DNA barcoding of deep‐water notacanthiform fishes (Teleostei,Elopomorpha)

Notacanthiformes Goodrich, 1909, is an order of deep‐sea teleost fishes with a leptocephalus larval stage whose biology and systematics are not widely known. The aim of this work was to apply the DNA barcode standard, based on COI sequence variation, to the delimitation of the species of this order, which is composed by the families Halosauridae (halosaurus) and Notacanthidae (spiny eels). The sequence data used for the analyses were obtained from two sources: 71 samples collected during oceanographic surveys in the North Atlantic Ocean (including the rare species Lipogenys gillii Goode & Bean, 1895) and 95 sequences collected from the BOLD data set. The neighbor‐joining analysis of the barcodes was successful in identifying 96% of the specimens, representing 9 of 16 and 9 of 10 of the recognised species of halosaurus and spiny eels, respectively, including all the current genera. The comparison between the Atlantic and the BOLD data sets also flagged the possibility of occurrences of misidentification and cryptic species. A modern molecular tool like the DNA barcoding supports the previously morphological‐based systematics of the order Notacanthiformes and will provide better access to the taxonomic knowledge of these deep‐water fishes.     

On a new species of Pseudocapillaria (Nematoda: Trichuroidea), P. lepidocephali,from the estuarine fish Lepidocephalus (Lepidocephalichthys) guntea (Hamilton)

Pseudocapillaria lepidocephali n. sp., parasitic in the intestine of the loach Lepidocephalus (Lepidocephalichthys) guntea from the Hooghly estuary at Kalyani, West Bengal, India, is described. The parasite is characterised mainly by its small body size, the structure of the male caudal end (the presence of mediumsized ventro-lateral lobes and the absence of a dorsal membrane), the presence of a non-spinous spicular sheath, the structure of the stichosome (26–34 stichocytes present), and the size and structure of the eggs. This is the first species of the genus Pseudocapillaria described from India and also from the genus Lepidocephalus.     

Production and characterization of asymmetric hybrids between upland cotton Coker 201 (Gossypium hirsutum) and wild cotton (G. klozschianum Anderss)

Asymmetric somatic hybrids were obtained between Gossypium hirsutum Coker 201 and wild cotton G. klozschianum Anderss. An investigation on the effect of ultraviolet (UV) irradiation on donor protoplasts was carried out, and the lethal dose was determined to be 38.7 J cm⁻². We firstly screened the putative hybrids by the color of the calli produced, followed by morphological, cytological, and molecular analysis of putative hybrid plants. Most regenerated plants derived from fused protoplasts displayed a recipient-like morphology, while some showed an intermediate phenotype between Coker 201 and G. klozschianum. Chromosome numbers in these somatic hybrids ranged from 54 to 74. The hybrids were verified by random amplified polymorphic DNA (RAPD) and simple sequence repeat (SSR). Absence or co-existence of parents’ genome DNA fragments was identified through molecular analysis. The heredity of cytoplasm was investigated by cleaved amplified polymorphic sequence (CAPS) analysis using mitochondrial and chloroplast universal primer pairs. The results indicated that recombination and rearrangements might have occurred in some regions of mitochondria (mt) and chloroplast (cp) DNA. To our knowledge, this is the first report about asymmetric protoplast fusion in cotton, and the hybrids obtained would be useful for breeding programs.     

Bactrocera dorsalis (Hendel) (Diptera: Tephritidae) is not invasive through Asia: It's been there all along

Oriental fruit fly, Bactrocera dorsalis (Hendel), is a highly polyphagous fruit fly which, in the last 15 years, has invaded (with or without establishment) Africa, Europe and North America. As a direct result of these invasions, there is increasing research interest in the invasion history and spread patterns of this fly. A statement being repeatedly used in the B. dorsalis invasion literature is that the species was first identified from Taiwan in 1912 and that it subsequently spread through South‐East and South Asia during the 20th century. This assumption is incorrect and stems from: (a) an incomplete knowledge of B. dorsalis taxonomic history; and (b) a confounding of first taxonomic record with first invasion record. Rather than being first detected in Taiwan in 1912, the first record of oriental fruit fly was from “East India” (India orientali) under the synonymous name of Musca ferruginea by Fabricius in 1794, and in the 1910s, it was known not only from Taiwan, but widely across tropical Asia with records from India, Burma, Bengal, Sri Lanka (as Ceylon), Singapore and Indonesia (multiple islands). The taxonomic literature is very clear that oriental fruit fly has not invaded the rest of Asia from Taiwan since 1912, and this error should not continue to be repeated in the literature.     

First molecular identification of Sarcocystis miescheriana (Protozoa, Apicomplexa) from wild boar (Sus scrofa) in Iran

Sarcocystis isolate obtained from the thigh muscle of a wild boar (Sus scrofa), captured from Gilan Province, northern Iran, was subjected to molecular analysis. Genomic DNA was obtained using a DNA extraction tissue kit and Polymerase chain reaction (PCR) for amplification of the 18S ribosomal DNA region yielded an 842 bp DNA band on agarose gel. Analysis of DNA sequencing by BLAST confirmed the isolate as Sarcocystis miescheriana and the sequence was deposited in GenBank by Accession No. GU395554. This is the first molecular identification of an isolate of S. miescheriana in Iran.     

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.     

Application of loop-mediated isothermal amplification (LAMP)-based technology for authentication of <Emphasis Type="Italic">Catharanthus roseus</Emphasis> (L.) G. Don

In this study, loop-mediated isothermal amplification (LAMP)-based molecular marker was developed for authentication of Catharanthus roseus, a medicinal plant. Samples of this plant were collected from different geographical locations in India. Random amplified polymorphic deoxyribonucleic acid (DNA) analysis of collected samples was carried out with 25 random primers. A 610-bp DNA fragment, common to all accessions, was eluted, cloned, and sequenced. Four LAMP primers were designed on the basis of sequence of 610 bp DNA fragment. LAMP reaction, containing 10× Bst DNA polymerase reaction buffer, Bst DNA polymerase, four in-house designed primers, dNTPs, MgSO₄, and betaine, was incubated at 65°C for 1 h. The resulting amplicon was visualized by adding SYBR Green I to the reaction tube. The data showed confirmatory results. Since the assay method is simple, sensitive, and cost-effective, it is a feasible method for identifying and authentication of C. roseus.     

Paracapillaria xenentodoni n. sp. (Nematoda: Trichuroidea) from the fishXenentodon cancila (Hamilton) from West Bengal,India

A new nematode,Paracapillaria xenentodoni n. sp. is described based on light microscope studies of the worms recovered from the migratory fishXenentodon cancila (Hamilton) from the Hooghly estuary at Kalyani, West Bengal, India. The worms are characterised by relatively large body size, the structure of the male caudal extremity (the presence of two wide, lobe-like, dorso-lateral caudal projections), the large size of the spicule (0.236–0.374 mm), the transversely wrinkled but non-spiny spicular sheath, the structure of the stichosome (30–40 stichocytes present), the slightly elevated anterior vulval lip, and the size (0.040–0.049 × 0.021–0.026 mm) and structure of the eggs. This represents the first species of the genusParacapillaria from India and also from fishes of the family Belonidae (Atheriniformes).     

DNA barcoding for identification of sand flies (Diptera: Psychodidae) in India

About 50 species of sand flies have been reported to be prevalent in India. We explored the utility of the DNA barcode approach towards species identification of these medically important insects. A total of 62 specimens belonging to seven morphologically identified species of two genera, Phlebotomus and Sergentomyia, collected from Puducherry Union Territory, Maharashtra and Rajasthan states of India were subjected to the analysis. Neighbor‐joining (NJ) analysis of DNA barcode sequences identified the individuals of seven morphological species into eight distinct species, as presented in the designed NJ tree. This methodology delineated morphologically identified species, S. bailyi, into two genetically isolated groups. Also, this study characterizes DNA barcodes of P. argentipes and P. papatasi, the vector species of leishmaniasis in India, for the first time.     

From Blood Oxygenation Level Dependent (BOLD) Signals to Brain Temperature Maps

A theoretical framework is presented for converting Blood Oxygenation Level Dependent (BOLD) images to brain temperature maps, based on the idea that disproportional local changes in cerebral blood flow (CBF) as compared with cerebral metabolic rate of oxygen consumption (CMRO ₂) during functional brain activity, lead to both brain temperature changes and the BOLD effect. Using an oxygen limitation model and a BOLD signal model, we obtain a transcendental equation relating CBF and CMRO ₂ changes with the corresponding BOLD signal, which is solved in terms of the Lambert W function. Inserting this result in the dynamic bioheat equation describing the rate of temperature changes in the brain, we obtain a nonautonomous ordinary differential equation that depends on the BOLD response, which is solved numerically for each brain voxel. Temperature maps obtained from a real BOLD dataset registered in an attention to visual motion experiment were calculated, obtaining temperature variations in the range: (−0.15, 0.1) which is consistent with experimental results. The statistical analysis revealed that significant temperature activations have a similar distribution pattern than BOLD activations. An interesting difference was the activation of the precuneus in temperature maps, a region involved in visuospatial processing, an effect that was not observed on BOLD maps. Furthermore, temperature maps were more localized to gray matter regions than the original BOLD maps, showing less activated voxels in white matter and cerebrospinal fluid.     

EVOLUTION OF POPULUS NIGRA (SECT. AIGEIROS):INTROGRESSIVE HYBRIDIZATION AND THE CHLOROPLAST CONTRIBUTION OF POPULUS ALBA (SECT. POPULUS)

Restriction site variation in chloroplast DNA and nuclear ribosomal DNA was examined in 16 accessions from the Salicaceae comprising ten species of Populus and one outgroup species of Salix. Forty-nine restriction site mutations in the chloroplast DNAs were used to generate one most parsimonious phylogenetic tree. This tree indicates that all varieties of P. nigra (black poplars of sect. Aigeiros) have a chloroplast genome, maternally inherited, derived from the clade including the white poplars (P. alba and segregate species of sect. Populus) and divergent from the American cottonwoods of their own section. Twenty-one restriction site mutations in the nuclear ribosomal DNAs generated a single most parsimonious phylogenetic tree that indicates that the nuclear genome ofP. nigra is distinct from both the white poplars and American cottonwoods. The incongruity of these independent molecular phylogenies provides evidence for an unusual origin of the black poplars. Populus alba or its immediate ancestor acted as the maternal parent in a hybridization event with the paternal lineage of P. nigra. Subsequent backcrosses to the paternal species gave rise to the extant P. nigra with a chloroplast genome of P. alba and the nuclear genome of the paternal species. These hybridization and introgression events must have pre-dated the divergence of the black poplar varieties. The biphyletic nature of the P. nigra genomes suggests that dependency on one class of molecular or morphological markers or the merging of the two kinds of data sets to derive accurate estimates of true phylogenies could be misleading in plants.     

First report of an endangered silurid catfish,Pterocryptis barakensis (Siluridae) from Brahmaputra drainage,North Eastern Himalayan region of India

The present communication reports an endangered catfish of the family Siluridae, Pterocryptis barakensis (Vishwanath & Sharma) for the first time outside its type locality from Brahmaputra drainage. The specimens were collected from the River Tissa, Longding district, Arunachal Pradesh foothills of Himalayan region of North East India. The current study describes morphometric and molecular characteristics of this endangered species.     

First description of the male of Gonatopus javanus (R.C.L. Perkins) determined by mitochondrial COI sequence (Hymenoptera: Dryinidae)

Gonatopus javanus (R.C.L. Perkins) was newly recorded from Japan and India. The males collected together with females of G. javanus from Japan were identified as previously unknown opposite sex of the species because they share identical sequences of mitochondrial COI. The sequence was different from that of G. clavipes (Thunberg) by 11%. The male of G. javanus was described as new to science. Doratulina producta (Matsumura) is implied as host in Japan. The utility of molecular marker to identify the dryinid taxa showing sexual dimorphism is discussed.     

Male-specific DNA markers from African catfish (Clarias gariepinus)

We searched for sex-specific DNA sequences in the male and female genomes of African catfish, Clarias gariepinus (Burchell, 1822) by comparative random amplified polymorphic DNA (RAPD) assays performed on pooled DNA samples. Two sex-linked RAPD markers were identified from the male DNA pool and confirmed on individual samples, showing good agreement with phenotypic sex. Both markers were isolated, cloned and characterized. The first marker (CgaY1) was nearly 2.6 kb long, while the length of second one (CgaY2) was 458 bp. Southern blot analysis with a CgaY1 probe showed strong hybridizing fragments only in males and not in females under stringent conditions, indicating the presence of multiple copies of CgaY1 in the male genome. When tested by zoo blot on the genomes of two closely related species from the Clariidae family, CgaY1 hybridized to the DNA of Heterobranchus longifilis and generated a faint male-specific band at low stringency. CgaY2 produced similar hybridization pattern in both sexes of C. gariepinus, C. macrocephalus and H. longifilis. Specific primers were designed to the sequences and the markers were amplified in multiplex PCR reactions together with a control band common to all individuals. This allowed for rapid, molecular sexing of the species on the basis of a simple three band (male) versus one band (female) pattern. According to our knowledge these are the first sex-specific DNA markers isolated from a siluroid fish species. This revised version was published online in July 2006 with corrections to the Cover Date.     

A Simple Method for the Efficient Isolation of Genomic DNA from Lactobacilli Isolated from Traditional Indian Fermented Milk (<Emphasis Type="Italic">dahi</Emphasis>)

A simple, inexpensive and effective genomic DNA isolation procedure for Lactobacillus isolates from traditional Indian fermented milk (dahi) is described. A total of 269 Lactobacillus isolates from fermented milk collected from four places in North and west India were tested for lysis by an initial weakening of the Gram positive cell wall with Ampicillin followed by Lysozyme treatment. The average genomic DNA yield was ~50 μg/ml log phase culture. Quality and repeatability of the method was found to be adequate for subsequent molecular applications. The quality of the genomic DNA isolated by this method was verified by restriction digestion and polymerase chain reaction (PCR). No inhibition was observed in subsequent PCR amplification and restriction digestion. The presented method is rapid, cheap and useful for routine DNA isolation from gram positive bacteria such as Lactobacillus.     

Molecular circumscription and intraspecific variation in Porella canariensis (F.Weber) Underw. (Porellaceae,Marchantiophyta)

Abstract

Fissidens subpulchellus Norkett in Gangulee is critically revised, and reduced to the synonymy of F. pulchellus Mitt. A new species, Fissidens longtonianus Z.Iwats. &; Tad.Suzuki, is described from India. This moss was collected on a branch in Jdukki District, South India, and is separated from F. pulchellus Mitt. by its smooth laminal cells, shorter setae and larger, smooth spores.     

Molecular confirmation of the occurrence of Elysia cf. tomentosa (Mollusca: Heterobranchia) in the Persian Gulf

The molluscan fauna of the Persian Gulf has recently been relatively well documented, yet there are few records of heterobranch sea slugs (opisthobranchs) from the Arabian parts and no report from the Iranian waters. Here we report for the first time the occurrence of one of these molluscs in the northern Persian Gulf (Bandar Abbas, Iran). Sacoglossan specimens were collected in association with the seaweed, Caulerpa sertularioides. Since morphological attributes were not adequately reliable for species identification, molecular approaches were carried out. Maximum-likelihood and Bayesian Inference analysis of partial DNA sequences of the mitochondrial cytochrome c oxidase subunit I (COI) locus were used for DNA barcoding of large-bodied specimens of Elysia. All Persian Gulf specimens were genetically confirmed as Elysia cf. tomentosa sp. 5, one of at least five morphologically similar but genetically distinct species in the taxonomically challenging and unresolved E. tomentosa complex. This species has previously been recorded only from Australia and Thailand and our finding adds another distant point to the geographic distribution of this species.     

RACIAL EVOLUTION IN ELEUSINE CORACANA SSP. CORACANA (FINGER MILLET)

Eleusine coracana ssp. coracana (finger millet, eleusine) is widely distributed in Africa and India as a cereal. The crop is cultivated in diverse eco-geographical areas. Over this range of distribution, eleusine displays high variability in vegetative, floral and seed morphology. The intent of this study is to establish correlations between morphology and distribution, and to determine the intraspecific taxonomy of the crop. Three eco-geographical races were determined: (1) an African highland race which is cultivated in the East African highlands, (2) a lowland race which is grown in the lowlands of Africa and South India, and (3) an Indian race with its center of distribution in Northeast India. In addition to these basic races, an Indian highland type was identified. The African highland race is the most primitive from which the lowland race evolved. The latter race was subsequently introduced to southern India where a secondary center of diversity became established. The Indian race originated from the lowland race, while the North Indian highland type can be derived from either or both of the two basic races in India. This study indicated that natural selection played a major role in the evolution of the crop. Artificial selection, although significant, was restricted within the limits imposed on it by the ultimate adaptation of the races to their environments.     

The origin of Indian Star tortoises (Geochelone elegans) based on nuclear and mitochondrial DNA analysis: A story of rescue and repatriation

The Indian Star tortoise (Geochelone elegans) belongs to the family Testunidae and is distributed in southwest India and Sri Lanka. In addition to facing loss of its natural habitat, the species is also illegally traded as food and as an exotic pet internationally. Here we report DNA-based analyses for identification and repatriation of these tortoises into their natural habitat. We have attempted to establish the geographical origin of these tortoises rescued from smugglers, by comparing the microsatellite and mitochondrial markers of rescued animals with animals of known provenance. Star tortoises exhibited strong genetic structure in India. The populations from western India were genetically distinct at microsatellite and mitochondrial loci from southern populations. The rescued individuals had similar multilocus genotypes and mitochondrial DNA haplotypes as the reference individuals from south India. However, the precise geographic origin of many of the rescued samples remains unresolved, because we could not assign them to southern populations and the Neighbor-Joining cluster analysis indicated that some of rescued tortoises formed distinct clusters. These data strongly suggest that the rescued group of tortoises is composed of a mix of individuals from differentiated source populations that are probably located in southern India and possibly Sri Lanka. Our study provides valuable information based on molecular markers for the assessment of genetic diversity in Indian Star tortoises.     

DNA barcoding of a new record of epi-endophytic green algae Ulvella leptochaete (Ulvellaceae,Chlorophyta) in India

Epi-endophytic green algae comprise one of the most diverse and phylogenetically primitive groups of green algae and are considered to be ubiquitous in the world’s oceans; however, no reports of these algae exist from India. Here we report the serendipitous discovery of Ulvella growing on intertidal green algae Cladophora glomerata and benthic red algae Laurencia obtusa collected from India. DNA barcodes at nuclear ribosomal DNA Internal Transcriber Spacer (nrDNA ITS) 1 and 2 regions for Indian isolates from the west and east coasts have been generated for the first time. Based on morphology and DNA barcoding, isolates were identified as Ulvella leptochaete. Phylogenetic reconstruction of concatenated dataset using Maximum Likelihood method differentiated Indian isolates from other accessions of this alga available in Genbank, albeit with low bootstrap support. Monophyly of Ulvella leptochaete was obvious in both of our phylogenetic analyses. With this first report of epi-endophytic algae from Indian territorial waters, the dire need to catalogue its cryptic diversity is highlighted and avenues of future research are discussed.