Bamboo tea: reduction of taxonomic complexity and application of DNA diagnostics based onrbcLandmatKsequence data

Adulteration of herbal products: Bamboo tea authentication

10.7287/peerj.preprints.2198 ◽

2016 ◽

Author(s):

Thomas Horn ◽

Annette Häser

Keyword(s):

Sequence Data ◽

Food Products ◽

Distinct Species ◽

Primary Concern ◽

Bamboo Species ◽

Herbal Products ◽

Dna Sequence Data ◽

Eu Legislation ◽

Bamboo Leaves ◽

Diagnostic Potential

Background. Names for ”substances” used in food products are rarely precise. The term bamboo (Bambusoideae, Poaceae) comprises over 1600 distinct species of which only few are well established sources for food products on the European market (i.e. bamboo sprouts). Methods. We analysed bamboo species and tea products containing an exotic ingredient (bamboo leaves) using anatomical leaf characters and DNA sequence data. Our primary concern was to determine the taxonomic origin of bamboo leaves to establish a baseline for EU legislation, to introduce a simple PCR based test to distinguish bamboo from other Poaceae leaf components and to assess the diagnostic potential of DNA Barcoding markers to resolve taxonomic entities within the bamboo subfamily and tribes. Results. Based on anatomical and DNA data we can pinpoint the taxonomic origin of genuine bamboo leaves used in commercial products to the genera Phyllostachys and Pseudosasa from the temperate ”woody” bamboo tribe (Arundinarieae). We detected adulteration by carnation in 4 of 8 tea products and, after adapting our objectives, could trace the taxonomic origin of the adulterant to Dianthus chinensis (Caryophyllaceae), a well known traditional Chinese medicine with counter indications for pregnant women.

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Adulteration of herbal products: Bamboo tea authentication

10.7287/peerj.preprints.2198v1 ◽

2016 ◽

Author(s):

Thomas Horn ◽

Annette Häser

Keyword(s):

Sequence Data ◽

Food Products ◽

Distinct Species ◽

Primary Concern ◽

Bamboo Species ◽

Herbal Products ◽

Dna Sequence Data ◽

Eu Legislation ◽

Bamboo Leaves ◽

Diagnostic Potential

Background. Names for ”substances” used in food products are rarely precise. The term bamboo (Bambusoideae, Poaceae) comprises over 1600 distinct species of which only few are well established sources for food products on the European market (i.e. bamboo sprouts). Methods. We analysed bamboo species and tea products containing an exotic ingredient (bamboo leaves) using anatomical leaf characters and DNA sequence data. Our primary concern was to determine the taxonomic origin of bamboo leaves to establish a baseline for EU legislation, to introduce a simple PCR based test to distinguish bamboo from other Poaceae leaf components and to assess the diagnostic potential of DNA Barcoding markers to resolve taxonomic entities within the bamboo subfamily and tribes. Results. Based on anatomical and DNA data we can pinpoint the taxonomic origin of genuine bamboo leaves used in commercial products to the genera Phyllostachys and Pseudosasa from the temperate ”woody” bamboo tribe (Arundinarieae). We detected adulteration by carnation in 4 of 8 tea products and, after adapting our objectives, could trace the taxonomic origin of the adulterant to Dianthus chinensis (Caryophyllaceae), a well known traditional Chinese medicine with counter indications for pregnant women.

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Morphological and molecular evidence places Maronina into synonymy with Protoparmelia (Ascomycota: Lecanorales)

The Lichenologist ◽

10.1017/s0024282911000284 ◽

2011 ◽

Vol 43 (6) ◽

pp. 561-567 ◽

Cited By ~ 15

Author(s):

K. PAPONG ◽

G. KANTVILAS ◽

H. T. LUMBSCH

Keyword(s):

Dna Sequence ◽

Sequence Data ◽

Distinct Species ◽

Genetic Distances ◽

Molecular Evidence ◽

New Combinations ◽

Secondary Chemistry ◽

Phenotypic Characters ◽

Dna Sequence Data ◽

Phylogenetic Placement

AbstractThe phylogenetic placement of the genus Maronina was studied, based chiefly on phenotypic characters such as thallus colour and anatomy, secondary chemistry, the anatomy of the excipulum and the ascus-type. DNA sequence data of mitochondrial and nuclear ribosomal loci from some of the species support the hypothesis that Maronina is nested within Protoparmelia. Hence, Maronina is reduced to synonymy with Protoparmelia. Comparison of genetic distances suggests that the two varieties within M. orientalis should be regarded as distinct species. Consequently, the new combinations Protoparmelia australiensis (Hafellner & R. W. Rogers) Kantvilas et al., P. corallifera (Kantvilas & Papong) Kantvilas et al., P. hesperia (Kantvilas & Elix) Kantvilas et al., P. multifera (Nyl.) Kantvilas et al., and P. orientalis (Kantvilas & Papong) Kantvilas et al. are proposed.

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Conflicts in sperm: how do genitalia coevolve with elaborate sperm?

ARPHA Conference Abstracts ◽

10.3897/aca.2.e37158 ◽

2019 ◽

Vol 2 ◽

Author(s):

Antonio Gomez ◽

David Maddison

Keyword(s):

Reproductive Tract ◽

Sequence Data ◽

Ground Beetles ◽

Storage Space ◽

Male And Female ◽

Dna Sequence Data ◽

Sexual Conflicts ◽

Storage Volume ◽

Phylogenetic Framework ◽

Sperm Traits

Some sperm traits are now recognized as ornaments akin to peacock’s tails evolving under cryptic female choice or weapons in sexual conflicts, but there are still few studies addressing patterns and process in sperm-female evolution. We are studying sperm-female evolution in ground beetles of the genus Dyschirius. Male Dyschirius make groups of sperm, termed conjugates, by pairing sperm to non-cellular rods, or spermatostyles. This pairing creates a conflict for storage space in the female’s reproductive tract between sperm and the spermatostyle, which is incapable of fertilizing eggs. We speculate that the conjugates of some Dyschirius that include large spermatostyles with few sperm are ornaments. We hypothesize that increased spermathecal storage volume is positively correlated with larger spermatostyles and that male genitalic complexity is negatively correlated with elaboration of sperm. We gathered morphological trait data on sperm conjugates and male and female genitalia from several species of Dyschirius. We analyzed these data in a phylogenetic framework using a robust Dyschirius species tree derived from DNA sequence data. We present preliminary results from this ongoing study and solicit feedback from the ECM community.

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Liparis wenshanensis, a new orchid species from China: Evidence from morphological and molecular analyses

Phytotaxa ◽

10.11646/phytotaxa.204.4.2 ◽

2015 ◽

Vol 204 (4) ◽

pp. 253 ◽

Cited By ~ 3

Author(s):

YONG-YU SU ◽

YI-LANG HUANG ◽

LI-JUN CHEN ◽

PEI-WEN ZHANG ◽

Zhong-Jian Liu ◽

...

Keyword(s):

Phylogenetic Analysis ◽

Dna Sequence ◽

Sequence Data ◽

Detailed Comparison ◽

Distinct Species ◽

Systematic Position ◽

Orchid Species ◽

Molecular Analyses ◽

Dna Sequence Data

A new orchid species, Liparis wenshanensis, discovered in Yunnan, China is described and illustrated in this study based on morphological and molecular analyses. A detailed comparison between the newly discovered orchid and other members of the genus, Liparis, was conducted. The new plant is characterized by the combination of the following features: a long rachis with 45 to 55 flowers; white sepals, petals and column; a greenish lip with a purplish center; strongly recurved and revolute dorsal sepals and petals; strongly recurved, oblong lateral sepals; a cordate lip that is strongly deflexed below the middle, with a two-lobed apex and a two-lobed callus at the base; an arcuate column with a lamella extending along the center almost to the stigma, and with a pair of broad wings toward the apex. These features distinguish the new orchid from all other known species of Liparis. We proceeded to a phylogenetic analysis to ascertain the systematic position of this enigmatic species. Molecular analyses based on nuclear ribosomal ITS and plastid matK DNA sequence data supports the recognition of L. wenshanensis as a distinct species.

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Cymbidium jiangchengense (Orchidaceae; Epidendroideae; Cymbidiinae), a new species from China: evidence from morphology and DNA sequences

Phytotaxa ◽

10.11646/phytotaxa.408.1.6 ◽

2019 ◽

Vol 408 (1) ◽

pp. 77-84

Author(s):

YING-LI PENG ◽

ZHUANG ZHOU ◽

SI-REN LAN ◽

ZHONG-JIAN LIU

Keyword(s):

Dna Sequences ◽

Yunnan Province ◽

Sequence Data ◽

Detailed Comparison ◽

Distinct Species ◽

Molecular Study ◽

Orchid Species ◽

Dna Sequence Data ◽

Pink Flower ◽

A New Species

A new orchid species, Cymbidium jiangchengense, from Yunnan Province, China, is described and illustrated. Its distinctiveness is evaluated with morphology and molecular analyses. A detailed comparison between the newly discovered orchid and other members of Cymbidium was performed. The new plant was characterized by stem-like pseudobulbs, narrowly oblong leaves, coriaceous leaves with an acute apex, a 2-flowered inflorescence, a purplish pink flower, narrowly elliptic sepals, petals, a obovate-lanceolate lip with a cordate midlobe, a yellow central callus, and a disc with a trough shape longitudinal lamella from the base extending to the base of the midlobe and a lamellae apex inflated to form two calluses that are not confluent apically. These features distinguish this new orchid from all other known species of Cymbidium. A molecular study based on nuclear ribosomal ITS and plastid matK and rbcL DNA sequence data indicates that C. jiangchengense is a distinct species that sister to C. wadae and a member of section Eburnea, subgenus Cyperorchis.

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Veterinary Fusarioses within the United States

Journal of Clinical Microbiology ◽

10.1128/jcm.01607-16 ◽

2016 ◽

Vol 54 (11) ◽

pp. 2813-2819 ◽

Cited By ~ 21

Author(s):

Kerry O'Donnell ◽

Deanna A. Sutton ◽

Nathan Wiederhold ◽

Vincent A. R. G. Robert ◽

Pedro W. Crous ◽

...

Keyword(s):

United States ◽

Dna Sequence ◽

Species Complex ◽

Sequence Data ◽

Phylogenetic Analyses ◽

Distinct Species ◽

The United States ◽

Content Type ◽

Dna Sequence Data ◽

Species Complexes

Multilocus DNA sequence data were used to assess the genetic diversity and evolutionary relationships of 67Fusariumstrains from veterinary sources, most of which were from the United States. Molecular phylogenetic analyses revealed that the strains comprised 23 phylogenetically distinct species, all but two of which were previously known to infect humans, distributed among eight species complexes. The majority of the veterinary isolates (47/67 = 70.1%) were nested within theFusarium solanispecies complex (FSSC), and these included 8 phylospecies and 33 unique 3-locus sequence types (STs). Three of the FSSC species (Fusarium falciforme,Fusarium keratoplasticum, andFusariumsp. FSSC 12) accounted for four-fifths of the veterinary strains (38/47) and STs (27/33) within this clade. Most of theF. falciformestrains (12/15) were recovered from equine keratitis infections; however, strains ofF. keratoplasticumandFusariumsp. FSSC 12 were mostly (25/27) isolated from marine vertebrates and invertebrates. Our sampling suggests that theFusarium incarnatum-equisetispecies complex (FIESC), with eight mycoses-associated species, may represent the second most important clade of veterinary relevance withinFusarium. Six of the multilocus STs within the FSSC (3+4-eee, 1-b, 12-a, 12-b, 12-f, and 12-h) and one each within the FIESC (1-a) and theFusarium oxysporumspecies complex (ST-33) were widespread geographically, including three STs with transoceanic disjunctions. In conclusion, fusaria associated with veterinary mycoses are phylogenetically diverse and typically can only be identified to the species level using DNA sequence data from portions of one or more informative genes.

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A newly recognised species that has been confused with the global polyphagous pest scale insect, Coccus hesperidum Linnaeus (Hemiptera: Coccomorpha: Coccidae)

Zootaxa ◽

10.11646/zootaxa.4320.3.10 ◽

2017 ◽

Vol 4320 (3) ◽

pp. 571 ◽

Cited By ~ 1

Author(s):

YEN-PO LIN ◽

HIROTAKA TANAKA ◽

LYN G. COOK

Keyword(s):

Adult Female ◽

Dna Sequences ◽

Sequence Data ◽

Distinct Species ◽

Scale Insect ◽

Scale Insects ◽

History Museum ◽

Dna Sequence Data ◽

Cryptic Species Complex ◽

Coccus Hesperidum

Coccus hesperidum L. (Hemiptera: Coccomorpha: Coccidae), the type species of the soft scale genus Coccus L., the family Coccidae and the whole of the scale insects (Coccoidea), is a cosmopolitan plant pest. Using DNA sequence data and morphological comparisons, we determine that there is a distinct species that is morphologically very similar to C. hesperidum. Here, we describe the species as Coccus praetermissus Lin & Tanaka sp. n., based on adult female specimens from Australia, Malaysia and Thailand. The adult female of C. praetermissus sp. n. differs from C. hesperidum in having dorsal setae with bluntly rounded tips, whereas they are sharply pointed in C. hesperidum. A detailed description of the newly recognised species is provided, incorporating adult female morphology and DNA sequences from mitochondrial and nuclear loci. Our examination of slides from The Natural History Museum, London, and several Australian institutions indicates that C. praetermissus sp. n. has been confused sometimes with C. hesperidum s. s. These findings have potential relevance to plant biosecurity and quarantine because C. hesperidum is cosmopolitan whereas C. praetermissus sp. n., which is also polyphagous and the two species can share many host plants, currently appears to be more geographically restricted. Additionally, there is deep genetic divergence within C. praetermissus sp. n. that might indicate that it is a cryptic species complex, but wider geographic sampling is required to test this possibility.

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Molecular phylogeny uncovers an overlooked species in the macrolichen family Parmeliaceae (Ascomycota) from India

Cryptogam Biodiversity and Assessment ◽

10.21756/cab.esp4 ◽

2018 ◽

Author(s):

Pradeep K. Divakar ◽

Ana Crespo

Keyword(s):

Sequence Data ◽

Molecular Data ◽

Fungal Species ◽

Species Boundaries ◽

Data Set ◽

Dna Sequence Data ◽

Distinct Lineage ◽

Phylogenetic Framework ◽

Phenotypic Features ◽

A New Species

Several obligately sexualy reproducing lichen-forming fungal species are disjunctly distributed in pantropical regions. Here, we aim to re-examine species boundaries within the sexually reproducing, disjunctly distributed species, Hypotrachyna intercalanda. We gathered a three-locus DNA sequence data set of Hypotrachyna subgen. Parmelinopsis, especially including the samples from India, and these data were analysed in a phylogenetic framework. Our results show that specimens of H. intercalanda, as currently circumscribed, do not form a monophyletic group but fall into two well-supported independent clades. Morphological and chemical features were re-evaluated. Corroborating with the phenotypic features, the sample recovered in clade 2 occurring in southern India are described as a new species, viz. Hypotrachyna upretii Divakar and A. Crespo sp. nov. Our study adds a further example of a previously overlooked, geographically distinct, lineage that was uncovered using molecular data. Additionally, our study underlines the need of critical reexamination of phenotypic features of samples falling into different clades.

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Molecular Phylogenetics of The Tody-Tyrant and Flatbill Assemblage of Tyrant Flycatchers (Tyrannidae)

The Auk ◽

10.1093/auk/124.1.134 ◽

2007 ◽

Vol 124 (1) ◽

pp. 134-154 ◽

Cited By ~ 2

Author(s):

Jose G. Tello ◽

John M. Bates

Keyword(s):

Molecular Phylogenetics ◽

Nuclear Dna ◽

Sequence Data ◽

Data Sets ◽

Skull Morphology ◽

Base Pairs ◽

Dna Sequence Data ◽

Phylogenetic Framework ◽

Data Partitions ◽

Tyrant Flycatchers

Abstract The tody-tyrant and flatbill assemblage, sensuLanyon (1988a), includes 12 genera of tyrant flycatchers known variously as “tody-tyrants” and “flatbills.” Lanyon supported the monophyly of the group based on similar skull morphology and nest form, and built intergeneric relationships based on syringeal characters. However, these comparisons were made without a phylogenetic framework. A more recent study assessing relationships in the tyrant flycatchers using published morphological and behavioral data failed to recover monophyly of this assemblage (Birdsley 2002). Using DNA sequence data, we test for the monophyly of the tody-tyrant and flatbill assemblage and compare and contrast phylogenetic signals from mitochondrial and nuclear DNA character systems. We discuss our results in light of results from previous studies. We include representatives of the other major tyrant flycatcher assemblages for a total of 42 individuals (representing 27 tyrannid genera and 36 species). We sequenced 3,022 base pairs (bp) of three mitochondrial genes (ND2, ND3, and cytochrome b) and one nuclear intron (FIB5). Our results resolve many of the basal relationships of the tody-tyrant and flatbill phylogeny, but separate and combined analyses of data partitions are necessary to understand the nature of conflict among data sets. The tody-tyrants constitute a monophyletic clade, but the genera Hemitriccus and Lophotriccus are not monophyletic, and the limits of Oncostoma-Lophotriccus need to be revised with more complete sampling at the species level. The flatbills as defined by Lanyon are not monophyletic (Onychorhynchus and Platyrinchus are not true flatbills). Pseudotriccus and Corythopis are sister taxa and, together with Leptopogon and Mionectes, are allied to the tody-tyrant and flatbill clade. Filogenia Molecular del Grupo de los Picochatos y Mosquiteros de la Familia Tyrannidae

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