scholarly journals Testing DNA barcoding in Usnea (Parmeliaceae) in Colombia using the internal transcribed spacer (ITS)

2020 ◽  
pp. 358-385
Author(s):  
Bibiana Moncada ◽  
Harrie Sipman ◽  
Robert Lücking
Keyword(s):  
Phylogenetic Analysis ◽  
Success Rate ◽  
Dna Barcoding ◽  
Reference Data ◽  
Integrative Taxonomy ◽  
Multiple Alignment ◽  
Its Sequences ◽  
Data Set ◽  
Reference Sequences ◽  
First Time

We tested the functionality of ITS-based DNA barcoding in lichen fungi using Colombian samples of the genus Usnea as an example. New ITS sequences were generated for 15 samples from five localities in two different ecoregions, representing varying morphologies and medullary chemistries. We employed five strategies to identify the samples: (1) BLASTn on the NCBI BLAST site with the original identifications of the best matching reference sequences; (2) as previous, but with revised identifications of the reference sequences based on a separately published revision of ITS sequences published for the genus; (3) local BLASTn in BioEdit using a separately published, revised and curated set of ITS reference sequences for the genus; (4) multiple alignment based phylogenetic analysis within the framework of all available ITS sequences for Usnea s.str.; and (5) integrative taxonomy, combining molecular phylogeny and comparative analysis of phenotype and chemical data. Using the latter approach as reference, we found that NCBI BLASTn with original identifications performed poorly, resulting in an identification success rate of only 7% (a single sample). NCBI BLASTn with revised identifications more than tripled identification success (23%), but was still unsatisfactory. Local BLASTn in BioEdit using the revised, curated reference data further doubled identification success (47%), but remained inadequate. Multiple alignment-based phylogenetic analysis achieved an identification success rate of 80% compared to the result from integrative taxonomy. Based on these results, we conclude that ITS-based DNA barcoding of the genus Usnea under the current circumstances performs poorly, but can be substantially improved using three strategies: (1) update identifications of reference sequences in primary repositories such as GenBank or alternatively use a curated reference data set; (2) perform local BLAST with a curated reference data set focusing on the target genus only, combined with multiple alignment-based phylogenetic analysis as a verification step; and (3) close substantial geographic and taxonomic gaps in the existing reference data. Our analyses suggest that if a near-complete reference data set with correct identifications existed for the genus, then standard BLAST approaches could achieve high levels of identification success close to 100%. As part of our DNA barcoding exercise, which generated the first 15 ITS sequences for Colombian samples of the genus Usnea, we confirm the presence of U. aranea and U. wasmuthii in Colombia and we report for the first time U. tenuicorticata for the country.

scholarly journals The Trichoptera barcode initiative: a strategy for generating a species-level Tree of Life

2016 ◽  
Vol 371 (1702) ◽  
pp. 20160025 ◽  
Author(s):  
Xin Zhou ◽  
Paul B. Frandsen ◽  
Ralph W. Holzenthal ◽  
Clare R. Beet ◽  
Kristi R. Bennett ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Dna Barcoding ◽  
Dna Sequences ◽  
Integrative Taxonomy ◽  
Tree Of Life ◽  
Species Level ◽  
Species Boundaries ◽  
Dna Barcodes ◽  
Index Numbers ◽  
Reference Specimens

DNA barcoding was intended as a means to provide species-level identifications through associating DNA sequences from unknown specimens to those from curated reference specimens. Although barcodes were not designed for phylogenetics, they can be beneficial to the completion of the Tree of Life. The barcode database for Trichoptera is relatively comprehensive, with data from every family, approximately two-thirds of the genera, and one-third of the described species. Most Trichoptera, as with most of life's species, have never been subjected to any formal phylogenetic analysis. Here, we present a phylogeny with over 16 000 unique haplotypes as a working hypothesis that can be updated as our estimates improve. We suggest a strategy of implementing constrained tree searches, which allow larger datasets to dictate the backbone phylogeny, while the barcode data fill out the tips of the tree. We also discuss how this phylogeny could be used to focus taxonomic attention on ambiguous species boundaries and hidden biodiversity. We suggest that systematists continue to differentiate between ‘Barcode Index Numbers’ (BINs) and ‘species’ that have been formally described. Each has utility, but they are not synonyms. We highlight examples of integrative taxonomy, using both barcodes and morphology for species description. This article is part of the themed issue ‘From DNA barcodes to biomes’.

New species of Mycena (Mycenaceae, Agaricales) with colored lamellae and three new species records from China

Phytotaxa ◽  
2018 ◽  
Vol 361 (3) ◽  
pp. 266 ◽  
Author(s):  
QIN NA ◽  
TOLGOR BAU
Keyword(s):  
Phylogenetic Analysis ◽  
New Species ◽  
Bayesian Inference ◽  
Maximum Likelihood ◽  
North America ◽  
Morphological Characters ◽  
Its Sequences ◽  
Monophyletic Clade ◽  
Three New Species ◽  
First Time

Four species of Mycena possessing a colored lamellar are reported. Of these, Mycena entolomoides is described as new and is distinguished by an incarnate color of the whole lamellae, and M. citrinomarginata, M. purpureofusca, and M. strobilinoidea are recorded for the first time in China. A complete description, drawings and photographs of the morphological characters of M. entolomoides sp. nov. are accompanied by comparisons with closely related taxa. The three species newly recorded in China are considered in agreement with those species in Europe and North America. Phylogenetic analysis based on ITS sequences showed that M. entolomoides sp. nov. forms a monophyletic clade, well supported by maximum likelihood and Bayesian inference.

Phylogenetic analysis of the genus Cylicocyclus (Nematoda: Strongylidae) based on nuclear ribosomal sequence data

2013 ◽  
Vol 58 (2) ◽  
Author(s):  
Yanzhen Bu ◽  
Hongxing Niu ◽  
Luping Zhang
Keyword(s):  
Phylogenetic Analysis ◽  
Internal Transcribed Spacer ◽  
Species Complex ◽  
Phylogenetic Trees ◽  
Sequence Data ◽  
Phylogenetic Analyses ◽  
Its Sequences ◽  
Data Sets ◽  
Reference Sequences ◽  
Second Internal Transcribed Spacer

AbstractSeven species of Cylicocyclus Ihle, 1922 (Nematoda: Strongylidae) were collected from donkeys from Henan Province, China. Five samples of each species were selected for sequencing. Sixteen different internal transcribed spacer (ITS) sequences representing the seven species of Cylicocyclus were obtained. Sequence differences in the first internal transcribed spacer (ITS-1) among species was lower than that of the second internal transcribed spacer (ITS-2). Phylogenetic analyses were conducted using the combined ITS-1 and ITS-2 data sets from the present study and using reference sequences from the GenBank database. The MP and ML trees were similar in topology. The phylogenetic trees were divided into two clades. Clade I included 8 species of Cylicocyclus; within this group, Cylicocyclus leptostomus (Kotlan, 1920) is nested between different samples of Cylicocyclus ashworthi (LeRoux, 1924), suggesting C. ashworthi may represent a species complex. Clade II included Cylicocyclus elongatus (Looss, 1900) and Cylicocyclus ultrajectinus (Ihle, 1920); however, these two species always clustered with the comparative species (Petrovinema poculatum (Looss, 1900) and Poteriostomum imparidentatum Quiel, 1919), suggesting that C. elongatus and C. ultrajectinus represent members of other genera.

scholarly journals Reassessment of the phylogenetic interrelationships of basal turtles (Testudinata)

2017 ◽  
Author(s):  
Jérémy Anquetin
Keyword(s):  
Phylogenetic Analysis ◽  
Data Matrix ◽  
Late Triassic ◽  
Character State ◽  
Additional Species ◽  
Data Set ◽  
Fossil Species ◽  
Turtle Species ◽  
Phylogenetic Placement ◽  
First Time

Recent discoveries from the Late Triassic and Middle Jurassic have significantly improved the fossil record of early turtles. These new forms offer a unique opportunity to test the interrelationships of basal turtles. Nineteen fossil species are added to the taxon sample of the most comprehensive morphological phylogenetic analysis of the turtle clade. Among these additional species are recently discovered forms (e.g., Odontochelys semitestacea, Eileanchelys waldmani, Condorchelys antiqua), taxa generally omitted from previous analyses (e.g., chengyuchelyids, Sichuanchelys chowi) and species included in a phylogenetic analysis for the first time (Naomichelys speciosa and Siamochelys peninsularis). The coding of several characters is reassessed in light of recent observations, but also in order to reduce unwarranted assumptions on character and character state homologies. Additional characters from previous analyses, as well as five new ones, are also included, resulting in a data matrix of 178 characters scored for 86 turtle species and 7 fossil outgroups.The data set resolves the relationships of most newly included taxa, with the exception of Sichuanchelys chowi and ‘Chengyuchelys’ dashanpuensis. The phylogenetic placement of Heckerochelys romani, Condorchelys antiqua and Eileanchelys waldmani as stem turtles more derived than Kayentachelys aprix but more basal than Meiolania platyceps and Mongolochelys efremovi is corroborated. The relationships of chengyuchelyids remain unclear and more investigation is needed regarding these forms, yet interestingly they are unstable with respect to stem turtles. In contrast to previous analyses, Arundelemys dardeni is placed within pleurosternids. Siamochelys peninsularis falls within xinjiangchelyids. Perhaps the most salient conclusion of the present study is the placement of Naomichelys speciosa as a basal member of a clade uniting meiolaniids, Mongolochelys efremovi and Otwayemys cunicularius. This clade of rather large stem turtles was spread worldwide during the Mesozoic at least and persisted up until the Pleistocene with meiolaniids.

Evaluation of the DNA barcoding approach to develop a reference data-set for the threatened flora of Sicily

2014 ◽  
Vol 150 (4) ◽  
pp. 631-640 ◽  
Author(s):  
A. Giovino ◽  
P. Marino ◽  
G. Domina ◽  
A. Scialabba ◽  
R. Schicchi ◽  
...  
Keyword(s):  
Dna Barcoding ◽  
Reference Data ◽  
Data Set

First report of Agaricus sect. Brunneopicti from Pakistan with descriptions of two new species

Phytotaxa ◽  
2018 ◽  
Vol 357 (3) ◽  
pp. 167 ◽  
Author(s):  
HIRA BASHIR ◽  
SHAH HUSSAIN ◽  
ABDUL NASIR KHALID ◽  
ABDUL REHMAN KHAN NIAZI ◽  
LUIS A. PARRA ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
New Species ◽  
Morphological Characters ◽  
Its Sequences ◽  
Saprophytic Fungi ◽  
Brown Discoloration ◽  
Two New Species ◽  
First Time ◽  
Desert Climate ◽  
Semi Arid

Agaricus is a genus of saprophytic fungi in the Basidiomycota. As part of ongoing studies on the genus Agaricus in Pakistan, we here describe and discuss two new species, A. pakistanicus sp. nov. and A. sparsisquamosus sp. nov. Morphological characters and phylogenetic analysis of ITS sequences were used to clarify their taxonomic affinities. Phylogenetic analysis indicated that both species belong to A. sect. Brunneopicti. This palaeotropical section, which has been recently reconstructed, is reported in Pakistan for the first time. Interestingly, these two new species exhibit a reddish or brown discoloration. With these two new species, the distribution of this section, which was previously restricted to tropical and subtropical humid regions, now extends to semi-arid and desert climate regions and the total number of species in the section increases to 20, including eight unnamed species.

Taxonomic review and cladistic analysis of Neotropical spider genus Epicratinus Jocqué & Baert, 2005 (Araneae: Zodariidae) with description of eleven new species

Zootaxa ◽  
2020 ◽  
Vol 4886 (1) ◽  
pp. 1-77
Author(s):  
RICARDO ANTONIO GONÇALVES ◽  
ANTONIO DOMINGOS BRESCOVIT
Keyword(s):  
Phylogenetic Analysis ◽  
Cladistic Analysis ◽  
Taxonomic Revision ◽  
Morphological Characters ◽  
Morphological Data ◽  
Data Set ◽  
Distribution Maps ◽  
Character Weighting ◽  
Males And Females ◽  
First Time

A taxonomic revision and phylogenetic analysis of the spider genus Epicratinus Jocqué & Baert, 2005 is presented. The phylogenetic analysis is based on a data set including 16 Epicratinus species plus 9 outgroups representing by five related zodariid gen­era and one of them considered most basal as the root. These taxa were scored for 49 morphological characters. Parsimony was used as the op­timality criterion and a sensitivity analysis was performed using different character weighting concavities. Five unambiguous synapomorphies support the monophyly of Epicratinus. Some internal clades within the genus are well-supported and their relationships are discussed. Epicratinus includes 16 species, all with males and females. A species identification key and distribution maps are provided for all. New morphological data are also pre­sented for five previously described species. All 16 species occur only in the New World. The following species are transferred to Epicratinus: E. perfidus (Jocqué & Baert), comb. nov. from Tenedos; Epicratinus perfidus Jocqué & Baert comb. nov. and newly synonymized with E. santacruz Grismado & Izquierdo and this last species is treated as the junior synonym. Epicratinus petropolitanus (Mello-Leitão) has the male described for the first time. The following 11 species are newly described as new: E. zangief sp. nov.; E. pegasus sp. nov.; E. pikachu sp. nov.; E. stitch sp. nov.; E. ehonda sp. nov.; E. anakin sp. nov.; E. vader sp. nov.; E. omegarugal sp. nov.; E. zelda sp. nov.; E. dookan sp. nov. and E. mauru sp. nov., all from Brazil. 

New and noteworthy lichen-forming and lichenicolous fungi 10

2020 ◽  
Vol 62 (1-2) ◽  
pp. 69-108
Author(s):  
S. Y. Kondratyuk ◽  
D. K. Upreti ◽  
G. K. Mishra ◽  
S. Nayaka ◽  
K. K. Ingle ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
South Korea ◽  
Eastern Europe ◽  
South Asia ◽  
New Combinations ◽  
Eastern Asia ◽  
Forest Zone ◽  
Mediterranean Europe ◽  
First Time ◽  
India And China

Eight species, new for science, i.e.: Lobothallia gangwondoana S. Y. Kondr., J.-J. Woo et J.-S. Hur and Phyllopsora dodongensis S. Y. Kondr. et J.-S. Hur from South Korea, Eastern Asia, Ioplaca rinodinoides S. Y. Kondr., K. K. Ingle, D. K. Upreti et S. Nayaka, Letrouitia assamana S. Y. Kondr., G. K. Mishra et D. K. Upreti, and Rusavskia indochinensis S. Y. Kondr., D. K. Upreti et S. Nayaka from India and China, South Asia, Caloplaca orloviana S. Y. Kondr. and Rusavskia drevlyanica S. Y. Kondr. et O. O. Orlov from Ukraine, Eastern Europe, as well as Xanthoria ibizaensis S. Y. Kondr. et A. S. Kondr. from Ibiza Island, Spain, Mediterranean Europe, are described, illustrated and compared with closely related taxa. Fominiella tenerifensis S. Y. Kondr., Kärnefelt, A. Thell et Feuerer is for the first time recorded from Mediterranean Europe, Huriella loekoesiana S. Y. Kondr. et Upreti is provided from Russia for the first time, and H. pohangensis S. Y. Kondr., L. Lőkös et J.-S. Hur for the first time from China, Phoma candelariellae Z. Kocakaya et Halıcı is new to Ukraine, and Staurothele frustulenta Vain. is recorded from the Forest Zone of Ukraine for the first time. Twelve new combinations, i.e.: Bryostigma apotheciorum (for Sphaeria apotheciorum A. Massal.), Bryostigma biatoricola (for Arthonia biatoricola Ihlen et Owe-Larss.), Bryostigma dokdoense (for Arthonia dokdoensis S. Y. Kondr., L. Lőkös, B. G. Lee, J.-J. Woo et J.-S. Hur), Bryostigma epiphyscium (for Arthonia epiphyscia Nyl.), Bryostigma lobariellae (for Arthonia lobariellae Etayo), Bryostigma lapidicola (for Lecidea lapidicola Taylor), Bryostigma molendoi (for Tichothecium molendoi Heufl. ex Arnold), Bryostigma neglectulum (for Arthonia neglectula Nyl.), Bryostigma parietinarium (for Arthonia parietinaria Hafellner et Fleischhacker), Bryostigma peltigerinum (for Arthonia vagans var. peltigerina Almq.), Bryostigma phaeophysciae (for Arthonia phaeophysciae Grube et Matzer), Bryostigma stereocaulinum (for Arthonia nephromiaria var. stereocaulina Ohlert), are proposed based on results of combined phylogenetic analysis based on mtSSU and RPB2 gene sequences. Thirty-one new combinations for members of the genus Polyozosia (i.e.: Polyozosia actophila (for Lecanora actophila Wedd.), Polyozosia agardhiana (for Lecanora agardhiana Ach.), Polyozosia altunica (for Myriolecis altunica R. Mamut et A. Abbas), Polyozosia antiqua (for Lecanora antiqua J. R. Laundon), Polyozosia bandolensis (for Lecanora bandolensis B. de Lesd.), Polyozosia behringii (for Lecanora behringii Nyl.), Polyozosia caesioalutacea (for Lecanora caesioalutacea H. Magn.), Polyozosia carlottiana (for Lecanora carlottiana C. J. Lewis et Śliwa), Polyozosia congesta (for Lecanora congesta Clauzade et Vězda), Polyozosia eurycarpa (for Lecanora eurycarpa Poelt, Leuckert et Cl. Roux), Polyozosia expectans (Lecanora expectans Darb.), Polyozosia flowersiana (Lecanora flowersiana H. Magn.), Polyozosia fugiens (for Lecanora fugiens Nyl.), Polyozosia invadens (for Lecanora invadens H. Magn.), Polyozosia juniperina (for Lecanora juniperina Śliwa), Polyozosia latzelii (for Lecanora latzelii Zahlbr.), Polyozosia liguriensis (for Lecanora liguriensis B. de Lesd.), Polyozosia massei (for Myriolecis massei M. Bertrand et J.-Y. Monnat), Polyozosia mons-nivis (for Lecanora mons-nivis Darb.), Polyozosia oyensis (for Lecanora oyensis M.-P. Bertrand et Cl. Roux), Polyozosia percrenata (for Lecanora percrenata H. Magn.), Polyozosia persimilis (for Lecanora hagenii subsp. persimilis Th. Fr.), Polyozosia poeltiana (for Lecanora poeltiana Clauzade et Cl. Roux), Polyozosia prominens (for Lecanora prominens Clauzade et Vězda), Polyozosia prophetae-eliae (for Lecanora prophetae-eliae Sipman), Polyozosia salina (for Lecanora salina H. Magn.), Polyozosia schofieldii (for Lecanora schofieldii Brodo), Polyozosia sverdrupiana (for Lecanora sverdrupiana Øvstedal), Polyozosia torrida (for Lecanora torrida Vain.), Polyozosia wetmorei (for Lecanora wetmorei Śliwa), Polyozosia zosterae (for Lecanora subfusca? zosterae Ach.)) are proposed.

RESULTS OF INTRALESIONAL TRIAMCINOLONE ACETONIDE FOR CHALAZION TREATMENT

2011 ◽  
pp. 100-104
Author(s):  
Thi Thu Nguyen ◽  
Viet Hien Vo ◽  
Thi Em Do
Keyword(s):  
Success Rate ◽  
Key Words ◽  
Triamcinolone Acetonide ◽  
Lower Eyelid ◽  
Upper Eyelid ◽  
Interventional Trial ◽  
The Mean ◽  
First Time

The study use intralesional triamcinolone acetonide injection proceduce for chalazion treatment.1. Objectives: To evaluate results of intralesional triamcinolone acetonide injection for chalazion treatment. 2. Method: This noncomparative prospective interventional trial included 72 chalazions of 61 patients. 3. Results: 61 patients (72 chalazions) with 19 males (31.1%) và 42 females (68.9%), the mean age was 24 ± 9,78 years. 31.1% patients was the first time chalazion and 68.9% patients was more than one times chalazion including 78.6% patients was recurrent at the first position and 21.4% patients occur at new position. 72 chalazions with 16 (22.2%) chalazions was treated before and 56 (77.8%) chalazions wasn’t done that. 72 chalazions with 49 chalazions (68.1%) are local in upper eyelid and 23 chalazions (31.9%) are local in lower eyelid. The mean of chalazion diameter is 6.99 ± 3.03mm. Intralesional triamcinolone acetonide is injected to treat 72 chalazions with 16 (22.2%) chalazions are injected through the route of skin and 56 (77.8%) chalazions are injected through the route of conjunctiva. After 2 weeks follow-up, the success rate was 93.1% and 6.9% failed. 4. Conclusion: intralesional triamcinolone acetonide injection for chalazion treatment is really effective. Key words: chalazion, intralesional triamcinolone acetonide.

scholarly journals Integrative Taxonomy and Molecular Phylogeny of the Plant-Parasitic Nematode Genus Paratylenchus (Nematoda: Paratylenchinae): Linking Species with Molecular Barcodes

Plants ◽  
2021 ◽  
Vol 10 (2) ◽  
pp. 408
Author(s):  
Phougeishangbam Rolish Singh ◽  
Gerrit Karssen ◽  
Marjolein Couvreur ◽  
Sergei A. Subbotin ◽  
Wim Bert
Keyword(s):  
18S Rrna ◽  
Parasitic Nematode ◽  
Integrative Taxonomy ◽  
Coi Gene ◽  
Integrated Analysis ◽  
Gene Sequences ◽  
Unknown Species ◽  
New Gene ◽  
First Time ◽  
Plant Parasitic

Pin nematodes of the genus Paratylenchus are obligate ectoparasites of a wide variety of plants that are distributed worldwide. In this study, individual morphologically vouchered nematode specimens of fourteen Paratylenchus species, including P. aculentus, P. elachistus, P. goodeyi, P. holdemani, P. idalimus, P. microdorus, P. nanus, P. neoamblycephalus, P. straeleni and P. veruculatus, are unequivocally linked to the D2-D3 of 28S, ITS, 18S rRNA and COI gene sequences. Combined with scanning electron microscopy and a molecular analysis of an additional nine known and thirteen unknown species originating from diverse geographic regions, a total of 92 D2-D3 of 28S, 41 ITS, 57 18S rRNA and 111 COI new gene sequences are presented. Paratylenchus elachistus, P. holdemani and P. neoamblycephalus are recorded for the first time in Belgium and P. idalimus for the first time in Europe. Paratylenchus is an excellent example of an incredibly diverse yet morphologically minimalistic plant-parasitic genus, and this study provides an integrated analysis of all available data, including coalescence-based molecular species delimitation, resulting in an updated Paratylenchus phylogeny and the corrective reassignment of 18 D2-D3 of 28S, 3 ITS, 3 18S rRNA and 25 COI gene sequences that were previously unidentified or incorrectly classified.

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