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Fish substitution in fish products is an important issue in fish markets, as it is a widespread practice. An authentication protocol for Rohu, Thaila and Tilapia was developed by multiplex PCR. Three species-specific and one degenerate common forward primer were designed using the Cytb gene of the mitochondrial genome. These primers for Labeo rohita, Labeo catla and Oreochromis niloticus showed the fragment size of 235 bp, 186 bp and 506 bp on the agarose gel, respectively. The primers for L. rohita and L. catla were sensitive to 0.1 ng of DNA template, while for O. niloticus this value was 1 ng of DNA template. A total of 230 commercial samples (160 fried and 70 processed fish products) were screened, where 60% mislabeling in fried and 30% mislabeling in processed fish were found. This multiplex PCR protocol could give useful insights for food inspection and enforcement of regulatory food control. [ABSTRACT FROM AUTHOR]

This study aimed to investigate the association between polymorphisms of ND1 and CYTB genes and in vitro early embryo development of Sanjabi sheep. Blood and ovarian samples were collected from a local slaughterhouse. The cumulus-oocyte complexes with a diameter greater than 3 mm were aspirated from follicles, and in vitro maturation (IVM) and in vitro culture (IVC) rates of them were recorded. A respective 1200 bp and 980 bp fragments of ND1 and CYTB genes were genotyped using a modified single strand conformation polymorphism (SSCP) method. The results of this study revealed that four different patterns, named as A, B, C, and D were observed for both ND1 and CYTB genes. The ND1 gene polymorphisms had significant effects on the IVM and IVC rate (p < 0.05). The pattern C of the ND1 gene significantly increased the IVM rate compared to the patterns A, B and D. For the IVC, the highest and lowest means were related to the C and B patterns, respectively. The CYTB gene polymorphisms also had significant effects on IVC (p < 0.01), but the IVM did not affected (p = 0.07). Here, the pattern D had the highest and the pattern C had the lowest means for both IVM and IVC rates. [ABSTRACT FROM AUTHOR]

Loxaulus hyalinus Pujade-Villar & Melika, 2014 was originally described as an asexual form but the recent collection of male samples confirms that it is, actually, a sexual form. The male of L. hyalinus is here morphologically described. With L. hyalinus being a sexual form, the reasonable question arises whether it may be the alternate generation of the only other Loxaulus species currently known from Mexico, L. laeta Pujade-Villar, 2014 (asex). An analysis of the phylogenetic relationships between L. hyalinus (sex) and L. laeta (asex) shows an uncorrected genetic distance variation between sympatric and allopatric individuals averaging 6.4% (range 5.9–6.9%) between the two species independently of the sampled locality. Four different species delimitation models – Automatic Barcode Gap Discovery (ABGD), Bayesian implementation of the Poisson tree processes (bPTP), Bayesian Phylogenetics and Phylogeography (BPP), and Bayesian Factor Delimitation (BFD) – support the distinctiveness of the two Loxaulus species. [ABSTRACT FROM AUTHOR]

Seven different methods of DNA extraction were performed and compared in order to have the better DNA recovery in terms of quality and quantity. A PCR assay was realised based on the Cytb mitochondrial gene to identify 53 commercial food products of wide range diversity (Scombridae Thunnus species) commercialised in the Tunisian market, and we checked whether these products were correctly labelled under European and national legislations. Phylogenetic analyses on Cytb mitochondrial gene were used to study the relationships among the considered species. Tuna species was easily differentiated and confirmed by direct sequencing. The results showed a high deficiency in labelling: 96% of canned tuna did not specify the species, although the name of the species had to be mentioned. Partial least squares regression (PLS) showed relatively high values (45%) in all analysed data, suggesting substantial difference between the extraction procedures and matrices with SDS/PCI method being the most convenient. [ABSTRACT FROM AUTHOR]

Cubilose, a valuable traditional Chinese medicine, is mainly composed of the saliva by several species of Aerodramus or Collocalia in the Apodidae. Due to rarity, high economic value and huge market demand, its fake or adulteration is frequently found in the market. Therefore, it is urgent to establish a simple and accurate method for authenticating cubilose. DNA barcoding, which is an easy, quick and reliable method, is widely used to trace the origin of traditional Chinese medicine. For identifying the original species of cubilose, cytb gene of 18 cubilose samples including 15 officer cubilose and 3 feather cubilose were amplified and entered into the GenBank database using the BLAST search tool. The genetic distances among 18 cubilose samples were calculated based on the Kimura two parameter (K2P) model. To construct the reference database, 18 cytb sequences of Aerodramus or Collocalia were downloaded from GenBank. The neighbor-joining (NJ) and unweighted pair group method with arithmetic average (UPGMA) trees were constructed based on sequences from GenBank and our dataset. Blast analysis showed that all cubilose samples had the highest similarity with A. fuciphagus, and the sequence similarity reached over 99%. Genetic distance of 18 cubilose samples ranged from 0.000–0.010. Trees constructed by NJ and UPGMA gave similar topology: all cubilose samples clustered together with A. fuciphagus. These result demonstrated that the original species of all 18 cubilose samples were A. fuciphagus, and cytb gene is a good candidate for identifying cubilose. [ABSTRACT FROM AUTHOR]

The crested loaches of the genus Paracobitis from the Sistan basin (Iran) are reviewed based on morphological and mitochondrial cytb and COI sequences characters to check the status of taxa in phylogenetic trees. Paracobitis rhadinaea (Regan, 1906) and P. vignai Nalbant & Bianco, 1998 were known only based on minor morphological differences (presence or absence of scales, caudal fin shape, colour pattern and fish size). We failed to find any diagnostic molecular and morphological characters between them. Therefore, we regard P. vignai as a junior synonym of P. rhadinaea. [ABSTRACT FROM AUTHOR]

Mitochondrial genetic markers have been extensively used to study the phylogenetics and phylogeography of many birds, including seabirds of the order Procellariiformes. Evidence suggests that part of the mitochondrial genome of Procellariiformes, especially albatrosses, is duplicated, but no DNA fragment covering the entire duplication has been sequenced. We sequenced the complete mitochondrial genome of a non-albatross species of Procellariiformes, Puffinus lherminieri (Audubon's shearwater) using the long-read MinION (ONT) technology. Two mitogenomes were assembled from the same individual, differing by 52 SNPs and in length. The shorter was 19 kb long while the longer was 21 kb, due to the presence of two identical copies of nad6, three tRNA, and two dissimilar copies of the control region (CR). Contrary to albatrosses, cob was not duplicated. We further detected a complex repeated region of undetermined length between the CR and 12S. Long-read sequencing suggests heteroplasmy and a novel arrangement within the duplicated region, indicating a complex evolution of the mitogenome in Procellariiformes. [ABSTRACT FROM AUTHOR]

The Italian wall lizard and the Balkan wall lizard have a series of taxonomic revisions. However, their phylogenetic relationships still remain uncertain in Turkey. In the present study, we have assessed taxonomic relationships, both of Podarcis siculus and Podarcis tauricus through estimation of phylogenetic relationships among 43 and 42 specimens, respectively, using mtDNA (16 S rRNA and cytb) from great main populations in Turkey. The genetic distances among the populations of P. siculus in Turkey were very low and they were ranged from 0.2 to 1.6% in 16 S rRNA while they were ranged from 0.0% to 3.3% in cytb. On the other hand, the p-distances among the populations of P. tauricus were ranged from 0.0 to 0.6% in 16 S rRNA while they were 0.2% cytb in Turkey. Finally, most of the topologically identical trees of phylogenetic analyses and p-distances showed that monophyly was found in extant populations of P. siculus and P. tauricus. The nominate subspecies, P. s. siculus and P. t. tauricus are representatives of these lizards in Turkey. [ABSTRACT FROM AUTHOR]

This study determines the presence of R. tanezumi from in Nepal using morphological and molecular analyses. Morphologically, it is indistinguishable with R. rattus owing to similar fur colour and morphometric data. However, molecular identification and phylogenetic analysis using sequences of the mitochondrial DNA (mtDNA) Cytochrome B (CytB) gene revealed two different species R. rattus and R. tanezumi from collected specimens. The genetic distance between R. rattus and R. tanezumi was found 0.043. In phylogenetic tree, the clade of R. tanezumi is distinguished into two sub-clades, R. tanezumi found in Nepal, and East Asian countries, China, Laos, Thailand, Viet Nam, and South Korea have genetic distance 0.031, suggesting the different lineages of R. tanezumi. This study confirmed the R. tanezumi present in Nepal. Our findings suggest that morphological analysis and molecular study should be carried out simultaneously for accurate identification of small sized cryptic mammals like R. tanezumi and R. rattus. [ABSTRACT FROM AUTHOR]

The Asian clam Corbicula fluminea is a small bivalve with high nutritional and medical values. However, natural resources of C. fluminea have declined in many areas of China including the Hongze Lake. In this study, 119 individuals from 10 sites of this lake and 2 outgroups were analyzed using a 456 bp mitochondrial cytochrome b (cytb) gene segment. Totally, 19 polymorphic sites were detected, which defined 16 haplotypes. Polymorphism varied among the 10 populations with those at the water inlet being more polymorphic. Most FST values among these populations were below 0.15 with the overall value of 0.060 (p < .05), meanwhile, the overall gene flow was 7.67, both of which indicated the low level of population differentiation in this lake. Neutrality test and mismatch analyses indicated that population explosion may have occurred in this lake. The results obtained in this study will provide useful information for artificial breeding and resource protection of this species in the Hongze Lake. [ABSTRACT FROM AUTHOR]

To reveal the dietary ecology of the peregrine falcon (Falco peregrinus), we conducted a molecular analysis for mitochondrial genes (COIandCYTB) to identify the prey species collected from a feeding place found on Sasu Island, South Korea. The results from noninvasive genetic analysis showed that the sequences obtained came from nine species of birds (Cuculus canorus,Eurystomus orientalis,Limosa limosa,Microscelis amaurotis,Oriolus chinensis,Phasianus colchicus,Sterna hirundo,Streptopelia orientalis, andTurdus pallidus). Five of the species (C.canorus,M.amaurotis,S.hirundo,S.orientalis, andT.pallidus) had previously been observed on this island, but the other four species (E. orientalis,L. limosa,O. chinensis, andP. colchicus) were newly identified as present. No mtDNA sequences of land animals such as amphibians, reptiles, and mammals were found in the dietary remains, suggesting that the peregrine falcon preys mostly on other birds rather than on other animals inhabiting Sasu Island. This island has rich avian diversity and abundant animal populations and therefore supplies sufficient dietary resources for the peregrine falcon. Our findings suggested that a DNA-based molecular method may be useful to identify the prey species of these birds and may be valuable in future studies of the Endangered peregrine falcon. [ABSTRACT FROM AUTHOR]

The spiny-tailed lizard of the genusDarevskiahave a series of taxonomic revisions, but still their phylogenetic relationships remain uncertain. In the present study, we have assessed taxonomic relationships amongDarevskia bithynicaandDarevskia rudispopulations through estimation of phylogenetic relationships among 96 specimens using microsatellite DNA (Du215,Du281,Du323andDu418loci) and 53 specimens using mtDNA (16S rRNA and cytb) from main populations in Turkey. AlthoughD. b. bithynicaandD. r. mirabiliswere separated based on the PCoA analysis at low level from otherD. rudisandD. bithynicapopulations, the distance values of Nei's genetic distance, Nei's unbiased genetic distance, Fst and Linear Fst were not high among taxa in microsatellite DNA. On the other hand, our phylogenetic analyses (NJ, ML, MP and BI) did not separateD. rudisandD. bithynicapopulations. Finally, most of the topologically identical trees of phylogenetic analyses and microsatellite results showed that the extant populations ofD. rudisandD. bithynicawere found to be polytomy. Based on our molecular phylogenetic study,D. rudiscomplex is still ongoing revisions. [ABSTRACT FROM PUBLISHER]

The population genetic structure of the rock bream (Oplegnathus fasciatus) along the coastal waters of China was estimated based on three mtDNA fragments (D-loop, COI, and Cytb). A total of 112 polymorphic sites were checked, which defined 63 haplotypes. A pattern with high levels of haplotype diversity (hCOI = 0.886 ± 0.034,hCytb = 0.874 ± 0.023) and low levels of nucleotide diversity (лCOI = 0.009 ± 0.005,лCytb = 0.006 ± 0.003) was detected based on the COI and Cytb fragments, and high levels of genetic diversity (hD-loop = 0.995 ± 0.007,лD-loop = 0.021 ± 0.011) were detected from the mtDNA D-loop. The population genetic diversity ofO. fasciatusin south China was significantly higher than those of north China. Three genealogical clades were checked in theO. fasciatuspopulations based on the NJ and MST analyses of mtDNA COI gene sequence, and the genetic distances among the clades ranged from 0.018 to 0.025. Significant population genetic differentiation was also checked based on theFst(0.331,p = 0.000) and exactp(0.000) test analyses. No significant population differentiations were checked based on mtDNA D-loop and Cytb fragments. Using a variety of phylogenetic methods, coalescent reasoning, and molecular dating interpreted in conjunction with paleoclimatic and physiographic evidences, we inferred that the genetic make-up of extant populations ofO. fasciatuswas shaped by Pleistocene environmental impacts on the historical demography of this species. Coalescent analyses (neutrality tests, mismatch distribution analysis, and Bayesian skyline analyses) showed that the species along coastline of China has experienced population expansions originated in its most recent history at about 169–175 kya before present. [ABSTRACT FROM PUBLISHER]

Pilos antler (Lu-Rong in Chinese) is a famous traditional medicine in China. Many adulterants have been discovered in Chinese markets in recent years. However, few DNA-based methods are effective for discrimination of this DNA-degraded animal medicine. Here, novel and deft amplification refractory mutation sequencing system (ARMSS), integrating the advantages of the amplification refractory mutation system (ARMS) and the short DNA barcode, was first developed to discriminate Pilos antler from its adulterants. We aimed to provide a new sight and inspiration for deft detection. The results showed that developed ARMS achieved strong specificity and high sensitivity in rapid identification, while the short Cytb gene was of excellent identification power in terms of accurate identification, which suggested that ARMSS successfully integrated the advantages of the ARMS and short DNA barcode, and that it was useful for deft detection. Our study determined that the deft ARMSS could be the well candidate for discrimination of Pilos antler, as well as be a valuable tool for deft identification of Chinese medicine. [ABSTRACT FROM AUTHOR]

The complete mitochondrial genome sequence was determined for a specimen ofCalotomus japonicus, a temperate parrotfish endemic to coastal East Asia. It was compared phylogenetically with previously published partial sequences from this species and other parrotfishes. The obtained tree indicated that the three cytb sequences ofC. japonicusfrom a recent molecular study (LC068806-8) probably resulted from introgression through intergeneric hybridization, or possibly from sample confusion. Taking the presently obtained mitogenome as representative ofC. japonicus, the species most closely related to this one among congeners isC. zonarchus, which is endemic to the Hawaiian islands. [ABSTRACT FROM PUBLISHER]

Background and aims. We analyzed a small and wide geographically distributed Neotropical freshwater fish, the Piabina argentea from the Upper Paraná Basin, to check the hypothesis that this species is composed of more than one biological unit, since it has a limited dispersion, through the DNA barcode technique. Materials and methods. Partial mitochondrial COI and CytB gene sequences were obtained for 58 specimens drawn from 13 localities. Results. Phylogenetic analysis revealed six major clusters of P. argentea. Kimura-two-parameter (K2P) genetic divergences among these six P. argentea clusters ranged from 2 to 5.6% and from 2.3 to 5.4% for COI and CytB genes, respectively, and these values were on average approximately nine times greater than intra-cluster K2P divergences. The fixation index ( FST) among clusters showed very high values and the haplotype network analysis displayed seven unconnected units. Conclusion. These results reinforce the hypothesis that the widely distributed P. argentea species concept as currently conceived actually represents more than one species (possibly six). These results demonstrate the efficacy of DNA barcoding for the discovery of hidden diversity in Neotropical freshwater fishes, and we conclude that barcoding is a useful tool for alpha taxonomy. [ABSTRACT FROM AUTHOR]

The complete mitochondrial genome sequence of the hybrid of blunt snout bream (Megalobrama amblycephala) (♀) × white Amur bream (Parabramis pekinesis) (♂) (M × P) was determined using the PCR-based method for the first time. The total length of the mitogenome was 16,623 bp in accordance with blunt snout bream. It contained 37 genes (13 protein-coding genes, 22 transfer RNA genes and 2 ribosomal RNA genes) and 2 main non-coding regions (the control region and the origin of the light strand replication). Compared with the complete mitochondrial genome of the parents, results showed the hybrid bream was consistent with a maternal inheritance; however, we also found a termination codon mutation inCytband a double-based site in 16S rRNA which was species-specific for the male parentP. pekinesis. The complete mitochondrial genome sequence of the M × P bream provided an important data set for further study in mitochondrial inheritance mechanism. [ABSTRACT FROM AUTHOR]