scholarly journals Semantic-based methods for morphological descriptions: An applied example for Neotropical species of genus Lepidocyrtus Bourlet, 1839 (Collembola: Entomobryidae)

Author(s):  
Luis Antonio González-Montaña

The production of semantic annotations has gained renewed attention due to the development of anatomical ontologies and the documentation of morphological data. Two methods are proposed in this production, differing in their methodological and philosophical approaches: class-based method and instance-based method. The first, the semantic annotations are established as class expressions, while in the second, the annotations incorporate individuals. An empirical evaluation of the above methods was applied in the morphological description of Neotropical species of the genus Lepidocyrtus (Collembola: Entomobryidae: Lepidocyrtinae). The semantic annotations are expressed as RDF triple, which is a language most flexible than the Entity-Quality syntax used commonly in the description of phenotypes. The morphological descriptions were built in Protégé 5.4.0 and stored in an RDF store created with Fuseki Jena. The semantic annotations based on RDF triple increase the interoperability and integration of data from diverse sources, e.g., museum data. However, computational challenges are present, which are related with the development of semi-automatic methods for the generation of RDF triple, interchanging between texts and RDF triple, and the access by non-expert users.

Plant Disease ◽  
2013 ◽  
Vol 97 (9) ◽  
pp. 1251-1251
Author(s):  
Y. H. Yun ◽  
S. Y. Son ◽  
S. H. Kim

Viburnum sargentii Koehne belongs to the family Caprifoliaceae. It is a deciduous shrub that grows in wet mountainous area in Korea, Japan, and China. On July 2011, rust symptoms were observed on V. sargentii Koehne in Balwang mountain, Gangwon Province, Korea, at an altitude of 1,450 meters. The specimen was coded as DUCC506 and used to study in detail. Rust symptoms were present on leaves, floral axes, and petioles. The infected lesions slightly swelled and leaflets and leaves were distorted. These caused sharp bends in the petioles and wart-like galls on twigs. Defoliation and deflowering could result when infection was severe. The first symptom was small and pale yellow spots on the upper surfaces of the leaves. As the spots increased in size, they turned brown and tanned. Bright orange or yellow powdery masses of spores were produced in tiny cup-like structures that appeared on the undersurfaces of leaves and the surface of floral axes and petioles. Aecia were gregarious, cupulate, yellowish, and erumpent with a peridium having a lacerate, somewhat recurved margin. Peridial cells were hyaline to whitish, rhomboidal, 18 to 25 (avg. 21.5) × 15 to 20 (avg. 18) μm, smooth to finely verrucose, and not observed in aecial stage on floral axes and petioles. Aeciospores were globose to ellipsoid, 14 to 16 (avg. 15.4) × 15 to 16.5 (avg. 16) μm, hyaline to yellowish, with many verrucose surface and hyaline walls. These morphological properties correspond to the aecial stage of Uromyces acuminatus (1,4). From extracted genomic DNA, the D1 and D2 region of 28S ribosomal DNA was amplified with LROR (5′- ACCCGCTGAACTTAAGC-3′) and LR4 (5′-ACCAGAGTTTCCTCTGG- 3′) primer set. The 28S rDNA sequence of DUCC506 was deposited in GenBank DNA database under accession number KC570451. A nucleotide sequence similarity search through BLAST in the GenBank database revealed that the DUCC506's 28S rDNA shared 98% (607/622) similarity with that of U. acuminatus LD1005 (GU058004). Aecidium magnatum Arthur is the anamorph of U. acuminatus (2). Aecial and telial hosts of U. acuminatus belong to several families of Angiosperms and Spartina spp., respectively. No telial host was found near the infected aecial host V. sargentii. These morphological and molecular results support the morphological data to identify DUCC506 specimen is A. magnatum. To our knowledge, this is the first report of rust caused by A. magnatum on V. sargentii in Korea or elsewhere in the world. Rust caused by A. viburni was reported on V. sargentii in Korea without any morphological description (3). Peoples in Asia are interested in this host plant as it is used for ornamental and medicinal purpose. Therefore, our report would be useful information for the management of V. sargentii. References: (1) G. B. Cummins. The Rust Fungi of Cereals, Grasses and Bamboos. Springer-Verlag, New York, 1971. (2) D. F. Farr et al. Fungi on Plants and Plant Products in the United States. Page 1009. American Phytopathological Society Press, St. Paul, MN, 1989. (3) C. J. Kim. Kor. J. Micorbiol. 1:51, 1963. (4) H. Y. Yun et al. Plant Dis. 94:279, 2010.


Zootaxa ◽  
2019 ◽  
Vol 4657 (3) ◽  
pp. 503-522
Author(s):  
MARIA VALLADOLID ◽  
IOANNIS KARAOUZAS ◽  
MERCEDES ARAUZO ◽  
BEATRIZ A. DORDA ◽  
ISABEL REY

The morphology of the different stages (larva, pupa, male, and female) of Rhyacophila fasciata kykladica Malicky & Sipahiler 1993 was examined as a basis for the description of the taxon. Morphological data were supplemented by molecular analysis of mitochondrial cytochrome C oxidase subunit I (mtCOI), which were compared with samples of the nominate subspecies Rhyacophila fasciata fasciata Hagen 1859, as well as with other new species in this group, Rhyacophila denticulata McLachlan 1879 and Rhyacophila sociata Navás 1916. Our results revealed genetic differences between all the taxa; therefore, a change of taxonomic status of R. fasciata kykladica to R. kykladica (stat. prom.) is proposed.


Phytotaxa ◽  
2020 ◽  
Vol 474 (3) ◽  
pp. 283-292
Author(s):  
ALI BAGHERI ◽  
FRANK R. BLATTNER ◽  
REINHARD M. FRITSCH

As a result of recent botanical expeditions to the north of Iran, we describe here a new endemic Allium species from Gilan province named Allium gilanense. Molecular and morphological data indicate that it belongs to Allium sect. Codonoprasum. We provide a morphological description, comparing Allium gilanense with the closest relative taxa A. lenkoranicum and A. paniculatum, the preliminary karyotype of the new species, and molecular phylogenetic data derived from the nuclear ribosomal DNA internal transcribed spacers (ITS) and the chloroplast intergenic spacer trnH-psbA. The chromosome number of the new species is 2n = 16 with 0-3 B chromosomes.


ZooKeys ◽  
2020 ◽  
Vol 909 ◽  
pp. 1-24 ◽  
Author(s):  
Adam Wang ◽  
Inga Elizabeth Conti-Jerpe ◽  
John Lawrence Richards ◽  
David Michael Baker

Phestilla subodiosussp. nov. (Nudibranchia: Trinchesiidae) is a novel species that feeds on corals in the genus Montipora (Scleractinia: Acroporidae) which are economically important in the aquarium industry. Nuclear-encoded H3, 28SC1-C2, and mitochondrial-encoded COI and 16S markers were sequenced. Phylogenetic analysis, Automatic Barcode Gap Discovery (ABGD), morphological data, and feeding specialization all support the designation of Phestilla subodiosussp. nov. as a distinct species. Although new to science, Phestilla subodiosussp. nov. had been extensively reported by aquarium hobbyists as a prolific pest over the past two decades. The species fell into a well-studied genus, which could facilitate research into its control in reef aquaria. Our phylogenetic analysis also revealed Tenellia chaetopterana formed a well-supported clade with Phestilla. Based upon a literature review, its original morphological description, and our phylogenetic hypothesis, we reclassified this species as Phestilla chaetopteranacomb. nov.


2015 ◽  
Vol 16 (3) ◽  
pp. 489 ◽  
Author(s):  
C. MAGGI ◽  
M. GONZÁLEZ-WANGÜEMERT

Parastichopus regalis (Cuvier, 1817) is the most expensive seafood product on the catalonian market (NE Spain), with prices around 130 €/Kg (fresh weight). Despite its ecological and economic importance, biological and genetic information on this sea cucumber species is scarce. We provided the first insight on the genetic structure of P. regalis using sequences of cytochrome oxidase I (COI) and 16S genes, as well as a morphological description of its populations. Individuals were collected in six locations along the Spanish Mediterranean coast, including an area under fishery pressure (Catalonia). We found high haplotype diversity and low nucleotide diversity for both genes, with higher levels of genetic diversity observed on COI gene. Population pairwise fixation index (FST), AMOVA and correspondence analysis (CA) based on COI, revealed significant genetic differentiation among some locations. However, further analysis using nuclear markers (e.g. microsatellites) would be necessary to corroborate these results. Moreover, the genetic and morphological data may indicate fishery effects on the Catalonian population with decrease of the size and weight average and lower genetic diversity compared to locations without fishery pressure. For an appropriate management of this species, we suggest: 1) an accurate assessment of the stocks status along the Spanish coasts; 2) the study of the reproductive cycle of this target species and the establishment of a closed fishery season according to it; 3) the founding of protected areas (i.e. not take zones) to conserve healthy populations and favour the recruitment on the nearby areas.


2014 ◽  
Vol 23 (2) ◽  
pp. 251-254
Author(s):  
Estevam Guilherme Lux Hoppe ◽  
José Hairton Tebaldi ◽  
Daniel Fontana Ferreira

The genus Habronema has four valid species, of which only two are properly known. The present study aimed to describe in detail the morphology of Habronema clarki through optical and scanning electron microscopy analyses. Our results showed that the labial morphology of this parasite is closer to H. muscae than to H. microstoma. Even so, the characteristic pseudolabia and the slightly convex border of the dorsal and ventral lips are sufficient to distinguish these nematodes. Additional morphological data are presented, thus contributing to the knowledge on this little known nematode. In addition, this study provides new locality records for this species.


2021 ◽  
pp. e1896
Author(s):  
Javier Isaac De la Fuente ◽  
Cesar Ramiro Martínez-González ◽  
Iván Oros-Ortega ◽  
Gonzalo Guevara ◽  
Víctor M. Bandala ◽  
...  

Background and Aims: The genus Melanogaster is characterized by its hypogeous to semi hypogeous habit, brownish basidiomata, gel-filled gleba locules, and globose to ellipsoid basidiospores. The genus is distributed in temperate zones, but sequences from Coccoloba root tips and a few basidiome collections have revealed its presence in the tropics. The aim of this article is to describe a new species of Melanogaster based on ecological, molecular, and morphological data. Methods: Specimens were collected in urban vegetation of Quintana Roo in the Yucatán Peninsula, Mexico. For morphological description, the classic protocols for sequestrate fungi were followed. The dried material was deposited in the mycological herbarium “José Castillo Tovar” of the Instituto Tecnológico de Ciudad Victoria (ITCV) and the herbarium of the Universidad Autónoma de Yucatán (UADY). Key results: Melanogaster coccolobae is presented as a new species from the urban gardens of Quintana Roo based on ecological, molecular, and morphological evidence. This species is characterized by its hypogeous to semi hypogeous basidioma, greyish orange, brown to reddish brown peridium composed of two layers, sweet smell, subglobose, ellipsoid or piriform basidiospores, and by its mycorrhizal association with Coccoloba spicata. Conclusions: Melanogaster coccolobae is the first species described from the Mexican Caribbean from urban gardens with Coccoloba spicata. More studies about the tropical sequestrate fungi are recommended.


Author(s):  
Jesús De Oliveira ◽  
Yudith Cardinale ◽  
Eduardo Blanco ◽  
Carlos Figueira

In distributed environments (e.g. grid platform) it is common to find pieces of reusable code distributed among multiple sites. The possibilities of compilation and execution with remote libraries have a great potential to facilitate the integration of pieces of software developed among different organizations. This chapter describes JaDiMa (Java Distributed Machine), a collaborative framework to construct Java applications on grid platforms. JaDiMa automatically manages library repositories to allow users to compile and execute applications which use distributed libraries, without keeping these libraries locally. JaDiMa services are implemented as Web Services following the SOA approach; library repositories are modeled as a JXTA P2P network; and semantic annotations of libraries assist developers on the tasks of discovering libraries. We describe an implementation of JaDiMa as part of SUMA/G, a Globus-based grid environment. We show experiences and an empirical evaluation of JaDiMa execution and compilation processes for an application which uses remote libraries for managing graph and network data.


Phytotaxa ◽  
2020 ◽  
Vol 441 (1) ◽  
pp. 47-59
Author(s):  
JIN-FEN HAN ◽  
FANG-RU NAN ◽  
JIA FENG ◽  
JUN-PING LV ◽  
QI LIU ◽  
...  

Four putative “Chantransia” isolates were collected from four locations in Hubei and Yunnan Provinces, China. Morphological analyses were conducted on all isolates. Two specimens (HB26 and YN2) fit the morphological description of A. pygmaea, while the other two isolates (YN1 and YN3) varied in morphology, but were within the circumscription of Audouinella hermannii. Due to the fact that the morphological characters of the “Chantransia” stages of order Batrachospermales and the species of genus Audouinella are too similar to be distinguished, a molecular analysis was performed to clarify the phylogenetic position of these four isolates based on rbcL and psbA sequences. Two “pygmaea” specimens collected from Jiugong Mountain, Hubei Province (HB26) and Shimen Gorge, Yunnan Province (YN2), such as S. jiugongshanensis and S. shimenxiaensis, are proposed primarily based on the DNA sequence data generated in this study. The description of these two new species provides more molecular data for phylogenetic analysis of the genus Sheathia. In addition to these newly described species, the results strongly support that those “hermannii” isolates (YN1 and YN3) collected from Yunnan Province were the “Chantransia” of S. arcuata. However, their gametophyte stages have not been found, meaning that critical diagnostic morphological features were unavailable and molecular methods were the only means for ascertaining their phylogenetic position. Considering the extensive application of the rbcL and psbA genes in phylogenetic analyses of freshwater red algae, we recommend using these two genes to identify species when no morphological characteristics are available.


2015 ◽  
pp. 201-212
Author(s):  
Adam Radziszewski ◽  
Marek Maziarz

Developing free morphological data for PolishA limiting factor in construction of Natural Language Processing (NLP) systems is often the availability of morphological resources. This indeed happens for Polish: the freely available corpus with manual morpho-syntactic annotation (part of the IPI PAN Corpus) is not coupled with any free morphological analyser. There exists a very large morphological dictionary of Polish available under a free licence – Morfologik. Unfortunately, its tagset differs significantly from the tagset of the corpus and, what is more, its morphological description lacks desired rigour. We amend this situation by performing a massive conversion of the dictionary into the tagset compliant with the corpus. The conversion results in a free dictionary containing entries for almost 3.5 million different word forms. In this article we report on our methodology, discuss some morphological and syntactic issues related to both tagsets and present the characteristics of the resulting dictionary.


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