K2P Model Research Articles

Global Terrapin Character-Based DNA Barcodes: Assessment of the Mitochondrial COI Gene and Conservation Status Revealed a Putative Cryptic Species.

Technological and analytical advances to study evolutionary biology, ecology, and conservation of the Southern River Terrapin (Batagur affinis ssp.) are realised through molecular approaches, including DNA barcoding. We evaluated the use of COI DNA barcodes in Malaysia's Southern River Terrapin population to better understand the species' genetic divergence and other genetic characteristics. We evaluated 26 sequences, including four from field specimens of Southern River Terrapins obtained in Bota Kanan, Perak, Malaysia, and Kuala Berang, Terengganu, Malaysia, as well as 22 sequences from global terrapins previously included in the Barcode of Life Database (BOLD) Systems and GenBank. The species are divided into three families: eight Geoemydidae species (18%), three Emydidae species (6%), and one Pelomedusidae species (2%). The IUCN Red List assigned the 12 species of terrapins sampled for this study to the classifications of critically endangered (CR) for 25% of the samples and endangered (EN) for 8% of the samples. With new haplotypes from the world's terrapins, 16 haplotypes were found. The intraspecific distance values between the COI gene sequences were calculated using the K2P model, which indicated a potential cryptic species between the Northern River Terrapin (Batagur baska) and Southern River Terrapin (Batagur affinis affinis). The Bayesian analysis of the phylogenetic tree also showed both species in the same lineage. The BLASTn search resulted in 100% of the same species of B. affinis as B. baska. The Jalview alignment visualised almost identical sequences between both species. The Southern River Terrapin (B. affinis affinis) from the west coast of Peninsular Malaysia was found to share the same haplotype (Hap_1) as the Northern River Terrapin from India. However, B. affinis edwardmolli from the east coast of Peninsular Malaysia formed Hap_16. The COI analysis found new haplotypes and showed that DNA barcodes are an excellent way to measure the diversity of a population.

Phylogenetic Analysis of the Economically Important Hymenopterans using cytochrome oxidase 1 Enzyme Sequences

Hymenoptera is the fourth diverse and the most economically important insect order comprising of bees, wasps, ants, sawflies etc. Being an important part of ecosystem, their conservation is of utmost importance. The first step towards conservation strategies is the identification of the species. The traditional morphological approach can sometimes lead to misidentification due to a lack of expertise. DNA barcoding using the small genomic fragments has been identified as an efficient tool in the identification as well as the phylogenetic analysis of the species. In the present study, we used the COI gene sequences as a tool for the characterization of Hymenoptera from different parts of the Jammu region. The collected samples were proceeded for the isolation of DNA, PCR for amplification of the COI gene, and then sequenced by Sanger dideoxy method. A total of 22 COI sequences belonging to 18 different species were successfully generated. Among which eight species sequences (Tachytes sp., Bombus trifasciatus, Rhynchium carnaticum, Ropalidia brevita, Lasioglossum marginatum, Camponotus pennsylvanicus, Tapinoma melanocephalum, Formica rufibarbis) are the novel contribution in the global database. NJ tree using the K2P model with 1000 bootstrap supporting values has been used to study the phylogeny of the species. Sequence analysis shows high AT content (67-77%) in the COI region of Hymenopterans. The generated COI sequence analysis also revealed less than 1% intra-specific divergence in the examined taxa, while the interspecific distances ranged between 8% to 38%. This study added significantly to the databases of DNA barcodes of Hymenopterans species from Jammu region.

Genetic identification and phylogenetic relationships of fish species at Panjnad , Abbasia and Abu Dahbi canals (Punjab, Pakistan) based on mitochondrial COI sequences

Fish is an extremely nutritious food that is abundant in important minerals, vitamin D, protein, and omega-3 fatty acids. Now a day, mislabeling of fish products is a major problem in the fish industry that affects the market prices and causes fluctuations. Phylogenetic analysis of nucleotide sequences is a technique that might be used to verify the identity of misidentified fish species. In this study five species (Cirrhinus mrigala, Hypophthalmichthys molitrix, two Actinopterygii sp., and Mastacembelus armatus) were used for phylogenetic analysis using the COI gene was amplified using the PCR, average product size is 658 base pairs. A comparison of obtained sequences was implemented through National Center for Biotechnology Information database (NCBI) and the Basic Local Alignment Search Tool (BLAST). Most resemble sequences were downloaded for comparison with our sequencing results. By using MAGA X the rates of different transitional substitutions are 11.33 and transversional substitutions are 6.83. The estimated Transition/Transversion bias (R) is 0.83. The K2P model was used for the estimation of this substitution pattern. Because most freshwater fish species were in the same order or family, phylogenetic tree analysis indicated that they grouped together. Using the InterPro database, the activity and regulatory pathways of the Cytochrome C Oxidase 1 gene are identified to show their activity on the protein level, especially for some important physiological functions. Each species of fish could be identified based on their speciation and node position and distance from their parent nodes. Based on the closest phylogenetic relations, DNA sequence-based study was developed for the accurate identification of fish species.

DNA barcoding and delimitation of critically endangered indigenous and introduced tilapias (pisces cichlidae) of Pangani catchment, Northern Tanzania

The Pangani catchment of Northern Tanzania harbours the critically endangered endemic tilapias of the genus Oreochromis. The introduction of non-native congenerics and consequent hybridization complicates taxa identification and phylogeny based on morphological systematics. We therefore morphologically and molecularly identified these tilapias and delimited their Molecular Operational Taxonomic Units (MOTUs) based on Cytochrome Oxidase Subunit I (CO1) gene for future management and conservation. A total of 132 indigenous and introduced tilapia specimens were morphologically identified, barcoded using the CO1 gene and delimited by Kimura 2 Parameter distance approaches, Automatic Barcode Gap Discovery (ABGD), Neighbour Joining (NJ) tree and haplotype analysis. Theoverall mean conspecific, congeneric and confamillial genetic distances based on the K2P model were 0.54%, 5.32% and 13.29% respectively. All taxa had a mean K2P distance < 2% and 90% (n = 10), were clearly delimited by the ABGD method. The NJ tree delimited tilapia taxa commensurate to the genetic distances depicted by DNA barcoding. However, DNA barcoding and NJ tree coherently failed to discriminate the morphologically distinct allopatric Oreochromis jipe and Oreochromis hunteri taxa. Moreover, the two methods depicted lack of monophyly in Oreochromis korogwe MOTUs implying that the taxon could consist of at least one MOTU. We conclude that the integration of morphological-based taxonomy and DNA barcoding among ichthyofaunal taxa herein will be invaluable in conservation and management of native tilapias in Pangani basin.

Detection of SNPs in Merremia and its related taxa for species identification using DNA barcode markers

Merremiae is one of the least defined tribes in the family Convolvulaceae. It contains number of species which are basically herbs and shrubs. Species identification is a tedious work in the tribe using morphological characters as these traits are often influenced by environmental factors. In the present piece of work, we have analysed five taxa (Merremia umbellata, Merremia vitifolia, Merremia tridentata (Pubescens) and Merremia tridentata (Alatipes) along with one species of Ipomoea - Ipomoea calycina) with help of DNA barcode marker. We have used seven DNA barcoding regions from organellar DNA. Clear and reproducible amplifications were obtained in most of the cases but we failed to observe remarkable variation in amplified fragment size. Variations were detected in the DNA sequence associated with matK and rbcL loci. Sequence analysis showed visible difference between the intra and inter specific genetic distance based on K2P model for both the loci. From the sequenced data we found unique SNPs and In/Dels for the different taxa included in the study. Based upon the matK and rbcL SNP variance table, two dendrograms were constructed and authentication of species of Merremia and its relative were carried out. This work will help in authentic identification of the different taxa in the tribe Merremiae.

Verification of Thai ethnobotanical medicine "Kamlang Suea Khrong" driven by multiplex PCR and powerful TLC techniques.

Kamlang Suea Khrong (KSK) crude drug, a traditional Thai medicine used for oral tonic and analgesic purposes, is obtained from three origins: the inner stem bark of Betula alnoides (BA) or the stems of Strychnos axillaris (SA) or Ziziphus attopensis (ZA). According to the previous reports, SA contains strychnine-type alkaloids that probably cause poisoning; however, only organoleptic approaches are insufficient to differentiate SA from the other plant materials. To ensure the botanical origin of KSK crude drug, powerful and reliable tools are desperately needed. Therefore, molecular and chemical identification methods, DNA barcoding and thin-layer chromatography (TLC), were investigated. Reference databases, i.e., the ITS region and phytochemical profile of the authentic plant species, were conducted. In case of molecular analysis, multiplex polymerase chain reaction (PCR) based on species-specific primers was applied. Regarding species-specific primers designation, the suitability of three candidate barcode regions (ITS, ITS1, and ITS2) was evaluated by genetic distance using K2P model. ITS2 presented the highest interspecific variability was verified its discrimination power by tree topology. Accordingly, ITS2 was used to create primers that successfully specified plant species of authentic samples. For chemical analysis, TLC with toluene:ethyl acetate:ammonia (1:9:0.025) and hierarchical clustering were operated to identify the authentic crude drugs. The developed multiplex PCR and TLC methods were then applied to identify five commercial KSK crude drugs (CK1-CK5). Both methods correspondingly indicated that CK1-CK2 and CK3-CK5 were originated from BA and ZA, respectively. Molecular and chemical approaches are convenient and effective identification methods that can be performed for the routine quality-control of the KSK crude drugs for consumer reliance. According to chemical analysis, the results indicated BA, SA, and ZA have distinct chemical profiles, leading to differences in pharmacological activities. Consequently, further scientific investigations are required to ensure the quality and safety of Thai ethnobotanical medicine known as KSK.

Application of COI Primers 30F/885R in Rotifers to Regional Species Diversity in (Sub)Tropical China

Rotifers are the most diverse group in freshwater zooplankton and play an important role in food webs and ecosystems. DNA barcoding has become a useful approach to investigate species diversity at local and regional scales, but its application is still limited by efficient primers for the group. To test a pair of primers 30F/885R recently designed for rotifers, we applied them to investigating regional species diversity in the freshwater of South China. We sequenced the cytochrome c oxidase subunit I (COI) gene of rotifers collected from the investigated 23 reservoirs in a large river basin and obtained 145 COI sequences from 33 species in 14 genera. The mean PCR success rate for all tested species was 50%. The 145 sequenced mtCOI in this study covered 33 of 64 identified morphological taxa, including most of the common species in the basin. The intraspecific genetic distance was calculated with a K2P model for 24 rotifer species occurring in the quantitative samples, in which 15 rotifers, such as Keratella cochlearis and Brachionus calyciflorus, had a genetic distance higher than 5%. The high intraspecific genetic differentiation indicates that cryptic species are probably common in (sub)tropical China.

Description of a new perchlet, Chelidoperca formosa, from southwestern Taiwan (Peciformes: Serranidae).

A new perchlet species is described on the basis of four specimens collected from southwestern Taiwan. It is similar to congeners with relatively few lateral-line scales (35-38) and can be distinguished by having third to sixth dorsal-fin spines notably long; eighth and ninth dorsal-fin spines notably short; developed gill rakers 1 + 7-8; scale rows between lateral line and sixth dorsal-fin spine 4 (the dorsalmost half-sized); tip of upper corner of caudal fin reddish; four reddish bands midlaterally on body with groups of melanophores in these bands. DNA barcoding analysis reveals the new species is a distinct lineage and closest to Chelidoperca microdon. The average interspecific genetic distance calculated by the K2P model is 15.4%, whereas the mean distance from the new species to C. microdon is 18.3%. The inferred phylogenetic tree supports monophyly of Chelidoperca. Including the new species, six nominal species of Chelidoperca are recognized in Taiwanese waters.

An Extension of the Kimura Two-Parameter Model to the Natural Evolutionary Process

Accurate estimates of genetic difference are required for research in evolutionary biology. Here we extend the Kimura two-parameter (K2P) model by considering gaps (insertions and/or deletions) and introduce a new measure for estimating genetic difference between two nucleotide sequences in terms of nucleotide changes that have occurred during the evolutionary process. Using the nuclear ribosomal DNA internal transcribed spacer 2 region from the genus Physalis, we demonstrate that species identification and phylogenetic studies strongly depend on evolutionary models. It is especially noteworthy that the use of different models affects the degree of overlap between intraspecific and interspecific genetic differences. We observe that the percentage of interspecific sequence pairs with values less than the maximum intraspecific genetic difference is 43.2% for the K2P model which is calculated by removing gap sites across all sequences, 22.7% for the K2P model which is calculated by removing gap sites for sequence pairs, and 16.9% for our model which is calculated without removing gap sites. Additionally, the numbers of sequence pairs with interspecific genetic differences of zero are 50 for the K2P model and 29 for our model. The genetic difference measure based on the K2P model, compared to our model, overestimates 21 sequence pairs that are not originally identical. These results indicate the importance of estimating genetic differences under the model of sequence evolution that includes insertions and deletions in addition to substitutions.

Identification and quality evaluation of Tripterygium wilfordii

With the extensive clinical application of Tripterygium wilfordii, there are many counterfeit products on the market. Traditional technology can not effectively identify the authenticity of the traditional Chinese medicine. Therefore, a strategy of accurate identification and quality evaluation of Tripterygium based on DNA barcode and chemical fingerprint spectrum was established. Based on DNA barcode technology, HMMer annotation method of hidden Markov model and K2P model were used to analyze genetic distance.BLAST1, nearest distance and phylogenetic tree (NJ-tree) methods were used to assess the identification efficiency of the ITS2 barcode. The fingerprint of 27 T. wilfordii was established by UPLC-PDA method, and the similarity of the fingerprint of different sources was evaluated. The main components of T. wilfordii were determined by LC-MS/MS. The results revealed that the intraspecific genetic distances of T. wilfordii were lower than the interspecific genetic distances between T. wilfordii and its adulterants. The results of similarity search showed that ITS2 sequence was used to identify T. wilfordii and its adulterants. The clustering of T. wilfordii and its adulterants was clear in the tree of NJ cluster, and 12 of 27 samples were identified as true T. wilfordii.The chemical fingerprint spectrum research indicates that the feature one region can distinguish the false product of tripterygium glycosides more intuitively. The cluster analysis of HCA-thermal map showed that the contents of six active components of T. wilfordii from different habitats were significantly different, which could be used to evaluate the quality of T. wilfordii. This paper is of guiding significance for the accurate identification and quality evaluation of Tripterygium medicinal plants.

First Record of African Angel Shark, Squatina africana (Chondricthyes: Squatinidae) in Indian Waters, Confirmed by DNA Barcoding

A single specimen of African angel shark, Squatina africana (Regan, 1908) was caught off Lakshadweep (11°5′47″ N; 72°2′21″ E), India in September 2016. The present study is a new report of the above species from Indian waters. In addition to classical methodologies, DNA barcoding was also adopted for species identification. The 650 bp-long region of mitochondrial Cytochrome Oxidase subunit I was sequenced to obtain the DNA barcode for the species under study. The sequence divergence value within species and between species was calculated using MEGA V.7.0, where Kimura 2 parameter (k2p) model was chosen as a distance model. The average k2p distance separating individuals within species was 1.76% and inter specific divergence was 8–10%. A neighbour joining network was constructed to provide a graphical representation of divergence between the species. Using the maximum identity with Gen Bank database, K2P divergence distance, NJ-network and traditional morphological approach, we could identify the given specimen as a mature male African angel shark.

ITS2 para la identificación de Califóridos (Diptera: Calliphoridae) de importancia forense en Colombia

La entomología forense es una disciplina que utiliza insectos para obtener información útil en la determinación del intervalo postmortem (IPM). Las moscas de la familia Calliphoridae son muy utilizadas en entomología forense, sin embargo, su identificación a nivel de especie puede dificultarse cuando el individuo se encuentra incompleto o en estadio inmaduro. En el presente trabajo, se evaluó el potencial de la región ITS2 del genoma nuclear para la identificación de especies de Calliphoridae en Colombia utilizando tres aproximaciones: comparando distancias genéticas utilizando la metodología de códigos de barra, haciendo una reconstrucción filogenética, y con enzimas de restricción (PCR-RFLPs). Se secuenciaron un total de 520 pb en 44 individuos pertenecientes a 16 especies. Se calcularon los valores de distancia intraespecífica e interespecíficas utilizando el modelo K2P. Los valores de distancia intraespecífica oscilaron entre 0 y 0,252 %, mientras que las distancias interespecíficas fluctuaron entre 3,6 y 18,9 %, evidenciándose que esta técnica puede ser utilizada como código de barras genético en la identificación de especies de la familia Calliphoridae. Tanto en los análisis de Neighbour-Joining como en los análisis bayesianos el 90 % de los géneros presentan una monofilia sustentada en probabilidad posterior de 0,89 a 1. En todos los casos la especie Blepharicnema splendens agrupa con el género Lucilia. Con base en las secuencias obtenidas se utilizó la aplicación NEBCutter para identificar cuatro enzimas de restricción las cuales se probaron en el laboratorio y se comprobó su utilidad para la identificación rápida de especies de Calliphoridae en Colombia.

Identification of commercial Ganoderma (Lingzhi) species by ITS2 sequences.

BackgroundDNA barcoding can be used to authenticate Ganoderma species for safe use. This study aims to identify commercial products containing Ganoderma using DNA barcoding.MethodsWe used 63 internal transcribed spacer (ITS) 2 sequences of Ganoderma species from 33 newly-sequenced wild samples, crude drugs, mycelia, spores, and authentic extracts and spore oils collected from various locations and markets, as well as 30 sequences from GenBank. Sequences were assembled and aligned using CodonCode Aligner V3.71. Intra- and inter-specific distances were estimated by MEGA 6.0, and phylogeny reconstruction was based on the K2P model. SNP(s) and RNA secondary structure of ITS2 were analyzed and compared among closely related Ganoderma species.ResultsG. lucidum cultivated in China was different from those cultivated in Europe. “Chizhi” (G. lucidum) and “Zizhi” (G. sinense) were clustered into two clades that were separated from the other Ganoderma species. The fruiting bodies and commercial products of G. lucidum and G. sinense were successfully distinguished from those of other Ganoderma species by comparing the ITS2 sequences and RNA secondary structures.ConclusionThe DNA barcoding method is applicable to the authentication of commercial products containing Ganoderma species.

DNA barcoding of marine ornamental fishes from India

India has rich marine ornamental fish diversity with 400 fish species distributed in Gulf of Munnar/Palk Bay, Gulf of Kutch, and in reefs around Andaman & Nicobar and Lakshadweep Islands. Marine ornamental fish identification at the field level is very difficult because of their high diversity and profound changes in appearance during their developmental stages and camouflage. To facilitate ornamental fish trading with ease and in compliance with the biodiversity act, DNA barcoding technique could be used to accurately identify species. In this study, DNA barcodes were generated for 31 species of commercially important marine ornamental fishes from India. The average genetic distance (K2P model) within species, genus, and family was 0.446, 13.08, and 20.09%, respectively. Intraspecific variation has increased several folds (15–20 times) after including conspecific sequences from different geographical locations. The presence of allopatric lineages/cryptic species was observed in the Indo-pacific region. The NJ tree constructed based on K2P values showed distinct clusters shared by congeneric species specific to populations.

Barcoding Neotropical birds: assessing the impact of nonmonophyly in a highly diverse group.

In this study, we verified the power of DNA barcodes to discriminate Neotropical birds using Bayesian tree reconstructions of a total of 7404 COI sequences from 1521 species, including 55 Brazilian species with no previous barcode data. We found that 10.4% of species were nonmonophyletic, most likely due to inaccurate taxonomy, incomplete lineage sorting or hybridization. At least 0.5% of the sequences (2.5% of the sampled species) retrieved from GenBank were associated with database errors (poor-quality sequences, NuMTs, misidentification or unnoticed hybridization). Paraphyletic species (5.8% of the total) can be related to rapid speciation events leading to nonreciprocal monophyly between recently diverged sister species, or to absence of synapomorphies in the small COI region analysed. We also performed two series of genetic distance calculations under the K2P model for intraspecific and interspecific comparisons: the first included all COI sequences, and the second included only monophyletic taxa observed in the Bayesian trees. As expected, the mean and median pairwise distances were smaller for intraspecific than for interspecific comparisons. However, there was no precise 'barcode gap', which was shown to be larger in the monophyletic taxon data set than for the data from all species, as expected. Our results indicated that although database errors may explain some of the difficulties in the species discrimination of Neotropical birds, distance-based barcode assignment may also be compromised because of the high diversity of bird species and more complex speciation events in the Neotropics.

Mitochondrial (COI) and nuclear (EF-1α) DNA variability of Rhopalosiphum padi and Rhopalosiphum nymphaeae (Hemiptera: Aphididae) in Lithuania

Partial sequences of mitochondrial COI and nuclear EF-1α genes have been analysed across the Lithuanian samples of Rhopalosiphum padi and R. nymphaeae (Hemiptera: Aphididae). In addition, samples from the adjacent countries of the Eastern Baltic region of Europe (Latvia, Estonia and Poland) and available sequences from GenBank and Bold Systems were used. The range of intraspecific pairwise R. padi COI sample (n = 44) divergences (K2P model) was 0.00–2.49% (average 0.61%). Out of 10 haplotypes, one was predominant (n = 25), with Worldwide distribution. The range of intraspecific pairwise R. nymphaeae COI sample (n = 20) divergences (K2P model) was 0.00–1.31% (average 0.22%). Out of 6 haplotypes, one was predominant (n = 13), sampled in Lithuania, Ukraine and Turkey (Asian part). The range of intraspecific pairwise sample divergences (K2P model) of EF-1α fragment was 0.00–0.40% (average 0.10%) for R. padi (n = 20) and 0.00–0.60% (average 0.13%) for R. nymphaeae (n = 17). Two COI haplotypes (including the Worldwide distributed one) and three EF-1α haplotypes (including the most common one) were detected in Lithuanian populations of R. padi. The present study suggests that R. padi populations from the Eastern Baltic region are predominantly holocyclic.

Molecular identification of Calliphoridae (Diptera: Calliphoridae) of forensic importance in Colombia

Recognizing the importance of the correct identification of insects associated with deceased bodies for an effective estimation of time of death, and taking into account the incidence of flies of the family Calliphoridae in corpses and the difficulty of their taxonomic determination, we evaluated the usefulness of COI mitochondrial gene sequences as a molecular diagnostic tool for identifying forensically important calliphorids in Colombia. Sequences obtained from samples collected in different regions of Colombia and other sequences taken from Genbank were used. Based on the genetic distances calculated using the K2P model, nucleotide divergence and neighbour-joining analyses were performed. Bayesian analyses were also developed and a graphical representation of the variation of the COI fragments for each species. A total 545 pb fragments were obtained; the values of intraspecific distance when all sequenced were included, ranged between 0% and 2.904% and the interspecific distance ranged between 0.188% and 18.07%, with an overlapping distance, caused mostly by the inclusion of species with only one sequence. When we excluded species with a single sequence and L. eximia was analyzed as two subgroups, a distance gap of 2.292% was obtained, which is an optimal value for the validation of this technique. Reciprocal monophyly was observed in most species. We conclude that the COI gene is a good marker for delineating species of the family Calliphoridae in Colombia.

Species delimitation in Cladonia (Ascomycota): a challenge to the DNA barcoding philosophy

The lichen-forming fungal genus Cladonia is species-rich with approximately 500 described species. The accepted barcode for fungi (ITS rDNA) often fails in identifying Cladonia spp. In order to find other markers that, in combination with the ITS rDNA region can be used for species identification in Cladonia, we studied the loci IGS rDNA, ef1α, rpb2 and cox1. A total of 782 sequences from 36 species have been analyzed. PCR amplification success rate, intraspecific and interspecific genetic distance variation, calculated using the K2P model, and the correct identification percentage (PCI) were taken into account to assess possible barcode regions. The marker showing the least intraspecific genetic distance range was cox1, followed by ITS rDNA and ef1α. Of the five studied markers only cox1 showed a barcoding gap. The rpb2 locus showed the highest PCI values, but it was the most difficult to amplify. The highest correct identification rates using blast method were obtained with rpb2.

Barcoding's next top model: an evaluation of nucleotide substitution models for specimen identification

Summary1. DNA barcoding studies use Kimura's two‐parameter substitution model (K2P) as thede factostandard for constructing genetic distance matrices. Distances generated under this model then provide the basis for most downstream analyses, but uncertainty in model choice is rarely explored and could potentially affect how reliably DNA barcodes discriminate species.2. Using information‐theoretic approaches for a data set comprising 14 472 DNA barcodes from 14 published studies, we tested whether the K2P model was a good fit at the species level and whether applying a better fitting model biased error rates or changed overall identification success.3. We report that the K2P was a poorly fitting model at the species level; it was never selected as the best model and very rarely selected as a credible alternative model. Despite the lack of support for the K2P model, differences in distance between best model and K2P model estimates were usually minimal, and importantly, identification success rates were largely unaffected by model choice even when interspecific threshold values were reassessed.4. Although these conclusions may justify using the K2P model for specimen identification purposes, we found simpler metrics such aspdistance performed equally well, perhaps obviating the requirement for model correction in DNA barcoding. Conversely, when incorporating genetic distance data into taxonomic studies, we advocate a more thorough examination of model uncertainty.

Geographically Widespread Swordfish Barcode Stock Identification: A Case Study of Its Application

BackgroundThe swordfish (Xiphias gladius) is a cosmopolitan large pelagic fish inhabiting tempered and tropical waters and it is a target species for fisheries all around the world. The present study investigated the ability of COI barcoding to reliably identify swordfish and particularly specific stocks of this commercially important species.MethodologyWe applied the classical DNA barcoding technology, upon a 682 bp segment of COI, and compared swordfish sequences from different geographical sources (Atlantic, Indian Oceans and Mediterranean Sea). The sequences of the 5′ hyper-variable fragment of the control region (5′dloop), were also used to validate the efficacy of COI as a stock-specific marker.Case ReportThis information was successfully applied to the discrimination of unknown samples from the market, detecting in some cases mislabeled seafood products.ConclusionsThe NJ distance-based phenogram (K2P model) obtained with COI sequences allowed us to correlate the swordfish haplotypes to the different geographical stocks. Similar results were obtained with 5′dloop. Our preliminary data in swordfish Xiphias gladius confirm that Cytochrome Oxidase I can be proposed as an efficient species-specific marker that has also the potential to assign geographical provenance. This information might speed the samples analysis in commercial application of barcoding.