DNA barcoding and evaluation of genetic diversity in Cyprinidae fish in the midstream of the Yangtze River

Using a DNA mini-barcode within the ITS region to identify toxic Amanita in mushroom poisoning cases

Mushroom poisoning contributes significantly to global foodborne diseases and related fatalities. Amanita mushrooms frequently cause such poisonings; however, identifying these toxic species is challenging due to the unavailability of fresh and intact samples. It is often necessary to analyze residues, vomitus, or stomach extracts to obtain DNA sequences for the identification of species responsible for causing food poisoning. This usually proves challenging to obtain usable DNA sequences that can be analyzed using conventional molecular biology techniques. Therefore, this study aimed to develop a DNA mini-barcoding method for the identification of Amanita species. Following the evaluation and optimization of universal primers for DNA mini-barcoding in Amanita mushrooms, we found that the internal transcribed spacer (ITS) gene sequence primer ITS-a was the most suitable DNA barcode primer for identifying Amanita species. Forty-three Amanita samples were subsequently amplified and sequenced. The sequences obtained were analyzed for intra- and inter-species genetic distances, and a phylogenetic tree was constructed. The findings indicated that the designed primers had strong universality among the Amanita samples and could accurately identify the target gene fragment with a length of 290 bp. Notably, the DNA mini-barcode accurately identified the 43 Amanita samples, demonstrating high consistency with the conventional DNA barcode. Furthermore, it effectively identified DNA from digested samples. In summary, this DNA mini-barcode is a promising tool for detecting accidental ingestion of toxic Amanita mushrooms. It may be used as an optimal barcode for species identification and traceability in events of Amanita-induced mushroom poisoning. KEY POINTS: • Development of a DNA mini-barcoding method for Amanita species identification without fresh samples. • The ITS-a primer set was optimized for robust universality in Amanita samples. • The mini-barcode is suitable for screening toxic mushroom species in mushroom poisoning cases.

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

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

Environmental DNA metabarcoding serves as a promising method for aquatic species monitoring and management: A review focused on its workflow, applications, challenges and prospects

Marine and freshwater biodiversity is under threat from both natural and manmade causes. Biological monitoring is currently a top priority for biodiversity protection. Given present limitations, traditional biological monitoring methods may not achieve the proposed monitoring aims. Environmental DNA metabarcoding technology reflects species information by capturing and extracting DNA from environmental samples, using molecular biology techniques to sequence and analyze the DNA, and comparing the obtained information with existing reference libraries to obtain species identification. However, its practical application has highlighted several limitations. This paper summarizes the main steps in the environmental application of eDNA metabarcoding technology in aquatic ecosystems, including the discovery of unknown species, the detection of invasive species, and evaluations of biodiversity. At present, with the rapid development of big data and artificial intelligence, certain advanced technologies and devices can be combined with environmental DNA metabarcoding technology to promote further development of aquatic species monitoring and management.

Divergence time of mites of the family Laelapidae based on mitochondrial barcoding region

Using the mitochondrial barcoding region to correlate research with 58 species in 19 genera of the family Laelapidae with the aim of determining the origin, phylogenetic relationships, and biogeographic historical distribution characteristics of mites in the family Laelapidae. Phylogenetic trees were obtained using Bayesian inference (BI) and Maximum-likelihood (ML) methods, based on three fossil records calibrated as molecular clock nodes, to estimate the divergence time of mites in the family Laelapidae as well as to apply Dispersal-Extinction-Cladogenesis (DEC) analyses to obtain biogeographic history inferences. The result showed species of the genera Hyperlaelaps and Haemolaelaps and some species of the genus Androlaelaps in the family Laelapidae were divided into clades of the genus Laelaps in both the BI and ML trees. Divergence time estimates and biogeographic history analysis revealed that the family Laelapidae likely diverged from other taxa during the Middle Jurassic (ca. 156.73 Mya), with Asia considered the most likely ancestral region for the family Laelapidae. Species of various genera began to undergo massive diversification events during the Cenozoic Tertiary. The results suggest that some genera in the family Laelapidae need to be re-defined or new genera need to be established; the Late Cretaceous to Late Neogene warm period would have promoted the divergence and expansion of species in the family Laelapidae. The divergence and dispersal of the family Laelapidae species is most likely a joint response to the continued northward drift of the Indian plate away from the Gondwana paleo-continent and gradually closer to Asia during the Late Cretaceous and the geological activity of the Tibetan Plateau during the Cenozoic Tertiary. The results strengthen our understanding of the origin and evolution of species in the family Laelapidae.

Integrative approach for validation of six important fish species inhabiting River Poonch of north-west Himalayan region (India)

Traditionally, species of fish are identified based on morphological characteristics. Although these taxonomic descriptions are essential, there are cases where the morphological characters distinguishing these species show marginal differences. For instance, in the Poonch River in the Himalayas, there are 21 species, out of which some are morphologically similar, and the taxonomic distinction between these species is unclear. Therefore, in this study, we used sequences from two mitochondrial genes, Cytochrome b (Cyt b) and a larger ribosomal subunit (16S rRNA), as well as the morphological analysis to address any taxonomic ambiguities among the six fish species. Maximum Likelihood results revealed that all the species were clustered according to their families and genera. The phenotypic analysis also supported this statement, as all the species of different genera like Schizothorax, Tor, Garra, Traqilabeo, and Glyptothorax are grouped in their particular cluster, it shows that species of a separate class share a mutual morphological characteristic. While genetic analyses of these species suggest nucleotide diversity (p) and haplotype diversity, with Hd values as 0.644 for Cyt b and 0.899 for 16S rRNA, confirming the rich genetic diversity in the river. Overall, we recommend that the integrative approach in delimiting the fish species is more effective than the individual one and can be used to rapidly diagnose a species and understand the evolutionary relationship between the species.

DNA barcoding and species delimitation of the genus Oxynoemacheilus (Teleostei: Nemacheilidae) in Anatolia

The DNA barcoding approach was used for the determination of evolutionary relationships and species delimitation of the genus Oxynoemacheilus (Teleostei: Nemacheilidae). The COI barcode region (615 bp amplicon) was used to barcode 444 individuals from 64 morphologically identified species in the genus Oxynoemacheilus and 189 haplotypes were identified. The average of the interspecific p distance (9.59%) was about 21-fold higher than the average intraspecific distance (0.44%). A general genetic threshold of 1.46% sequence divergence was defined for species delimitation. The multiple species delimitation methods (BCM, GMYC, bPTP and TCS) revealed a total of 62 molecular operational taxonomic units for 64 morphospecies with a new loach species from the BuyukMelen River. Neighbour-joining, maximum likelihood and Bayesian inference analyses indicated that all haplotypes were clustered into 62 clades, which corresponded to Oxynoemacheilus species, with strong bootstrap support (≥95%). Furthermore, all samples grouped in concurrence with the taxonomic status of the species except for species groups (O. germencicus-O. cinicus-O. mesudae and O. leontinae-O. namiri) that were showed intraspecific overlap in genetic diversity for COI-based barcodes. In conclusion, our analyses indicate that COI-based barcodes provide reliable species discrimination. Therefore, we currently recommend COI barcodes as the suitable barcode for genus Oxynoemacheilus.

Morphological Identification and Phylogenetic Analysis of Laelapin Mite Species (Acari: Mesostigmata: Laelapidae) from China

Laelapinae mites are involved in transmission of microbial diseases between wildlife and humans, with an impact on public health. In this study, 5 mite members in the subfamily Laelapinae (laelapin mites; LM) were morphologically identified by light microscopy, and the phylogenetic relationship of LM was analyzed in combination with the sequence information of part of the LM cytochrome oxidase subunit I (cox1) gene. The morphological identification revealed that 5 mites belonged to the genera Laelaps and Haemolaelaps, respectively. Sequence analysis showed that the ratio of non-synonymous mutation rate to synonymous mutation rate of LM was less than 1, indicating that the LM cox1 gene had undergone purifying selection. Phylogenetic analysis showed that the Laelapinae is a monophyletic group. The genera Haemolaelaps and Hyperlaelaps did not separated into distinct clades but clustered together with species of the genus Laelaps. Our morphological and molecular analyses to describe the phylogenetic relationships among different genera and species of Laelapinae provide a reference for the improvement and revision of the LM taxonomy system.

Large scale DNA barcoding of the subfamily Culterinae (Cypriniformes: Xenocyprididae) in East Asia unveils geographic scale effect, taxonomic warnings and cryptic diversity

Geographical scale might be expected to impact significantly the efficiency of DNA barcoding as spatially comprehensive sampling provides opportunities to uncover intricate relationships among closely related species and to detect cryptic diversity for widespread taxa. Here, we present a DNA barcoding study on a Xencyprididae subfamily (Culterinae) involving the production of 998 newly generated DNA barcodes from East Asian drainages (80 localities). Together with 513 barcodes mined from BOLD and GenBank, a reference library consisting of 1511 DNA barcodes (116 localities) for 42 species was assembled, accounting for 66% of known Culterinae species. Intraspecific genetic distances are positively correlated to geographical scale, while a negative correlation is detected between interspecific genetic distances and geographical scale. The present study demonstrates that geographical scale influences the efficiency of DNA barcoding by narrowing the width of the barcoding gap. DNA‐based species delimitation analyses delimited 44 molecular operational taxonomic units (MOTUs). Rampant cryptic diversity is detected within eight species with multiple MOTUs, whereas 25 species present mismatch between morphological and molecular delimitations. A total of 18 species are lumped into nine MOTUs due to low interspecific divergence and/or mixed lineages. Several MOTU divergences are hypothesized to relate to known biogeographical barriers and geological events during the Pliocene and Pleistocene. This study provides new insights into the taxonomy and phylogeography of the subfamily Culterinae.

Complete mitogenomes of four Trichiurus species: A taxonomic review of the T.lepturus species complex

Four Trichiurus species, T.japonicus, T.lepturus, T.nanhaiensis, and T.brevis, from the coasts of the China Seas, have been identified and their entire mitochondrial genomes (mitogenomes) have been sequenced by next-generation sequencing technology. A comparative analysis of five mitogenomes was conducted, including the mitogenome of T.gangeticus. The mitogenomes contained 16.568-16.840 bp and encoded 36 typical mitochondrial genes (13 protein-coding, 2 ribosomal RNA-coding, and 21 transfer RNA-coding genes) and two typical noncoding control regions. Although tRNAPro is absent from Trichiurus mitogenomes, when compared with the 22 tRNAs reported in other vertebrates, the gene arrangements in the mitogenomes of the studied species are consistent with those in most teleost mitogenomes. The full-length sequences and protein-coding genes (PCGs) in the mitogenomes of the five species had obvious AT biases and negative GC skew values. Our study indicate that the specimens in the Indian Ocean are neither T.lepturus nor T.nanhaiensis but they are T.gangeticus; the Trichiurus species composition in the Indian Ocean is totally different from that in Pacific and Atlantic oceans; there are at least two Trichiurus species in Indian Ocean; and the worldwide systematics and diversity of the genus Trichiurus need to be reviewed.

A new species of deep-sea grunt, Rhonciscus pauco (Lutjaniformes: Haemulidae), from Puerto Rico

A fourth species of the genus Rhonciscus (Lutjaniformes: Haemulidae) is described from various specimens collected by small-scale fishers from the insular upper slope of western Puerto Rico. The new species was molecularly recovered as sister to the Eastern Pacific R. branickii, to which it bears many morphological similarities. It is distinguished from other Rhonciscus species by the number of scale rows between the dorsal fin and the lateral line (7), larger and thus fewer scales along the lateral line (48-50), large eyes (9.4-10.4 times in SL), longer caudal peduncle (15.2-20% of SL), larger sized penultimate (14.7-19.1% in SL) and last (7.4-9.5% in SL) dorsal fin spines which translates to a less deeply notched dorsal fin, and its opalescent silver with golden specks live coloration. This grunt, only now recognized by ichthyologists, but well known by local fishers that target snappers and groupers between 200 and 500 m in depth, occurs in far deeper waters than any western Atlantic grunt.

Evaluation of fish diversity and abundance in the Kabul River with comparisons between reaches above and below Kabul City, Afghanistan

The fish fauna of the Kabul River downstream of the City of Kabul face threats from increasing human population such as pollution, overfishing, and increased development. Despite the rapid increase of these activities leading to threats to fishes in the Kabul River, no studies have examined the changes in diversity, distribution, and abundance of fish fauna in the Kabul River surrounding of Kabul City.  In this study, the Kabul River was divided into two zones (upstream and downstream) consisting of six sampling sites (3 sites per zone). Of the total of 1,190 fishes collected, Cypriniformes was the dominant order with one family, six genera, and eight species. Cyprinidae was the dominant family of that order with 81.4% (n= 969) of total individuals. Species abundance was higher in the upstream reaches in almost all analyses. Upstream sites recorded 11 species, while seven species were recorded from downstream sites. Fish species richness was significantly higher upstream versus downstream reaches (9.67 ± 1.53 vs.  6.33 ± .58; U= .00, z= -1.99, p= .04, r= .81). Species diversity upstream was significantly higher than downstream (H’= 1.90 ± 0.15, D1= 0.81 ± 0.02). Similarly, species evenness was also higher upstream than downstream (J’= 0.84 ± 0.01). Low diversity, abundance, and evenness in downstream reaches are likely due to anthropogenic activities affecting the river in and around Kabul City.

Molecular diversity of Uzbekistan's fishes assessed with DNA barcoding

Uzbekistan is one of two doubly landlocked countries in the world, where all rivers are endorheic basins. Although fish diversity is relatively poor in Uzbekistan, the fish fauna of the region has not yet been fully studied. The aim of this study was to establish a reliable barcoding reference database for fish in Uzbekistan. A total of 666 specimens, belonging to 59 species within 39 genera, 17 families, and 9 orders, were subjected to polymerase chain reaction amplification in the barcode region and sequenced. The length of the 666 barcodes was 682 bp. The average K2P distances within species, genera, and families were 0.22%, 6.33%, and 16.46%, respectively. The average interspecific distance was approximately 28.8 times higher than the mean intraspecific distance. The Barcode Index Number (BIN) discordance report showed that 666 specimens represented 55 BINs, of which five were singletons, 45 were taxonomically concordant, and five were taxonomically discordant. The barcode gap analysis demonstrated that 89.3% of the fish species examined could be discriminated by DNA barcoding. These results provide new insights into fish diversity in the inland waters of Uzbekistan and can provide a basis for the development of further studies on fish fauna.

Species diversity of freshwater shrimp in Henan Province, China, based on morphological characters and COI mitochondrial gene

Freshwater shrimp are a rich species group, with a long and problematic taxonomic history attributed to their wide distribution and similar morphological characteristics. Shrimp diversity and species identification are important cornerstones for fisheries management. However, identification based on morphological characteristics is a difficult task for a nonspecialist. Abundant freshwater shrimp species are distributed in the waters of Henan Province, but investigations of freshwater shrimp are limited in this region, especially concerning molecular features. Here, we combined morphology and DNA barcodes to reveal the species diversity of freshwater shrimp in Henan province. A total of 1,200 freshwater shrimp samples were collected from 46 sampling sites, and 222 samples were chosen for further microscopic examination and molecular delimitation. We used tree-based methods (NJ, ML, and bPTP) and distance-based methods (estimation of the paired genetic distances and ABGD) to delimit species. The results showed that there were nine morphospecies based on morphological characteristics; all could effectively be defined by molecular methods, among which bPTP and ABGD defined 13 and 8 MOTUs, respectively. The estimation of the paired genetic distances of K2P and the p-distances had similar results. Mean K2P distances and p-distances within species were both equal to 1.2%. The maximum intraspecific genetic distances of all species were less than 2%, with the exception of Palaemon modestus and M. maculatum. Various analyses have shown that P. modestus and M. maculatum have a large genetic differentiation, which may indicate the existence of cryptic species. By contrast, DNA barcoding could unambiguously discriminate 13 species and detect cryptic diversity. Our results demonstrate the high efficiency of DNA barcoding to delimit freshwater shrimp diversity and detect the presence of cryptic species.

DNA barcoding of coral reef fishes from Chuuk State, Micronesia

The fish diversity of Chuuk Micronesia is currently under threat due to rapid changes in the coral reef ecosystem. Thus, accurate fish identification using DNA barcodes is fundamental for exploring species biodiversity and resource protection. In this study, we analyzed 162 fish mitochondrial DNA cytochrome c oxidase I (COI) barcodes from Chuuk Micronesia. Consequently, we identified 95 species from 53 genera in 26 families and seven orders. The average Kimura 2-parameter genetic distances within species, genera, families, and orders were calculated as 0.17%, 11.78%, 15.63%, and 21.90%, respectively. Also, we have utilized DNA barcodes to perform genetic divergence and phylogenetic analysis of families recognized as dominant groups in Chuuk State. Our findings confirm that DNA barcodes using COI are an effective approach in identifying coral reef fish species. We anticipate that the results of this study will provide baseline data for the protection of coral reef fish biodiversity at Chuuk Micronesia.

Molecular Detection Mapping and Analysis Platform for R (MDMAPR) facilitating the standardization, analysis, visualization, and sharing of qPCR data and metadata

Quantitative polymerase chain reaction (qPCR) has been used as a standard molecular detection tool in many scientific fields. Unfortunately, there is no standard method for managing published qPCR data, and those currently used generally focus on only managing raw fluorescence data. However, associated with qPCR experiments are extensive sample and assay metadata, often under-examined and under-reported. Here, we present the Molecular Detection Mapping and Analysis Platform for R (MDMAPR), an open-source and fully scalable informatics tool for researchers to merge raw qPCR fluorescence data with associated metadata into a standard format, while geospatially visualizing the distribution of the data and relative intensity of the qPCR results. The advance of this approach is in the ability to use MDMAPR to store varied qPCR data. This includes pathogen and environmental qPCR species detection studies ideally suited to geographical visualization. However, it also goes beyond these and can be utilized with other qPCR data including gene expression studies, quantification studies used in identifying health dangers associated with food and water bacteria, and the identification of unknown samples. In addition, MDMAPR’s novel centralized management and geospatial visualization of qPCR data can further enable cross-discipline large-scale qPCR data standardization and accessibility to support research spanning multiple fields of science and qPCR applications.

DNA Barcoding and geographical scale effect: The problems of undersampling genetic diversity hotspots

DNA barcoding identification needs a good characterization of intraspecific genetic divergence to establish the limits between species. Yet, the number of barcodes per species is many times low and geographically restricted. A poor coverage of the species distribution range may hamper identification, especially when undersampled areas host genetically distinct lineages. If so, the genetic distance between some query sequences and reference barcodes may exceed the maximum intraspecific threshold for unequivocal species assignation. Taking a group of Quercus herbivores (moths) in Europe as model system, we found that the number of DNA barcodes from southern Europe is proportionally very low in the Barcoding of Life Data Systems. This geographical bias complicates the identification of southern query sequences, due to their high intraspecific genetic distance with respect to barcodes from higher latitudes. Pairwise intraspecific genetic divergence increased along with spatial distance, but was higher when at least one of the sampling sites was in southern Europe. Accordingly, GMYC (General Mixed Yule Coalescent) single-threshold model retrieved clusters constituted exclusively by Iberian haplotypes, some of which could correspond to cryptic species. The number of putative species retrieved was more reliable than that of multiple-threshold GMYC but very similar to results from ABGD and jMOTU. Our results support GMYC as a key resource for species delimitation within poorly inventoried biogeographic regions in Europe, where historical factors (e.g., glaciations) have promoted genetic diversity and singularity. Future European DNA barcoding initiatives should be preferentially performed along latitudinal gradients, with special focus on southern peninsulas.

DNA barcoding and phylogenetics of freshwater fish fauna of Ranganadi River, Arunachal Pradesh

Arunachal Pradesh, the largest state of North-East India covers almost 60.93% of the Eastern Himalayan hotspot. Fish diversity and species identification is utmost important for fisheries management. But, in some cases morphological characteristics based identification is difficult for a non-specialist to perform. In view of the above, the present study emphasized on the assessment of DNA barcoding, phylogenetics and genetic diversity of fish species in the Ranganadi River, Arunachal Pradesh, India. India. Arunachal Pradesh, the largest state of North-East India covers almost 60.93% of the Eastern Himalayan hotspot. Altogether 114 specimens, representing 22 species, belonging to 3 orders and 5 families were successfully barcoded and found to be 98-100% identical from both GenBank and BOLD databases. Out of these 22 fish species, it was found that one species assessed was Endangered, three species as Near Threatened and one species as Vulnerable. A Neighbour Joining (NJ) tree was constructed using Rstudio for the purpose of a phylogenetic analysis of the identified species. The barcoding gap analysis using K2P, P-distance and Jukes-Cantor was done to detect the presence of cryptic species and barcoding success. The nucleotide base composition and genetic distance analysis were also performed, using MEGA 6.0. DNA Sequence Polymorphism v6.12.03 analysis revealed the nucleotide diversity (p) and haplotype diversity (Hd). The Hd for the whole dataset was found to be 0.975, which showed high genetic diversity in the Ranganadi River. Both morphological key identifying characters and molecular data corroborated the phylogenetic analysis. This COI barcode library, generated in the present study, not only helped in species identification and molecular study, but also in cryptic species identification.

DNA barcoding for identification of fish species from freshwater in Enugu and Anambra States of Nigeria

Within Enugu and Anambra States, Nigeria, identification of fishes has been based on morphological traits and do not account for existing biodiversity. For DNA barcoding, assessment of biodiversity, conservation and fishery management, 44 fish sampled from Enugu and Anambra States were isolated, amplified and sequenced with mitochondrial cytochrome oxidase subunit I (COI). Twenty groups clustering at 100% bootstrap value including monophyletic ones were identified. The phylogenetic diversity (PD) ranged from 0.0397 (Synodontis obesus) to 0.2147 (Parachanna obscura). The highest percentage of genetic distance based on Kimura 2-parameter was 37.00 ± 0.0400. Intergeneric distances ranged from 15.8000 to 37.0000%. Congeneric distances were 6.9000 ± 0.0140–28.1000 ± 0.0380, with Synodontis as the existing synonymous genus. Confamilial distances in percentage were 16.0000 ± 0.0140 and 25.7000 ± 0.0300. Forty-two haplotypes and haplotype diversity of 0.9990 ± 0.0003 were detected. Nucleotide diversity was 0.7372, while Fu and Li’s D* test statistic was 2.1743 (P < 0.02). Tajima’s D was 0.2424 (P > 0.10) and nucleotide frequencies were C (17.70%), T (29.40%), A (24.82%), G (18.04%) and A + T (54.22%). Transitional mutations were more than transversions. Twenty species (99–100%) were identified with the e-value, maximum coverage and bit-score of 1e−43, 99–100 and 185–1194, respectively. Seventeen genera and 12 families were found and Clariidae (n = 14) was the most dominant among other families. The fish species resolution, diversity assessment and phylogenetic relationships were successfully obtained with the COI marker. Clariidae had the highest number of genera and families. Phylogenetic diversity analysis identified Parachanna obscura as the most evolutionarily divergent one. This study will contribute to fishery management, and conservation of freshwater fishes in Enugu and Anambra States, Nigeria.

Population genetics and sympatric divergence of the freshwater gudgeon, Gobiobotia filifer, in the Yangtze River inferred from mitochondrial DNA

The ecosystem and Pleistocene glaciations play important roles in population demography. The freshwater gudgeon, Gobiobotia filifer, is an endemic benthic fish in the Yangtze River and is a good model for ecological and evolutionary studies. This study aimed to decode the population structure of G. filifer in the Yangtze River and reveal whether divergence occurred before or after population radiation. A total of 292 specimens from eight locations in the upper and middle reaches of the Yangtze River were collected from 2014 to 2016 and analyzed via mitochondrial DNA Cyt b gene sequencing. A moderately high level of genetic diversity was found without structures among the population. However, phylogenetic and network topology showed two distinct haplotype groups, and each group contained a similar proportion of individuals from all sampled sites. This suggested the existence of two genetically divergent source populations in G. filifer. We deduced that a secondary contact of distinct glacial refugia was the main factor creating sympatric populations of G. filifer, and climate improvement promoted population expansion and colonization.

DNA barcoding of marine fishes from Saudi Arabian waters of the Gulf

We used the cytochrome oxidase subunit I (coI) gene DNA to barcode 117 endemic Gulf and cosmopolitan Indo-West Pacific fish species belonging to 54 families and 13 orders. Novel DNA barcodes were provided for 18 fish species (Trachinocephalus sp., Nematalosa sp., Herklotsichthys lossei, Upeneus doriae, Trachurus indicus, Apogonichthyoides taeniatus, Verulux cypselurus, Favonigobius sp., Suezichthus gracilis, Sillago sp., Brachirus orientalis, Pegusa sp., Lepidotrigla bispinosa, Lepidotrigla sp., Grammoplites suppositus, Hippichthys sp., Paramonacanthus sp. and Triacanthus sp.). The species delimitation analysis, conducted with Poisson tree processes- Bayesian PTP (PTP-bPTP) and nucleotide-divergence-threshold (NDT) models), found 137 and 119 entities respectively. Overall, NDT method, neighbour-joining species tree and the prior taxonomic assessment provided similar results. Among the 54 families considered, only 10 (Ariommatidae, Ephippidae, Leiognathidae, Nemipteridae, Plotosidae, Pomacanthidae, Pomacentridae, Priacanthidae and Rachycentridae) showed the occurrence of molecular diagnostic pure characters. The DNA barcoding database developed during this study will help ichthyologists to identify and resolve the taxonomic ambiguities they may encounter with the fishes occurring in The Gulf and throughout the region.

DNA Barcoding Reveals High Levels of Divergence among Mitochondrial Lineages of Brycon (Characiformes, Bryconidae)

Brycon is an important group of Neotropical fish and the principal genus of the family Bryconidae, with 44 valid species that are found in some Central American rivers and practically all the major hydrographic basins of South America. These fish are medium to large in size, migratory, omnivorous, important seed dispersers for riparian forests, and bioindicators of environmental quality, given that they are found preferentially in rivers with clean, well oxygenated water. Many Brycon species are important fishery resources and some are farmed. Morphological and molecular studies have nevertheless indicated that the group is not monophyletic and has a number of unresolved taxonomic problems. Given this, the present study aimed to identify the Molecular Operational Taxonomic Units (MOTUs) of the genus using the mitochondrial cytochrome c oxidase I (COI) gene, with analyses of genetics distance (NJ), maximum likelihood (ML), and Bayesian Inference (BI), combined with two different species delimitation approaches (GMYC and ABGD). The results indicate that at least 31 MOTUs exist within the 18 species identified a priori based on their morphology. Many of these lineages require further investigation for a more definitive classification.

Comprehensive analysis of population genetics of Phoxinus phoxinus ujmonensis in the Irtysh River: Abiotic and biotic factors

As a widely distributed species along the Irtysh River, Phoxinus phoxinus ujmonensis (Kaschtschenko, 1899) was used as a model to investigate genetic diversity and population structure as well as the influence of environmental factors on population genetics. In this study, we specifically developed 12 polymorphic microsatellite loci. The analysis of microsatellite and mtDNA markers revealed a high and a moderate genetic diversity across seven populations, respectively. Moderate differentiation was also detected among several populations, indicating the impact of habitat fragmentation and divergence. The absence of isolation by distance implied an extensive gene flow, while the presence of isolation by adaptation implied that these populations might be in the process of adapting to divergent habitats. Correlation analysis showed that abiotic factors like dissolved oxygen, pH, total dissolved solids, and conductivity in water as well as biotic factors like plankton diversity and fish species diversity had impact on genetic diversity and divergence in P. phoxinus ujmonensis populations. The results of this study will provide an insight into the effect of environmental factors on genetic diversity and contribute to the study of population genetics of sympatric species.

Influence of pairwise genetic distance computation and reference sample size on the reliability of species identification using Cyt b and COI gene fragments in a group of native passerines

Species identification is fundamental to wildlife forensic practice. The desirability of molecular genetic methods is increasing rapidly. The sequence of a marker, rather than its particular diagnostic nucleotides, provides greater safety through comparisons between intra- and inter-specific pairwise genetic distances. However, it has not been well described how reliability of species assignment is influenced by distance computing methods and reference sample sizes. In this study, the influences were tested using 12 species from 4 genera of passerine birds and the sequences of partial Cytochrome b (Cyt b) and Cytochrome Oxidase subunit I (COI) genes. Results showed that different substitution types have different outcomes of pairwise genetic distance estimation and this influences the risk of false inclusion and exclusion. Transition (Ts) is the most effective substitution type to reveal optimal species resolution for both Cyt b and COI gene fragments no matter whether K2P and p-distance are used. Sample size required to accurately estimate pairwise distance is essentially determined by the genetic diversity of a species in reference to a given strictness of predefined acceptable accuracy. These findings suggest that for future forensic work on birds by use of Cyt b and COI gene fragments, transition should be used exclusively for marker validation and identification practice when targeting closely related species. Meanwhile, the reference database should sufficiently represent overall genetic diversity of the species. The minimum sample size should be estimated based on existing knowledge of genetic diversity. Special caution should be used for species assignment when only several reference data are available for animals that are considered likely to have high genetic diversity.

Species diversity of drifting fish eggs in the Yangtze River using molecular identification

The dam constructions greatly changed the hydrologic conditions in the Yangtze River, and then significantly affected the spawning activities of indigenous river fish. Monitoring the species composition of drifting eggs during spawning season is important for protection issues. In this study, we have sampled drifting fish eggs in nine locations from 2014 to 2016. Eggs were identified using the mitochondrial cyt b gene sequence. A total of 7,933 fish eggs were sequenced successfully and blasted into the NCBI database. Thirty-nine fish species were identified, and were assigned to four families and two orders. Approximately 64% of the species identified, and 67% of the eggs, were classified in the Family Cyprinidae. Abundance and Shannon–Wiener diversity index of species were higher in the main river than in tributaries of the river. However, tributaries may be important spawning grounds for some fish species. The Jaccard’s similarity index and river-way distances among sampled stations were negatively correlated suggesting the environment shapes species composition in the sampled spawning grounds. These results showed that mitochondrial DNA sequence is a powerful and effective tool for fish egg identification in Yangtze River and these data are useful for conservation efforts.

Molecular characterization of small indigenous fish species (SIS) of Bangladesh through DNA barcodes

The mitochondrial DNA gene cytochrome oxidase subunit I (COI) has been adopted as a global bioidentification system for animals. This study represents the comprehensive molecular identification of small indigenous fish species (SIS) of Bangladesh assessed by DNA barcoding. DNA barcodes were generated from 81 SIS species belongs to the orders Clupeiformes, Cypriniforms, Siluriformes, Perciformes, Synbranchiformes, Beloniformes and Tetraodontiformes representing 55 genera and 24 families. For all the samples, %G were significantly lowered compared to other nucleotides and %GC compared to %AT. Also, a significantly lowered GC content was observed in second and third codon position compared to the first codon position in all samples. The average Kimura two-parameter (K2P) distances within genera, families, and orders were 15.83%, 19.14%, and 25.07%, respectively. The minimum and maximum K2P distance based genetic divergences were 0.19% and 57.14% respectively. Members of Cypriniformes, Siluriformes, and Perciformes were clustered separately in the neighbour-joining (NJ) tree. Nucleotide composition, GC distribution across codon positions, K2P distance, genetic divergence, and phylogenetic analyses reveal that these freshwater SIS fishes are genetically very diverse. Along with morphological data, we have confirmed the existence of seven new records of SIS fishes in Bangladesh using such barcode approach. These findings suggest that fishes can be discriminated using these barcode data without any confusion.

DNA barcoding of economically important freshwater fish species from north-central Nigeria uncovers cryptic diversity

This study examines the utility of morphology and DNA barcoding in species identification of freshwater fishes from north-central Nigeria. We compared molecular data (mitochondrial cytochrome c oxidase subunit I (COI) sequences) of 136 de novo samples from 53 morphologically identified species alongside others in GenBank and BOLD databases. Using DNA sequence similarity-based (≥97% cutoff) identification technique, 50 (94.30%) and 24 (45.30%) species were identified to species level using GenBank and BOLD databases, respectively. Furthermore, we identified cases of taxonomic problems in 26 (49.00%) morphologically identified species. There were also four (7.10%) cases of mismatch in DNA barcoding in which our query sequence in GenBank and BOLD showed a sequence match with different species names. Using DNA barcode reference data, we also identified four unknown fish samples collected from fishermen to species level. Our Neighbor-joining (NJ) tree analysis recovers several intraspecific species clusters with strong bootstrap support (≥95%). Analysis uncovers two well-supported lineages within Schilbe intermedius. The Bayesian phylogenetic analyses of Nigerian S. intermedius with others from GenBank recover four lineages. Evidence of genetic structuring is consistent with geographic regions of sub-Saharan Africa. Thus, cryptic lineage diversity may illustrate species' adaptive responses to local environmental conditions. Finally, our study underscores the importance of incorporating morphology and DNA barcoding in species identification. Although developing a complete DNA barcode reference library for Nigerian ichthyofauna will facilitate species identification and diversity studies, taxonomic revisions of DNA sequences submitted in databases alongside voucher specimens are necessary for a reliable taxonomic and diversity inventory.

DNA barcoding for identification of fish species in the Taiwan Strait

DNA barcoding based on a fragment of the cytochrome c oxidase subunit I (COI) gene in the mitochondrial genome is widely applied in species identification and biodiversity studies. The aim of this study was to establish a comprehensive barcoding reference database of fishes in the Taiwan Strait and evaluate the applicability of using the COI gene for the identification of fish at the species level. A total of 284 mitochondrial COI barcode sequences were obtained from 85 genera, 38 families and 12 orders of fishes. The mean length of the sequences was 655 base pairs. The average Kimura two parameter (K2P) distances within species, genera, families, orders and classes were 0.21%, 6.50%, 23.70% and 25.60%, respectively. The mean interspecific distance was 31-fold higher than the mean intraspecific distance. The K2P neighbor-joining trees based on the sequence generally clustered species in accordance with their taxonomic classifications. High efficiency of species identification was demonstrated in the present study by DNA barcoding, and we conclude that COI sequencing can be used to identify fish species.