scholarly journals Community metabarcoding uncovers vast diversity and a lack of barcode references for aquatic invertebrates in Carpathian spring fens

2021 ◽  
Vol 4 ◽  
Author(s):  
Magdalena Gajdošová ◽  
Arne Beermann ◽  
Jindřiška Bojková ◽  
Vendula Polášková ◽  
Jana Schenková ◽  
...  
Keyword(s):  
Molecular Diversity ◽  
Morphological Characters ◽  
Western Carpathians ◽  
Coi Gene ◽  
Glacial Refugium ◽  
Operational Taxonomic Units ◽  
Spring Fens ◽  
Biogeographic History ◽  
Species Complexes ◽  
Model Community

Recent studies on diversity of stream amphipods proposed that the Western Carpathians have served as an important glacial refugium of freshwater fauna. If this scenario is true, a considerably high molecular diversity can be expected in this biogeographic region also for other taxa. In our project, we aimed to uncover and characterize molecular diversity of benthic macroinvertebrate fauna of spring fens, a well studied and hence convenient model community. Using a DNA metabarcoding approach, we sequenced a fragment of the COI gene of pooled spring fen invertebrate communities from 21 localities in the Western Carpathians. The preliminary analysis of the sequences revealed a substantially higher amount of operational taxonomic units (OTUs), when compared to the number of taxa identified in the same spring fens based on morphological characters. The lack of reference sequences in public databases (Barcoding of Life Database, GenBank) for the majority of the detected OTUs indicates that the Western Carpathian region is not yet sufficiently covered by barcoding efforts, and suggests that there indeed may be a considerable unrecognized diversity of macrozoobenthos. However, most newly uncovered diversity is concentrated in a few taxa such as the dipteran families Tabanidae and Ceratopogonidae, annelid species (complexes) Eiseniella tetraedra and Helobdella stagnalis or the amphipod genus Gammarus. In the future, these findings will be the basis for several levels of research: detailed investigation of seemingly hyperdiverse taxa (phylogeography, phylogeny, reference coverage) and comparison of overall molecular diversity of these communities in the Western Carpathians and neighbouring Bohemian Massif, a region where we expect much lower diversity due to different biogeographic history.

Use of DNA barcode in the identification of fish species from Ribeira de Iguape Basin and coastal rivers from São Paulo State (Brazil)

DNA Barcodes ◽  
2015 ◽  
Vol 3 (1) ◽  
Author(s):  
Jefferson Monteiro Henriques ◽  
Guilherme José Costa Silva ◽  
Fernando Yuldi Ashikaga ◽  
Robert Hanner ◽  
Fausto Foresti ◽  
...  
Keyword(s):  
Species Identification ◽  
Species Concept ◽  
Dna Barcode ◽  
Distinct Species ◽  
Coi Gene ◽  
Morphological Identification ◽  
Operational Taxonomic Units ◽  
Paulo State ◽  
Species Complexes ◽  
Definition Of

AbstractSpecies identification is a difficult task, ranging from the definition of the species concept itself to the definition of the threshold for speciation. DNA Barcode technology uses a fragment of the Cytochrome Oxidase I (COI) gene as a molecular tool that many studies have already validated as a tool for species identification. DNA barcode sequences for COI were generated and analyzed from 805 specimens. The General Mixed Yule Coalescent (GMYC) analysis recognized 99 independent evolution units, and the Barcode Index Numbers (BIN) approach pointed to the existence of 104 BINs (interpreted as distinct species). By cross-tabulating the results of all approaches, we identified 109 Molecular Operational Taxonomic Units (MOTU) by at least one methodology. In most cases (89 MOTUs), the genetic approaches are in agreement with morphological identification, and the discrepant results of MOTUs are in the complex groups, which have many morphological similarities but may represent species complexes.

scholarly journals Sand fly identification and screening for Leishmania spp. in six provinces of Thailand

2021 ◽  
Vol 14 (1) ◽  
Author(s):  
Orawan Phuphisut ◽  
Chanyapat Nitatsukprasert ◽  
Nattaphol Pathawong ◽  
Boonsong Jaichapor ◽  
Arissara Pongsiri ◽  
...  
Keyword(s):  
Dna Barcoding ◽  
Distinct Species ◽  
Morphological Characters ◽  
Sand Fly ◽  
Morphological Identification ◽  
Sand Flies ◽  
Operational Taxonomic Units ◽  
Species Complexes ◽  
Human Leishmaniasis ◽  
Leishmania Spp

Abstract Background Phlebotomine sand flies are vectors of Leishmania spp. At least 27 species of sand flies have been recorded in Thailand. Although human leishmaniasis cases in Thailand are mainly imported, autochthonous leishmaniasis has been increasingly reported in several regions of the country since 1999. Few studies have detected Leishmania infection in wild-caught sand flies, although these studies were carried out only in those areas reporting human leishmaniasis cases. The aim of this study was therefore to identity sand fly species and to investigate Leishmania infection across six provinces of Thailand. Methods Species of wild-caught sand flies were initially identified based on morphological characters. However, problems identifying cryptic species complexes necessitated molecular identification using DNA barcoding in parallel with identification based on morphological characters. The wild-caught sand flies were pooled and the DNA isolated prior to the detection of Leishmania infection by a TaqMan real-time PCR assay. Results A total of 4498 sand flies (1158 males and 3340 females) were caught by trapping in six provinces in four regions of Thailand. The sand flies were morphologically classified into eight species belonging to three genera (Sergentomyia, Phlebotomus and Idiophlebotomus). Sergentomyia iyengari was found at all collection sites and was the dominant species at most of these, followed in frequency by Sergentomyia barraudi and Phlebotomus stantoni, respectively. DNA barcodes generated from 68 sand flies allowed sorting into 14 distinct species with 25 operational taxonomic units, indicating a higher diversity (by 75%) than that based on morphological identification. Twelve barcoding sequences could not be assigned to any species for which cytochrome c oxidase subunit I sequences are available. All tested sand flies were negative for Leishmania DNA. Conclusions Our results confirm the presence of several sand fly species in different provinces of Thailand, highlighting the importance of using DNA barcoding as a tool to study sand fly species diversity. While all female sand flies tested in this study were negative for Leishmania, the circulation of Leishmania spp. in the investigated areas cannot be ruled out. Graphical abstract

Morphological and molecular diversity of rissoellids (Mollusca, Gastropoda, Heterobranchia) from the Northwest Pacific island of Hokkaido, Japan

Zootaxa ◽  
2019 ◽  
Vol 4551 (4) ◽  
pp. 415
Author(s):  
LUIS E. CHIRA SIADÉN ◽  
KEVIN C. WAKEMAN ◽  
STEPHEN C. WEBB ◽  
KAZUNORI HASEGAWA ◽  
HIROSHI KAJIHARA
Keyword(s):  
Molecular Diversity ◽  
Morphological Characters ◽  
Coi Gene ◽  
Northwest Pacific ◽  
Dorsal Margin ◽  
Visceral Mass ◽  
Lateral Projection ◽  
The Family ◽  
Central Tooth ◽  
Different Color

This study deals with four species of marine microgastropods of the family Rissoellidae. Rissoella elatior (Golikov, Gulbin & Sirenko, 1987), R. golikovi (Gulbin, 1979), R. japonica n. sp., and Rissoella sp. 1 were collected in different locations around the island of Hokkaido, Japan. Light and scanning electron microscopy (SEM) were used to study the general morphology of the shell and radula, and a region of the mitochondrial cytochrome c oxidase subunit I (COI) gene was amplified for 26 specimens. Rissoella elatior is morphologically characterized by a highly asymmetrical radula with a deep notch encircled by 10–13 minute secondary cusps on the left dorsal margin of the central tooth. Rissoella golikovi is characterized by a skeneiform shell and possession of three teeth per row on the radula. Rissoella japonica n. sp. shows five teeth per row on the radula; central tooth higher than wide; lateral and marginal teeth narrow with an outer lateral projection at the base; all teeth presenting numerous small cusps on the cutting edge. Rissoella sp. 1 is distinguished from R. japonica n. sp. in having i) very short oral lobes, ii) a mantle with a large, black patch and whitish blotches inside, and iii) different color patterns associated with the visceral mass. Although Rissoella sp. 1 probably represents an undescribed species, additional specimens are needed to complete its description. This study represents a first molecular approach to the family Rissoellidae. Studies of traditional morphological characters indicated four species, the addition of COI data raised the count to eight potential species, suggesting the occurrence of cryptic species among rissoellids. 

Comparative Analysis of Genetic and Morphological Variation within the Platanthera hyperborea Complex (Orchidaceae)

2020 ◽  
Vol 45 (4) ◽  
pp. 767-778
Author(s):  
Eranga Wettewa ◽  
Nick Bailey ◽  
Lisa E. Wallace
Keyword(s):  
North America ◽  
Diploid Species ◽  
Morphological Characters ◽  
Evolutionary Patterns ◽  
Founding Population ◽  
Multiple Origins ◽  
Geographic Structure ◽  
Species Complexes ◽  
Nuclear Its ◽  
Cryptic Taxa

Abstract—Species complexes present considerable problems for a working taxonomy due to the presence of intraspecific variation, hybridization, polyploidy, and phenotypic plasticity. Understanding evolutionary patterns using molecular markers can allow for a more thorough assessment of evolutionary lineages than traditional morphological markers. In this study, we evaluated genetic diversity and phylogenetic patterns among taxa of the Platanthera hyperborea (Orchidaceae) complex, which includes diploid (Platanthera aquilonis) and polyploid (Platanthera hyperborea, P. huronensis, and P. convallariifolia) taxa spanning North America, Greenland, Iceland, and Asia. We found that three floral morphological characters overlap among the polyploid taxa, but the diploid species has smaller flowers. DNA sequence variation in a plastid (rpL16 intron) and a nuclear (ITS) marker indicated that at least three diploid species have contributed to the genomes of the polyploid taxa, suggesting all are of allopolyploid origin. Platanthera convallariifolia is most like P. dilatata and P. stricta, whereas P. huronensis and P. hyperborea appear to have originated from crosses of P. dilatata and P. aquilonis. Platanthera huronensis, which is found across North America, has multiple origins and reciprocal maternal parentage from the diploid species. By contrast, P. hyperborea, restricted to Greenland and Iceland, appears to have originated from a small founding population of hybrids in which P. dilatata was the maternal parent. Geographic structure was found among polyploid forms in North America. The area of Manitoba, Canada appears to be a contact zone among geographically diverse forms from eastern and western North America. Given the geographic and genetic variation found, we recommend continued recognition of four green-flowered species within this complex, but caution that there may be additional cryptic taxa within North America.

Are Tetranychus macfarlanei Baker & Pritchard and Tetranychus malaysiensis Ehara (Acari: Tetranychidae) one species? Morphological and molecular evidences for synonymy between these two spider mite species and a note on invasiveness of T. macfarlanei on okra and eggplant in India

2017 ◽  
Vol 22 (4) ◽  
pp. 467
Author(s):  
Mahran Zeity ◽  
Nagappa Srinivas ◽  
Chinnamade Channegowde Gowda
Keyword(s):  
Spider Mite ◽  
Morphological Characters ◽  
Molecular Data ◽  
Mite Species ◽  
Coi Gene ◽  
High Similarity ◽  
Mitochondrial Coi ◽  
Mitochondrial Coi Gene ◽  
High Degree ◽  
Degree Of Similarity

Study of morphological characters of Tetranychus macfarlanei Baker & Pritchard and Tetranychus malaysiensis Ehara revealed high similarity by comparing all the important characters in addition to the characters pointed out by Ehara to separate those two species. Molecular phylogeny of seven Indian populations of T. macfarlanei and one population of T. malaysiensis from Philippines along with few distantly related species of Tetranychus was attempted. High degree of similarity between these two species at mitochondrial COI gene (96%) as well as ITS2 (rDNA) (96–99%) region was evident. Based on both morphological features and molecular data, T. malaysiensis is proposed as a junior synonym of T. macfarlanei based on ICZN’s law of priority. Also more female characters are prompted in this study to distinctly discriminate T. macfarlanei from its most resembling species, Tetranychus ludeni Zacher. Tetranychus macfarlanei has emerged as a pest of several cultivated crop plants in India. 

Intraspecific variability of morphological characters in the species-rich deep-sea genus Acantholaimus Allgén, 1933 (Nematoda: Chromadoridae)

Nematology ◽  
2016 ◽  
Vol 18 (4) ◽  
pp. 455-473 ◽  
Author(s):  
Dmitry M. Miljutin ◽  
Maria A. Miljutina
Keyword(s):  
Deep Sea ◽  
Intraspecific Variability ◽  
Morphological Characters ◽  
Molecular Data ◽  
Species Discrimination ◽  
Species Differentiation ◽  
Lateral Field ◽  
Operational Taxonomic Units ◽  
General Arrangement ◽  
Taxonomic Approach

Acantholaimusis a species-rich genus of deep-sea nematodes, often with dozens of species found at the same locality but each represented by single or few individuals. Species discrimination by morphological characters in this genus is therefore often difficult due to transitional forms that may be referred to several species because of lack of data on intraspecific variability. The aim of this study was to evaluate the intraspecific variability of morphological characters that are most often used inAcantholaimustaxonomy, in order to distinguish those which are most informative for species differentiation. A reverse taxonomic approach was applied for initial species discrimination. Two loci, one each from small and large subunits of rRNA, were sequenced for 59Acantholaimusspecimens from two deep-sea locations. Twenty-seven Molecular Operational Taxonomic Units (MOTU) were identified, of which 12 were represented by more than one individual. These were then analysed for intraspecific variability in morphological characters. Some of the examined characters showed high intraspecific variability; specifically: length of cephalic setae; distance from anterior end to amphid; shape of anterior setae; position and arrangement of cervical setae. In the absence of genetic data, these characters should be used with caution for differential diagnoses or species discrimination. Other characters were more conservative within the same MOTU: body proportions; length of outer labial setae; amphidial diam.; appearance of lateral field; general arrangement of cervical setae; and shape of tail. These characters may be successfully used for species discrimination in the absence of molecular data.

scholarly journals Molecular diversity of bacteria in commercially available “Spirulina” food supplements

PeerJ ◽  
2016 ◽  
Vol 4 ◽  
pp. e1610 ◽  
Author(s):  
Elisabeth Vardaka ◽  
Konstantinos A. Kormas ◽  
Matina Katsiapi ◽  
Savvas Genitsaris ◽  
Maria Moustaka-Gouni
Keyword(s):  
Natural Product ◽  
454 Pyrosequencing ◽  
Molecular Diversity ◽  
Arthrospira Platensis ◽  
Food Supplements ◽  
Health Issues ◽  
Operational Taxonomic Units ◽  
Health Promoting ◽  
First Time ◽  
Pyrosequencing Analysis

The cyanobacteriumArthrospirais among the most well-known food supplements worldwide known as “Spirulina.” While it is a widely recognized health-promoting natural product, there are no reports on the molecular diversity of commercially available brands of “Spirulina” supplements and the occurrence of other cyanobacterial and heterotrophic bacterial microorganisms in these products. In this study, 454-pyrosequencing analysis of the total bacterial occurrence in 31 brands of “Spirulina” dietary supplements from the Greek market was applied for the first time. In all samples, operational taxonomic units (OTUs) ofArthrospira platensiswere the predominant cyanobacteria. Some products contained additional cyanobacterial OTUs including a few known potentially toxic taxa. Moreover, 469 OTUs were detected in all 31 products collectively, with most of them being related to the Proteobacteria, Firmicutes, Bacteroidetes, Actinobacteria and Verrucomicrobia. All samples included heterotrophic bacterial OTUs, ranging from 9–157 per product. Among the most common OTUs were ones closely related to taxa known for causing health issues (i.e.,Pseudomonas,Flavobacterium,Vibrio,Aeromonas,Clostridium,Bacillus,Fusobacterium,Enterococcus). The observed high cyanobacterial and heterotrophic bacterial OTUs richness in the final product is a point for further research on the growth and processing ofArthrospirabiomass for commercial purposes.

scholarly journals New records of Celaenorrhinus pyrrha de Nicéville, 1889 and C. munda (Moore, 1884) from China (Lepidoptera, Hesperiidae)

ZooKeys ◽  
2020 ◽  
Vol 985 ◽  
pp. 61-70
Author(s):  
Guo-Xi Xue ◽  
Yutaka Inayoshi ◽  
Meng Li ◽  
Fu-Ming Zhang ◽  
Da-Kun Lai ◽  
...  
Keyword(s):  
Gene Sequence ◽  
New Records ◽  
Morphological Characters ◽  
Coi Gene ◽  
Distribution Map ◽  
Male Specimen ◽  
Autonomous Region ◽  
Tibet Autonomous Region ◽  
First Time ◽  
The Tibet Autonomous Region

Celaenorrhinus pyrrha de Nicéville, 1889, a rare species of Hesperiidae previously known to be distributed from northeastern India to Indochina, is reported from southwestern Yunnan and southwestern Chongqing, China. A 658 bp COI gene sequence of this species is published for the first time. Although Chongqing is obviously isolated from the main distribution range, morphological characters of the specimens from this locality do not indicate a subspecies differentiation. Another rare taxon, C. munda munda (Moore, 1884), is also recorded from China for the first time based upon a male specimen from Cuona County in the Tibet Autonomous Region. This is the second specimen of C. munda from China, over 100 years after the holotype of C. munda joka Evans, 1949. The genitalia of both species are illustrated and described. Some taxonomic notes and a distribution map are provided as well.

Taxonomic Synopsis of Eriosema (Leguminosae: Papilionoideae, Phaseoleae) in Brazil

Phytotaxa ◽  
2019 ◽  
Vol 416 (2) ◽  
pp. 91-137 ◽  
Author(s):  
ELISA SILVA CÂNDIDO ◽  
WANDERLEIA DE VARGAS ◽  
LUÍSA MARIA DE PAULA ALVES BEZERRA ◽  
VIDAL DE FREITAS MANSANO ◽  
MOHAMMAD VATANPARAST ◽  
...  
Keyword(s):  
Field Work ◽  
Morphological Characters ◽  
Second Step ◽  
Correct Identification ◽  
Type Specimens ◽  
Distribution Maps ◽  
Savanna Vegetation ◽  
Tropical Environments ◽  
Species Complexes ◽  
Representative Species

Eriosema is a pantropical genus occurring mostly in savanna vegetation and grasslands of tropical environments, with approximately 150 species and two centers of diversity, one in Africa with about 110 species, and the other in the Neotropics with about 40 species. Considering the large number of Eriosema taxa in Brazil, including five recently described, and the lack of recent study that encompasses all species that occur in the country, a taxonomic synopsis of the Brazilian species of Eriosema was needed and is presented here. Herbaria collections, including type specimens, were consulted and field work was carried out in Brazil. Our study records 35 Eriosema species in Brazil, which concentrates most of the diversity of the genus in the Americas (85%; 35 out of 41 species). Most of this diversity occurs in the Central Brazilian savannas, particularly in the states of Goiás (29 taxa, eight endemic), and Minas Gerais (26 taxa, four endemic). Among all American species in the genus, Eriosema simplicifolium and E. crinitum have the broadest geographical distributions, and occur throughout Brazil and most part of the American continent. They form species complexes and future detailed studies will be necessary in order to understand taxon boundaries and delimitations. An identification key, taxon descriptions, information about type specimens as well as information on the habitat, phenological and geographical records, together with distribution maps, images of representative species in the field and the main morphological characters are provided to assist in the correct identification of this group of savanna plants. We also present 15 lectotypifications, out of which three are second-step.

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