scholarly journals Barcoding type specimens helps to identify synonyms and an unnamed new species in Eumunida Smith, 1883 (Decapoda : Eumunididae)

2011 ◽  
Vol 25 (4) ◽  
pp. 322 ◽  
Author(s):  
Nicolas Puillandre ◽  
Enrique Macpherson ◽  
Josie Lambourdière ◽  
Corinne Cruaud ◽  
Marie-Catherine Boisselier-Dubayle ◽  
...  
Keyword(s):  
Species Delimitation ◽  
Preliminary Analysis ◽  
Taxonomic Revision ◽  
Distinct Species ◽  
Molecular Clusters ◽  
Dna Barcodes ◽  
Type Specimens ◽  
Important Challenge ◽  
Identification Tool

The primary purpose of DNA-barcoding projects is to generate an efficient expertise and identification tool. This is an important challenge to the taxonomy of the 21st century, as the demand increases and the expert capacity does not. However, identifying specimens using DNA-barcodes requires a preliminary analysis to relate molecular clusters to available scientific names. Through a case study of the genus Eumunida (Decapoda : Eumunididae), we illustrate how naming molecule-based units, and thus providing an accurate DNA-based identification tool, is facilitated by sequencing type specimens. Using both morphological and unlinked molecular markers (COI and 28S genes), we analysed 230 specimens from 12 geographic areas, covering two-thirds of the known diversity of the genus, including type specimens of 13 species. Most hypotheses of species delimitation are validated, as they correspond to molecular units linked to only one taxonomic name (and vice versa). However, a putative cryptic species is also revealed and three entities previously named as distinct species may in fact belong to a single one, and thus need to be synonymised. Our analyses, which integrate the current naming rules, enhance the α-taxonomy of the genus and provide an effective identification tool based on DNA-barcodes. They illustrate the ability of DNA-barcodes, especially when type specimens are included, to pinpoint where a taxonomic revision is needed.

DNA barcodes for species delimitation in Chironomidae (Diptera): a case study on the genusLabrundinia

2013 ◽  
Vol 145 (6) ◽  
pp. 589-602 ◽  
Author(s):  
Fabio Laurindo da Silva ◽  
Torbjørn Ekrem ◽  
Alaide Aparecida Fonseca-Gessner
Keyword(s):  
Species Delimitation ◽  
Pupal Stage ◽  
Coi Gene ◽  
Life Stages ◽  
Dna Barcodes ◽  
Paulo State ◽  
Taxon Identification ◽  
Excellent Tool ◽  
Barcode Gap

AbstractIn this study, we analysed the applicability of DNA barcodes for delimitation of 79 specimens of 13 species of nonbiting midges in the subfamily Tanypodinae (Diptera: Chironomidae) from São Paulo State, Brazil. Our results support DNA barcoding as an excellent tool for species identification and for solving taxonomic conflicts in genusLabrundinia.Molecular analysis of cytochrome c oxidase subunit I (COI) gene sequences yielded taxon identification trees, supporting 13 cohesive species clusters, of which three similar groups were subsequently linked to morphological variation at the larval and pupal stage. Additionally, another cluster previously described by means of morphology was linked to molecular markers. We found a distinct barcode gap, and in some species substantial interspecific pairwise divergences (up to 19.3%) were observed, which permitted identification of all analysed species. The results also indicated that barcodes can be used to associate life stages of chironomids since COI was easily amplified and sequenced from different life stages with universal barcode primers.

On the type specimens of the recently described Sulawesi pitviper Tropidolaemus laticinctus Kuch, Gumprecht & Melaun 2007 (Squamata: Viperidae)

Zootaxa ◽  
2008 ◽  
Vol 1721 (1) ◽  
pp. 65
Author(s):  
ANDRÉ KOCH
Keyword(s):  
Taxonomic Revision ◽  
Distinct Species ◽  
Sensu Stricto ◽  
The Philippines ◽  
Type Specimens ◽  
Venomous Snakes ◽  
South Vietnam ◽  
Southern Thailand ◽  
Green Form

Until recently, the Asiatic pitviper genus Tropidolaemus Wagler, 1830 comprised only two species, the rare T. huttoni (Smith, 1949) from India and T. wagleri (Boie, 1827) (for discussion about authorship and data of publication see Vogel et al. 2007), which is known to represent a polytypic complex of morphologically distinct species occurring in South Vietnam and from the Malaysian Peninsula through Sumatra, Borneo, the Philippines and on Sulawesi (Iskandar & Colijn 2001, Vogel 2006). In a first paper of a comprehensive taxonomic revision of the T. wagleri complex, Vogel et al. (2007) demonstrated that these widespread and medically important venomous snakes actually represent at least three different taxa (wagleri, subannulatus, and philippensis), of which T. wagleri sensu stricto is restricted to Southern Thailand, West Malaysia as well as Sumatra and some adjacent islands. Therein, the green form of Sulawesi pitviper population (in addition to those of Borneo, and most Philippine islands) was preliminary assigned to the taxon subannulatus Gray, 1842.

Distinct species hidden in the widely distributed coral Coelastrea aspera (Cnidaria, Anthozoa, Scleractinia)

2021 ◽  
Author(s):  
Yuta Mitsuki ◽  
Naoko Isomura ◽  
Yoko Nozawa ◽  
Hiroyuki Tachikawa ◽  
Danwei Huang ◽  
...  
Keyword(s):  
Species Delimitation ◽  
Scleractinian Coral ◽  
Species Differences ◽  
Distinct Species ◽  
Molecular Data ◽  
Type Specimens ◽  
Morphological Studies ◽  
Morphological And Molecular Data ◽  
Northern Taiwan ◽  
Planula Larvae

Species identification is key for coral reef conservation and restoration. Recent coral molecular-morphological studies have indicated the existence of many cryptic species. Coelastrea aspera (Verrill, 1866) is a zooxanthellate scleractinian coral that is widely distributed in the Indo-Pacific. In Japan, this species is distributed from the subtropical reef region to the high-latitudinal non-reef region. Previous studies have reported that C. aspera colonies in the non-reef region release egg-sperm bundles (bundle type), whereas those in the reef region release eggs and sperm separately (non-bundle type) and release planula larvae after spawning. This difference in reproduction might be relevant to species differences. To clarify the species delimitation of C. aspera, the reproduction, morphology and molecular phylogeny of C. aspera samples collected from reef and non-reef regions in Japan were analysed, along with additional morphological and molecular data of samples from northern Taiwan. The results show that C. aspera is genetically and morphologically separated into two main groups. The first group is the non-bundle type, distributed only in reef regions, whereas the second group is the bundle type, widely distributed throughout the reef and non-reef regions. Examination of type specimens of the taxon’s synonyms leads us to conclude that the first group represents the true C. aspera, whereas the second is Coelastrea incrustans comb. nov., herein re-established, that was originally described as Goniastrea incrustans Duncan, 1886, and had been treated as a junior synonym of C. aspera.

scholarly journals How to Render Species Comparable Taxonomic Units Through Deep Time: a Case Study on Intraspecific Osteological Variability in Extant and Extinct Lacertid Lizards

2021 ◽  
Author(s):  
Emanuel Tschopp ◽  
James G Napoli ◽  
Lukardis C M Wencker ◽  
Massimo Delfino ◽  
Paul Upchurch
Keyword(s):  
Species Delimitation ◽  
Intraspecific Variability ◽  
Distinct Species ◽  
Deep Time ◽  
Extinct Species ◽  
Naturally Occurring ◽  
Extant Species ◽  
Lacertid Lizards ◽  
Single Genus

Abstract Generally, the species is considered to be the only naturally occurring taxon. However, species recognised and defined using different species delimitation criteria cannot readily be compared, impacting studies of biodiversity through Deep Time. This comparability issue is particularly marked when comparing extant with extinct species, because the only available data for species delimitation in fossils is derived from their preserved morphology, which is generally restricted to osteology in vertebrates. Here, we quantify intraspecific, intrageneric, and intergeneric osteological variability in extant species of lacertid lizards using pairwise dissimilarity scores based on a dataset of 253 discrete osteological characters for 99 specimens referred to 24 species. Variability is always significantly lower intraspecifically than between individuals belonging to distinct species of a single genus, which is in turn significantly lower than intergeneric variability. Average values of intraspecific variability and associated standard deviations are consistent (with few exceptions), with an overall average within a species of 0.208 changes per character scored. Application of the same methods to six extinct lacertid species (represented by 40 fossil specimens) revealed that intraspecific osteological variability is inconsistent, which can at least in part be attributed to different researchers having unequal expectations of the skeletal dissimilarity within species units. Such a divergent interpretation of intraspecific and interspecific variability among extant and extinct species reinforces the incomparability of the species unit. Lacertidae is an example where extant species recognised and defined based on a number of delimitation criteria show comparable and consistent intraspecific osteological variability. Here, as well as in equivalent cases, application of those skeletal dissimilarity values to palaeontological species delimitation potentially provides a way to ameliorate inconsistencies created by the use of morphology to define species.

A Novel Integrated Reliability Test System for BEOL TDDB Study

2012 ◽  
Author(s):  
Jifeng Chen ◽  
Peilin Song ◽  
Thomas M. Shaw ◽  
Franco Stellari ◽  
Lynne Gignac ◽  
...  
Keyword(s):  
Preliminary Analysis ◽  
Dielectric Breakdown ◽  
Test System ◽  
Accurate Information ◽  
Reliability Test ◽  
Electrical Measurements ◽  
Time Dependent Dielectric Breakdown ◽  
Microscopy Images ◽  
Insight Into

Abstract In this paper, we propose a new methodology and test system to enable the early detection and precise localization of Time-Dependent-Dielectric-Breakdown (TDDB) occurrence in Back-End-of-Line (BEOL) interconnection. The methodology is implemented as a novel Integrated Reliability Test System (IRTS). In particular, through our methodology and test system, we can easily synchronize electrical measurements and emission microscopy images to gather more accurate information and thereby gain insight into the nature of the defects and their relationship to chip manufacturing steps and materials, so that we can ultimately better engineer these steps for higher reliable systems. The details of our IRTS will be presented along with a case study and preliminary analysis results.

scholarly journals Comparative genomics suggests a taxonomic revision of the Staphylococcus cohnii species complex

2021 ◽  
Author(s):  
Anna Lavecchia ◽  
Matteo Chiara ◽  
Caterina De Virgilio ◽  
Caterina Manzari ◽  
Carlo Pazzani ◽  
...  
Keyword(s):  
Comparative Genomics ◽  
Species Complex ◽  
Large Scale ◽  
Genomic Sequence ◽  
Bacterial Species ◽  
Taxonomic Revision ◽  
Distinct Species ◽  
The Novel ◽  
Staphylococcus Cohnii ◽  
Taxonomic Assignments

Abstract Staphylococcus cohnii (SC), a coagulase-negative bacterium, was first isolated in 1975 from human skin. Early phenotypic analyses led to the delineation of two subspecies (subsp.), Staphylococcus cohnii subsp. cohnii (SCC) and Staphylococcus cohnii subsp. urealyticus (SCU). SCC was considered to be specific to humans whereas SCU apparently demonstrated a wider host range, from lower primates to humans. The type strains ATCC 29974 and ATCC 49330 have been designated for SCC and SCU, respectively. Comparative analysis of 66 complete genome sequences—including a novel SC isolate—revealed unexpected patterns within the SC complex, both in terms of genomic sequence identity and gene content, highlighting the presence of 3 phylogenetically distinct groups. Based on our observations, and on the current guidelines for taxonomic classification for bacterial species, we propose a revision of the SC species complex. We suggest that SCC and SCU should be regarded as two distinct species: SC and SU (Staphylococcus urealyticus), and that two distinct subspecies, SCC and SCB (SC subsp. barensis, represented by the novel strain isolated in Bari) should be recognized within SC. Furthermore, since large scale comparative genomics studies recurrently suggest inconsistencies or conflicts in taxonomic assignments of bacterial species, we believe that the approach proposed here might be considered for more general application.

Mitochondrial phylogeny and taxonomic revision of Italian and Slovenian fluvio-lacustrine barbels, Barbus sp. (Cypriniformes, Cyprinidae)

BMC Zoology ◽  
2021 ◽  
Vol 6 (1) ◽  
Author(s):  
Giovanni Rossi ◽  
Federico Plazzi ◽  
Gianluca Zuffi ◽  
Andrea Marchi ◽  
Salvatore De Bonis ◽  
...  
Keyword(s):  
Taxonomic Revision ◽  
Nuclear Data ◽  
Distinct Species ◽  
Sensu Stricto ◽  
Zoological Nomenclature ◽  
Conservation Policies ◽  
D Loop ◽  
Cyprinid Fishes ◽  
Northern Croatia ◽  
And Control

Abstract Background Barbels are ray finned cyprinid fishes of the Old-World with partially unresolved, intricate taxonomy. Within the Barbus sensu lato paraphyletic assemblage, Barbus sensu stricto is a monophyletic tetraploid lineage of Europe, northern Africa and Middle East, including two monophyletic sibling genera: Barbus and Luciobarbus. Italy, Slovenia and northern Croatia are natively inhabited by several entities of the genus Barbus, whose relationships and taxonomic ranks are still unclear. Aim of the present work is to focus on phylogeography of Italian and Slovenian barbels, with an appraisal of their current taxonomy. Results One hundred fifty specimens were collected in 78 sampling sites from 33 main watersheds, widely distributed along Italian and Slovenian ichthyogeographic districts. We amplified two mitochondrial markers, cytochrome b (cytb) and control region (D-loop), to infer a robust phylogeny for our sample and investigate on species delimitation. Our results strongly indicate all Italian and Adriatic Slovenian fluvio-lacustrine barbels to be comprised into at least three distinct species. We provide a proposal of taxonomic revision and a list of synonymies for two of them and a new description under the International Code of Zoological Nomenclature rules for the third one. Conclusions If nuclear data will confirm our findings, at least three specific entities should be acknowledged across our sampling area. Namely, the three species are (i) Barbus plebejus, in the Padano-Venetian district; (ii) Barbus tyberinus, in the Tuscany-Latium district; (iii) Barbus oscensis Rossi & Plazzi sp. nov., in the Tyrrhenian and southernmost-Adriatic parts of Apulia-Campania district. Finally, we briefly discuss the implications of such a taxonomic scenario on conservation policies.

A taxonomic revision of Hypogastrura crassaegranulata (Stach, 1949) (Collembola, Hypogastruridae)

Zootaxa ◽  
2006 ◽  
Vol 1109 (1) ◽  
pp. 27
Author(s):  
DARIUSZ SKARŻYŃSKI
Keyword(s):  
Taxonomic Revision ◽  
Distinct Species

The polytypic species Hypogastrura crassaegranulata (Stach, 1949) is revised, mostly based on types. H. crassaegranulata dobsinensis (Stach, 1949) is synonymized with H. crassaegranulata sensu nov. and H. crassaegranulata estaranhensis Cassagnau, 1959 and H. crassaegranulata burgundiana Gisin, 1960 are synonymized with H. franconiana stat. nov. H. crassaegranulata carpatica Nosek, 1962 is recognized as a distinct species. Achorutes schäfferi Carl, 1901 (= A. affinis Schäffer, 1900), suspected as identical with H. crassaegranulata franconiana, is considered as a probable synonym of H. purpurescens (Lubbock, 1867). Redescriptions are provided and lectotypes are designated for H. crassaegranulata (Stach, 1949) sensu nov. and H. franconiana (Stach, 1949) stat. nov.

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