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Phylogram of relationships of Bangladeshi fish species, based on Bayesian analysis of the standard DNA barcode fragment of the mitochondrial coi gene. The scale bar indicates expected number of substitutions per site. Terminals are identified by NRM or DU tissue sample collection identifiers (metadata, including GenBank Accession Numbers, in Supplementary Table S2).
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We sequenced the standard DNA barcode gene fragment in 694 newly collected specimens, representing 243 species level Operational Barcode Units (OBUs) of freshwater fishes from Bangladesh. We produced coi sequences for 149 out of the 237 species already recorded from Bangladesh. Another 83 species sequenced were not previously recorded for the count...
Citations
... Hebert et al. (2003) proposed DNA barcoding technology using mitochondrial cytochrome c oxidase subunit I (COI) gene sequence, for which the intraspecific diversity is significantly lower than the interspecific diversity, as a barcode for species identification and classification. For over a decade, the COI gene has been widely used for classifying and identifying Cyprinid fishes (Hubert et al. 2008(Hubert et al. , 2015Keskin and Atar 2013;Chakraborty and Ghosh 2014;Geiger et al. 2014;Karim et al. 2016;Lakra et al. 2016;Bayçelebi et al. 2018;Aksu and Bektas 2019;Bektas et al. 2019b;Rahman et al. 2019;Bahadır et al. 2020;Bektas et al. 2022). So far, the COI-based DNA barcode has been used to identify a limited number of cyprinid fish genera or species in Turkey (Keskin et al. 2012;Keskin and Atar 2013;Geiger et al. 2014;Bektas et al. 2019b) in Turkey. ...
The present study investigated the ability of DNA barcoding to reliably identify the endemic freshwater species in Turkey, known as biodiversity hotspots. The barcode region (652 bp) of the mitochondrial cytochrome c oxidase subunit I (COI) was used to barcode 153 individuals from 13 morphologically identified species of the genus Alburnoides . Based on the Kimura two-parameter (K2P) evolution model, the average interspecific distance (0.0595) was 31-fold higher than the average intraspecific distance (0.0019). There was a clear-cut barcode gap (0.0158–0.0187) between maximum intraspecific distance ( A. tzanevi and A. velioglui ) and minimum nearest-neighbour distance ( A. freyhofi and A. kurui ) for Anatolian Alburnoides species and a common genetic threshold of 0.0158 sequence divergence was defined for species delimitation. The multiple species delimitation methods (ABGD, ASAP, GMYC and bPTP) revealed a total of 11 molecular operational taxonomic units (MOTUs) for 13 morphospecies. Neighbour-joining (NJ), Maximum Likelihood (ML) and Bayesian Inference (BI) tree analysis indicated that all haplotypes were clustered into two major clades, which corresponded to eleven Alburnoides species clusters, with strong bootstrap support. Furthermore, all the specimens clustered in concurrence with the morpho-taxonomic status of the species, except for two species ( A. coskuncelebii and A. emineae ) that were morphologically differentiated, but showed overlap in variation for COI-based DNA barcode data with other species. Overall, present results identified that COI-based DNA barcoding is effective for species identification and cataloguing of genus Alburnoides in Turkey.
... However, after molecular and post mating isolation studies, it has been found that F. limnocharis divided into three groups which named was given as F. small type, F. middle type and F. large type (Islam et al., 2008;Hasan et al., 2012). This kind of species complexity also exists in the freshwater species in Bangladesh (Habib et al., 2019;Rahman et al., 2019;Hasan and Tripti, 2021). Therefore, we assume that more than one species might be incorporated into this family unintentionally. ...
... Therefore, we assume that more than one species might be incorporated into this family unintentionally. This speculation is supported by the recent molecular work of Rahman et al. (2019). As a result, now it is highly time demanding appeal to do molecular work to unveil the true species identification of these groups. ...
A checklist of 110 species of fishes belonging to 10 orders, 31 families and 78 genera was recorded with their scientific, common and Bangla or local names. These fish specimens were collected from the rivers, beels, haors, ponds and swamps of middle to North-east Bangladesh (Jamalpur, Netrokona, Kishorganj, Munshiganj and Bogra Districts). The order Cypriniformes (37%) was recorded higher followed by Perciformes (24%), Siluriformes (23%), Clupeiformes (6%). The global and national IUCN categories of these species are also provided. Based on local IUCN criteria, around 23% fish species belongs to threatened level and 5, 8 and 10% are denoted as critically endangered (CR), endangered (EN) and vulnerable (VU), respectively. Although collection and preservation is comparatively hassle-free, however, due to mingle nature of few fish species; it seems difficult to error free identification of the collected fishes by morphological traits alone. Two individuals from Sanondabari, Jamalpur (MHBSFMSTU Fish 92 and Ghaglajur Bazar, Netrokona (MHBSFMSTU Fish 84), morphologically very similar but they are completely two separated species i.e. Gagata cenia and G. youssoufi, respectively. Phenotypic plasticity is a barrier to name the fish species accurately, suggesting the presence of putative candidate species or existence of hidden diversity in the collected specimens of Sisoridae family. Due to anthropological effects, the biodiversity and fishing grounds are losing their qualities, resulting the low number of freshwater fish species in these sampling sites. The systematic, ecology, distribution, habitats of these fish fauna need to be studied exclusively and a well-planned conservation strategy need to implement as early as possible for protecting our valuable freshwater tasty fishes. Further, the output of the current study will also guide the government and non-government organization to come forward and take necessary measure for the betterment of the country, its economy, and fisheries resources.
... Labels in red, grey, and black represent sequences from specimens collected in Texas, Bangladesh, and India, respectively. and those also collected in eastern Bangladesh (Rahman et al. 2019) and West Bengal, India (Britz et al. 2021). ...
The native range of Ophichthys cuchia includes part of Bangladesh, Bhutan, India, Myanmar, and Nepal. Ophichthys cuchia has also been collected within six states in the USA (Louisiana, Maryland, Michigan, New Jersey, New York, and Pennsylvania) and an established invasive population exists in New Orleans (Louisiana). We provide the first record of O. cuchia from Texas and the second report of an established non-native population in the USA based on 26 museum vouchered specimens collected from a series of urban ponds within the Houston metro area (Fort Bend Co.).
... org) aimed to barcode all fish in the world. The COI gene has successfully discriminated a wide range of fishes from marine (Bakar et al. 2018;Chu et al. 2019;Rabaoui et al. 2019;Thu et al. 2019;Fadli et al. 2020) to freshwater environments (Muchlisin et al. 2013;Barman et al. 2018;Rahman et al. 2019;Tan et al. 2019). However, the success of species identification through DNA barcoding approach depends on the accuracy of species identification in DNA barcode library, namely GenBank and BOLD System (Seah et al. 2017). ...
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.
... org) aimed to barcode all fish in the world. The COI gene has successfully discriminated a wide range of fishes from marine (Bakar et al. 2018;Chu et al. 2019;Rabaoui et al. 2019;Thu et al. 2019;Fadli et al. 2020) to freshwater environments (Muchlisin et al. 2013;Barman et al. 2018;Rahman et al. 2019;Tan et al. 2019). However, the success of species identification through DNA barcoding approach depends on the accuracy of species identification in DNA barcode library, namely GenBank and BOLD System (Seah et al. 2017). ...
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.
... Anal-fin rays 15 (8), 16(15), 17(7) or 18(1) with first two rays unbranched (32) and last unbranched (26) or branched (6). Number of anal-fin pterygiophores in front of first haemal spine: 0(7), 1(11) or 2 (15). Last anal-fin pterygiophore inserted in front of haemal spine of vertebra 22 (14), 23(15) or 24 (3). ...
... Danionella cerebrum was not found at the surface, but at a depth below ca. 30 cm where the water is significantly 15 , the significance of which is unknown. Interestingly, we were also able to identify two adenin insertions in the coxI gene in the whole genome sequence of D. cerebrum provided by Kadobianskyi et al. 16 (GenBank accession SRMA00000000 as D. translucida) as well as the expected mt DNA tRNAs flanking the coxI, hundreds of base pairs up and downstream of the coxI region sequenced in our study, suggesting a genuine mitochondrial origin of our coxI sequences rather than a nuclear pseudogene (NUMT). ...
The four described species of Danionella are tiny, transparent fishes that mature at sizes between 10–15 mm, and represent some of the most extreme cases of vertebrate progenesis known to date. The miniature adult size and larval appearance of Danionella, combined with a diverse behavioral repertoire linked to sound production by males, have established Danionella as an important model for neurophysiological studies. The external similarity between the different species of Danionella has offered an important challenge to taxonomic identification using traditional external characters, leading to confusion over the identity of the model species. Using combined morphological and molecular taxonomic approaches, we show here that the most extensively studied species of Danionella is not D. translucida, but represents an undescribed species, D. cerebrum n. sp. that is externally almost identical to D. translucida, but differs trenchantly in several internal characters. Molecular analyses confirm the distinctiveness of D. cerebrum and D. translucida and suggest that the two species are not even sister taxa. Analysis of the evolution of sexual dimorphisms associated with the Weberian apparatus reveals significant increases in complexity from the simpler condition found in D. dracula, to most complex conditions in D. cerebrum, D. mirifica and D. translucida.
... DNA barcoding, the use of cytochrome oxidase I (COI) as a species tag for automated identification, opened new perspectives for the characterization of Sundaland's ichthyofauna by helping to clarify taxonomic confusion within several groups [15,21,22], by identifying discrepancies in historical species records [9] and by detecting a substantial amount of morphologically similar, yet highly divergent lineages (i.e., cryptic diversity) within numerous species [9,15,[21][22][23][24][25][26][27][28]. Several molecular studies that aimed at characterizing patterns of genetic diversity in Barbonymus led to conflicting species identities associated with sequences submitted to international repositories [9,16,[29][30][31][32][33][34][35][36]. ...
... Most sequences of BOLD:ADD1940 from mainland Asia were attributed to B. gonionotus [29,32,33,36], while sequences from Sundaland were called B. balleroides [9,16]. Sequences from BOLD:AAU0688 from Java were assigned to B. gonionotus, while previously published and newly generated sequences from Sumatra and Borneo were assigned to B. schwanefeldii. ...
Biodiversity hotspots often suffer from a lack of taxonomic knowledge, particularly those in tropical regions. However, accurate taxonomic knowledge is needed to support sustainable management of biodiversity, especially when it is harvested for human sustenance. Sundaland, the biodiversity hotspot encompassing the islands of Java, Sumatra, Borneo, and Peninsular Malaysia, is one of those. With more than 900 species, its freshwater ichthyofauna includes a large number of medium- to large-size species, which are targeted by inland fisheries. Stock assessment requires accurate taxonomy; however, several species groups targeted by inland fisheries are still poorly known. One of those cases is the cyprinid genus Barbonymus. For this study, we assembled a consolidated DNA barcode reference library for Barbonymus spp. of Sundaland, consisting of mined sequences from BOLD, as well as newly generated sequences for hitherto under-sampled islands such as Borneo. A total of 173 sequences were analyzed using several DNA-based species delimitation methods. We unambiguously detected a total of 6 Molecular Operational Taxonomic Units (MOTUs) and were able to resolve several conflicting assignments to the species level. Furthermore, we clarified the identity of MOTUs occurring in Java.
... The barcoding region has also shown significant utility in biodiversity studies that aim to rapidly identify unknown specimens collected from various habitat and sample types such as soil [17,18], water [19], feces [20,21], and dietary products [22,23]. Moreover, it has been used to construct regional and local DNA barcode libraries for further biodiversity assessment [24,25]. The use of integrative methods in systematics has shown remarkable ability to resolve species identification problems in organismal groups [26,27]. ...
The diversity of Indochinese prawns in genus Macrobrachium is enormous due to the habitat diversification and broad tributary networks of two river basins: the Chao Phraya and the Mekong. Despite long-standing interest in SE-Asian decapod diversity, the subregional Macrobrachium fauna is still not yet comprehensively clarified in terms of taxonomic identification or genetic diversification. In this study, integrative taxonomic approaches including morphological examination, DNA barcoding, and molecular species delimitation were used to emphasize the broad scale systematics of Macrobrachium prawns in Indochina. Twenty-seven nominal species were successfully re-verified by traditional and molecular taxonomy. Barcode gap analysis supported broad overlapping of species boundaries. Taxonomic ambiguity of several deposited samples in the public database is related to inter- and intraspecific genetic divergence as indicated by BOLD discordance. Diagnostic nucleotide positions were found in six Macrobrachium species. Eighteen additional putative lineages are herein assigned using the consensus of species delimitation methods. Genetic divergence indicates the possible existence of cryptic species in four morphologically complex and wide-ranging species: M . lanchesteri , M . niphanae , M . sintangense , and some members of the M . pilimanus group. The geographical distribution of some species supports the connections and barriers attributed to paleo-historical events of SE-Asian rivers and land masses. Results of this study show explicitly the importance of freshwater ecosystems in Indochinese subregions, especially for the Mekong River Basin due to its high genetic diversity and species composition found throughout its tributaries.
... 3 Specific gene regions have been chosen as markers that can distinguish between different species. [4][5][6] For animal groups, cytochrome c oxidase 1 gene (COI) is used as a barcode, while matK and rbcL are used for identifying land plants, and ITS is used for fungi. 7 The problem then translates into classifying barcodes to a known species in a fast and efficient way. ...
... We first create an empty frequency dictionary, and then populate it with all possible k-mer combinations of A, G, C and T along with initial frequency value of 0 (lines 1-3). Next, we loop over the BOLD Systems dataset until there are no samples left (lines [4][5][6][7][8][9][10][11][12][13][14][15][16][17]. In each iteration, we skip a DNA string if its length is smaller than 657, since the full length of COI segment used as a DNA barcode is 657 bp (lines 5-7). ...
Accurately identifying organisms based on their partially available genetic material is an important task to explore the phylogenetic diversity in an environment. Specific fragments in the DNA sequence of a living organism have been defined as DNA barcodes and can be used as markers to identify species efficiently and effectively. The existing DNA barcode-based classification approaches suffer from three major issues: (i) most of them assume that the classification is done within a given taxonomic class and/or input sequences are pre-aligned, (ii) highly performing classifiers, such as SVM, cannot scale to large taxonomies due to high memory requirements, (iii) mutations and noise in input DNA sequences greatly reduce the taxonomic classification score. In order to address these issues, we propose a multi-level hierarchical classifier framework to automatically assign taxonomy labels to DNA sequences. We utilize an alignment-free approach called spectrum kernel method for feature extraction. We build a proof-of-concept hierarchical classifier with two levels, and evaluated it on real DNA sequence data from Barcode of Life Data Systems. We demonstrate that the proposed framework provides higher f1-score than regular classifiers. Besides, hierarchical framework scales better to large datasets enabling researchers to employ classifiers with high classification performance and high memory requirement on large datasets. Furthermore, we show that the proposed framework is more robust to mutations and noise in sequence data than the non-hierarchical classifiers.
... 3 Specific gene regions have been chosen as markers that can distinguish between different species. [4][5][6] For animal groups, cytochrome c oxidase 1 gene (COI) is used as a barcode, while matK and rbcL are used for identifying land plants, and ITS is used for fungi. 7 The problem then translates into classifying barcodes to a known species in a fast and efficient way. ...
... We first create an empty frequency dictionary, and then populate it with all possible k-mer combinations of A, G, C and T along with initial frequency value of 0 (lines 1-3). Next, we loop over the BOLD Systems dataset until there are no samples left (lines [4][5][6][7][8][9][10][11][12][13][14][15][16][17]. In each iteration, we skip a DNA string if its length is smaller than 657, since the full length of COI segment used as a DNA barcode is 657 bp (lines 5-7). ...
Accurately identifying organisms based on their partially available genetic material is an important task to explore the phylogenetic diversity in an environment. Specific fragments in the DNA sequence of a living organism have been defined as DNA barcodes and can be used as markers to identify species efficiently and effectively. The existing DNA barcode-based classification approaches suffer from three major issues: (i) most of them assume that the classification is done within a given taxonomic class and/or input sequences are pre-aligned, (ii) highly performing classifiers, such as SVM, cannot scale to large taxonomies due to high memory requirements, (iii) mutations and noise in input DNA sequences greatly reduce the taxonomic classification score. In order to address these issues, we propose a multi-level hierarchical classifier framework to automatically assign taxonomy labels to DNA sequences. We utilize an alignment-free approach called spectrum kernel method for feature extraction. We build a proof-of-concept hierarchical classifier with two levels, and evaluated it on real DNA sequence data from Barcode of Life Data Systems. We demonstrate that the proposed framework provides higher f1-score than regular classifiers. Besides, hierarchical framework scales better to large datasets enabling researchers to employ classifiers with high classification performance and high memory requirement on large datasets. Furthermore, we show that the proposed framework is more robust to mutations and noise in sequence data than the non-hierarchical classifiers.
