Interspecific Divergence Values Research Articles

RETRACTED: SEQUENCE ANALYSIS OF MITOCHONDRIAL CYTOCHROME C OXIDASE I GENE IN CATFISHES: AN INSIGHT INTO BARCODING AND PHYLOGENY

The standard methodology of DNA barcoding consists of clustering a taxonomic group using the Neighbour-joining (NJ) clustering method, which utilizes the divergence gap between species as a yardstick of species differentiation. With this approach, the present study is framed to decipher the divergence trend in catfish species - Clarias batrachus, C. gariepinus, Heteropneustes fossilis, Sperata seenghala, Wallago attu and Rita rita. The partial segment of the mitochondrial cytochrome c oxidase I subunit gene was used as the molecular marker of investigation. The intraspecific and interspecific divergence values were compared where a considerable gap was found between them. The average intraspecific divergence was found to be < 1%, while the average interspecific divergence found in the range of 16-24% which encompasses the divergence even at the family level. The NJ clustering has differentiated these species and has also shown phylogenetic insights as well. The species relatedness which appeared in NJ clustering was then reconfirmed using the Maximum likelihood (ML) approach with bootstrap support to trace their phylogenetic relationship. Interestingly, both NJ and ML clustering were found parallel, which assured the presence of phylogenetic signals in NJ tree too. Our study has successfully shown the role of intraspecific and interspecific divergence in species differentiation in catfishes, and simultaneously highlights the appearance of phylogenetic relationships in the NJ tree. A more comprehensive way of sampling is also discussed that could assist in looking deep into the divergence role to differentiate higher taxonomic levels.
 
 Retraction Notice: This paper has been retracted from the journal after receipt of written complains regarding authorship dispute. This journal is determined to promote integrity in research publication. This retraction is in spirit of the same. After formal procedures editor(s) and publisher have retracted this paper on 19th December-2022.

DNA barcoding ferns in an unexplored tropical montane cloud forest area of southeast Oaxaca, Mexico

DNA barcoding can be useful for species identification and phylogenetic analysis, but its effectivity has not been verified in most neotropical cloud forest plants. We tested three plastid barcodes, rbcLa, matK, and trnH-psbA, in selected pteridophytes, a well-represented group in these forests, from a little-explored area in Oaxaca, Mexico, applying the CBOL criteria for barcoding. We used BLASTn, genetic distance, and monophyly tree-based analyses employing neighbor-joining (NJ), maximum likelihood (ML), and Bayesian inference methods. Universal primers for rbcLa and trnH-psbA were successfully amplified and bi-directionally sequenced, but matK could not be amplified for most species. rbcLa showed the highest species discrimination in BLASTn (66.67%). trnH-psbA exhibited higher significant interspecific divergence values than rbcL and rbcLa + trnH-psbA (two-sample sign test, P value < 2.2e−16). Using NJ and ML phylogenetic trees, monophyletic species were successfully resolved (100%), differing only in support values and displaying full agreement with the most recent fern classification. ML trees showed the highest mean support value (80.95%). trnH-psbA was the only barcode that could detect the Elaphoglossoideae subfamily. Species discrimination did not increase using rbcLa + trnH-psbA. rbcLa is useful for fern barcoding, trnH-psbA is most helpful for phylogenetic analyses, and matK may not work as a universal barcoding marker.

Revision of the Genus Sirodotia Kylin (Batrachospermales, Rhodophyta) with Description of Four New Species

Most genera of the freshwater red algal order Batrachospermales have been systematically revised using molecular and morphological data, but Sirodotia Kylin remains to be thoroughly reviewed. In this investigation, DNA sequence data for the rbcL, COI-5P and LSU markers of specimens collected worldwide were combined with morphological observations to assess their specific diversity, infer their relationships and evaluate the morphological characters relevant for species identification. Phylogenetic analyses showed the genus to be a monophyletic lineage with high support. Inter- and intra-specific divergence values were well-delineated with higher interspecific (2.1-7% and 4.4-10.5%) and lower intraspecific (0-2.4% and 0-3.8%) variations for rbcL and COI-5P sequences, respectively. LSU sequences revealed lower interspecific divergence values than the COI-5P sequences (0.7-3.3%) indicating less resolution as a barcode marker. Nine species are recognized based on DNA sequence data, morphological characters and geographic distribution. Five species were previously described (S. assamica Necchi, Rossignolo, Yasmin, J.A.West & Ganesan, S. delicatula Skuja, S. huillensis (Welwitsch ex West & GSWest) Skuja, S. kennedyi A.L.Szinte, J.C.Taylor & M.L.Vis and S. suecica Kylin) and four new species are proposed (S. amazonica Necchi, N.L.Rossignolo & M.O.Paiano, sp. nov., S. aquiloamericana Necchi, N.L.Rossignolo & M.L.Vis, sp. nov., S. cryptica Necchi, N.L.Rossignolo & M.O.Paiano, sp. nov. and S. delicatuliformis Necchi, N.L.Rossignolo & M.O.Paiano, sp. nov.). Diagnostic characters for the genus are confirmed to be carpogonia asymmetric with a basal protuberance and carposporophytes diffuse with indeterminant prostrate filaments producing determinate erect branches terminating in carposporangia. The following morphological characters were applied to distinguish species: primary fascicle cell number, spermatangial arrangement, origin of gonimoblast filament and size of carposporangia. Based on morphology, S. sinica, S. segawae and S. yutakae are proposed as synonyms of S. suecica and S. ateleia Skuja of S. delicatula. The status of three species (S. cirrhosa Skuja ex M.S.Balakr. & B.B.Chaugule, S. gardneri Skuja ex Flint and S. huangshanensis Z.X.Shi & S.L.Xie) could not be confirmed due to lack of type specimens and published information on informative diagnostic characters.

Guidelines for DNA barcoding of coralline algae, focusing on Lithophylloideae (Corallinales) from Brazil

AbstractMultiple-marker (COI-5P, UPA,psbA andrbcL-3P) and two algorithmic approaches [automatic barcode gap discovery (ABGD) and Poisson tree process (PTP)] were used for species delimitation of Lithophylloideae in Brazil. The integrative approach was mostly congruent between markers and algorithmic methods of species delimitation, suggesting the occurrence of 24 species. Based on morphology and molecular data,Amphiroa rigida,Amphiroa vanbosseae,Lithophyllum atlanticum,Lithophyllum kaiseri,Lithophyllum margaritae,Titanoderma pustulatum,Titanoderma prototypumandPaulsilvella huveorum, which were previously reported for Brazil, are confirmed in this work. Six new species are distinguished by both molecular and morphological traits, and they are provisionally named asAmphiroasp. 1,Amphiroasp. 2,Amphiroasp. 3,Lithophyllumsp. 1,Lithophyllumsp. 2 andLithophyllumsp. 3. Another 10 species are cryptic and cannot be distinguished based on traditionally used morphological traits. These includeAmphiroasp. 4,Lithophyllumsp. 4, three species that are morphologically named underAmphiroa beauvoisii, and six that share the morphology described forAmphiroa fragilissima. All four markers used were useful for species delimitation. However, a combination of practical aspects and levels of intra- and interspecific divergence values led us to propose the use ofrbcL-3P as a standard DNA barcode marker for the Corallinales.

Reassessing the species status of Pseudodiaptomus malayalus Wellershaus, 1969 and P. binghami Sewell, 1912 (Calanoida: Pseudodiaptomidae) from India based on morphology and mitochondrial cytochrome oxidase I gene sequences

Pseudodiaptomus binghami Sewell, 1912 was first described from the Rangoon River (now Yangon River) estuary, Myanmar. Pseudodiaptomus malayalus Wellershaus, 1969 previously known as P. binghami malayalus, is a typical brackish-water calanoid copepod from Cochin Estuary, Kerala. Morphological examination of P. malayalus and P. binghami collected from Cochin Estuary and the Nambur canal in Andhra Pradesh revealed crucial differences between the two congeners. Female specimens of P. malayalus exhibited marked differences from those described by Wellershaus. They are (1) the number of terminal spines on P5, (2) ornamentation of GS, (3) ornamentation of Ur1–4, (4) length ratio of the Ur and CR segments and (5) length:width ratio of the CR setae. Furthermore, significant and discrete morphological differences were observed between the two Indian species in their P5 and urosome. But the male specimens of P. malayalus did not show any major differences from the original description. In addition, distance matrix data revealed 22% interspecific divergence values which in turn confirmed the status of P. malayalus and P. binghami as two distinct species.

Mitochondrial COI gene as a tool in the taxonomy of mosquitoes Culex subgenus Melanoconion

The subgenus Melanoconion is the second largest subgenus within the genus Culex, with 160 described species. Several of the species are proven vectors of arboviruses, including West Nile virus, Venezuelan equine encephalitis virus complex and Eastern equine encephalomyelitis virus. Species of Melanoconion are well distributed from southern North America to most countries of South America and display the highest species diversity in tropical regions. Taxonomical identification within this group has been primarily based on morphological characters, with the male genitalia as the source of the most solid diagnostic features. The difficulty in reaching accurate species determinations when studying specimens of Culex (Melanoconion) has been extensively documented as a real limitation to expand knowledge of these insects. We tested the utility of the mitochondrial gene COI as a complementary tool in the taxonomy of Melanoconion. Using a data set of 120 COI sequences from Culex specimen captured in several localities in Brazil, the utility of COI barcodes for species delimitation is discussed through the evaluation of genetic divergences among specimens and the clustering patterns of species in three topologies obtained with Neighbor Joining, Maximum Likelihood and Bayesian phylogenetic inference. For all specimens included in this study a previous morphological examination was performed, and most of the taxonomical determinations were corroborated using the COI barcode. We generated COI sequences that belong to 48 species of Melanoconion, with a mean intraspecific K2P genetic divergence of 3%; and all interspecific divergence values higher than the intraspecific divergence values. This is the first comprehensive study of subgenus Melanoconion, with evidence of COI as a useful and accessible DNA barcode.

Deoxyribonucleic Acid Barcoding of Some Indian Coelogyninae (Orchidaceae)

Subtribe Coelogyninae (Epidendroideae, Orchidaceae) comprises of 16 genera. The present study is undertaken to develop DNA barcodes of subtribe Coelogyninae using rbcL. It reveals the sectional delineation and its relationship with Pholidota. DNA barcoding is a technique which helps identification of species even if only small fragment of organism is available at any stage. The rbcL (Rubisco large subunit) from chloroplast genome is tested for effective barcoding. The interspecific divergence values and species discrimination rates were calculated by Kimura 2 parameter using MEGA 4.0. The rbcL with average interspecific divergence values yielded 72.72 % species resolution, thus it could distinguish all the species of Coelogyne and Pholidota. Invariably the genus Pholidota shows close affinity with Coelogyne. This supports the inclusion of genus Pholidota in the subtribe Coelogyninae of tribe Coelogyneae.

Taxonomy of Grateloupia (Halymeniales, Rhodophyta) by DNA barcode marker analysis and a description of Pachymeniopsis volvita sp. nov.

We applied DNA barcoding analysis to the red alga Grateloupia because it is one of the most complicated taxa in the family Halymeniaceae. We used two DNA barcoding markers, the 5′ end of the cytochrome c oxidase I gene and the universal plastid amplicon of the 23S rRNA gene, to define levels of genetic diversity and species relationships within rbcL phylogeny. We detected nine species of Grateloupia, four species of Pachymeniopsis, and one Kintokiocolax in Korea: G. angusta, G. asiatica, G. catenata, G. divaricata, G. imbricata, G. jejuensis, G. kurogii, G. subpectinata, G. turuturu, P. elliptica, P. gargiuli, P. lanceolata, a new species, and K. aggregato-cerantha. The COI-5P barcode successfully differentiated species, with interspecific divergence values ranging between 3.7 and 14 %. Barcoding data provided a rapid and accurate methodology for species-level identification and for taxonomic explorations when used in combination with morphological data. We describe Pachymeniopsis volvita sp. nov. based on DNA barcoding analysis. Fourteen species detected in four different subclades with strong bootstrap support within rbcL phylogenetic tree.

DNA barcodes and molecular diagnostics for distinguishing introduced Xyleborus (Coleoptera: Scolytinae) species in China

Members of the large and complex genus Xyleborus (Coleoptera: Scolytinae: Xyleborini) are the most commonly intercepted beetles associated with solid wood-packing materials at ports of entry in China. The accurate identification of species is critical in preventing the invasion of exotic insects. Considering the difficulties in morphological identification, genetic divergences of mitochondrial cytochrome c oxidase subunit I (COI) genes have been used in insect species identification. In this study, 32 Xyleborus and 2 outgroup species were collected from Jiangsu ports and selected to evaluate the effectiveness of DNA barcoding for Xyleborus species. The results showed that the mean interspecific divergence values (23.6%) were 15-fold higher than the observed intraspecific divergence (1.6%), except Xyleborus affinis. The results supported the inference that the barcode variation within species of insects is somewhat higher than interspecific ones. Thus, this study validated the effectiveness of barcoding for the identification of Xyleborus species.

DNA barcoding of endangered Indian Paphiopedilum species

The indiscriminate collections of Paphiopedilum species from the wild for their exotic ornamental flowers have rendered these plants endangered. Although the trade of these endangered species from the wild is strictly forbidden, it continues unabated in one or other forms that elude the current identification methods. DNA barcoding that offers identification of a species even if only a small fragment of the organism at any stage of development is available could be of great utility in scrutinizing the illegal trade of both endangered plant and animal species. Therefore, this study was undertaken to develop DNA barcodes of Indian species of Paphiopedilum along with their three natural hybrids using loci from both the chloroplast and nuclear genomes. The five loci tested for their potential as effective barcodes were RNA polymerase-β subunit (rpoB), RNA polymerase-β' subunit (rpoC1), Rubisco large subunit (rbcL) and maturase K (matK) from the chloroplast genome and nuclear ribosomal internal transcribed spacer (nrITS) from the nuclear genome. The intra- and inter-specific divergence values and species discrimination rates were calculated by Kimura 2 parameter (K2P) method using mega 4.0. The matK with 0.9% average inter-specific divergence value yielded 100% species resolution, thus could distinguish all the eight species of Paphiopedilum unequivocally. The species identification capability of these sequences was further confirmed as each of the matK sequences was found to be unique for the species when a blast analysis of these sequences was carried out on NCBI. nrITS, although had 4.4% average inter-specific divergence value, afforded only 50% species resolution. DNA barcodes of the three hybrids also reflected their parentage.

Molecular species identification with rich floristic sampling: DNA barcoding the pteridophyte flora of Japan.

BackgroundDNA barcoding is expected to be an effective identification tool for organisms with heteromorphic generations such as pteridophytes, which possess a morphologically simple gametophyte generation. Although a reference data set including complete coverage of the target local flora/fauna is necessary for accurate identification, DNA barcode studies including such rich taxonomic sampling on a countrywide scale are lacking.Methodology/Principal FindingsThe Japanese pteridophyte flora (733 taxa including subspecies and varieties) was used to test the utility of two plastid DNA barcode regions (rbcL and trnH-psbA) with the intention of developing an identification system for native gametophytes. DNA sequences were obtained from each of 689 (94.0%) taxa for rbcL and 617 (84.2%) taxa for trnH-psbA. Mean interspecific divergence values across all taxon pairs (K2P genetic distances) did not reveal a significant difference in rate between trnH-psbA and rbcL, but mean K2P distances of each genus showed significant heterogeneity according to systematic position. The minimum fail rate of taxon discrimination in an identification test using BLAST (12.52%) was obtained when rbcL and trnH-psbA were combined, and became lower in datasets excluding infraspecific taxa or apogamous taxa, or including sexual diploids only.Conclusions/SignificanceThis study demonstrates the overall effectiveness of DNA barcodes for species identification in the Japanese pteridophyte flora. Although this flora is characterized by a high occurrence of apogamous taxa that pose a serious challenge to identification using DNA barcodes, such taxa are limited to a small number of genera, and only minimally detract from the overall success rate. In the case that a query sequence is matched to a known apogamous genus, routine species identification may not be possible. Otherwise, DNA barcoding is a practical tool for identification of most Japanese pteridophytes, and is especially anticipated to be helpful for identification of non-hybridizing gametophytes.

Six new species ofAsphondylia(Diptera: Cecidomyiidae) damaging flower buds and fruit of AustralianAcacia(Mimosaceae)

Six species of gall midge are described from Australian acacias. Asphondylia bursicola Kolesik sp.n. and A. occidentalis Kolesik sp.n. form galls on fruit; A. germinis Kolesik sp.n., A. pilogerminis Kolesik sp.n .a ndA. glabrigerminis Kolesik sp.n. induce severe deformation of flower buds; and A. acaciae Kolesik sp.n. causes galls on both fruit and flower buds. Galled flower buds do not produce flowers, and galled fruit produce no or undeveloped seeds. Host ranges of the new species comprise between two and eight acacia hosts. Larval, pupal and male morphology, together with phylogenetic analyses of a 410-bp fragment of the mitochondrial cytochrome b gene, were used to characterize the new species. For A. bursicola, A. germinis, A. pilogerminis, A. glabrigerminis and A. acaciae, the intraspecific divergence values were between 0.2 and 3.4%, and the interspecific divergence values ranged between 5.1 and 10.5%. For A. occidentalis, the only species with geographical distribution confined solely to Western Australia, the intraspecific divergence was between 6.6 and 10.3%, and the interspecific difference from the other five new species was between 9.3 and 13.9%. In contrast to Dasineura spp. from Acacia, for which the morphology was more informative in species recognition than the cytochrome b sequence, in Asphondylia spp. treated here the partial cytochrome b sequence data provided better species recognition than did the morphology. Several of the new Asphondylia have potential as biological control agents in ecosystems in which Australian acacias are invasive and their sexual reproduction needs to be restricted. A list of Australian acacias whose reproductive organs are destroyed by known gall midges, all belonging to Dasineura and Asphondylia, is provided.

Nine new species of Dasineura (Diptera: Cecidomyiidae) from flowers of Australian Acacia (Mimosaceae)

Abstract. Thirteen species of Australian acacias are invasive plants in agricultural and native vegetation areas of South Africa. Biological control programmes for Australian acacias in South Africa have been implemented and are aimed at suppressing reproductive vigour and, in some cases, vegetative growth of these weeds. Gall‐forming midges are under consideration as potential biological control agents for invasive acacias in South Africa. Entomological surveys in southern Australia found a diverse cecidomyiid fauna associated with the buds, flowers and fruits of Acacia species. Nine new Dasineura species are described and two species, D. acaciaelongifoliae (Skuse) and D. dielsi Rübsaamen, are redescribed. The newly described taxa are D. fistulosasp.n., D. furcatasp.n., D. glaucasp.n., D. glomeratasp.n., D. oldfieldiisp.n., D. oshanesiisp.n., D. piliferasp.n., D. rubiformissp.n. and D. sulcatasp.n. All eleven species induce galls on ovaries and prevent the formation of fruit. Two general types of gall are caused. Type A comprises woody, tubular galls with larvae living inside ovaries (D. acaciaelongifoliae, D. dielsi, D. fistulosa, D. furcata, D. glauca, D. glomerata, D. oldfieldii). Type B includes soft‐tissued, globose galls that belong to four subtypes: inflated, baglike, hairy galls with larvae living between ovaries (D. pilifera); pyriform, pubescent swellings with larvae living inside ovaries (D. rubiformis); globose, hairy, swellings with larvae living superficially on ovaries in ovoid chambers (D. oshanesii); and inconspicuous, glabrous swellings with larvae living superficially on ovaries in shallow groovelike chambers (D. sulcata). The gall types are associated with a particular pupation pattern. In type A galls, larvae pupate within larval chambers in galls, whereas in type B galls pupation takes place between ovaries in galls or in the soil beneath the host tree. Gall midges responsible for the same general gall type are morphologically related and differ from species causing the other gall type. Phylogenetic analysis of a 410 bp fragment of the mitochondrial cytochrome b gene supports the division of the gall midge species into two groups except for D. sulcata, which appears as a subgroup of the group causing type A galls. The interspecific divergence values in group A species were between 0.5 and 3.9% with intraspecific divergence estimates of 0–0.2%. Gall midges causing type B galls had interspecific divergence values of 4.6–7.3% and intraspecific divergence values of 0–3.7%. Closely related biology and morphology together with low cytochrome b divergence estimates suggest a more recent speciation in group A when compared with species of group B. Dasineura rubiformis and D. dielsi are proposed as potential biological control agents for Acacia mearnsii De Wild. and Acacia cyclops A. Cunn. ex G. Don, respectively, in South Africa due to their narrow host range and ability to form high population densities that reduce seed formation. Both species produce galls with low biomass, which makes them compatible with commercial exploitation of their host species in Africa.