scholarly journals What Have Been and What Can Be Delimited as Species Using Molecular Data Under the Multi-Species Coalescent Model? A Case Study Using Hercules beetles (Dynastes; Dynastidae)

2018 ◽  
Vol 2 (2) ◽  
Author(s):  
Jen-Pan Huang
Keyword(s):  
Molecular Data ◽  
Coalescent Model ◽  
As Species

ESP corpus design: compilation of the Veterinary Nursing Medical Chart Corpus and the Veterinary Nursing Wordlist

Corpora ◽  
2020 ◽  
Vol 15 (2) ◽  
pp. 125-140
Author(s):  
Yukiko Ohashi ◽  
Noriaki Katagiri ◽  
Katsutoshi Oka ◽  
Michiko Hanada
Keyword(s):  
Word List ◽  
English For Specific Purposes ◽  
Regular Expressions ◽  
Annotation Scheme ◽  
Corpus Design ◽  
As Species ◽  
Lexical Items ◽  
Access To Data ◽  
General Service

This paper reports on two research results: ( 1) designing an English for Specific Purposes (esp) corpus architecture complete with annotations structured by regular expressions; and ( 2) a case study to test the design to cater for creating a specific vocabulary list using the compiled corpus. The first half of this study involved designing a precisely structured esp corpus from 190 veterinary medical charts with a hierarchy of the data. The data hierarchy in the corpus consists of document types, outline elements and inline elements, such as species and breed. Perl scripts extracted the data attached to veterinary-specific categories, and the extraction led to creating wordlists. The second part of the research tested the corpus mode, creating a list of commonly observed lexical items in veterinary medicine. The coverage rate of the wordlists by General Service List (gsl) and Academic Word List (awl) was tested, with the result that 66.4 percent of all lexical items appeared in gsl and awl, whereas 33.7 percent appeared in none of those lists. The corpus compilation procedures as well as the annotation scheme introduced in this study enable the compilation of specific corpora with explicit annotations, allowing teachers to have access to data required for creating esp classroom materials.

scholarly journals Computational Design of Sensitized Combustion Chemistry Experiments

2021 ◽  
Vol 7 ◽  
Author(s):  
Cody Ising ◽  
Pedro Rodriguez ◽  
Daniel Lopez ◽  
Jeffrey Santner
Keyword(s):  
Shock Tube ◽  
Initial Conditions ◽  
Computational Design ◽  
Reaction Rates ◽  
Oxidation Reactions ◽  
Combustion Chemistry ◽  
Experimental Conditions ◽  
As Species ◽  
User Friendly

In combustion chemistry experiments, reaction rates are often extracted from complex experiments using detailed models. To aid in this process, experiments are performed such that measurable quantities, such as species concentrations, flame speed, and ignition delay, are sensitive to reaction rates of interest. In this work, a systematic method for determining such sensitized experimental conditions is demonstrated. An open-source python script was created using the Cantera module to simulate thousands of 0D and hundreds of 1D combustion chemistry experiments in parallel across a broad, user-defined range of mixture conditions. The results of the simulation are post-processed to normalize and compare sensitivity values among reactions and across initial conditions for time-varying and steady-state simulations, in order to determine the “most useful” experimental conditions. This software can be utilized by researchers as a fast, user-friendly screening tool to determine the thermodynamic and mixture parameters for an experimental campaign. We demonstrate this software through two case studies comparing results of the 0D script against a shock tube experiment and results of the 1D script against a spherical flame experiment. In the shock tube case study we present mixture conditions compared to those used in the literature to study H + O2 (+M)→HO2(+M). In the flame case study, we present mixture conditions compared to those in the literature to study formyl radical (HCO) decomposition and oxidation reactions. The systematically determined experimental conditions identified in the present work are similar to the conditions chosen in the literature.

Monographic revision of the endemic Helix mazzullii De Cristofori & Jan, 1832 complex from Sicily and re-introduction of the genus Erctella Monterosato, 1894 (Pulmonata, Stylommatophora, Helicidae)

Zootaxa ◽  
2011 ◽  
Vol 3134 (1) ◽  
pp. 1 ◽  
Author(s):  
M. STELLA COLOMBA ◽  
ARMANDO GREGORINI ◽  
FABIO LIBERTO ◽  
AGATINO REITANO ◽  
SALVATORE GIGLIO ◽  
...  
Keyword(s):  
Molecular Study ◽  
Molecular Data ◽  
Comprehensive Analysis ◽  
Molecular Dating ◽  
12S Rrna ◽  
Ecological Significance ◽  
Ecological Features ◽  
As Species ◽  
Individual Segment ◽  
Nuclear Its

Helix mazzullii De Cristofori & Jan, 1832 s.l.(Pulmonata, Stylommatophora, Helicidae) is an endemic, rupicolous, saxicavous taxon of northwestern Sicily. Its populations are vulnerable and it is of great ecological significance. However, its taxonomy, phylogeny and biogeography are still uncertain. The present paper reports on a comprehensive analysis of morphological diagnostic characters (shell and genitalia) joined by the molecular study of two mitochondrial (16S rRNA and 12S rRNA) and one nuclear (ITS-2) partial gene sequences, investigated by individual segment analyses or combining the three gene fragments with a concatenate analysis. Our results corroborated the hypothesis that this species is rather a group (i.e., the mazzullii group) including three different taxa (mazzullii, cephalaeditana and insolida) recognized as species. Moreover, molecular dating of lineages suggests that this complex might have occurred long before the Messinian salinity crisis. Finally, peculiar morphological and ecological features along with molecular data strongly support the proposal to re-introduce the genus Erctella Monterosato, 1894 for the H. mazzullii complex. Synonyms and bibliographic references are reported in the systematic part; collection records are listed in Appendix 1.

scholarly journals The Palynological Compass: A Case Study In Viticoideae (Vitex L.)

2008 ◽  
Vol 14 (S3) ◽  
pp. 158-161 ◽  
Author(s):  
C. Cabral ◽  
M. Möller ◽  
F. Sales
Keyword(s):  
Molecular Data ◽  
Systematic Relationships ◽  
The Way

The concept of palynological compass was introduced in 1969 by Erdtman to express the way palynological evidence points to systematic relationships. Recent evidence shows that, in the cases studied, the palynological compass points to the same phylogenetic direction as the molecular data.

Dunnarts from Boullanger Island: new evidence and reassessment of a taxonomic issue with resource implications.

2006 ◽  
Vol 28 (1) ◽  
pp. 51 ◽  
Author(s):  
A. N. Start ◽  
D. Moro ◽  
M. Adams ◽  
R. Bencini
Keyword(s):  
Genetic Study ◽  
Molecular Data ◽  
Morphological Data ◽  
Island Population ◽  
New Taxon ◽  
Fresh Tissue ◽  
New Subspecies ◽  
New Evidence ◽  
Molecular Characters

Crowther et al. (1999) described an island population of an Australian dasyurid marsupial, Sminthopsis griseoventer, as a new subspecies on molecular (allozyme) and morphological grounds despite a previously published, contradictory genetic study and evidence of sympatry with its mainland conspecific. The legitimacy of this taxonomic arrangement has implications for the allocation of scarce management resources because the new taxon could be considered 'Critically Endangered'. Samples of the original tissues from which the molecular data cited by Crowther et al. were obtained no longer exist. Therefore, salient components of that work were rerun with fresh tissue and the results used to reassess evidence that the island population warrants recognition as a subspecies. We conclude that neither the molecular nor the morphological data supports differentiation at taxonomic or evolutionarily significant levels. Nevertheless, there is a good case for recognising the island population as an important management unit. This case study emphasises the importance of sound taxonomy determined by macro and molecular characters as a prerequisite to allocating resources for conservation.

scholarly journals Is there a need for accepting paraphyletic taxa? A case study in the Sardinian endemic Cymbalaria muelleri (Plantaginaceae)

2019 ◽  
Vol 191 (3) ◽  
pp. 325-338 ◽  
Author(s):  
Pau Carnicero ◽  
Peter Schönswetter ◽  
Núria Garcia-Jacas ◽  
Mercè Galbany-Casals
Keyword(s):  
Genome Size ◽  
Phylogenetic Trees ◽  
Fragment Length Polymorphism ◽  
Habitat Preferences ◽  
Molecular Data ◽  
Disjunct Distribution ◽  
Morphological Differences ◽  
A New Species ◽  
The Mediterranean Basin

Abstract Evolution does not always result in dichotomous phylogenetic trees. For instance, in anacladogenetic speciation, where a new species originates by budding, the ancestral taxon is often initially paraphyletic. Here we study Cymbalaria muelleri (Plantaginaceae), a chasmophytic species endemic to Sardinia, a major island in the Mediterranean Basin. Its distribution range is divided into two well-delimited geographical groups with some morphological differences. Using a combination of morphology, molecular data (amplified fragment length polymorphism fingerprinting) and relative genome size, we found that the two geographical groups should be considered two separate taxa, which split through anacladogenesis. Accordingly, we formally describe the new paraphyletic subspecies C. muelleri subsp. villosa as the ancestor, from which C. muelleri subsp. muelleri originated by budding. Morphological analyses support the differentiation of the two subspecies, and there are strong diagnostic characters to differentiate them. In addition to morphology and genetics, slightly divergent habitat preferences and the disjunct distribution of the two subspecies also support the recognition of two taxa. Genome size data obtained for the two subspecies are consistent with the previously established hexaploidy of C. muelleri.

Conflict between morphological and molecular data: A case study of Ficus krishnae (Moraceae)

Phytotaxa ◽  
2016 ◽  
Vol 247 (2) ◽  
pp. 143 ◽  
Author(s):  
KUMAR K. ANAND ◽  
SATYA N. JENA ◽  
LAL B. CHAUDHARY ◽  
MUNNA SINGH
Keyword(s):  
Gene Expression ◽  
Molecular Level ◽  
Molecular Data ◽  
Nodal Anatomy ◽  
Aerial Roots ◽  
Dna Contents ◽  
Morphological Differences ◽  
Morphological And Molecular Data ◽  
Peculiar Nature

Ficus krishnae, considered as highly sacred plant species in India, is well known for its peculiar nature of cup-shaped leaves. The species distinctly differs from its allied species F. benghalensis not only in the cup formation in leaves but also in the height of plants, aerial roots, stipules, petiole and its leafy appendages, ostiolar bracts of the receptacle and pollinator wasps, in addition to slight differences in the karyotype, DNA contents, stomatal and parenchymatous cells and nodal anatomy. In spite of having several morphological differences, F. krishnae is considered by some authors as a synonym of F. benghalensis, which does not seem to be convincing. Contrary to the morphological differences, the sequence analysis of nuclear and plastid regions of both the species conducted in the present study does not reveal any significant variations and thus infers no differentiation between the species at molecular level. This may be due to mutations at one or few coding loci or differences in gene expression associated with morphogenesis with significant phenotypic appearance.

scholarly journals Cytogenetic analysis of Hypomasticus copelandii and H. steindachneri: relevance of cytotaxonomic markers in the Anostomidae family (Characiformes)

2021 ◽  
Vol 15 (1) ◽  
pp. 65-76
Author(s):  
Filipe Schitini Salgado ◽  
Marina Souza Cunha ◽  
Silvana Melo ◽  
Jorge Abdala Dergam
Keyword(s):  
Sex Chromosome ◽  
5S Rdna ◽  
Molecular Data ◽  
Banding Patterns ◽  
As Species ◽  
Heteromorphic Sex Chromosomes ◽  
Species Groups ◽  
Phylogenetic Hypotheses ◽  
Morphological And Molecular Data ◽  
Species Specific

Recent phylogenetic hypotheses within Anostomidae, based on morphological and molecular data, resulted in the description of new genera (Megaleporinus Ramirez, Birindelli et Galetti, 2017) and the synonymization of others, such as the reallocation of Leporinus copelandii Steindachner, 1875 and Leporinus steindachneri Eigenmann, 1907 to Hypomasticus Borodin, 1929. Despite high levels of conservatism of the chromosomal macrostructure in this family, species groups have been corroborated using banding patterns and the presence of different sex chromosome systems. Due to the absence of cytogenetic studies in H. copelandii (Steindachner, 1875) and H. steindachneri (Eigenmann, 1907), the goal of this study was to characterize their karyotypes and investigate the presence/absence of sex chromosome systems using different repetitive DNA probes. Cytogenetic techniques included: Giemsa staining, Ag-NOR banding and FISH using 18S and 5S rDNA probes, as well as microsatellite probes (CA)15 and (GA)15. Both species had 2n = 54, absence of heteromorphic sex chromosomes, one chromosome pair bearing Ag-NOR, 18S and 5S rDNA regions. The (CA)15 and (GA)15 probes marked mainly the subtelomeric regions of all chromosomes and were useful as species-specific chromosomal markers. Our results underline that chromosomal macrostructure is congruent with higher systematic arrangements in Anostomidae, while microsatellite probes are informative about autapomorphic differences between species.

scholarly journals Contribution to chromosome numbers and phylogeny of Turkish Vincetoxicum Wolf (Apocynaceae, Asclepiadoideae)

2019 ◽  
Author(s):  
Seher Güven ◽  
Serdar Makbul ◽  
Kamil Coşkunçelebì
Keyword(s):  
Chromosome Numbers ◽  
Phylogenetic Analyses ◽  
Molecular Data ◽  
Sensu Stricto ◽  
Species Level ◽  
Nrdna Its ◽  
Chromosome Counts ◽  
As Species ◽  
Molecular Phylogenetic

We report chromosome counts for ten taxa of Vincetoxicum sensu stricto (s. str.) (Apocynaceae) from Turkey (of which two are endemic), including the first chromosome counts for V. canescens subsp. pedunculata, V. funebre, V. fuscatum subsp. boissieri, V. parviflorum and V. tmoleum. Two taxa of V. fuscatum proved to be tetraploid (2n=44) and the remaining eight taxa diploid (2n=22). Molecular phylogenetic analyses based on nrDNA (ITS) and cpDNA (trnT-trnL) (including 31 newly generated sequences) confirm the position of the Turkish Vincetoxicum in the Vincetoxicum s. str. clade. Vincetoxicum fuscatum, V. parviflorum, V. speciosum, as well as the Turkish endemic V. fuscatum subsp. boissieri, were clearly resolved as species-level clades, whereas the delimitation of the rest of the Turkish taxa was less clear based on molecular data.

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