DNA barcodes of fish of the Scotia Sea, Antarctica indicate priority groups for taxonomic and systematics focus

2008 ◽  
Vol 20 (3) ◽  
pp. 253-262 ◽  
Author(s):  
J. Rock ◽  
F.O. Costa ◽  
D.I. Walker ◽  
A.W. North ◽  
W.F. Hutchinson ◽  
...  
Keyword(s):  
Dna Barcoding ◽  
Sequence Data ◽  
Molecular Classification ◽  
Molecular Data ◽  
Species Level ◽  
Scotia Sea ◽  
Life History Stages ◽  
Additional Sequence ◽  
Taxonomic Framework ◽  
Taxonomic Studies

AbstractWe analysed cytochrome oxidase I (COI) barcodes for 35 putative fish species collected in the Scotia Sea, and compared the resultant molecular data with field-based morphological identifications, and additional sequence data obtained from GenBank and the Barcode of Life Data System (BOLD). There was high congruence between morphological and molecular classification, and COI provided effective species-level discrimination for nearly all putative species. No effect of geographic sampling was observed for COI sequence variation. For two families, including the Liparidae and Zoarcidae, for which morphological field identification was unable to resolve taxonomy, DNA barcoding revealed significant species-level divergence. However, the dataset lacked sufficient sensitivity for resolving species within theBathydracoandArtedidracogenera. Analysis of cytochromebfor these two genera also failed to resolve taxonomic identity. The data are discussed in relation to emergent priorities for additional taxonomic studies. We emphasize the utility of DNA barcoding in providing a valuable taxonomic framework for fundamental population studies through assigning life history stages or other morphologically ambiguous samples to parental species.

scholarly journals DNA Barcoding: Mixed results for big-headed flies (Diptera: Pipunculidae)

Zootaxa ◽  
2007 ◽  
Vol 1423 (1) ◽  
pp. 1-26 ◽  
Author(s):  
JEFFREY H. SKEVINGTON ◽  
CHRISTIAN KEHLMAIER ◽  
GUNILLA STÅHLS
Keyword(s):  
Dna Barcoding ◽  
Sequence Data ◽  
Phylogenetic Signal ◽  
Morphological Characters ◽  
Molecular Data ◽  
Morphological Data ◽  
Base Pairs ◽  
Data Set ◽  
Taxonomic Decision ◽  
Morphological Species

Sequence data from 658 base pairs of mitochondrial cytochrome c oxidase I (cox1) were analysed for 28 described species of Pipunculidae (Diptera) in an effort to test the concept of DNA Barcoding on this family. Two recently revised but distantly related pipunculid lineages with presumed different evolutionary histories were used for the test (Clistoabdominalis Skevington, 2001 and Nephrocerus Zetterstedt, 1838). An effort was made to test the concept using sister taxa and morphologically similar sibling species swarms in these two genera. Morphological species concepts for Clistoabdominalis taxa were either supported by cox1 data or found to be too broad. Most of the discordance could be accounted for after reassessing morphological characters. In these cases, the molecular data were invaluable in assisting taxonomic decision-making. The radiation of Nearctic species of Nephrocerus could not be diagnosed using cox1. The ability of cox1 to recover phylogenetic signal was also tested on Clistoabdominalis. Morphological data for Clistoabdominalis were combined with the molecular data set. The pipunculid phylogeny from molecular data closely resembles the published phylogeny based on morphology. Partitioned Bremer support is used to localize areas of conflict between the datasets.

scholarly journals Intraspecific mitochondrial gene variation can be as low as that of nuclear rRNA

F1000Research ◽  
2020 ◽  
Vol 9 ◽  
pp. 339 ◽  
Author(s):  
Tshifhiwa G. Matumba ◽  
Jody Oliver ◽  
Nigel P. Barker ◽  
Christopher D. McQuaid ◽  
Peter R. Teske
Keyword(s):  
Dna Barcoding ◽  
Dna Sequences ◽  
Sequence Data ◽  
Mitochondrial Gene ◽  
Population Expansion ◽  
Species Level ◽  
Molecular Dating ◽  
Coi Gene ◽  
28S Rrna ◽  
Mtdna Sequence

Background: Mitochondrial DNA (mtDNA) has long been used to date historical demographic events. The idea that it is useful for molecular dating rests on the premise that its evolution is neutral. Even though this idea has long been challenged, the evidence against clock-like evolution of mtDNA is often ignored. Here, we present a particularly clear and simple example to illustrate the implications of violations of the assumption of selective neutrality. Methods: DNA sequences were generated for the mtDNA COI gene and the nuclear 28S rRNA of two closely related rocky shore snails, and species-level variation was compared. Nuclear rRNA is not usually used to study intraspecific variation in species that are not spatially structured, presumably because this marker is assumed to evolve so slowly that it is more suitable for phylogenetics.  Results: Even though high inter-specific divergence reflected the faster evolutionary rate of COI, intraspecific genetic variation was similar for both markers. As a result, estimates of population expansion times based on mismatch distributions differed between the two markers by millions of years. Conclusions: Assuming that 28S evolution is more clock-like, these findings can be explained by variation-reducing purifying selection in mtDNA at the species level, and an elevated divergence rate caused by diversifying selection between the two species. Although these two selective forces together make mtDNA suitable as a marker for species identifications by means of DNA barcoding because they create a ‘barcoding gap’, estimates of demographic change based on this marker can be expected to be highly unreliable. Our study contributes to the growing evidence that the utility of mtDNA sequence data beyond DNA barcoding is limited.

An expanded phylogenetic analysis of Austrostipa (Poaceae: Stipeae) to test infrageneric relationships

2012 ◽  
Vol 25 (1) ◽  
pp. 1 ◽  
Author(s):  
Anna E. Syme ◽  
Daniel J. Murphy ◽  
Gareth D. Holmes ◽  
Stuart Gardner ◽  
Rachael Fowler ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Sequence Data ◽  
Strong Support ◽  
Molecular Data ◽  
Species Level ◽  
Internal Transcribed Spacer Region ◽  
Deep Coalescence ◽  
History Of ◽  
Levels Of Support

Although the Australasian grass genus Austrostipa is species rich, abundant and ecologically significant, the subgeneric classification of its 62 species has not been comprehensively tested with molecular data. We used three molecular markers from 51 species to determine a phylogeny of the genus and found strong support for the following seven of the existing subgenera: Falcatae, Austrostipa, Aulax, Lobatae, Bambusina, Lancea and Longiaristatae. The molecular data do not support Tuberculatae and Eremophilae, which could be combined with subgenus Austrostipa. The data are equivocal or insufficient regarding monophyly of Ceres, Arbuscula, Petaurista and Lanterna. Data from the nuclear internal transcribed spacer region appear to be suitable for phylogenetic analysis of this group, and the degree of sequence variability resolves species-level relationships with good levels of support. In contrast, chloroplast sequence data from the matK and rbcL genes do not resolve most relationships at the species level, and the inferred phylogeny hints at gene duplication, chloroplast capture, or deep coalescence in the evolutionary history of Austrostipa.

scholarly journals Limitations of DNA barcoding in determining the origin of smuggled seahorses and pipefishes

2020 ◽  
Author(s):  
Conny P. Serite ◽  
Ofentse K. Ntshudisane ◽  
Eugene Swart ◽  
Luisa Simbine ◽  
Graça L. M. Jaime ◽  
...  
Keyword(s):  
Dna Barcoding ◽  
Sequence Data ◽  
Country Of Origin ◽  
Species Level ◽  
Dna Barcodes ◽  
Region Of Origin ◽  
Genetic Population ◽  
Aquarium Fish ◽  
Hippocampus Kuda ◽  
Pacific Species

AbstractSeahorses and pipefishes are heavily exploited for use in Traditional Chinese Medicine (TCM), and less frequently for curio markets or as aquarium fish. A number of recent studies have used DNA barcoding to identify species sold at TCM markets in East Asia, but the usefulness of this approach in determining the region of origin remains poorly explored. Here, we generated DNA barcodes of dried seahorses and pipefishes destined for TCM that were confiscated at South Africa’s largest airport because they lacked the export permits required for the CITES-listed seahorses. These were compared with published sequences and new sequences generated for Mozambican seahorses, with the aim of determining whether it is possible to identify their country of origin. All pipefishes were identified as Syngnathoides biaculeatus, a widespread Indo-Pacific species, but the published sequence data did not provide sufficient resolution to identify the region of origin. The same was true of the majority of seahorses, which could not even be identified to species level because they clustered among an unresolved species complex whose sequences were published under the names Hippocampus kuda, H. fuscus and H. capensis. The presence of a few specimens of a second seahorse, H. camelopardalis, suggests that the shipment originated from East Africa because the range of this seahorse is centred around this region, but again, it was not possible to determine their country of origin. Even though seahorses and pipefishes have high levels of genetic population structure because of their low dispersal potential, DNA barcoding was only suitable to tentatively identify species, but not their region of origin. DNA barcoding is increasingly used to identify illegally traded wildlife, but our results show that more sophisticated methods are needed to monitor and police the trade in seahorses and pipefishes.

Genes, morphology, development and photosynthetic ability support the resurrection of Elysia cornigera (Heterobranchia:Plakobranchoidea) as distinct from the 'solar-powered' sea slug, E. timida

2011 ◽  
Vol 25 (6) ◽  
pp. 477 ◽  
Author(s):  
Patrick J. Krug ◽  
Katharina Händeler ◽  
Jann Vendetti
Keyword(s):  
Population Genetic ◽  
Molecular Data ◽  
Genetic Distances ◽  
Species Level ◽  
Sea Slugs ◽  
Interspecific Divergence ◽  
Integrative Study ◽  
Solar Powered ◽  
Taxonomic Framework ◽  
High Degree

Some groups of marine heterobranch sea slugs (formerly Opisthobranchia) have few discrete characters or hard parts and many ‘cosmopolitan’ species, suggesting an overly conservative taxonomy in need of integrative approaches. Many herbivorous sea slugs in the clade Sacoglossa retain algal chloroplasts that remain functionally photosynthetic for 1–2 weeks, but at least four species can sustain chloroplasts for several months. To better understand the origins of long-term kleptoplasty, we performed an integrative study of the highly photosynthetic species Elysia timida from the Mediterranean and Caribbean populations that were described as E. cornigera but later synonymised with E. timida. Nominal E. cornigera were distinct in their anatomy and aspects of larval development, and had dramatically reduced chloroplast retention compared with E. timida. Mean divergence at three genetic loci was determined for ten pairs of sister species in the genus Elysia, confirming that E. cornigera and E. timida have species level differences. Both taxa had a high degree of population genetic subdivision, but among-population genetic distances were far less than interspecific divergence. In an integrative taxonomic framework, E. cornigera is thus restored to species rank and fully redescribed, and baseline molecular data are presented for evaluating species level differences in the Sacoglossa.

scholarly journals Intraspecific mitochondrial gene variation can be as low as that of nuclear rRNA

F1000Research ◽  
2020 ◽  
Vol 9 ◽  
pp. 339 ◽  
Author(s):  
Tshifhiwa G. Matumba ◽  
Jody Oliver ◽  
Nigel P. Barker ◽  
Christopher D. McQuaid ◽  
Peter R. Teske
Keyword(s):  
Dna Barcoding ◽  
Dna Sequences ◽  
Sequence Data ◽  
Mitochondrial Gene ◽  
Population Expansion ◽  
Species Level ◽  
Molecular Dating ◽  
Coi Gene ◽  
28S Rrna ◽  
Mtdna Sequence

Background: Mitochondrial DNA (mtDNA) has long been used to date historical demographic events. The idea that it is useful for molecular dating rests on the premise that its evolution is neutral. Even though this idea has long been challenged, the evidence against clock-like evolution of mtDNA is often ignored. Here, we present a particularly clear and simple example to illustrate the implications of violations of the assumption of selective neutrality. Methods: DNA sequences were generated for the mtDNA COI gene and the nuclear 28S rRNA of two closely related rocky shore snails, and species-level variation was compared. To our knowledge, this is the first study to use nuclear rRNA at this taxonomic level, presumably because this marker is assumed to evolve so slowly that it is only suitable for phylogenetics.   Results: Even though high inter-specific divergence reflected the faster evolutionary rate of COI, intraspecific genetic variation was similar for both markers. As a result, estimates of population expansion times based on mismatch distributions differed between the two markers by millions of years. Conclusions: Assuming that 28S evolves effectively clock-like, these findings can be explained by variation-reducing purifying selection in mtDNA at the species level, and an elevated divergence rate caused by diversifying selection between the two species. Although these two selective forces together make mtDNA suitable as a marker for species identifications by means of DNA barcoding because they create a ‘barcoding gap’, estimates of demographic change based on this marker can be expected to be highly unreliable. Our study contributes to the growing evidence that the utility of mtDNA sequence data beyond DNA barcoding is limited.

Identification of a species of deer fly attacking human and live stocks in Assam, India

ENTOMON ◽  
2019 ◽  
Vol 44 (3) ◽  
pp. 237-240
Author(s):  
Dipankar Biswas ◽  
Dibya Ranjan Bhattacharyya ◽  
Kaushal Yadav ◽  
Pranjal Jyoti Baruah ◽  
Biswa Jyoti Borkakoty
Keyword(s):  
Present Article ◽  
Sequence Data ◽  
Molecular Data ◽  
Northeast India ◽  
Species Level ◽  
Coi Gene ◽  
Mitochondrial Coi ◽  
Preliminary Examination ◽  
Mitochondrial Coi Gene ◽  
Sudden Appearance

During April 2018, a sudden appearance of some unknown flies was observed in some villages under Sibsagar district of Assam, Northeast India. The flies attacked in groups and had more attraction towards human than livestock. The present article describes the entomological and molecular identification of the fly at species level in Sibsagar district of Assam, northeast India. Preliminary examination revealed the fly to be an insect of order Diptera, Family Tabanidae and Genus Chrysops as they posses short proboscis, ocelli, third antennal joint with five divisions and wings demarcated with dark median cross-band. This was supported by molecular data where the partial nucleotide sequences of Mitochondrial COI gene revealed maximum identity (90.6%-92.3%) with genus Chrysops. The mitochondrial COI sequence data of Chrysops flavocinctus has been made available in NCBI Gen Bank. Gen Bank Accession No. MH998226.

The status of Myriangiaceae (Dothideomycetes)

Phytotaxa ◽  
2014 ◽  
Vol 176 (1) ◽  
pp. 219 ◽  
Author(s):  
ASHA J. DISSANAYAKE ◽  
RUVISHIKA S. JAYAWARDENA ◽  
SARANYAPHAT BOONMEE ◽  
KASUN M. THAMBUGALA ◽  
QING TIAN ◽  
...  
Keyword(s):  
Sequence Data ◽  
Molecular Data ◽  
Molecular Sequence Data ◽  
Molecular Sequence ◽  
The Family ◽  
The Status ◽  
Sexual State ◽  
Morphological And Molecular Data ◽  
Asexual State ◽  
Molecular Characters

The family Myriangiaceae is relatively poorly known amongst the Dothideomycetes and includes genera which are saprobic, epiphytic and parasitic on the bark, leaves and branches of various plants. The family has not undergone any recent revision, however, molecular data has shown it to be a well-resolved family closely linked to Elsinoaceae in Myriangiales. Both morphological and molecular characters indicate that Elsinoaceae differs from Myriangiaceae. In Elsinoaceae, small numbers of asci form in locules in light coloured pseudostromata, which form typical scab-like blemishes on leaf or fruit surfaces. The coelomycetous, “Sphaceloma”-like asexual state of Elsinoaceae, form more frequently than the sexual state; conidiogenesis is phialidic and conidia are 1-celled and hyaline. In Myriangiaceae, locules with single asci are scattered in a superficial, coriaceous to sub-carbonaceous, black ascostromata and do not form scab-like blemishes. No asexual state is known. In this study, we revisit the family Myriangiaceae, and accept ten genera, providing descriptions and discussion on the generic types of Anhellia, Ascostratum, Butleria, Dictyocyclus, Diplotheca, Eurytheca, Hemimyriangium, Micularia, Myriangium and Zukaliopsis. The genera of Myriangiaceae are compared and contrasted. Myriangium duriaei is the type species of the family, while Diplotheca is similar and may possibly be congeneric. The placement of Anhellia in Myriangiaceae is supported by morphological and molecular data. Because of similarities with Myriangium, Ascostratum (A. insigne), Butleria (B. inaghatahani), Dictyocyclus (D. hydrangea), Eurytheca (E. trinitensis), Hemimyriangium (H. betulae), Micularia (M. merremiae) and Zukaliopsis (Z. amazonica) are placed in Myriangiaceae. Molecular sequence data from fresh collections is required to confirm the relationships and placement of the genera in this family.

scholarly journals EPEN-45. NORMALIZING AND FACILITATING GENOMIC TESTING AT DIAGNOSIS IN PEDIATRIC EPENDYMOMA

2020 ◽  
Vol 22 (Supplement_3) ◽  
pp. iii317-iii317
Author(s):  
Emily Owens Pickle ◽  
Ana Aguilar-Bonilla ◽  
Amy Smith
Keyword(s):  
Current Practice ◽  
Molecular Classification ◽  
Molecular Data ◽  
Molecular Profiling ◽  
Genomic Testing ◽  
Molecular Testing ◽  
Newly Diagnosed ◽  
Pediatric Ependymoma ◽  
Need Support ◽  
Almost All

Abstract The current consensus is that diagnosis and treatment of ependymoma should be based upon clinical and molecular classification. As we move into this paradigm, it is important all ependymoma cases undergo tumor collection, preservation, and molecular profiling at diagnosis. Our group of 6 sites gathered data on a cohort of 72 ependymoma cases. Sites were asked to report known molecular findings; 60/68 eligible cases (88%) did not include genetic findings. The low number of cases with molecular findings was surprising and since cases were diagnosed from as early as 2004, we asked collaborators to share their current practice in profiling (e.g., how frequently; in what setting were ependymomas sent for testing) to try and better understand current practice at sites. Since the publication of ependymoma molecular data, sites with a neuro-oncology program report sending almost all newly diagnosed ependymomas for molecular testing, whereas current practices at sites without dedicated neuro-oncology were less consistent. Profiling in the setting of relapse was more frequently reported at all centers. The implementation of molecular testing at diagnosis may need support at sites without dedicated neuro-oncology. Lead investigators for upcoming ependymoma clinical trials will need to think carefully about the logistics of profiling at centers where this is not standard practice at diagnosis.

scholarly journals Genetic Diversity and Pathogenic Variability Among Isolates of Colletotrichum Species from Strawberry

2003 ◽  
Vol 93 (2) ◽  
pp. 219-228 ◽  
Author(s):  
Béatrice Denoyes-Rothan ◽  
Guy Guérin ◽  
Christophe Délye ◽  
Barbara Smith ◽  
Dror Minz ◽  
...  
Keyword(s):  
Sequence Analysis ◽  
Sequence Data ◽  
Random Amplified Polymorphic Dna ◽  
Molecular Data ◽  
Its2 Sequence ◽  
Host Specialization ◽  
Pathogenicity Tests ◽  
Colletotrichum Spp ◽  
Rapd Polymorphism ◽  
Pathogenic Variability

Ninety-five isolates of Colletotrichum including 81 isolates of C. acutatum (62 from strawberry) and 14 isolates of C. gloeosporioides (13 from strawberry) were characterized by various molecular methods and pathogenicity tests. Results based on random amplified polymorphic DNA (RAPD) polymorphism and internal transcribed spacer (ITS) 2 sequence data provided clear genetic evidence of two subgroups in C. acutatum. The first subgroup, characterized as CA-clonal, included only isolates from strawberry and exhibited identical RAPD patterns and nearly identical ITS2 sequence analysis. A larger genetic group, CA-variable, included isolates from various hosts and exhibited variable RAPD patterns and divergent ITS2 sequence analysis. Within the C. acutatum population isolated from strawberry, the CA-clonal group is prevalent in Europe (54 isolates of 62). A subset of European C. acutatum isolates isolated from strawberry and representing the CA-clonal and CA-variable groups was assigned to two pathogenicity groups. No correlation could be drawn between genetic and pathogenicity groups. On the basis of molecular data, it is proposed that the CA-clonal subgroup contains closely related, highly virulent C. acutatum isolates that may have developed host specialization to strawberry. C. gloeosporioides isolates from Europe, which were rarely observed were either slightly or nonpathogenic on strawberry. The absence of correlation between genetic polymorphism and geographical origin in Colletotrichum spp. suggests a worldwide dissemination of isolates, probably through international plant exchanges.

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