (PCA), factor analysis (FA), canonical variate analysis (CVA), and cluster analysis (CA) were performed. Six principal components explained 91.50% of the variation in TMR, while seven principal components explained 73.425% of the variation in ITNA. CVA, using traditional methods and ratios were correctly classified as 65.0%, 42.0%, 64.2%, 89.3%, and 77.5% for Danu, Padma, Jamuna, Dhorala, and Atrai River stocks, respectively, based on original grouped classes. CVA using ITNA was correctly classified as 90.0%, 80.0%, 77.4%, 94.6%, and 98.6% for Danu, Padma, Jamuna, Dhorala, and Atrai River stocks, respectively, based on original grouped classes. CVA analysis based on TMR and ITNA showed that cannonical variates (CV1 to CV3) are related to the whole-body shape. Both TMR and ITNA formed two clusters. In the first cluster, the Jamuna and Atrai River stocks combinedly formed a separate stock based on (TMR). In ITNA, the Dhorala and Atrai River formed as separate stocks from the other four stocks. According to this study, combining TMR and ITNA analysis aids in the differentiation of various B. dario stocks. The stock separation of this species was supposed to be geographic disconnection, waterway nature, and temperature variations. The B. dario stocks are heavily exploited and the species is an ideal nominee for species variation to boost the aquaculture yield. Within-stock distinctions were revealed in this study, necessitating the identification of gene pools and molecular studies to achieve a deeper understanding of the stocks. Through a more scientific approach, this stock structure study may aid in the development of conservation programs for this endangered species.

Understanding the molecular evolution of tiger diversity through DNA barcoding marker ND4 and NADH dehydrogenase complex using computational biology

BACKGROUND

Currently, Tigers (the top predator of an ecosystem) are on the list of endangered species. Thus the need is to understand the tiger's population genomics to design their conservation strategies.

OBJECTIVE

We analyzed the molecular evolution of tiger diversity using NADH dehydrogenase subunit 4 (ND4), a significant electron transport chain component.

METHODS

We have analyzed nucleotide composition and distribution pattern of ND genes, molecular evolution, evolutionary conservation pattern and conserved blocks of NADH, phylogenomics of ND4, and estimating species divergence, etc., using different bioinformatics tools and software, and MATLAB programming and computing environment.

RESULTS

The nucleotide composition and distribution pattern of ND genes in the tiger genome demonstrated an increase in the number of adenine (A) and a lower trend of A+T content in some place of the distribution analysis. However, the observed distributions were not significant (P > 0.05). Evolutionary conservation analysis showed three highly align blocks (186 to 198, 406 to 416, and 527 to 545). On mapping the molecular evolution of ND4 among model species (n = 30), we observed its presence in a broader range of species. ND4 based molecular evolution of tiger diversity and time divergence for a tiger (20 different other species) shows that genus Panthera originated more or less at a similar time.

CONCLUSIONS

The nucleotide composition and nucleotide distribution pattern of tiger ND genes showed the evolutionary pattern and origin of tiger and Panthera lineage concerning the molecular clock, which will help to understand their adaptive evolution.

Towards retrieving the Promethean treasure: a first molecular assessment of the freshwater fish diversity of Georgia

In this study, we provide a first estimation of the molecular diversity of the freshwater fishes of Georgia. In addition to field collections, we integrated DNA barcode data obtained from recent works and public databases (BOLD and NCBI GenBank). Currently, the DNA barcode reference library for freshwater fishes of Georgia comprises 352 DNA barcodes for 50 species, 36 genera and 15 families (52% of total Georgian freshwater fish diversity), from which 162 DNA barcodes belonging to 41 species were newly generated as part of this study. A total of 22 species are reported from the Caspian Sea basin and 31 from the Black Sea basin. Amongst the studied taxa, seven species were found with large interspecific divergences (> 2%) while 11 species were found to share DNA barcodes within our dataset. In the course of the study, we found the first evidence of the existence of Gymnocephaluscernua (Linnaeus, 1758) and also confirm the second occurrence of invasive Rhinogobiuslindbergi (Berg, 1933) in Georgia. Based on the evaluation of currently-available barcode data for Georgian fishes, we highlighted major gaps and research needs to further progress DNA-based biodiversity studies in Georgia. Though this study lays a solid base for DNA, based biodiversity assessment and monitoring approaches, further efforts within the recently started CaBOL (Caucasus Barcode Of Life) project are needed to obtain reference data for the species still lacking DNA barcodes.

DNA barcoding of commercially important reef fishes in Weh Island, Aceh, Indonesia

Knowledge on the precise identification of fish resources is critical for sustainable fisheries management. This study employs the DNA barcoding approach to generate a molecular taxonomic catalogue of commercially important reef fishes in the waters of Weh Island (Aceh Province), the most northerly inhabited island in the biodiverse Indonesian Archipelago. The waters not only support artisanal fisheries but also a feeder for the industry in the greater island of Aceh. In total, 230 specimens from 72 species belonging to 32 genera and 17 families were DNA barcoded, representing a major segment of the captured reef fish taxa and a quarter of fish species diversity that had previously been recorded. The sequence read lengths were 639 bp revealing 359 conserved sites, 280 variable sites, 269 parsimony informative and 11 singletons. Our molecular findings paralleled the morphological identification with no evidence of cryptic species or new species discovery. This study is a significant contribution to the fisheries statistics of this area, which would facilitate assessment of species catch composition and hence for strategizing management plans. It is an important input to the DNA barcode library of Indonesian marine fishes and to the global DNA barcode entries in general.

Cytochrome Oxidase I (COI) Divergence Assessment of Family Nemipteridae from Malaysian Waters

DNA Barcoding, primarily focusing on cytochrome c oxidase subunit I (COI) gene has been appraised as an effective tool for species identification. Nonetheless, species identification based on molecular approach is essential for discrimination of look-alike species. In this study, we focused on the marine fishes Family Nemipteridae, one of the commercially important group distributed within the surrounding seas of Malaysia. Some of the samples were collected during the National Demersal Trawl Survey in the Exclusive Economic Zone of East Coast Peninsular Malaysia by the Department of Fishery Malaysia. A 652bp region of COI was sequenced for 74 individuals from nine putative species. Additional 34 COI sequences from GenBank were also included in this study making the total number of samples analysed to 108 individuals. The average Kimura 2-parameter (K2P) nucleotide divergence was 0.34% among individuals within species and 6.97% within genera. All putative species formed monophyletic clades in both Neighbour-joining (NJ) and Maximum-likelihood (ML) trees. However, there was a potential misidentification in specimen identified as Nemipterus tambuloides, as the specimen did not group with their own taxa. It was genetically grouped in Nemipterus thosaporni clade. This study supports the effectiveness of COI gene in species discrimination of Family Nemipteridae.

Species identification of juvenile fishes of the genus Pseudoblennius using mitochondrial DNA barcoding

Species identification is important in natural science and should be precise. Six specimens of juvenile Pseudoblennius were collected from the eastern coastal waters of the Korean Peninsula and Jeju Island in 2016-2017, and identified for the first time using DNA barcoding based on mitochondrial DNA cytochrome oxidase subunit I sequences. DNA barcoding analysis supported three adult species of genus Pseudoblennius (P. cottoides, P. marmoratus, and P. percoides) being quite distinct from each other. Six juvenile specimens were completely identified: two as P. cottoides; two more as P. marmoratus; and the final two as P. percoides. Mitochondrial DNA COI can be effective as a means of species identification method for the genus Pseudoblennius.

Detection of Potential Problematic Cytb Gene Sequences of Fishes in GenBank

Fishes are, by far, the most diverse group of vertebrates. Their classification relies heavily on morphology. In practice, the correct morphological identification of species often depends on personal experience because many species vary in their body shape, color and other external characters. Thus, the identification of a species may be prone to errors. Due to the rapid development of molecular biology, the number of sequences of fishes deposited in GenBank has grown explosively. These published data likely contain errors owing to invalid or incorrectly identified species. The erroneous data can lead to downstream problems. Thus, it is critical that such errors get identified and corrected. A strategy based on DNA barcoding can detect potentially erroneous data, especially when intraspecific K2P variation exceeds interspecific K2P divergence. Analyses of the most used DNA marker for fishes (mitochondrial Cytb) discovers that intraspecific differences of fishes are generally less than 1%, while interspecific differences are generally higher than 10%. Based on this ruler, our analyses identify 1,303 potential problematic Cytb sequences of fishes in GenBank and point to taxonomic problems, errors in identification, genetic introgression and other concerns. Care must be taken to avoid the perpetuation of errors when using these available data.

Harnessing the Power of Genomics to Secure the Future of Seafood

Best use of scientific knowledge is required to maintain the fundamental role of seafood in human nutrition. While it is acknowledged that genomic-based methods allow the collection of powerful data, their value to inform fisheries management, aquaculture, and biosecurity applications remains underestimated. We review genomic applications of relevance to the sustainable management of seafood resources, illustrate the benefits of, and identify barriers to their integration. We conclude that the value of genomic information towards securing the future of seafood does not need to be further demonstrated. Instead, we need immediate efforts to remove structural roadblocks and focus on ways that support integration of genomic-informed methods into management and production practices. We propose solutions to pave the way forward.