No full-text available
To read the full-text of this research,
you can request a copy directly from the authors.
DNA barcodes of the native ray-finned fishes in Taiwan
Abstract
Species identification based on the DNA sequence of a fragment of the cytochrome c oxidase subunit I (COI) gene in the mitochondrial genome, DNA barcoding, is widely applied to assist in sustainable exploitation of fish resources and the protection of fish biodiversity. The aim of this study was to establish a reliable barcoding reference database of the native ray-finned fishes in Taiwan. A total of 2,993 individuals, belonging to 1,245 species within 637 genera, 184 families, and 29 orders of ray-finned fishes and representing approximately 40% of the recorded ray-finned fishes in Taiwan, were PCR amplified at the barcode region and bidirectionally sequenced. The mean length of the 2,993 barcodes is 549 bp. Mean congeneric K2P distance (15.24%) is approximately 10-fold higher than the mean conspecific one (1.51%), but roughly 1.4-fold less than the mean genetic distance between families (20.80%). The Barcode Index Number (BIN) discordance report shows that 2,993 specimens represent 1,275 BINs and, among them, 86 BINs are singletons, 570 BINs are taxonomically concordant, and the other 619 BINs are taxonomically discordant. Barcode gap analysis also revealed that more than 90% of the collected fishes in this study can be discriminated by DNA barcoding. Overall, the barcoding reference database established by this study reveals the need for taxonomic revisions and voucher specimen rechecks, in addition to assisting in the management of Taiwan's fish resources and diversity. This article is protected by copyright. All rights reserved.
... These catches may include species not usually consumed directly but often caught as bycatch. Taiwan is renowned for its rich marine biodiversity and resources, with over 3000 finfish species recorded in its waters, including more than 200 species of sharks [7,8]. Consequently, highly active coastal fisheries in Taiwan inevitably lead to the direct or indirect utilization of these abundant and diverse shark species [9][10][11][12]. ...
... The number, composition, and abundance (reads) of fish species varied across the four seasons and among the main species groups (Figs. [5][6][7][8]. Private fishery sources and preferences may influence the differences in fish species between samples from different producers and seasons. Seasonal variations in fish species can be attributed to the availability of species, as fishing seasons in Taiwan differ for various species [43]. ...
Fish surimi products are traditional foods primarily made from fish meat and may contain a complex species composition. In Taiwan, the abundant fishery resources and diverse fish species lead to local catches being widely used as ingredients in fish surimi products. However, due to growing market demand and increasingly scarce resources, some surimi products contain sensitive species, such as sharks, posing potential threats to the ecological environment and biodiversity. In this study, by applying metabarcoding techniques, we analyzed 120 fish surimi product samples from different brands and types throughout the four seasons in Taiwan's market. The main fish species identified included milkfish (Chanos chanos), dolphinfish (Coryphaena hippurus), Pomfret (Taractes rubescens), swordfish (Istiophorus spp.) and cartilaginous. Moreover, at least 37 species of cartilaginous fish, including 26 endangered species, were found. Through comprehensive and accurate species identification of surimi product ingredients, we unveiled the usage of sensitive species in products on the market. This finding is important for the surimi industry's quality control and market supervision. Furthermore, it can promote the sustainable use of Taiwan's fishery resources and protect biodiversity.
... The similarity of the nucleotide sequence of the specimen studied in the present research and P. pavoninus (MW380722) from a paper by Shadrin et al. [2] is 82.6%, indicating that the two representatives of the Soleidae are very clearly differentiated based on the mitochondrial COI gene. Moreover, GenBank contains three reference sequences of L. melanospilos deposited by three independent teams of researchers [4,11,42] and two matching accessions under the name P. pavoninus deposited by Zhang [46]. A photograph presented in the publication by Zhang [46] leaves no doubt that, despite the significant color variability in L. melanospilos [10,23,44], the author studied L. melanospilos but not P. pavoninus. ...
... With completion of differentiation of the digestive system to the functional state, the number of myomeres of the trunk region in the larvae of L. melanospilos apparently reached the definitive value, which was also observed in other studied soleids at these developmental stages, particularly in Pegusa lascaris [34], Barnardichthys fulvomarginatus, Heteromycteris capensis, Austroglossus microlepis [3], Dicologlossa cuneata [17], Microchirus ocellatus [28], and Pardachirus pavoninus [2]. When characterizing soleid larvae, Leis and Carson-Ewart [20] provided a segmental formula of a much wider range for the trunk region (4)(5)(6)(7)(8)(9)(10)(11)(12)(13)(14)(15)(16)(17)(18)(19)(20); however, we failed to find specific examples in the literature of species with such strong deviations from a value of 9−10 trunk vertebrae. ...
Late embryonic and larval development of the carpet sole Liachirus melanospilos was followed until completion of metamorphosis and transition to the juvenile state. Illustrations and morphological descriptions of the early developmental stages are presented. The material of L. melanospilos was obtained from ichthyoplankton samples (Central Vietnam) and incubated under laboratory conditions at a temperature of about 24°C. Ta-xonomic identification of the species was carried out based on the analysis of a partial sequence of the mitochondrial cytochrome c oxidase subunit 1 (COI) gene.
... More significant genetic differentiation was detected between Clade C (ZZ and ST) and Clades A, B, which was inconsistent with geographical distance among different sampling locations. This genetic pattern is also found in other marine organisms ( (Chang et al., 2017). There is different marine habitat in Taiwan Strait, including coral reefs, estuaries, and mangrove forests, resulting in a wide range of differences in water depths and water temperatures (Shao, 2009). ...
... There is different marine habitat in Taiwan Strait, including coral reefs, estuaries, and mangrove forests, resulting in a wide range of differences in water depths and water temperatures (Shao, 2009). Besides, due to the influence of the South China Sea, Kuroshio and China coast currents, specific genetic structure of marine organisms is easily generated (Chang et al., 2017). To investigate and protect genetic resources, further research on population genetics of species in Taiwan Strait is necessary. ...
Amphioctopus fangsiao (Cephalopoda: Octopodidae) is an important commercial species in the coastal waters of China. In recent years, however, the resource of A. fangsiao have declined because of habitat destruction and overfishing. To analyze the genetic variations of A. fangsiao caused by the fluctuation of resources, the population genetic structure of nine sampling locations collected from the Bohai Sea to the South China Sea were investigated, using mtDNA COI fragments and microsatellite DNA. The results of F-statistics, AMOVA, STRUCTURE and PCA analyses showed three phylogeographic clades (Clades A, B and C), revealing limited genetic exchange between north and south populations. These clades diverged in 2.23 (Clades A and B) and 3.67 (Clades A, B and C) million years ago, during the dramatic environmental fluctuations, such as sea level and temperature changes, have exerted great influence on the survival distribution pattern of global organisms. Our results for low genetic connectivity among A. fangsiao populations provide insights into the development of management strategies, that is, to manage this species as separate management unit.
... The similarity of the nucleotide sequence of the specimen studied in the present research and P. pavoninus (MW380722) from a paper by Shadrin et al. [2] is 82.6%, indicating that the two representatives of the Soleidae are very clearly differentiated based on the mitochondrial COI gene. Moreover, GenBank contains three reference sequences of L. melanospilos deposited by three independent teams of researchers [4,11,42] and two matching accessions under the name P. pavoninus deposited by Zhang [46]. A photograph presented in the publication by Zhang [46] leaves no doubt that, despite the significant color variability in L. melanospilos [10,23,44], the author studied L. melanospilos but not P. pavoninus. ...
... With completion of differentiation of the digestive system to the functional state, the number of myomeres of the trunk region in the larvae of L. melanospilos apparently reached the definitive value, which was also observed in other studied soleids at these developmental stages, particularly in Pegusa lascaris [34], Barnardichthys fulvomarginatus, Heteromycteris capensis, Austroglossus microlepis [3], Dicologlossa cuneata [17], Microchirus ocellatus [28], and Pardachirus pavoninus [2]. When characterizing soleid larvae, Leis and Carson-Ewart [20] provided a segmental formula of a much wider range for the trunk region (4)(5)(6)(7)(8)(9)(10)(11)(12)(13)(14)(15)(16)(17)(18)(19)(20); however, we failed to find specific examples in the literature of species with such strong deviations from a value of 9−10 trunk vertebrae. ...
... 15,53 Such taxonomic uncertainty seriously complicates accurate species determination and the search for valid information on aspects such as species distribution, biology, ecology and status. As pointed out by, 54 the ability to precisely identify the fish species in fisheries catches or waters is important for moving towards more sustainable exploitation of fish resources and better protection of fish diversity. An increasingly common molecular approach to species identification is DNA barcoding; this involves the sequencing of a fragment of DNA which is highly conserved within species but differs between species of the taxonomic group being studied. ...
... 2, 56 In addition to species identification, phenotypic traits are important for taxonomy and to support fisheries management. 54,57,58 From a biodiversity and responsible fisheries management point of view, it was considered important to determine the native species currently present in Bolano Sau Lake. This study combined molecular biology methods (DNA barcoding) to identify the payangka in Bolano Sau Lake with classic methods to describe phenotypic characters, in particular external morphology (morphometric and meristic characters) and growth pattern (length-weight relationship). ...
Background : The freshwater ichthyofauna of Wallacea is diverse and understudied. A baseline survey of Bolano Sau Lake in Parigi Moutong District, Central Sulawesi Province, Indonesia in 2019 found an eleotrid goby (local name payangka) with characters conforming to the genus Giuris , long considered monophyletic as G. margaritacea/G. margaritaceus but recently found to comprise at least eight species. This study focused on the molecular (DNA barcoding) identification and phenotypic characters of the payangka.
Methods : Payangka samples were collected from August to December 2019 in collaboration with local fishermen, weighed and measured, and preserved in 75% ethanol. Length, weight, sex (n=111) and 17 morphometric characters/six meristic counts (n=42) were recorded. DNA barcoding was performed on a fin clipping preserved in 96% ethanol. Homologous nucleotide sequences were obtained from public (GenBank and BOLD) databases, analysis conducted in MEGA X, and phylogenetic trees edited in the Interactive Tree of Life (iToL).
Results : Within the deeply divided Giuris clade, the payangka sequence resolved into a sub-clade identified as Giuris laglaizei (Sauvage 1880), a recently resurrected taxon, based on a sequence provided by Philippe Keith. The length-weight relationship (L = 0.0087∙W3.162) indicated mildly allometric positive growth. Size distribution differed significantly between male and female fish with significantly larger mean size of males (13.56 cm) than females (11.62 cm). The meristic formula was: D VI-I,8 A I,8 P 13 V I,5 C15. Phylogenetic analysis indicated four Giuris species in wetlands around Tomini Bay and five in Sulawesi.
Conclusions : This first record of G. laglaizei in Indonesia advances knowledge of Wallacean and Indo-Pacific Gobiiformes biogeography and highlights the need for a revision of the conservation status of the taxa currently grouped under Giuris margaritacea/G. margaritaceus in the IUCN Red List and FishBase databases. The data will inform biodiversity and fisheries management at local and regional levels.
... 15,53 Such taxonomic uncertainty seriously complicates accurate species determination and the search for valid information on aspects such as species distribution, biology, ecology and status. As pointed out by, 54 the ability to precisely identify the fish species in fisheries catches or waters is important for moving towards more sustainable exploitation of fish resources and better protection of fish diversity. An increasingly common molecular approach to species identification is DNA barcoding; this involves the sequencing of a fragment of DNA which is highly conserved within species but differs between species of the taxonomic group being studied. ...
... 2,56 In addition to species identification, phenotypic traits are important for taxonomy and to support fisheries management. 54,57,58 From a biodiversity and responsible fisheries management point of view, it was considered important to determine the native species currently present in Bolano Sau Lake. This study combined molecular biology methods (DNA barcoding) to identify the payangka in Bolano Sau Lake with classic methods to describe phenotypic characters, in particular external morphology (morphometric and meristic characters) and growth pattern (length-weight relationship). ...
Background : The freshwater ichthyofauna of Wallacea is diverse and understudied. A baseline survey of Bolano Sau Lake in Parigi Moutong District, Central Sulawesi Province, Indonesia in 2019 found an eleotrid goby (local name payangka ) with characters conforming to the genus Giuris , long considered monophyletic as G. margaritacea/G. margaritaceus but recently found to comprise at least eight species. This study focused on the molecular (DNA barcoding) identification and phenotypic characters of the payangka .
Methods : Payangka samples were collected from August to December 2019 in collaboration with local fishermen, weighed and measured, and preserved in 75% ethanol. Length, weight, sex (n=111) and seventeen morphometric characters/six meristic counts (n=42) were recorded. DNA barcoding was performed on a fin clipping preserved in 96% ethanol. Homologous nucleotide sequences were obtained from public (GenBank and BOLD) databases, analysis conducted in MEGA X, and phylogenetic trees edited in the Interactive Tree of Life (iToL).
Results : Within the polyphyletic Giuris clade, the payangka sequence resolved into a sub-clade identified as Giuris laglaizei (Sauvage 1880), a recently resurrected taxon, based on a sequence provided by Philippe Keith. The length-weight relationship (L = 0.0087∙W3.162) indicated mildly allometric positive growth. Size distribution differed significantly between male and female fish with significantly larger mean size of males (13.56 cm) than females (11.62 cm). The meristic formula was: D VI-I,8 A I,8 P 13 V I,5 C15. Phylogenic analysis indicated four Giuris species in wetlands around Tomini Bay and five in Sulawesi.
Conclusions : This first record of G. laglaizei in Indonesia advances knowledge of Wallacean and Indo-Pacific gobioid biogeography and highlights the need for a revision of the conservation status of the taxa currently grouped under Giuris margaritacea/G. margaritaceus in the IUCN Red List and FishBase databases. The data will inform biodiversity and fisheries management at local and regional levels.
... Currently, species identification using mitochondrial genes as genetic markers has been widely applied (Chang et al 2017). Mitochondrial 16S rRNA gene that has some highly conserved regions in its sequence has been used as a molecular marker for identification studies of various animal species (Yang et al 2014). ...
The genus Ompok is one of the catfish which include local fishery resources from the Riau Province of Indonesia. Research on the genetic character of the genus Ompok in Indonesia is still very rare. This study aimed to determine genetic characterization and phylogenetic reconstruction of the genus Ompok from Riau Province of Indonesia using mitochondrial 16S rRNA gene sequences. A total of 15 fish samples were used in this study consisting of six samples of Ompok eugeneiatus and nine samples of Ompok hypophthalmus. The fish samples were collected from Kampar River, Tapung River and Indragiri River of Riau Province, Indonesia. Total genome was extracted from muscle tissue of fish using DNeasy Blood and Tissue Kit (Qiagen). The mitochondrial 16S rRNA gene was amplified using polymerase chain reaction (PCR) technique. The PCR reaction component follows protocol of the TopTaq Master Mix Kit (Qiagen). The analysis of genetic characterization and phylogenetic relationship was conducted using MEGA version 6.0 software. The results of multiple alignment of 16S rRNA gene sequences of O. eugeneiatus and O. hypophthalmus from Riau Province of Indonesia obtained 454 bp of nucleotides. The base composition on the 16S rRNA gene showed that the base composition was adenine (A) > thymine (T/U), and guanine (G) < cytosine (C). The composition of the nucleotide bases in the 16S rRNA gene showed that the A+T value was higher than that of G+C. Transition substitution mutations are more common than transversion substitution. The results of genetic distance to 16S rRNA sequences in O. eugeneiatus and O. hypophthalmus species found that interspecies genetic distance > intraspecies. The phylogenetic tree reconstruction using the 16S rRNA gene showed that this gene could differentiate interspecies between O. eugeneiatus and O. hypohthalmus from Riau Province, Indonesia. This accuracy is indicated by the formation of separate groups between the species O. eugeneiatus and O. hypophthalmus from Riau Province, with comparison Ompok bimaculatus and Clarias gariepinus from GenBank data.
... Nasren et al., 2020, uncovered that the COI gene serves as a genetic marker for a more precise differentiation of Hypselobarbus jerdoni and H. pulchellus sister species, while lateral line scales (llsc) are utilized as a morphological characteristic in their identification. A significant amount of genetic data pertaining to ambassid fishes primarily consists of DNA barcoding information, specifically cytochrome c oxidase subunit I (COX1) data (Chang et al., 2017;Khedkar et al., 2014), which have yielded consistent findings. Three vouchers were matched with OL638214.1, ...
Fish species identification is of paramount importance in biological research, serving as a fundamental component for understanding species biology. In our study, we collected a total of 34 specimens, glassy perchlet fish (Parambassis lala) from the Surma River, Singari beel and Ratargul swamp forest. Those total length (TL) were ranging from 2.1 to 3.9 cm. The collected specimens showed morphological variation in meristic features and coloration, which can be resolved through molecular study. For molecular identification, we meticulously selected three individual fish samples, conducted DNA extraction, polymerase chain reaction (PCR), and subsequent sequencing. These efforts resulted in sequences of 638 base pairs each for the Cytochrome C Oxidase subunit I (COI) gene. In our genetic analysis, three specimens-demonstrated a high degree of sequence similarity, ranging from 97.76% to 98.56%, when compared to the reference sequence OL638214.1. This outcome confirms their classification as Parambassis lala, despite morphological differences.
... The mitochondrial COI gene shows an increase level of conserved genes within genera and species, and some levels of genetic variation between different genera and species. The mitochondrial COI gene analysis was used for the identification of Mediterranean fishes (Karahan et al. 2017), Taiwan ray-finned fishes (Chang et al. 2017), Indian freshwater fishes (Chakraborty & Ghosh 2014), and Japanese marine fishes (Zhang & Hanner 2011). The selected primers applied in the present work proved effective in amplifying the target region without any insertions or deletions, revealing that DNA barcoding can be used as a gold standard method for characterizing organisms. ...
In this study, the collected fish species were identified based on morphological observations and then evaluated by DNA barcoding. The COI gene has been recognized as a biological marker for fish species identification and the objective of this study is to analyze the variable region of the COI gene in subunit I. The mitochondrial cytochrome (COI) oxidase subunit I gene was analyzed as a suitable molecular maker for the identification of three specimens of the fish species Hipposcarus harid, widely distributed in the Red Sea. The COI gene sequences in the variable region revealed variations among the fish species. The COI gene sequences in the variable region were similar to the variable region of Hipposcarus harid collected from the Northern Red Sea and all three were named: H. harid H13, H. harid H2c, and H. harid H12. The identification of the fish species collected from the Red Sea in Saudi Arabia would help ichthyologists improve the management, conservation and monitoring of economically important long-nose parrotfish species in Saudi Arabia.
... DNA barcoding involving mitochondrial cytochrome C oxidase subunit I (mtCOI) has been successfully implemented for various taxonomic groups and has been used in identifying rays from several locations, including Taiwan (Chang et al., 2017), Indonesia (Madduppa et al., 2016), Australia (Ward et al., 2008), India (Bineesh et al., 2017) and Northeastern Atlantic Ocean and Mediterranean Sea (Ferrari et al., 2023). To date, a limited number of mtCOI sequences of African stingrays are publicly available in global databases. ...
1. The coastal marine stingrays (genus Fontitrygon) include two endemic and highly threatened species (Fontitrygon margaritella and Fontitrygon margarita) from the African Gulf of Guinea. However, the lack of robust diagnostic features due to similar external features hinders species identification, thus limiting species-specific conservation efforts.
2. The present study aims to examine the morphological characteristics and apply a DNA barcoding tool through amplifying mitochondrial cytochrome C oxidase subunit I (mtCOI) to accurately identify F. margaritella and F. margarita from coastal waters in Nigeria, Cameroon, Côte d'Ivoire, Guinea Bissau and Senegal.
3. Morphological evaluation revealed differences in colour pattern, eye shade, mouth shape and pectoral radial count between F. margarita and F. margaritella. We generated 25 mtCOI barcode sequences that included F. margaritella (n = 22) and F. margarita (n = 3). Our query search in the National Center for Biotechnology Information (NCBI) GenBank and Barcode of Life Data system (BOLD) showed a sequence match of our newly collected F. margaritella with other F. margaritella in the global databases, while mtCOI sequences of F. margarita were new to the NCBI GenBank and BOLD databases. The phylogenetic clustering analyses based on the maximum-likelihood tree grouped morphospecies into highly supported monophyletic units.
4. Our study demonstrates the potential of combined molecular and morphological approaches in the identification of coastal marine stingrays from the Gulf of Guinea. Our study is helpful in future scientific studies and in forming future conservation plans.
... Although traditional fish species identification has relied heavily on external morphological characters, there is a growing trend to use molecular taxonomy for this purpose . A few molecular markers have been previously used in Barathronus species for taxonomic or phylogenetic purposes: cytochrome c oxidase subunit I (COI) (Chang et al., 2017;Evseenko et al., 2018;Nielsen et al., 2019), 16S ribosomal RNA (16S) and NADH (Nicotinamide Adenine Dinucleotide + Hydrogen) dehydrogenase subunit 4 (ND4) (Evseenko et al., 2018;Møller et al., 2016;Near et al., 2013), and recombination activating protein 1 (RAG1) (Evseenko et al., 2018;Near et al., 2013). ...
Barathronus is a genus of blind cusk eels comprising 11 valid species. In this paper, we report the second specimen ever documented of Barathronus roulei (Bythitidae) obtained from the Porcupine Bank by R.V. Vizconde de Eza using a bottom trawl at a depth of 1349 m. Morphological description and illustrations, including a radiograph, are provided. In addition, three new sequences corresponding to three different genes, cytochrome c oxidase subunit I (COI)‐DNA barcoding, 16S ribosomal RNA (16S), and recombination activating protein 1 (RAG1), have been added to the molecular repositories, representing the first sequences for the species.
... The absence of species hits on the database is expected given the paucity of genetic data on Symphysanodontidae. Available sequences were mostly directly submitted or unpublished and those that had publications associated with the sequence record were generated from barcoding studies (e.g., Valdez-Moreno et al. 2010;Chang et al. 2017). ...
Two individuals of wavy jaw slopefish, Cymatognathus aureolateralis, were collected from a fish landing area in the coastal municipality of Governor Generoso in Davao Gulf, Philippines. This extends the species’ known geographic distribution northward, approximately 579 kilometers from Bitung, North Sulawesi, Indonesia, where it was first described. The specimens collected from Davao Gulf have similar overall appearance, including the elevated tooth patch that is distinct for this genus. Morphological and meristic characters were also comparable with the measurements and counts provided for the specimen from Indonesia. Although interconnectivity of C. aureolateralis between southern Mindanao and North Sulawesi is possible given the similar bathymetric contour along the stretch of the Sangihe arc, larval transport remains unclear due to the prevailing oceanographic currents. The new records of marine fishes reported recently in Davao Gulf emphasizes the importance of strengthened management measures through an ecosystem-based approach to sustain biodiversity amid various anthropogenic threats.
... However, available scientific references on D. anguillare were mainly limited to the nutrition and feeding habits (Zhang and Tang 2003), the dynamics of spatial-temporal distribution (Miller et al. 2002;Liu and Xian 2009), as well as physiological and ecological researches (Yang et al. 2020;Yang et al. 2022a, b). To the present, the genetic information of this eel is almost blank except for sporadic mitochondrial DNA sequences (Chen et al. 2014;Chang et al. 2016;Wang et al. 2019). ...
Dysomma anguillare is a demersal eel widespread distributing in tropical waters of the Indo-West Pacific and Atlantic. As an important component of the coastal fishery and marine ecosystem, the lack of genomic information for this species severely restricts the progress of relevant researches. In this study, the abecedarian genome-wide characteristics and phylogenetic relationships analyses were carried out based on next-generation sequencing (NGS) platform. The revised genome size was approximately 1 310 Mb, with the largest scaffold length reaching 23 878 bp through K-mer (K = 17) method. The heterozygosity, repetitive rate and average GC content were about 0.94%, 51.93% and 42.23%, respectively. A total of 1 160 104 microsatellite motifs were identified from the de novo assembled genome of D. anguillare, in which dinucleotide repeats accounted for the largest proportion (592 234, 51.05%), the highest occurrence frequency (14.58%) as well as the largest relative abundance (379.27/Mb). The high-polymorphic and moderate-polymorphic loci composed around 73% of the total single sequence repeats (SSRs), showing a latent capacity for subsequent population genetic structure and genetic diversity appraisal researches. Another byproduct of whole-genome sequencing, the double-stranded and circular mitogenome (16 690 bp) was assembled to investigate the evolutionary relationships of D. anguillare. The phylogenic tree constructed with maximum likelihood (ML) method showed that D. anguillare was closely related to Synaphobranchidae species, and the molecular systematic results further supported classical taxonomy status of D. anguillare.
... Percentage of LH Asis et al., 2013;Chang et al., 2016;Dahruddin et al., 2016;Hubert et al., 2012;Keith et al., 2011;McMahan et al., 2021;Steinke et al., 2016;Thu et al., 2019). The ML tree analysis using replication model by Kimura (1980) was carried out using the software MEGA X (Kumar et al., 2018). ...
A new species of the genus Awaous (Oxudercidae), Awaous motla sp. nov., is described based on 18 specimens collected from the Mahanadi River near Sonepur, Subarnapur District, and 3 specimens from the same river near Boudh bridge, Boudh District of Odisha, India. This species is distinct from its congeners by having a combination of characteristics: relatively small eyes, diameter of 6.6–8.4 in head length (LH); robust and long snout, 2.0–2.6 in LH; eye diameter 2.7–4.1 in snout length; cephalic sensory pore system interrupted with eight pores; predorsal scales 13–15; longitudinal scale series 55–58; gill rakers 2 + 1 + (6–7) on the first gill arch; teeth small, conical, and in a single row on the upper jaw and multiserial (2–3) on the lower jaw. This species is also differentiated from some of its congeners in the nucleotide composition of the cytochrome c oxidase I gene by 8.3%–13.8% Kimura two‐parameter (K2P) distance and belongs to a separate cluster in the maximum likelihood tree analysis. This finding is also supported by the species delimitation analysis based on Assemble Species by Automatic Partitioning. The new species holds high commercial value in its locality and needs special conservation attention for sustainable utilization.
... Mitochondrial cytochrome c oxidase subunit I (COI) was amplified from extracted gDNA using the polymerase chain reaction (PCR). Primer sets and PCR conditions follow Chang et al. (2017). Sanger sequencing was outsourced to the Australian Genome Research Facility (Canberra, Australia). ...
Australian species of the cirrhilabrin labrid genus Paracheilinus are reviewed. Four species of Paracheilinus are report- ed from Australian waters: P. amanda, new species, from Flora, Holmes, and Osprey Reefs, Coral Sea, off northeast Queensland, and Harrier Reef, Great Barrier Reef; P. filamentosus from Lizard Island, Great Barrier Reef; P. flavianalis from Evans and Flinders Shoals, Timor Sea, off northeast Darwin, Northern Territory, and Ashmore, Scott, Seringapatam, and Hibernia Reefs in the north-western shelf of Western Australia; and P. nursalim from Flinders Shoal, Timor Sea, off northern Darwin, Northern Territory. Paracheilinus amanda, new species, has previously been confused for P. rubricaudalis from Melanesia, but molecular analysis of mitochondrial COI recovers both species as re- ciprocally monophyletic lineages, differing from each other by 1–1.2% in genetic distance. They further differ in as- pects of live coloration of terminal phase (TP) males. Both species are allopatric and do not overlap in distribution. The new species is described on the basis of six specimens: the holotype and two paratypes from Harrier Reef, Great Barrier Reef, one paratype from Flora Reef, Coral Sea, and from two paratypes collected off Hula in southern Papua New Guinea, along the north-western margin of the Coral Sea. The discovery of P. nursalim in Australia represents a new and significant range extension from previous locality records of West Papua and Ambon Bay. Paracheilinus is rediagnosed, and keys, diagnoses, photographs, and Australian distribution records are presented for all species herein.
... Increasing genetic distances in higher taxonomic levels ( Fig. 3, Table 3) conform with many previous barcoding studies (e.g. 3,4,[46][47][48] Fig. S3, Table 4), suggesting either insufficient resolution of the used marker or the requirement for additional taxonomic revisions of these taxa. After careful comparison, all topologies of non-monophyletic genera based on COI sequences are similar to those in phylogenetic studies conducted with multi-loci or genome-wide data, in which their taxonomies are usually contentious (Table 4 and reference therein). ...
A morphology-based barcoding library of market teleost fishes (Teleostei) in Cebu is built based on cytochrome c oxidase subunit I (COI) sequences and voucher specimens which aimed to establish a reliable reference of frequently traded fishes in the province, a biodiversity hotspot at the center of the Philippine archipelago. A total of 1721 specimens were collected from 18 fish markets and landing sites around the province, in which 538 specimens were sequenced belonging to 393 species from 229 genera, 86 families, and 37 orders. Most speciose families are coral reef or reef-related shallow-water species. Twelve species from 11 families are newly recorded in the Philippine waters, among which 7 species are deep-sea inhabitants, while 3 species have expanded their distribution range. Only 20 taxa could not be identified to the species level due to the difficulty in morphological examinations, absence of matched reference sequences in online databases, and/or problematic species awaiting further studies. This first comprehensive DNA barcoding survey of Cebu fishes can facilitate further taxonomic research as well as the conservation and management of fisheries in the Philippines.
... Challenges associated with suspected cryptic species and, conversely, morphological variation within accepted species, as well as the variety of past and present nomenclature and putative diagnostic traits, all contribute to greatly complicate the identification of mangrove clams of the Cyrenidae, especially the nominal genera Polymesoda and Geloina (Carter 2014). However, correct species identification is vital in many fields (Carter 2014), including in the effective management of exploited taxa (Chang et al 2017;Abdullah et al 2020;Razi et al 2021). ...
Mangrove clams of the Cyrenidae family are widely collected for human consumption. Despite reports of declining populations, data are limited, while taxonomic revisions highlight the need for correct species identification to support effective management. Mangrove clam collection contributes to food security and income in Tolongano Village, Donggala District, Central Sulawesi Province, Indonesia. This study conducted from September to October 2020 aimed to identify the mangrove clams collected in Tolongano using molecular biology methods (DNA barcoding-Cytochrome Oxidase I Mitochondrial DNA, Sanger sequencing) and to evaluate the clam population status and characteristics based on size-frequency, morphometric and weight data. Clams purchased from collectors were measured, weighed, and sorted into size classes. The NCBI BLAST-n routine and phylogenetic tree constructed in MEGA 11 gave the closest sequence matches (99.47-99.61% identity) with Geloina expansa, a species with many (non-valid) synonyms including Polymesoda erosa, consonant with identification based on morphological traits. However, phylogenetic analysis revealed multiple clades within the G. expansa/G. erosa complex and precluded definitive species-level identification. Clam shell length and weight ranges were 24.38-65.03 mm and 6-127 g, respectively. Clam size distribution was strongly left-skewed with very few individuals over 44 mm. The common and maximum sizes were small compared to SeaLifeBase data (70 mm, 100 mm). The results indicate high levels of clam harvesting and a need for appropriate regulation.
... The explicit germplasm genetic characteristics of fishery species are considered to be the indispensable prerequisite for effective fisheries management (Hemmer-Hansen et al. 2018). However, the available genetic data for this species are still scarce and only partial mitochondrial and nuclear gene sequences have hitherto been reported and analysed (Chen et al. 2014, Chang et al. 2016. Microsatellite DNA, also named simple sequence repeats (SSRs) are short tandem duplications (typically 1-6 nucleotide repeats and mostly less than 100 bp in length), ubiquitous occurring in eukaryotic organisms. ...
Microsatellite loci were screened from the genomic data of Dysomma anguillare and their composition and distribution were analysed by bioinformatics for the first time. The results showed that 4,060,742 scaffolds with a total length of 1,562 Mb were obtained by high-throughput sequencing and 1,160,104 microsatellite loci were obtained by MISA screening, which were distributed on 770,294 scaffolds. The occurrence frequency and relative abundance were 28.57% and 743/Mb, respectively. Amongst the six complete microsatellite types, dinucleotide repeats accounted for the largest proportion (592,234, 51.05%), the highest occurrence frequency (14.58%) and the largest relative abundance (379.27/Mb). A total of 1488 microsatellite repeats were detected in the genome of D. anguillare , amongst which the hexanucleotide repeat motifs were the most abundant (608), followed by pentanucleotide repeat motifs (574), tetranucleotide repeat motifs (232), trinucleotide repeat motifs (59), dinucleotide repeat motifs (11) and mononucleotide repeat motifs (4). The abundance of microsatellites of the same repeat type decreased with the increase of copy numbers. Amongst the six types of nucleotide repeats, the preponderance of repeated motifs are A (191,390, 43.77%), CA (150,240, 25.37%), AAT (13,168, 14.05%), CACG (2,649, 8.14%), TAATG (119, 19.16%) and CCCTAA (190, 19.16%, 7.65%), respectively. The data of the number, distribution and abundance of different types of microsatellites in the genome of D. anguillare were obtained in this study, which would lay a foundation for the development of high-quality microsatellite markers of D. anguillare in the future.
... This COI Region is the region that some gene markers have agreed on globally for molecular identification. Research on barcoding of several aquatic biota has been carried out such as for marine fish in Australia (Ward et al. 2005), marine fish in India (Lakra et al. 2011), marine fish in Turkey (Keskİn & Atar 2013), marine fish in China (Wang et al. 2012;Zhang & Hanner 2012), and marine fish in Taiwan (Chang et al. 2017;Bingpeng et al. 2018). Whereas research on fish molecular identification in Aceh has been carried out on some species such as groupers (Kamal et al. 2019), and Scomber spp. ...
The enormous potential of marine resources possessed by Banda Aceh Province is expected to be utilised optimally. Accuracy in marine fish resource identification is a critical requirement to support their utilisation and preservation in Banda Aceh Province. In this study, a molecular identification approach was carried out in addition to conducting a morphological identification, commonly used by several scientists. The results were 47 COI sequences generated representing 33 genera, 19 families, and five orders. From the resulting COI partial sequences, there is one potential haplotype from the Scombridae family (Auxis thazard), two potential haplotypes from the Carangidae family (Elagatis bipinnulata and Decapterus macarellus), and two potential haplotypes from the Serranidae family (Variola albimarginata and Cephalopholis sonnerati). This study is essential for fisheries biological studies and other fisheries studies to support the sustainable utilisation of marine fisheries potential in Banda Aceh.
... Color codes in line represent the clades found in Elops species. Asterisks (*) at nodes indicate posterior probability > 0.9 [35][36][37][38][39][40][41][42][43][44][45][46][47][48]. Data Availability Statement: All data from this study are available in the databases used. ...
Elopidae is the most speciose family within the Elopiformes, comprising seven valid species. Despite this reduced number of species, the family presents poorly resolved systematics, mainly owing to its wide distribution and highly conserved anatomic features. Therefore, we aimed to explore the species diversity of the Elopidae using species delimitation, genetic diversity, and phylogenetic analysis combined with DNA barcoding of the COI gene. The results from the delimitation analysis grouped the species into a single cluster, while the genetic diversity analysis among the groups showed a distance ranging between 1.29 and 2.78%. Both phylogenetic and haplotype network analysis grouped the species into four clades, associated with the distribution of the organisms. The lack of resolution in the species delimitation analysis might be directly associated with the recent radiation of the group, a hypothesis corroborated by both the low genetic diversity (close to the 2% threshold) and the few mutations that separate the haplotypes observed among the species. Interestingly, our data supported a new arrangement for the Elops species. In addition, the data available in public databases present taxonomic errors at several levels. Although some issues remain unsolved, our results can be used in the identification of taxa and provide information to assist taxonomic revisions of the Elopidae.
... Local and adjacent oceanic fish COI sequences of Trichiurus spp. were cited from reliable literatures for secondary analysis should the aforementioned criteria not be met (Hsu et al., 2009;Tzeng and Chiu, 2012;Chang et al., 2017;Hou et al., 2018). A neighbor-joining (NJ) tree was reconstructed to illustrate lineage diversity via phylogenetic topology, based on the Kimura 2-parameter model (K2P, Kimura, 1980) with 1,000 bootstrap replicates by MEGA v6.0 (Tamura et al., 2013). ...
... The cytochrome c oxidase subunit 1 (CO1) barcoding method follows Chang et al. (2016). PCR amplification of the 5′ region of the CO1 gene (approximately 650 bp) was performed and all the successfully amplified sequences were aligned (Clustal W), trimmed, constructed, and saved as FASTA format by using BioEdit ver. ...
A recently-described butterflyfish, Roa haraguchiae Uejo, Senou et Motomura, 2020, is herewith for the first time reported from northeast Taiwan. In Taiwan, the genus Roa has been known represented by a single species, Roa modesta (Temminck et Schlegel, 1844). This study presents a comparison of R. haraguchiae with its congeners and includes diagnostic characters on the basis of morphology and genetic differences by life-barcoding. Our specimens have some differences that may be attributed to the individual variations, which are compared and discussed.
... DNA barcoding has been extensively used as a species identification tool for a wide range of fish species (Zhang and Hanner 2011;Ward et al. 2005;Mat Jaafar et al. 2012;Chang et al. 2017;Bakar et al. 2018;Fadli et al. 2020). However, in the process of building up a reference library, deep genetic divergences within nominal species are commonly found, as observed in the current study. ...
Species of genus Carangoides also known as trevallies are one of the commercially exploited groups of fishes in Malaysia. The genus Carangoides consists of fishes with mixed morphological and meristic characteristics. Due to this, species within this genus are often reported as single collective group, rather than as an individual species. Thus, fisheries landing statistics do not reflect the precise number of individual species harvested and the true status of species exploitation pattern will hinder efficient sustainable exploitation of a particular species. In this study, an annotated list of the 13 species of Carangoides known from Malaysian waters is presented with two species (C. oblongus and C. talamparoides) recorded as first specimen-based records and two species (C. chrysophrys and C. fulvoguttatus) as additional specimen-based distribution records in Malaysia. All species are briefly described, and a key is provided to identify Malaysian species of Carangoides. The mitochondrial Cytochrome c oxidase subunit I (COI) gene was also analyzed for genetic identification of 271 samples representing all of the species in the study. The average within species K2P distance was 0.4% with C. oblongus and C. praeustus showing the lowest intraspecific divergence (0%) and C. coeruleopinnatus showed the highest (1.3%). A maximum-likelihood tree generated from haplotype sequences clearly grouped all 13 putative species into their own clade. However, C. coeruleopinnatus and C. gymnostethus showed deep intraspecific divergence (9.1% and 3.5%) which formed three and two clusters with their own respective taxa. A more detailed analysis on the taxonomic status of some individuals within these species is required.
... While building the COI dataset and comparing the samples sequenced in this study to sequence data for threadfins databased and distributed through BOLD and/or GenBank, a number of previously generated sequences were found to be misidentified or mislabelled. These came from a variety of published(Betancur-R et al., 2013a,b;Chang et al., 2017;Horne et al., 2011;Khedkar et al., 2014;Lakra et al., 2011;Ribeiro et al., 2012;Shihab et al., 2017;Thu et al., 2019;Qu et al., 2020;Zhong et al., 2021) and unpublished works. The recent study byGopalakrishnan et al. (2021) similarly highlighted mislabelled or misidentified samples of threadfins native to India. ...
Threadfins (Teleostei: Polynemidae) are a group of fishes named for their elongated and threadlike pectoral‐fin rays. These fishes are commonly found in the world's tropical and subtropical waters, and are an economically important group for people living in these regions, with more than 100,000 t harvested in recent years. However, we do not have a detailed understanding of polynemid evolutionary history such that these fishes can be monitored, managed and conserved as an important tropical food source. Recent studies hypothesize at least one genus of threadfins is polyphyletic, and no studies have focused on generating a hypothesis of relationship for the Polynemidae using DNA sequences. In this study, we analyse a genomic dataset of ultraconserved‐element and mitochondrial loci to construct a phylogeny of the Polynemidae. We recover the threadfins as a clade sister to flatfishes, with the most taxonomically rich genus, Polydactylus, being resolved as polyphyletic. When comparing our dataset to data from previous studies, we find that a few recent broad‐scale phylogenies of fishes have incorporated mislabelled, misidentified or chimeric terminals into their analyses, impacting the relationships of threadfins they recover. We highlight these problematic sequences, providing revised identifications based on the data sequenced in this study. We then discuss the intrarelationships of threadfins, highlighting morphological or ecological characters that support the clades we recover.
... DNA barcoding has been extensively used as a species identification tool for a wide range of fish species (Zhang and Hanner 2011;Ward et al. 2005;Mat Jaafar et al. 2012;Chang et al. 2017;Bakar et al. 2018;Fadli et al. 2020). However, in the process of building up a reference library, deep genetic divergences within nominal species are commonly found, as observed in the current study. ...
Species of genus Carangoides also known as trevallies are one of the commercially exploited groups of fishes in Malaysia. The genus Carangoides consists of fishes with mixed morphological and meristic characteristics. Due to this, species within this genus are often reported as single collective group, rather than as an individual species. Thus, fisheries landing statistics do not reflect the precise number of individual species harvested and the true status of species exploitation pattern will hinder efficient sustainable exploitation of a particular species. In this study, an annotated list of the 13 species of Carangoides known from Malaysian waters is presented with two species (C. oblongus and C. talamparoides) recorded as first specimen-based records and two species (C. chrysophrys and C. fulvoguttatus) as additional specimen-based distribution records in Malaysia. All species are briefly described, and a key is provided to identify Malaysian species of Carangoides. The mitochondrial Cytochrome c oxidase subunit I (COI) gene was also analyzed for genetic identification of 271 samples representing all of the species in the study. The average within species K2P distance was 0.4% with C. oblongus and C. praeustus showing the lowest intraspecific divergence (0%) and C. coeruleopinnatus showed the highest (1.3%). A maximum-likelihood tree generated from haplotype sequences clearly grouped all 13 putative species into their own clade. However, C. coeruleopinnatus and C. gymnostethus showed deep intraspecific divergence (9.1% and 3.5%) which formed three and two clusters with their own respective taxa. A more detailed analysis on the taxonomic status of some individuals within these species is required.
The lizardfish Saurida elongata (Temminck and Schlegel 1846) described from three specimens collected from Japan, has had a confused nomenclatural history and the name has long been misapplied. Re-examination of the type specimens in the Naturalis Biodiversity Center, Leiden, has shown that they comprise two distinct species, and two of the three specimens are recognised as lectotype and paralectotype, respectively. Based on these specimens and others examined here, S. elongata is redescribed. Saurida eso Jordan and Herre 1907, previously considered a synonym of S. elongata, is resurrected as a valid species, and also redescribed. Saurida wanieso Shindo and Yamada 1972 is now included as a synonym of S. elongata; and Saurida microlepis Wu and Wang 1931 is included as a synonym of S. eso. The name Saurida japonica Jordan and Evermann 1902 (not Cobitis japonica Houttuyn 1782), previously unrecognised, is considered to be an available name, but because of its poor description is regarded as a nomen dubium. Consequently, even though predating S. eso, S. japonica of Jordan and Evermann is relegated as an uncertain synonym of S. eso. Saurida elongata has been included by some authors as a synonym of Saurida argyrophanes (Richardson 1846). The latter species, however, is based solely on a painting in the Reeves collection of Chinese fish drawings now in the Natural History Museum, London, and lacks important diagnostic features. As such, S. argyrophanes cannot be confidently referred to any known species of Saurida and is also regarded here as a nomen dubium.
The taxonomy of the Parachela–Oxygaster–Macrochirichthys clade of Xenocyprididae has been confused since the original descriptions of Parachela oxygastroides and Parachela hypophthalmus in the mid‐19th century. The confusion seems attributable to the substantial intraspecific variation in color and other morphological characteristics of species of Oxygaster and Parachela. Morphological data on 401 specimens from throughout the range of Parachela and molecular phylogenetic analyses indicate that six available species names for Parachela are valid: Parachela cyanea, P. hypophthalmus, Parachela ingerkongi, Parachela johorensis (removed from the synonymy of P. oxygastroides), P. oxygastroides, and Parachela williaminae. In addition, two new species of Parachela, Parachela melanosticta and Parachela microlepis, are described. Chela pointoni is a synonym of P. oxygastroides, not a valid species of Oxygaster as previously hypothesized, and Parachela maculicauda is a synonym of Parachela johorensis. Considerable morphological and genetic variation is present in all well‐sampled species of Parachela.
The present study contributes to the taxonomy of the family Sillaginidae, with comments on the distribution of its species in the Indian Ocean and an emphasis on the taxonomy and distribution of Sillago sihama. Thirty described and putative species with Indian Ocean distribution are listed, and a distribution range for each species is provided based on published data and results from the present study. A comprehensive phylogenetic analysis of the barcoding portion of the mitochondrial COI gene is provided together with three approaches for molecular species delimitation, which includes 44 to 47 genetic lineages (depending on the species delimitation approach used) in the family Sillaginidae, 33 of them applying to described species and also 8 putative species, formerly misidentified as S. sihama. Inclusion of specimens from South Africa, Iran, Pakistan, India, Bangladesh and the southern Red Sea (type locality) reveals one genetic lineage representing the true Sillago sihama. Distribution of the species is confined to the Red Sea and the Indian Ocean, and other records under the name S. sihama are based on misidentifications. Several undescribed species identified as S. sihama are distributed in the Indo-West Pacific region and closely resemble S. sihama, but are not identical with this species and can be identified as members of different evolutionary lineages. Two species, S. sihama and S. soringa, reported from Bangladesh, represent the easternmost record of both species. These two species are described in detail, including swimbladder morphology. The study also shows that specimens from India identified as Sillago ingenuua McKay, 1985 are nested within a lineage previously referred to as S. ingenuua A, but are different from the lineage S. ingenuua B, representing a confirmed record of the clade S. ingenuua in the northern Indian Ocean. Comments on misidentifications of S. sihama from the Indian Ocean and western Pacific are provided. Furthermore, we propose that Sillago erythraea should be resurrected from its synonymy with S. sihama. As Sillago suezensis is identical with the former species, it becomes a junior synonym of S. erythraea.
The present study contributes to the taxonomy of the family Sillaginidae, with comments on the distribution of its
species in the Indian Ocean and an emphasis on the taxonomy and distribution of Sillago sihama. Thirty described and
putative species with Indian Ocean distribution are listed, and a distribution range for each species is provided based on
published data and results from the present study. A comprehensive phylogenetic analysis of the barcoding portion of the
mitochondrial COI gene is provided together with three approaches for molecular species delimitation, which includes
44 to 47 genetic lineages (depending on the species delimitation approach used) in the family Sillaginidae, 33 of them
applying to described species and also 8 putative species, formerly misidentified as S. sihama. Inclusion of specimens
from South Africa, Iran, Pakistan, India, Bangladesh and the southern Red Sea (type locality) reveals one genetic lineage
representing the true Sillago sihama. Distribution of the species is confined to the Red Sea and the Indian Ocean, and other
records under the name S. sihama are based on misidentifications. Several undescribed species identified as S. sihama
are distributed in the Indo-West Pacific region and closely resemble S. sihama, but are not identical with this species
and can be identified as members of different evolutionary lineages. Two species, S. sihama and S. soringa, reported
from Bangladesh, represent the easternmost record of both species. These two species are described in detail, including
swimbladder morphology. The study also shows that specimens from India identified as Sillago ingenuua McKay, 1985
are nested within a lineage previously referred to as S. ingenuua A, but are different from the lineage S. ingenuua B,
representing a confirmed record of the clade S. ingenuua in the northern Indian Ocean. Comments on misidentifications of
S. sihama from the Indian Ocean and western Pacific are provided. Furthermore, we propose that Sillago erythraea should
be resurrected from its synonymy with S. sihama. As Sillago suezensis is identical with the former species, it becomes a
junior synonym of S. erythraea.
The identification of indigenous small, wild, or less noteworthy fish species heavily relies on morphometric and meristic traits. However, morphometric and meristic trait varies during the life stage which underprops the preference toward molecular methodologies for species documentation. The identification and characterization of indigenous small fishes are prerequisites for fish experts, planners, and culture specialists. Molecular taxonomic approaches enable precise species identification of these small fishes. The mitochondrial DNA (mtDNA) along with the nuclear gene is well-suited for molecular taxonomic studies. mtDNA is particularly well-suited for molecular taxonomic studies due to its accessibility, rapid evolution rates, and clonal inheritance pattern. However, mtDNA has limitations due to interspecific hybridization, the inclusion of nuclear copies (paralogy), and differential sorting of polymorphisms. The nuclear marker along with the mtDNA marker will overcome these limitations. DNA barcoding technology based on cytochrome c oxidase subunit I (CO1) is an important marker of choice for molecular identification. The nuclear gene, recombination activating 2 (rag2) fragments along with the CO1 gene will give a clear resolution for species identification and documentation. The molecular taxonomy will enhance our understanding of commercially significant indigenous small fishes.
The Persian Gulf is a semi-enclosed marginal sea with a subtropical climate in southern Iran. One of the most productive coastal habitats in this region is the mangrove forests which support rich biodiversity and play an essential role in sustainable fisheries. Because of the fish's dependence on this ecosystem as a nursery habitat and its vulnerability to various natural and anthropogenic stresses and disturbances, it seems critical to identify and classify the fish species in this region and screen biodiversity. A segment (593 bp) of the cytochrome oxidase subunit I (COI) gene was used to identify the fish in the largest mangrove area of the Persian Gulf. In the present study, we created a comprehensive fish barcoding database for 53 species belonging to 39 genera, 32 families, and 17 orders. For six species, novel DNA barcodes to the global gene databases of GenBank and BOLD were introduced (Ilisha megaloptera, Pseudosynanceia melanostigma, Sillago sp., Hyporhamphus sindensis, Johnius sp., Strongylura sp.). Congeneric genetic distances were 46-fold higher than conspecific distances, and a DNA barcoding gap was observed. The tree constructed using maximum likelihood clearly displayed phylogenetic signals at different taxonomic levels. Our results indicated that DNA barcodes served as a valuable tool for studying fish diversity and also for the identification and discovery of fish species in the Persian Gulf. The database developed during this study will contribute to assessing fish biodiversity, conservation, and fisheries management.
Introduction
Accurate species identification and biodiversity assessment of larval fish are essential for effective management and conservation of fisheries resources, as it allows for the estimation of parent stocks, assessment of future recruitment, and prediction of spawning and nursing grounds. However, traditional morphology-based identification methods have inherent limitations, highlighting the need for accurate and efficient techniques to address these challenges effectively. The Luzon Strait, a crucial channel connecting the South China Sea to Western Pacific Ocean, is renowned for its fish biodiversity. However, our knowledge of the biodiversity status of larval fish species in this region remains insufficient.
Methods
Here we employed DNA barcoding to assess larval fish species diversity in the Luzon Strait and adjacent waters. We investigated the species composition, diversity, and geographical distribution of larval fish communities in the region. Moreover, we assessed habitat types, human uses, and IUCN conservation status of each larval fish species.
Results
A total of 385 larval fish individuals were collected from 15 stations, and 354 individuals were successfully barcoded and identified, representing 147 species from 93 genera, 44 families, and 22 orders. The interspecific Kimura 2-parameter (K2P) divergence exhibited a significant increase of approximately 55-fold higher than intraspecific divergence. The phylogenetic neighbor-joining tree confirmed the distinct lineages for each taxonomic level, demonstrating the feasibility of DNA barcoding. We observed notable variations in fish species diversity and community composition among sampling stations. Non-metric multidimensional scaling analysis revealed greater diversity and dissimilarity of larval fish community compositions in the western regions compared to the eastern regions. This pattern corresponded to the grouping based on the path of the Kuroshio current, suggesting its influence on the fish community structure. Additionally, economically valuable species were identified at these stations, highlighting their ecological significance as potential spawning or nursery grounds for larval fish. We also examined the habitat type, human use, and conservation status of each larval fish species, providing comprehensive insights into their ecological significance and conservation needs.
Discussion
The establishment of a local DNA sequences database through DNA barcoding will greatly enhance the accuracy of species identification in environmental DNA (eDNA) metabarcoding applications. Altogether, this study offers valuable information for identifying important spawning and nursing grounds of fish populations, thereby supporting sustainable management and conservation of fisheries resources in this region.
One of the largest bony fishes on earth, the family Regalecidae is very rare. So, they remain largely unknown. They are often misidentified each other because they tend to be usually found in a damaged condition. Therefore, we firstly provide detailed morphological traits of R. russellii based on three voucher specimens (total length, 170e422 cm; damaged bodies) collected from Uljin, Ulsan and Jeju-do Island, Korea during 2018e2022. Based on color patterns, the numbers of dorsal fin rays, and gill rakers, our specimens were identified as R. russellii. The morphology of our specimens nearly matched that of the Eastern Pacific R. russellii. Molecular analysis based on mitochondrial DNA cytochrome c oxidase subunit I (506 bp) sequences showed that our specimens almost matched R. russellii recorded from Taiwan (Kimura-2-parameter distance ¼ 0.44%). Our detailed morphological and molecular analysis results highlight the importance of voucher specimens to prevent misidentification.
Since 2006, an ophidiiform larva with an ovoid body, elongate anterior dorsal-fin ray, and long trailing fleshy filament has been identified as Pycnocraspedum squamipinne. Similarly, the larvae of the ophidiid genus Luciobrotula have been tentatively identified since 1988, with posteriorly displaced dorsal fins and bulging or exterilium guts. However, neither of these larval forms morphologically agree with their adult counterparts. Recently, blackwater divers captured and photographed specimens of larval Luciobrotula and Pycnocraspedum off the coast of Hawaiʻi and Florida, making them available for both morphological and molecular sampling. After examining these larvae and analyzing DNA barcode sequences, as well as a newly captured and sequenced adult of Pycnocraspedum phyllosoma, we revise the previously identified “Pycnocraspedum” larvae to species of Luciobrotula. We describe the larvae of Luciobrotula bartschi and Luciobrotula corethromycter for the first time, highlighting an extraordinary loss of multiple anterior dorsal-fin elements in their ontogeny. We also generate the first DNA sequences for L. corethromycter and P. phyllosoma, adding to the depauperate number of sequences available for ophidiiforms. For the previously identified “Luciobrotula” larvae, neither morphological nor molecular characters provide definitive identification other than recovering them among the Bythitidae. We provide new morphological observations, revised descriptions, and generate a phylogeny of ophidiiform fishes based on COI to place these larvae in a phylogenetic context, prompting further investigation into the relationships of the Ophidiiformes using additional genetic markers. Our study emphasizes the importance of blackwater diving to improving our understanding of marine larval fishes and the need for additional molecular sampling of the diverse order of brotulas, cusk-eels, pearlfishes, and their allies.
Synopsis
Extreme abiotic factors in deep-sea environments, such as near-freezing temperatures, low light, and high hydrostatic pressure, drive the evolution of adaptations that allow organisms to survive under these conditions. Pelagic and benthopelagic fishes that have invaded the deep sea face physiological challenges from increased compression of gasses at depth, which limits the use of gas cavities as a buoyancy aid. One adaptation observed in deep-sea fishes to increase buoyancy is a decrease of high-density tissues. In this study, we analyze mineralization of high-density skeletal tissue in rattails (family Macrouridae), a group of widespread benthopelagic fishes that occur from surface waters to greater than 7000 m depth. We test the hypothesis that rattail species decrease bone density with increasing habitat depth as an adaptation to maintaining buoyancy while living under high hydrostatic pressures. We performed micro-computed tomography (micro-CT) scans on 15 species and 20 specimens of rattails and included two standards of known hydroxyapatite concentration (phantoms) to approximate voxel brightness to bone density. Bone density was compared across four bones (eleventh vertebra, lower jaw, pelvic girdle, and first dorsal-fin pterygiophore). On average, the lower jaw was significantly denser than the other bones. We found no correlation between bone density and depth or between bone density and phylogenetic relationships. Instead, we observed that bone density increases with increasing specimen length within and between species. This study adds to the growing body of work that suggests bone density can increase with growth in fishes, and that bone density does not vary in a straightforward way with depth.
The taxonomic status of the keeled back mullets (Teleostei: Mugilidae) has been reinvestigated. Two nominal mugilid species having keeled backs from East Asia: Mugil lauvergnii Eydoux & Souleyet, 1850 and Mugil affinis Günther, 1861 have been re-evaluated through examination of the holotypes and fresh specimens. Comparison of morpho-meristic characters of the holotypes shows that both species are identical. Phylogenetic analysis based on mitochondrial cytochrome c oxidase 1 (CO1) confirmed morphological data by highlighting presence of a single clade from East Asia. Mugil lauvergnii (=Planiliza lauvergnii) is thus the sole keeled back mullet from East Asia and a senior synonym of Mugil affinis (=Planiliza affinis). The taxonomic status of two other keeled back mullets, Planiliza carinata and P. klunzingeri, is also contentious due to their similar morphology. Meristic and morphometric variation as well as sequence divergence between the two species are limited but phylogenetic analyses delineate well-supported clades consistent with biogeography and currently accepted taxonomy. Planiliza carinata and P. klunzingeri share a recent common ancestor in a Maximum Likelihood tree, with separate distribution ranges while P. lauvergnii formed a paraphyletic lineage. Based on present findings, we suggest maintenance of the taxonomic distinction of P. klunzingeri and P. carinata and discuss its evolutionary significance.
Torquigener flavimaculosus Hardy & Randall (1983) was described based on specimens collected from the Gulf of Aqaba, Gulf of Suez, and Gulf of Aden, which has then penetrated the Mediterranean Sea, becoming one of the most abundant invasive tetraodontids. A comparison of samples collected from the northern Levant coasts of Türkiye between 2007 and 2020 showed that morphometric and meristic characteristics do not fully match either with T. flavimaculosus, or the closely related congeneric species T. hypselogeneion and T. altipinnis. Multivariate analysis carried out by 16 morphometric and six meristic characters did not show any discrimination between the above-mentioned species and exhibited almost identical sequences in genetic analysis. The results strongly suggest that T. flavimaculosus and T. hypselogeneion are conspecific, making the former species a junior synonym of the latter.
For 175 years, an unremarkable bass, the Grape-eye Seabass (Hemilutjanus macrophthalmos), has been known from coastal waters in the Eastern Pacific. To date, its phylogenetic placement and classification have been ignored. A preliminary osteological examination of Hemilutjanus hinted that it may have affinities with the Acropomatiformes. To test this hypothesis, we conducted a phylogenetic analysis using UCE and Sanger sequence data to study the placement of Hemilutjanus and the limits and relationships of the Acropomatiformes. We show that Hemilutjanus is a malakichthyid, and our results corroborate earlier studies that have resolved a polyphyletic Polyprionidae; accordingly, we describe Stereolepididae, new family, for Stereolepis. With these revisions, the Acropomatiformes is now composed of the: Acropomatidae; Banjosidae; Bathyclupeidae; Champsodontidae; Creediidae; Dinolestidae; Epigonidae; Glaucosomatidae; Hemerocoetidae; Howellidae; Lateolabracidae; Malakichthyidae; Ostracoberycidae; Pempheridae; Pentacerotidae; Polyprionidae; Scombropidae; Stereolepididae, new family; Symphysanodontidae; Synagropidae; and Schuettea. Finally, using our new hypothesis, we demonstrate that acropomatiforms repeatedly evolved bioluminescence and transitioned between shallow waters and the deep sea.
Oxyurichthys omanensis sp. nov. is described as a new gobiid species from a mudflat/estuary habitat in northern Oman. The new species is diagnosed among all currently recognised congeners by the following combination of character states: elongate tentacle on dorsoposterior surface of the eye; nape with well-developed membranous crest; nape scaled to above anterior half of opercle along sides with naked median along membranous crest, scales never reaching to above preopercle; opercle and pectoral base naked; scales ctenoid laterally on trunk posterior to base of second dorsal fin 3rd element; lateral scale rows 51–58, usually 51–56; transverse forward scale rows 23–29, usually 24–28; transverse rearward scale rows 14–16, usually 14–15; upper lip usually constricted at premaxillary symphysis; infraorbital transverse papillae row 2 reaching eye margin dorsally and markedly short of longitudinal row d ventrally; additional short transverse papillae rows between rows 2 and 3i present; dark saddle present over caudal peduncle; snout length 34.9–45.4% HL; second dorsal-fin longest ray 1.1–1.6 head depth; pelvic fin always reaching or passing anal-fin origin. The K2P genetic distances (%) in the mtDNA COI barcode region between O. omanensis and the other Oxyurichthys species were all high (11.2–30.6%) with the K2P nearest neighbor distance of 11.2% to O. cornutus and O. ophthalmonema.
The study used morphological and genetic approach for the DNA barcoding analysis of the inter- and intra-species
relationships among catadromous Philippine freshwater eels. Past DNA barcoding studies on Philippine anguillid eels
came from Northern Luzon. This study aimed to determine the DNA barcodes of the freshwater eels of the Philippines
using the cytochrome c oxidase 1 (CO1) gene of the mitochondrial DNA. Specimens were collected from six sites in the
Philippines. Four Anguilla species - Anguilla bicolor pacifica Schmidt, 1928, A. celebesensis Kaup, 1856, A. interioris
Whitney, 1938 and A. marmorata Quoy & Gaimard, 1824 and one Monopterus species– Monopterus javanensis
Lacepéde, 1800 were collected and identified. Morphological features varied from the taxonomic guides for Anguilla
celebesensis and A. interioris with their body color and fin length. Genetic divergence estimates using Kimura 2-
parameter substitution model showed an intraspecific variation of 0–0.4% and interspecific variation of 4.1– 27.6%. The
ML tree generated was similar to the previous studies and indicated the monophyly of the Indo–Pacific freshwater
anguillid eel lineage. This study also reports the first genetic record of M. javanensis sampled from Batac, Ilocos Norte,
Philippines.
Glossogobius is the most speciose among all the genera of the family Gobiidae. Eight species of Glossogobius have been reported in the Philippines, which include the most abundant and commercially important species, G. aureus. In this study, Glossogobius specimens were collected from nine lakes in the Philippines. A total of 113 specimens were DNA barcoded using the mitochondrial cytochrome c oxidase subunit I (COI) gene. Additional sequences of Glossogobius were mined from GenBank. The neighbor-joining (NJ) tree showed that all the specimens from Laguna de Bay, Naujan, Buluan, Bato, Buhi, and Paoay lakes clustered with G. aureus sequences from GenBank with a 99% bootstrap support. Ten of the 14 specimens from Taal Lake were also included in this cluster; the other four specimens morphologically identified as G. illimis formed a separate cluster. The specimens from Lake Lanao formed two separate groups: one group clustered with G. aureus, while the other group formed a separate cluster and were designated as G. cf. aureus because they are morphologically similar to G. aureus, but are genetically divergent from it. All the 20 specimens from Lake Mainit formed a separate cluster and are most likely a new and still undescribed species. DNA barcoding also lends support to previous studies which showed, based on morphological data, that G. giuris and G. celebius are species complexes. Within-species genetic distances suggest that G. callidus, G. bicirrhosus, and G. circumspectus are also species complexes. The discovery of possibly new species from Lake Mainit, cryptic species from Lake Lanao, and the presence of species complexes in Glossogobius have implications on the proper conservation and management of these important fishery resources.
Among the Egyptian catch fisheries, marine shrimp species represent the
most economically important invertebrate. Likewise, this species is distributed
all over the world as a diverse one. The current study merged DNA barcoding
as a valuable complementary tool with morphology-based species
identification. Ten different maritime shrimp species were phenotypically
delineated and identified, based on the structure of the carapace; the crest,
groove, and spines, the rostrum with its teeth; dorsally and ventrally, sex
determination; the shape of the petasma and thelycum, armed or unarmed
telson, and the body colour. Phylogenetic relationships between ten Egyptian
shrimp species were examined with the nucleotide sequence data stored in the
GenBank database of partly region for the mitochondrial subunit I of
cytochrome oxidase gene (COI). Most of the produced sequences had 99–
100% similarity to conspecific sequences. Sequence assessment of the COI
gene for the phylogenetic tree distinguished all ten shrimp species into three
definite clades, which are genetically distinct from one another and
demonstrated the same phylogenetic reservations to their respective genus. The
percent GC content ranged between 41.4% in Metapenaeus monoceros and
36.6 % in Trachypenaeus curvirostris and Marsupenaeus japonicas. The
highest genetic distance (0.3) was found between Palaemon serratus and
Parapenaeus longirostris of Egypt, and Penaeus semisulcatus of India and
Trachypenaeus curvirostris of Egypt. The lowest genetic distance (0.0) was
observed between Parapenaeus longirostris of Egypt and Turkey, and
Xiphopenaeus kroyeri of Egypt, Mexico, and the USA, overlapping each other.
The current study clearly shows that DNA barcoding may be used for the
differentiation between shrimp species, which will help researchers better
understand the biology of evolution and conservation.
Omobranchus punctatus is native to the Indo-Pacifc region and invasive in the Atlantic region, currently being considered one of the most widely distributed blenny species. However, recent molecular studies indicated that O. punctatus is a complex of species, with three divergent mtDNA lineages identifed to date, stressing the need for a taxonomic revision. In this study, we used an integrative approach, combining morphological and genetic data, to shed light on the taxonomy and distribution of O. punctatus. Moreover, we provide the frst genetic records of introduced populations in Brazil and discuss the introduction pattern of this species in this region. Morphological data shows that O. punctatus consists of at least fve distinct and geographically restricted species: O. punctatus sensu stricto, O. dispar, O. sewalli, O. cf. kochi, and O. cf. japonicus. Species delimitation analyses performed using the mtDNA data available confrmed that O. punctatus sensu stricto, O. dispar and O. sewalli correspond to diferent species that started to diverge about 2.6 Mya. Furthermore, O.
sewalli was identifed as the invasive species colonizing Atlantic shores. The existence of historical oceanographic barriers, such as the emergence of the Sunda Shelf in the Eastern Indian Ocean during
the Pleistocene, and the biological traits of these blennies are the most likely factors responsible for their genetic diferentiation and subsequent speciation.
By far, very few studies have dealt with the ichthyoplankton diversity in Guanghai Bay (China), which is a potential spawning ground for many important fish species. In this study, fish eggs collected in Guanghai Bay were identified through molecular method combined with visual taxonomic method. We employed two mitochondrial gene regions of cytochrome c oxidase subunit I (COI) and 16S ribosomal RNA (16S rRNA) as genetic markers for species identification. Through sequence identification at NCBI, 121 eggs with overlapping size range and easy to be confused were discriminated as four economically important species: seven as silver sillago Sillago sihama, 48 as black-banded sillago Sillago nigrofasciata, 38 as yellow drum Nibea albiflora, and 28 as Pacific seabream Acanthopagrus pacificus. Phylogenetic analyses showed that these 121 eggs clustered in four groups with strong support. To testify the validity of these identification results, species identification through five BarcodingR package methods was also carried out using sequences of 33 fish specimens as a reference library covering four target species. Finally, a highly consensus of species assignment results was achieved across different methods. Morphological characteristics and detailed photographs for eggs from these four species were supplied here. Eggs of each species are pelagic, round, have a smooth chorion and one single oil globule. Embryonic pigment patterns vary as eggs develop and can be used for species distinguishing. Eggs from S. nigrofasciata and A. pacificus were described for the first time in this study. One simple and accurate method for identifying N. albiflora eggs was additionally provided. Moreover, the morphological differences between two Sillago eggs offered supportive evidence for the recent separation of S. nigrofasciata as a new species from S. sihama. All these results would be critical for the discrimination of eggs from these four species and the estimation for their spawning areas. Meanwhile, our study would contribute to the stock assessment and fishery management in Guanghai Bay.
The monocle bream Scolopsis vosmeri species complex is revised. Three species in the complex are recognized: Scolopsis vosmeri (Bloch, 1792), widespread in the Indo-West Pacific, from the northern Indian Ocean (Pakistan, western India, Sri Lanka, Bay of Bengal, and the Andaman Sea, but not recorded from the Red Sea or Arabian Gulf, east African coast or Madagascar) to western Indonesia and Borneo; S. japonica (Bloch, 1793), restricted to the western Pacific Ocean from western Indonesia and north-western Australia east to the Philippines and north to southern Japan; and S. curite Cuvier, 1815, widespread from the western to the eastern Indian Ocean, including the Red Sea and Arabian Gulf. All three species are similar morphologically, and have been confused taxonomically, but phylogenetic analysis of the COI barcoding region shows they are evolutionarily divergent. The three species are redescribed in detail and characters found to distinguish them. Scolopsis vosmeri is easily distinguished from S. japonica and S. curite in having a white band along the side of the body; having a black spot on most body scales (versus greenish yellow spot in S. japonica and S. curite); in lacking a distinct black spot (sometimes a small and faint spot present) on the upper pectoral-fin base (versus small black wedge-shaped spot present in S. japonica and S. curite); caudal peduncle whitish in live individuals (versus caudal peduncle usually yellowish in S. japonica and S. curite); and pelvic and anal fins crimson to orange-red (versus yellow in S. japonica and S. curite). Scolopsis japonica and S. curite are indistinguishable by color pattern but differ in the degree of spination on the preopercular margin. Neotypes are designated for Scolopsis japonica and S. curite. Nomenclatural problems, including validity of the genus Scolopsis, are discussed. We regard Scolopsis curite Cuvier, 1815 as a valid binomial name and thus the type species of Scolopsis Cuvier, 1814 by subsequent monotypy.
The carangid genus Carangoides Bleeker 1851 has been considered to include 19 valid species, although the genus has been shown to be paraphyletic with molecular-phylogenetic methods. In this account, the previous Carangoides and its related genera (Alectis Rafinesque 1815, Atropus Oken 1817, Parastromateus Bleeker 1864, Selene Lacepède 1802, Ulua Jordan and Snyder 1908, and Uraspis Bleeker 1855) are reorganized into 15 (including five new and four resurrected) genera based on both molecular-phylogenetic results and morphological analyses. The members of the previously recognised Alectis are split into two genera, Alectis [Alectis ciliaris (Bloch 1787)] and Scyris Cuvier 1829 [Scyris alexandrina (Geoffroy St. Hilaire 1817) and Scyris indica Rüppell 1830]. Two new genera, Euprepocaranx and Paraselene are established for Carangoides dorsalis Gill 1863 [= Carangoides otrynter (Jordan and Gilbert 1883)] and Selene orstedii Lütken 1880, respectively. The genus Selene is valid, including six species except for Selene orstedii. Atropus atropos (Bloch and Schneider 1801), two species of Ulua and two species previously known in Carangoides [Carangoides armatus (Forsskål in Niebuhr 1775) and Carangoides hedlandensis (Whitley 1934)] composed the newly redefined Atropus. Craterognathus and Flavocaranx are new monotypic genera, consisting of the previous species Carangoides plagiotaenia Bleeker 1857 and Carangoides bajad (Fabricius in Niebuhr 1775), respectively. Platycaranx is also a new genus comprising three species, previous Carangoides chrysophrys (Cuvier in Cuvier and Valenciennes 1833), Carangoides malabaricus (Bloch and Schneider 1801) and Carangoides talamparoides Bleeker 1852. Resurrected genera, Carangichthys Bleeker 1853, Ferdauia Jordan, Evermann and Wakiya in Jordan, Evermann and Tanaka 1927, and Turrum Whitley 1932 are composed of a few species previously assigned to Carangoides: Carangoides dinema Bleeker 1851, Carangoides humerosus (McCulloch 1915) and Carangoides oblongus (Cuvier in Cuvier and Valenciennes 1833); Carangoides ferdau (Fabricius in Niebuhr 1775) and Carangoides orthogrammus (Jordan and Gilbert 1882); and Carangoides coeruleopinnatus (Rüppell 1830), Carangoides fulvoguttatus (Forsskål in Niebuhr 1775) and Carangoides gymnostethus (Cuvier in Cuvier and Valenciennes 1833), respectively. Parastromateus and Uraspis continue to be valid genera, including Parastromateus niger (Bloch 1795), and Uraspis helvola (Forster in Bloch and Schneider 1801) and Uraspis uraspis (Günther 1860), respectively. The revised Carangoides consists of only two species, resurrected Carangoides ire (Cuvier in Cuvier and Valenciennes 1833) and Carangoides praeustus (Anonymous [Bennett] 1830). Diagnosis and brief description are provided for each genus.
Ponyfish (Perciformes: Leiognathidae) are a diverse group of mainly small, planktivorous fishes that comprise much of the teleost component found in the by-catch of trawlers in Thai waters. The generic taxonomy of ponyfish has been revised many times, which has resulted in confusion in the historical records of fishing data. Moreover, since two monsoon seasons affect the different coasts of Thailand at different times of the year, their effects are likely to have separate impacts on marine fish diversity in Thailand according to the time of year. By-catch samples totaling 25,439 ponyfish were collected from commercial fishing vessels during three sampling episodes in each of two Andaman Sea provinces and three provinces in the Gulf of Thailand. Ponyfish samples were identified to the species level and taxonomical ambiguity was dealt with by DNA sequencing against GenBank to identify the specie. From these data, the spatial and temporal community diversity and abundance were calculated. Richness and total abundance were significantly different between seasons but not between the two sides of the Thai peninsula. Diversity of ponyfish in bycatch was least during the monsoon transition period or the dry season. Morphological variation of Photopectoralis bindus has been a source of taxonomic confusion in the past, but here, the use of DNA sequencing in addition to body ratio data analysis reinforces taxonomic clarity and suggests population-level structuring that may explain these issues. These findings indicate the role of seasonal fluctuations in biodiversity maintenance for fisheries management in Thailand.
The data collected through ichthyoplankton monitoring surveys provide valuable insight into the spawning dynamics of multiple species. Fish eggs, more than larvae, offer a more precise evaluation of species-specific spawning characteristics; however, egg collections are greatly underused because of the limitations associated with morphology- based identifications. In recent years, a new means of molecular identification, termed DNA barcoding, has made species identification readily available across a broad range of taxa. We used DNA barcoding to identify ethanol-preserved fish eggs collected during 2002–2012 along the northeastern U.S. continental shelf. A subsampling protocol was used to select 1603 unidentified eggs for analysis. DNA sequences were successfully obtained from 1495 (93.26%) of these eggs, representing 50 species—many of which have either never before been identified to the species-level as eggs or have been identified previously only to a higher taxonomic level or during specific developmental egg stages. In comparison with past attempts at morphological identification, our molecular identifications comprise a broader diversity of eggs and provide a technique with high success rates of unambiguous identifications that is not sensitive to egg stage. Overall, this work shows that DNA barcoding of fish eggs is sufficiently advanced to be incorporated into long-term, regional-scale ichthyoplankton monitoring programs. © 2016, National Marine Fisheries Service. All rights reserved.
The Indo-west Pacific damselfish Neopomacentrus cyanomos was first recorded in the West Atlantic in 2013, when it was found to be common on reefs near Coatzacoalcos, in the extreme southwest corner Gulf of Mexico. During 2014-2015 this species also was found on reefs further afield in that area, but not in the northwest Gulf, nor the north-eastern tip of the Yucatan peninsula. These data, and information from public databases on invasive reef fishes, indicate that N. cyanomos currently is widely distributed in, but restricted to, the southwest Gulf of Mexico. Barcodes of N cyanomos from that area match those for this species from its natural range, but do not indicate the ultimate origin of the Gulf of Mexico fish. Possible modes of introduction to the Gulf of Mexico, and the potential for its further spread with negative effects on the native reef-fish fauna are discussed, and directions for future research suggested.
The long-term species diversity patterns in marine fish communities are garnering increasing attention from ecologists and conservation biologists. However, current databases on quantitative abundance information lack consistent long-term time series, which are particularly important in exploring the possible underlying mechanism of community changes and evaluating the effectiveness of biodiversity conservation measures. Here we describe an impinged fish assemblage dataset containing 1, 283, 707 individuals from 439 taxa. Once a month over 19 years (1987–1990 and 2000–2014), we systematically collected the fish killed by impingement upon cooling water intake screens at two nuclear power plants on the northern coast of Taiwan. Because impingement surveys have low sampling errors and can be carried out over many years, they serve as an ideal sampling tool for monitoring how fish diversity and community structure vary over an extended period of time.
Although much biological research depends upon species diagnoses, taxonomic expertise is collapsing. We are convinced that the sole prospect for a sustainable identification capability lies in the construction of systems that employ DNA sequences as taxon 'barcodes'. We establish that the mitochondrial gene cytochrome c oxidase I (COI) can serve as the core of a global bioidentification system for animals. First, we demonstrate that COI profiles, derived from the low-density sampling of higher taxonomic categories, ordinarily assign newly analysed taxa to the appropriate phylum or order. Second, we demonstrate that species-level assignments can be obtained by creating comprehensive COI profiles. A model COI profile, based upon the analysis of a single individual from each of 200 closely allied species of lepidopterans, was 100% successful in correctly identifying subsequent specimens. When fully developed, a COI identification system will provide a reliable, cost-effective and accessible solution to the current problem of species identification. Its assembly will also generate important new insights into the diversification of life and the rules of molecular evolution.
Introduced predators pose ecological impacts upon prey species and receiving ecosystems. Understanding such ecological interactions creates technical challenges including species-specific identification of partially digested prey items in the stomachs of piscivorous predators. We present the first evaluation of DNA barcoding to identify piscine prey in the stomachs of North American catfishes (Family Ictaluridae). Fish prey items of non-native Blue Catfish Ictalurus furcatus and Flathead Catfish Pylodictis olivaris were obtained by gastric lavage and ranked as lightly, moderately, or heavily digested. We used an established cocktail of universal fish primers (FishF2_t1, FishR2_t1, VF2_t1, and FR1d_t1) to amplify the cytochrome oxidase I (COI-3) region of mitochondrial DNA from these samples. Amplification products were subjected to Sanger sequencing, and edited sequences were compared to entries in GenBank. Eighty-six percent of the sequences generated for lightly or moderately digested samples and 66 % of those for heavily digested samples could be assigned to the species level based on similarity with archived COI-3 sequences. While traditional morphological identification led to species-level identification of 65 % of fish prey items, addition of DNA barcoding resulted in identification to species of 88 % of fish prey items overall. Diet items identified by DNA markers included anadromous Striped Bass Morone saxatilis and herrings and shads Alosa spp. that are the focus of fishery restoration programs in these rivers. We found DNA barcoding to be an efficient and cost-effective addition to diet studies of non-native predators.
Human-dominated marine ecosystems are experiencing accelerating loss of populations and species, with largely unknown consequences. We analyzed local experiments, long-term regional time series, and global fisheries data to test how biodiversity loss affects marine ecosystem services across temporal and spatial scales. Overall, rates of resource collapse increased and recovery potential, stability, and water quality decreased exponentially with declining diversity. Restoration of biodiversity, in contrast, increased productivity fourfold and decreased variability by 21%, on average. We conclude that marine biodiversity loss is increasingly impairing the ocean's capacity to provide food, maintain water quality, and recover from perturbations. Yet available data suggest that at this point, these trends are still reversible.
The identification of fish larvae from two neotropical hydrographic basins using traditional morphological taxonomy and DNA barcoding revealed no conflicting results between the morphological and barcode identification of larvae. A lower rate (25%) of correct morphological identification of eggs as belonging to migratory or non-migratory species was achieved. Accurate identification of ichthyoplankton by DNA barcoding is an important tool for fish reproductive behaviour studies, correct estimation of biodiversity by detecting eggs from rare species, as well as defining environmental and management strategies for fish conservation in the neotropics.
© 2015 The Fisheries Society of the British Isles.
DNA bar-coding is a taxonomic method that uses small genetic markers in organisms' mitochondrial DNA (mt DNA) for identification of particular species. It uses sequence diversity in a 658-base pair fragment near the 5' end of the mitochondrial cytochrome c oxidase subunit 1 (CO1) gene as a tool for species identification. DNA barcoding is more accurate and reliable method as compared with the morphological identification. It is equally useful in juveniles as well as adult stages of fishes. The present study was conducted to identify three farm fish species of Pakistan (Cyprinus carpio, Cirrhinus mrigala, and Ctenopharyngodon idella) genetically. All of them belonged to family cyprinidae. CO1 gene was amplified. PCR products were sequenced and analyzed by bioinformatic software. Conspecific, congenric, and confamilial k2P nucleotide divergence was estimated. From these findings, it was concluded that the gene sequence, CO1, may serve as milestone for the identification of related species at molecular level.
We isolated, amplified, and sequenced the mtDNA from insect fragments found in the feces of big brown bats (Eptesicus fuscus) caught in apple orchards, to determine whether the bats were consuming prey of economic interest, especially common pests of apples. Comparison of sequences to those in a reference database (Barcode of Life Database) allowed identification of 58 sequences from 40 bats to the level of family, genus, or species; 40 (69%) of the 58 sequences of insects matched to species, 6 (10%) to only genus, and 12 (21%) to only family. Forty-nine (84%) of the 58 matches, from 34 (85%) of the 40 bats, were to taxa within the order Coleoptera and most represented taxa within the family Carabidae; other orders included Diptera, Ephemeroptera, and Hymenoptera. Eighteen different species were identified, including several important pests, such as various mosquitoes (Aedes), the spotted cucumber beetle (Diabrotica undecimpunctata), and pavement ants (Tetramorium caespitum), although no pests specific to apples were discovered.
Beetles are the most diverse group of animals, and are crucial for ecosystem functioning. In many countries, they are heavily used for environmental impact assessment, but even in the well-studied Central European fauna, species identification can be very difficult. A comprehensive and taxonomically well curated DNA barcode library could remedy this deficit and also could link hundreds of years of traditional knowledge with next generation sequencing technology. However, such a beetle library is missing to date. This study provides the globally largest DNA barcode reference library for Coleoptera for 15,948 individuals belonging to 3,514 well-identified species (53% of the German fauna) with representatives from 97 of 103 families (94%). This study is the first comprehensive regional test of the efficiency of DNA barcoding for beetles with a focus on Germany. Sequences >500bp were recovered from 63% of the specimens analyzed (15,948 of 25,294) with short sequences from another 997 specimens. Whereas mostspecimens (92.2%) could be unambiguously assigned to a single known species by sequence diversity at CO1, 1089 specimens (6.8%) were assigned to more than one Barcode Index Number (BIN), creating 395 BINs which need further study to ascertain if they represent cryptic species, mitochondrial introgression, or simply regional variation in widespread species. We found 409 specimens (2.6%) that shared a BIN assignment with another species, most involving a pair of closely allied species as 43 BINs were involved. Most of these taxa were separated by barcodes although sequence divergences were low. Only 155 specimens (0.97%) show identical or overlapping clusters. This article is protected by copyright. All rights reserved.
This article is protected by copyright. All rights reserved.
Hybridization in the ocean was once considered rare, a process prohibited by the rapid evolution of intrinsic reproductive barriers in a high-dispersal medium. However, recent genetic surveys have prompted a reappraisal of marine hybridization as an important demographic and evolutionary process. The Hawaiian Archipelago offers an unusual case history in this arena, due to the recent arrival of the widely distributed Indo-Pacific Sergeant (Abudefduf vaigiensis), which is hybridizing with the endemic congener, A. abdominals. Surveys of mtDNA and three nuclear loci across Hawai'i (N = 396, A. abdominalis and N = 314, A. vaigiensis) reveal that hybridization is significantly higher in the human-perturbed southeast archipelago (19.8%), tapering off to 5.9% in the pristine northwest archipelago. While densities of the two species varied throughout Hawai'i, hybridization was highest in regions with similar species densities, contradicting the generalization that the rarity of one species promotes interspecific mating. Our finding of later generation hybrids throughout the archipelago invokes the possibility of genetic swamping of the endemic species. An exaptation, an adaptation with unintended consequences, may explain these findings: the endemic species has transient yellow coloration during reproduction, whereas the introduced species has yellow coloration continuously as adults, in effect a permanent signal of reproductive receptivity. Haplotype diversity is higher in Hawaiian A. vaigiensis than in our samples from the native range, indicating large-scale colonization almost certainly facilitated by the historically recent surge of marine debris. In this chain of events, marine debris promotes colonization, exaptation promotes hybridization, and introgression invokes the possible collapse of an endemic species.This article is protected by copyright. All rights reserved.
Abstract This paper reviews progress in research on
taxonomy and systematics of larval marine and estuarine
fishes in the Indo-Pacific since the first Indo-Pacific Fish
Conference in 1981. In 1981, the literature on development
of fish larvae in the vast Indo-Pacific region was sparse,
scattered and of very uneven quality. During the intervening
33 years, taxonomy of adult Indo-Pacific fishes has
improved greatly, the proceedings of the landmark Ahlstrom
Symposium were published, a large number of larval-
fish atlases, or identification guides, have been
produced, and the quality of descriptions of larval-fish
development in journals has greatly increased. This has
resulted in a great improvement in our ability to identify
Indo-Pacific fish larvae, particularly oceanic taxa. However,
much remains to be done, with the large majority of
families having <50 % of species with described larvae,
and with only a small proportion of species descriptions
based on full developmental series of larvae. DNA technology
has helped to establish identities of larvae, but only
a small proportion of the larvae so identified have been
described, so the potential for DNA to advance larval
taxonomy is largely untapped. An integrative approach
combining genetics and morphology is required. Online
publication of descriptions of larval development and of
interactive identification guides to larvae is the most efficient
way to make such information available and useful to
a variety of users. The great potential for larval-fish
ontogeny to contribute to the study of phylogeny of marine
fishes has been under-realized. The ageing of current larval-fish
taxonomists, and the lack of positions for younger
replacement researchers, is a major obstacle to further
progress.
The hairtail (currently recognized as Trichiurus lepturus in Korea) is one of the most important commercial fish species in Korea, Japan, China, and Taiwan. Because the amount of catches has been steadily declining, we must determine the early life stages of the hairtail from the viewpoint of resource management. Furthermore, the taxonomic status of the hairtail is unclear among ichthyologists, potentially creating management difficulties. Therefore, the purpose of this study was to compare morphological and molecular information on eggs, larvae, and adults of hairtail from Korea with that of T. lepturus from the Atlantic Ocean, and to review the taxonomic status of the hairtail. A total of 510 base pairs of the mitochondrial DNA cytochrome oxidase subunit I sequences of 12 eggs, 2 larvae, and 11 adults of the hairtail from the Korean waters clearly matched those of Trichiurus japonicus adults (d = 0.000-0.014) from the East China Sea rather than those of T. lepturus (d = 0.100-0.110) from the Atlantic Ocean. Our results also showed that larvae of the Korean hairtail are different than those in the Atlantic Ocean in having no melanophores along the ventral edge of the lower jaw. Therefore, our findings suggest that the hairtail in the Korean waters may not be T. lepturus, but T. japonicus.
A genetic identification method (DNA barcoding) was used to compare the community compositions of planktonic fish eggs and larvae within a coastal embayment, testing the hypothesis that the composition of the planktonic larval fish community proportionately reflects the composition of the planktonic fish egg community (excluding species with non-planktonic eggs). By genetically identifying 843 individual eggs, we preserved the quantitative aspects of traditional community analysis. The studied embayment has restricted hydrodynamic connectivity to other coastal waters. A circulation model containing simulated particles estimated average egg movement of approximately 1 km between times of spawning and sample collection, indicating locally spawned eggs were likely to be retained within the survey area. Thirteen of 14 collected egg taxa (88% of egg specimens) could be genetically identified to species level, with the 14th taxon identified to genus level. This novel approach revealed a high degree of spatial heterogeneity in fish egg compositions within the embayment. Species that dominated the egg community (Eugerres plumieri, Cynoscion nebulosus, Centropomus undecimalis, and Prionotus spp.) were not particularly abundant amongst the 276 larvae identified, and the most abundant larval species (Achirus lineatus and Cynoscion arenarius) only comprised a minor proportion of the identified eggs. Overall, there was no correlation between the percent compositions of the egg and larval communities (r = -0.07, n = 15, p = 0.81). The clear disparities observed between the species compositions of the eggs and larvae highlight the need for directly identifying eggs when studying habitat connectivity or performing stock assessment with egg production model-based methods.
Fresh waters in lakes, ponds, rivers, estuaries and wetlands are only 0·3% of available global surface water yet support 47–53% (> 15 000) of all extant fish species. Freshwater fishes are globally valuable yet threatened everywhere through overfishing, pollution, habitat loss, damming, alien invasive species and climate change. Hence, they are in dire need of effective and sustained conservation action, including through zoo and aquarium programmes in the wild and ex situ. To address these challenges, zoo and aquarium staff need to be familiar with the substantial issues, develop greater expertise, and become better integrated in wider regional and global initiatives in freshwater-fish conservation and sustainability. Resolving diverse issues requires knowledge of the many different values in the conservation of freshwater fishes, including sustainable commercial fisheries and the aquarium trade. It is necessary to assess and mitigate threats to fish survival through research and monitoring. An improved conservation-orientated science of threatened fish species is also needed in terms of taxonomy and biology. From this, the implementation and dissemination of appropriate conservation policies, strategies and legislation can be developed. All these factors enable direct practical action for fish conservation, in conjunction with improved zoo education, training and public communication. Finally, review and evaluation of the efficacy of various conservation actions must be carried out in order to plan future undertakings.
We announce the release of an advanced version of the Molecular Evolutionary Genetics Analysis (MEGA) software, which currently contains facilities for building sequence alignments, inferring phylogenetic histories, and conducting molecular evolutionary analysis. In version 6.0, MEGA now enables the inference of timetrees, as it implements our RelTime method for estimating divergence times for all branching points in a phylogeny. A new Timetree Wizard in MEGA6 facilitates this timetree inference by providing a graphical user interface (GUI) to specify the phylogeny and calibration constraints step-by-step. This version also contains enhanced algorithms to search for the optimal trees under evolutionary criteria and implements a more advanced memory management that can double the size of sequence data sets to which MEGA can be applied. Both GUI and command-line versions of MEGA6 can be downloaded from www.megasoftware.net free of charge.
With almost 40 000 species, the spiders provide important model systems for studies of sociality, mating systems, and sexual dimorphism. However, work on this group is regularly constrained by difficulties in species identification. DNA-based identification systems represent a promising approach to resolve this taxonomic impediment, but their efficacy has only been tested in a few groups. In this study, we demonstrate that sequence diversity in a standard segment of the mitochondrial gene coding for cytochrome c oxidase I (COI) is highly effective in discriminating spider species. A COI profile containing 168 spider species and 35 other arachnid species correctly assigned 100% of subsequently analyzed specimens to the appropriate species. In addition, we found no overlap between mean nucleotide divergences at the intra- and inter-specific levels. Our results establish the potential of COI as a rapid and accurate identification tool for biodiversity surveys of spiders.
'Biodiversity' means the variety of life and it can be studied at different levels (genetic, species, ecosystem) and scales (spatial and temporal). Last decades showed that marine biodiversity has been severely underestimated at all levels. In order to investigate diversity patterns and underlying processes, there is a need to know what species live in the marine environment. An emerging tool for species identification, DNA barcoding can reliably assign unknown specimens to known species, also flagging potential cryptic species and genetically distant populations. This paper will review the role of DNA barcoding for the study of marine biodiversity at the species level. © 2010 by the authors; licensee Molecular Diversity Preservation International, Basel, Switzerland.
Preface. Part I: Background: 1. Introduction. Why Employ Molecular Genetic Markers? Why Not Employ Molecular Genetic Markers? 2. History of Molecular Phylogenetics. Debates and Diversions from Molecular Systematics. Molecular Phylogenetics. 3. Molecular Tools. Protein Assays. DNA Assays. References to Laboratory Protocols. 4. Interpretative Tools. Categorical Subdivisions of Molecular Genetic Data. Molecular Clocks. Procedures for Phylogeny Reconstruction. Gene Trees versus Species Trees. Part II: Applications: 5. Individuality and Parentage. Genetic Identity versus Non-Identity. Parentage. 6. Kinship and Intraspecific Phylogeny. Close Kinship and Family Structure. Geographic Population Structure and Gene Flow. Phylogeography. Microtemporal Phylogeny. 7. Speciation and Hybridization. The Speciation Process. Hybridization and Introgression. 8. Species Phylogenies and Macroevolution. Rationales for Phylogeny Estimation. Special Approaches to Phylogeny Estimation. Prospectus for a Global Phylogeny. Special Topics in Molecular Phylogenetics. 9. Conservation Genetics. Issues of Heterozygosity. Issues of Phylogeny. Literature Cited. Index to Taxonomic Genera. General Index.
Among the 899 species of freshwater fishes reported from Sundaland biodiversity hotspot, nearly 50% are endemics. The functional integrity of aquatic ecosystems is currently jeopardized by human activities and landscape conversion led to the decline of fish populations in several part of Sundaland, particularly in Java. The inventory of the Javanese ichthyofauna has been discontinuous and the taxonomic knowledge is scattered in the literature. The present study provides a DNA barcode reference library for the inland fishes of Java and Bali with the aim to streamline the inventory of fishes in this part of Sundaland. Owing to the lack of available checklist for estimating the taxonomic coverage of the present study, a checklist was compiled based on online catalogs. A total of 95 sites were visited and a library including 1,046 DNA barcodes for 159 species was assembled. Nearest neighbor distance was 28-fold higher than maximum intra-specific distance on average and a DNA barcoding gap was observed. The list of species with DNA barcodes displayed large discrepancies with the checklist compiled here as only 36% (i.e. 77 species) and 60% (i.e.24 species) of the known species were sampled in Java and Bali, respectively. This result was contrasted by a high number of new occurrences and the ceiling of the accumulation curves for both species and genera. These results highlight the poor taxonomic knowledge of this ichthyofauna and the apparent discrepancy between present and historical occurrence data is to be attributed to species extirpations, synonymy and misidentifications in previous studies. This article is protected by copyright. All rights reserved.
Attempts were made to identify species in commercial frozen shrimp meat samples collected in Taiwan. First, approximately 20 fresh specimens of each of the 10 common commercial shrimp species were identified by morphological methods. A 401 to 407-bp fragment of the cytochrome b gene was amplified from the shrimp meat by polymerase chain reaction (PCR) using the primer pair UCYTB151F/270R. By comparing the gene sequences and PCR-restriction fragment length polymorphism (RFLP) maps obtained using the endonucleases Alu I, Ssp I and Hae III, the 10 species of shrimp could be successfully differentiated. The PCR-RFLP method was proved applicable for the species identification of 10 marketed shrimp samples.
Illegal trade threatens the survival of many wild species, and molecular forensics can shed light on various questions raised during the investigation of cases of illegal trade. Among these questions is the identity of the species involved. Here we report a case of a man who was caught in a Brazilian airport trying to travel with 58 avian eggs. He claimed they were quail eggs, but authorities suspected they were from parrots. The embryos never hatched and it was not possible to identify them based on morphology. As 29% of parrot species are endangered, the identity of the species involved was important to establish a stronger criminal case. Thus, we identified the embryos' species based on the analyses of mitochondrial DNA sequences (cytochrome c oxidase subunit I gene [COI] and 16S ribosomal DNA). Embryonic COI sequences were compared with those deposited in BOLD (The Barcode of Life Data System) while their 16S sequences were compared with GenBank sequences. Clustering analysis based on neighbor-joining was also performed using parrot COI and 16S sequences deposited in BOLD and GenBank. The results, based on both genes, indicated that 57 embryos were parrots (Alipiopsitta xanthops, Ara ararauna, and the [Amazona aestiva/A. ochrocephala] complex), and 1 was an owl. This kind of data can help criminal investigations and to design species-specific anti-poaching strategies, and demonstrate how DNA sequence analysis in the identification of bird species is a powerful conservation tool.
© The American Genetic Association 2015. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.
This study evaluates the utility of DNA barcoding to traditional morphology-based species identifications for the fish fauna of the north-eastern Congo basin. We compared DNA sequences (COI) of 821 samples from 206 morphologically identified species. Best Match, Best Close Match and All Species Barcoding analyses resulted in a rather low identification success of 87.5%, 84.5% and 64.1%, respectively. The ratio 'nearest-neighbour distance/maximum intraspecific divergence' was lower than 1 for 26.1% of the samples, indicating possible taxonomic problems. In ten genera, belonging to six families, the number of species inferred from mtDNA data exceeded the number of species identified using morphological features; and in four cases indications of possible synonymy were detected. Finally, the DNA barcodes confirmed previously known identification problems within certain genera of the Clariidae, Cyprinidae and Mormyridae. Our results underscore the large number of taxonomic problems lingering in the taxonomy of the fish fauna of the Congo basin, and illustrate why DNA barcodes will contribute to future efforts to compile a reliable taxonomic inventory of the Congo basin fish fauna. Therefore, the obtained barcodes were deposited in the reference barcode library of the Barcode of Life Initiative. This article is protected by copyright. All rights reserved.
This article is protected by copyright. All rights reserved.
Seahorse, which has a unique appearance and exhibits male pregnancy, is a useful component of traditional Chinese medicine (TCM). With the growing demand for TCM, vast amounts of seahorses are harvested from the wild every year and traded internationally. This study investigated 58 dried seahorse samples collected from 23 Chinese herbal medicine stores across Taiwan using molecular forensics. Results showed that eight seahorse species were present in the Taiwan TCM market. Among them, Knysna seahorse (Hippocampus capensis) has an endangered status according to the International Union for Conservation of Nature (IUCN) Red List, while the West African seahorse (Hippocampus algiricus), tiger tail seahorse (Hippocampus comes), thorny seahorse (Hippocampus histrix), great seahorse (Hippocampus kelloggi), yellow seahorse (Hippocampus kuda), hedgehog seahorse (Hippocampus spinosissimus), and three-spot seahorse (Hippocampus trimaculatus) have vulnerable status. Copyright
The objective of this study was to test a variety of ground meat products sold on the U.S. commercial market for the presence of potential mislabeling. Forty-eight ground meat samples were purchased from online and retail sources, including both supermarkets and specialty meat retailers. DNA was extracted from each sample in duplicate and tested using DNA barcoding of the cytochrome c oxidase I (COI) gene. The resulting sequences were identified at the species level using the Barcode of Life Database (BOLD). Any samples that failed DNA barcoding went through repeat extraction and sequencing, and due to the possibility of a species mixture, they were tested with real-time polymerase chain reaction (PCR) targeting beef, chicken, lamb, turkey, pork and horse. Of the 48 samples analyzed in this study, 38 were labeled correctly and 10 were found to be mislabeled. Nine of the mislabeled samples were found to contain additional meat species based on real-time PCR, and one sample was mislabeled in its entirety. Interestingly, meat samples ordered from online specialty meat distributors had a higher rate of being mislabeled (35%) compared to samples purchased from a local butcher (18%) and samples purchased at local supermarkets (5.8%). Horsemeat, which is illegal to sell on the U.S. commercial market, was detected in two of the samples acquired from online specialty meat distributors. Overall, the mislabeling detected in this study appears to be due to either intentional mixing of lower-cost meat species into higher cost products or unintentional mixing of meat species due to cross-contamination during processing.
