scholarly journals A re-analysis of the data in Sharkey et al.’s (2021) minimalist revision reveals that BINs do not deserve names, but BOLD Systems needs a stronger commitment to open science

2021 ◽  
Author(s):  
Rudolf Meier ◽  
Bonny Blaimer ◽  
Eliana Buenaventura ◽  
Emily Hartop ◽  
Thomas von Rintelen ◽  
...  
Keyword(s):  
Open Science ◽  
Type Specimens ◽  
Public And Private ◽  
Character System ◽  
Private Data ◽  
As Species ◽  
Public Data ◽  
Assessment And Monitoring ◽  
Time Of Divergence ◽  
Species Descriptions

AbstractHalting biodiversity decline is one of the most critical challenges for humanity, but biodiversity assessment and monitoring are hampered by taxonomic impediments. We here distinguish between a “dark taxon impediment” caused by a large number of undescribed species and a “superficial description impediment” caused by species descriptions so imprecise that type specimens have to be consulted in order to resolve species identities. Recently, Sharkey et al. (2021) proposed to address the dark taxon impediment for Costa Rican braconid wasps by describing 403 species based on barcode clusters (“BINs”) computed by BOLD Systems. The default assumption of the revision is that BIN=Species (e.g., BOLD:ACM9419 becomes Bracon federicomatarritai Sharkey, sp. nov.) and therefore the diagnoses of most species consist only of a consensus barcode. We here argue that this type of “minimalist revision” is unnecessary and undesirable. It is unnecessary because barcode clusters (e.g. BINs) already provide grouping statements that overcome many of the obstacles associated with dark taxon impediments. However, minimalist revisions are also undesirable and problematic because the diagnoses are only based on one character system – that in the case of Sharkey et al. was poorly analyzed. Furthermore, the revision relies on units that violate basic rules of reproducibility because the BINs were delimited by a proprietary algorithm (RESL) that is applied to a mixture of public and private data. Here, we illustrate that many of the BINs described as species are unstable when the available public data are reanalyzed, reiterate that COI mostly measures time of divergence, and that BOLD Systems violates key principles of open science. We conclude by urging authors, reviewers, editors, and grantors to only publish and fund projects that adhere to modern standards of reproducibility.

Systematic studies of Festuca (Poaceae) occurring in China compared with taxa in North America

2003 ◽  
Vol 81 (10) ◽  
pp. 1008-1028 ◽  
Author(s):  
Xiang Chen ◽  
Susan G Aiken ◽  
Michael J Dallwitz ◽  
Patrice Bouchard
Keyword(s):  
North America ◽  
Software Package ◽  
Description Language ◽  
Type Specimens ◽  
Cd Rom ◽  
As Species ◽  
Flora Of China ◽  
Centre Of Diversity ◽  
Species Descriptions ◽  
Chinese And English

Members of the genus Festuca in China were studied from an illustrated database developed using the DELTA (DEscription Language for Taxonomy) software package. The database includes the place of valid publication of scientific names; the location of type specimens when known; whether we have examined the type specimens; synonymy; information on habitat, distribution, subgeneric classification, and taxonomic notes; and approximately 200 images. Five subgenera and 58 species including aggregates are recognized. Six taxa are not assigned to a subgenus at this time. Species descriptions of 400–500 words were generated in Chinese and English and are available on the Internet at http://cdelta.ibcas.ac.cn and as a CD-ROM in English and Chinese from the first author. INTKEY has been used to produce parallel and diagnostic descriptions of 120–130 words for 58 species of the genus Festuca for the Flora of China treatment in English. INTKEY and other DELTA programs were used to assess taxa throughout the database and in a detailed study of 11 flat-leaved taxa that appear to have their centre of diversity in China. The awnless taxa from China that were considered belong to the genus Festuca, not Poa. All the flat-leaved Festuca studied are sufficiently morphologically unique to be treated as species distinct from any found in North America. Clustering and phylogenetic methodologies were used to assess subgeneric and sectional classifications. A new section is proposed, Parviglumae sect. nov.Key words: Festuca, Subulatae, DELTA, China, systematics.

A new species of genus Hexacentrus Serville, 1831 from Taiwan (Orthoptera: Tettigoniidae: Hexacentrinae)

Zootaxa ◽  
2021 ◽  
Vol 4933 (4) ◽  
pp. 543-556
Author(s):  
PO-WEI CHEN ◽  
HUI-CONG XIE ◽  
XUE WU ◽  
CHU-ZE SHEN ◽  
ZHU-QING HE
Keyword(s):  
New Species ◽  
Gene Tree ◽  
Species Level ◽  
National Museum ◽  
Type Specimens ◽  
As Species ◽  
Wide Range ◽  
Similar Appearance ◽  
One New Species ◽  
A New Species

There are 29 species or subspecies in genus Hexacentrus occurring in Asia, Africa and Australia. Because of its similar appearance, it is not easy to distinguish them by traditional methods. In this study, we collected samples and sequenced COI genes from wide range. By reconstructing the gene tree, we found one new species, H. formosanus Chen et He sp. nov., from Taiwan. The new species is similar to H. expansus or H. inflatissimus, but differs from the former in male Cu2 vein of left tegmina curved and slender, and spectrum of male left tegmina slender and subsquare; differs from the later by body size smaller and female tegmina narrow and short. The type specimens are deposited in National Museum of Natural Science, Taichung, Taiwan (NMNS). H. japonicus hareyamai is treated as species level, H. hareyamai stat. nov. 

scholarly journals Photo images, 3D models and CT scanned data of loaches (Botiidae, Cobitidae and Nemacheilidae) of Japan

2018 ◽  
Vol 6 ◽  
pp. e26265 ◽  
Author(s):  
Yuichi Kano ◽  
Jun Nakajima ◽  
Takeshi Yamasaki ◽  
Jyun-ichi Kitamura ◽  
Ryoichi Tabata
Keyword(s):  
Public Interest ◽  
3D Models ◽  
Open Science ◽  
Type Specimens ◽  
Genetic Studies ◽  
Digital Archiving ◽  
Fish Biology ◽  
Freshwater Habitats ◽  
Further Development

Loach is one of the major cypriniform fishes in freshwater habitats of Japan; 35 taxa/clades have, until now, been recognised. Parallel to genetic studies, morphological examinations are needed for further development of loach study, eventually ichthyology and fish biology. Digital archiving, concerning taxonomy, ecology, ethology etc., is one of the progressive challenges for the open science of biology. This paper aimed to online publish photo images, 3D models and CT scanned data of all the known clades of loaches inhabiting Japan (103 individuals in total with several type specimens), contributing to ichthyology and public interest of biodiversity/biology.Photo images, 3D models and CT scanned data of all the known 35 taxa/clades of loaches inhabiting in Japan were online published at http://ffish.asia/loachesOfJapan and http://ffish.asia/loachesOfJapan3D.

The Toxic Side of Nanotechnology: An Insight into Hazards to Health and the Ecosystem

2021 ◽  
Vol 13 ◽  
Author(s):  
Sarita Kumari Yadav ◽  
Zulfequar Ahmed Khan ◽  
Brahmeshwar Mishra ◽  
Shiv Bahadur ◽  
Ajay Kumar ◽  
...  
Keyword(s):  
Aquatic Organisms ◽  
Risk Assessments ◽  
Proper Treatment ◽  
Public And Private ◽  
Regulatory Guidelines ◽  
Assessment And Monitoring ◽  
Treatment And Disposal ◽  
Human And Nature ◽  
Insight Into ◽  
Detailed Nature

: The objective of the present article is to provide an insight into the toxicity aspect of Nanoparticles on health and ecosystem along with risk assessment and monitoring. After a detailed screening of various research reports from the peer-reviewed journals, books, and research news, the article was prepared. Due to nanotechnology's various significant advantages over conventional technologies, it has been explored for diverse research and commercial needs such as cosmetics, medical, pharmaceuticals, biotechnology, electronics, catalysts, robotics, and so on. However, nanotechnology has several challenging elements for the health, environmental, societal and economic aspects, and unpredictable consequences can happen due to its unknown detailed nature, which needs to be identified. Therefore, in this review, an attempt has been made to cover the two most important aspects of the toxicity of nanoparticles i.e. influence on health and the ecosystem. The health hazards to various organs, especially lungs, gastrointestinal tract and dermis and aquatic organisms, have been elaborated. Further, the ecotoxicological aspect describing fate, mechanism of ecotoxicity, ecotoxicological challenges and solutions to ecotoxicologist are discussed. Risk assessments, related to the approaches that can be used for the optimization of nanotechnology, are also mentioned. Its high time when nanotechnology field needs reconsideration and uncompromising attention at a public and private level about its use, handling, storage, proper treatment and disposal. Also, risk analysis and establishment of regulatory guidelines for optimization and safe practice of nanotechnology for human and nature welfare are recommended.

scholarly journals A genomic perspective on the taxonomy of the subtribe Carcharodina (Lepidoptera: Hesperiidae: Carcharodini)

Zootaxa ◽  
2020 ◽  
Vol 4748 (1) ◽  
pp. 182-194 ◽  
Author(s):  
JING ZHANG ◽  
ERNST BROCKMANN ◽  
QIAN CONG ◽  
JINHUI SHEN ◽  
NICK V. GRISHIN
Keyword(s):  
Dna Sequences ◽  
Type Species ◽  
Phylogenetic Trees ◽  
Type Specimens ◽  
African Species ◽  
Protein Coding ◽  
Coding Regions ◽  
As Species ◽  
Close Relatives ◽  
Genomic Regions

We obtained whole genome shotgun sequences and phylogenetically analyzed protein-coding regions of representative skipper butterflies from the genus Carcharodus Hübner, [1819] and its close relatives. Type species of all available genus-group names were sequenced. We find that species attributed to four exclusively Old World genera (Spialia Swinhoe, 1912, Gomalia Moore, 1879, Carcharodus Hübner, [1819] and Muschampia Tutt, 1906) form a monophyletic group that we call a subtribe Carcharodina Verity, 1940. In the phylogenetic trees built from various genomic regions, these species form 7 (not 4) groups that we treat as genera. We find that Muschampia Tutt, 1906 is not monophyletic, and the 5th group is formed by currently monotypic genus Favria Tutt, 1906 new status (type species Hesperia cribrellum Eversmann, 1841), which is sister to Gomalia. The 6th and 7th groups are composed of mostly African species presently placed in Spialia. These groups do not have names and are described here as Ernsta Grishin, gen. n. (type species Pyrgus colotes Druce, 1875) and Agyllia Grishin, gen. n. (type species Pyrgus agylla Trimen, 1889). Two subgroups are recognized in Ernsta: the nominal subgenus and a new one: Delaga Grishin, subgen. n. (type species Pyrgus delagoae Trimen, 1898). Next, we observe that Carcharodus is not monophyletic, and species formerly placed in subgenera Reverdinus Ragusa, 1919 and Lavatheria Verity, 1940 are here transferred to Muschampia. Furthermore, due to differences in male genitalia or DNA sequences, we reinstate Gomalia albofasciata Moore, 1879 and Gomalia jeanneli (Picard, 1949) as species, not subspecies or synonyms of Gomalia elma (Trimen, 1862), and Spialia bifida (Higgins, 1924) as a species, not subspecies of Spialia zebra (Butler, 1888). Sequencing of the type specimens reveals 2.2-3.2% difference in COI barcodes, the evidence that combined with wing pattern differences suggests a new status of a species for Spialia lugens (Staudinger, 1886) and Spialia carnea (Reverdin, 1927), formerly subspecies of Spialia orbifer (Hübner, [1823]). 

Data dissemination best practices and challenges identified through NOAA’s Big Data Project

2020 ◽  
Author(s):  
Meredith Richardson ◽  
Ed Kearns ◽  
Jonathan O'Neil
Keyword(s):  
Big Data ◽  
Best Practices ◽  
Data Dissemination ◽  
Public And Private ◽  
Data Formats ◽  
Data Authentication ◽  
Start Up ◽  
Public Data ◽  
Amazon Web Services ◽  
Public And Private Stakeholders

<p>Through satellites, ships, radars, and weather models, the National Oceanic and Atmospheric Administration (NOAA) generates and handles tens of terabytes of data per day. Many of NOAA’s key datasets have been made available to the public through partnerships with Google, Microsoft, Amazon Web Services, and more as part of the Big Data Project (BDP). This movement of data to the Cloud has enabled access for researchers from all over the world to vast amounts of NOAA data, initiating a new form of federal data management as well as exposing key challenges for the future of open-access data. NOAA researchers have run into challenges of providing “analysis-ready” datasets to which researchers from varying fields can easily access, manipulate, and use for different purposes. This issue arises as there is no agreed-upon format or method of transforming traditional datasets for the cloud across research communities, with each scientific field or start up expressing differing data formatting needs (cloud-optimized, cloud-native, etc.). Some possible solutions involve changing data formats into those widely-used throughout the visualization community, such as Cloud-Optimized GeoTIFF. Initial findings have led NOAA to facilitate roundtable discussions with researchers, public and private stakeholders, and other key members of the data community, to encourage the development of best practices for the use of public data on commercial cloud platforms. Overall, by uploading NOAA data to the Cloud, the BDP has led to the recognition and ongoing development of new best practices for data authentication and dissemination and the identification of key areas for targeting collaboration and data use across scientific communities.</p>

scholarly journals SPIN: A Blockchain-Based Framework for Sharing COVID-19 Pandemic Information across Nations

2021 ◽  
Vol 11 (18) ◽  
pp. 8767
Author(s):  
Yazeed Alabdulkarim ◽  
Abdulmajeed Alameer ◽  
Mohammed Almukaynizi ◽  
Abdulaziz Almaslukh
Keyword(s):  
Private Information ◽  
International Travel ◽  
Security And Privacy ◽  
Shopping Malls ◽  
Economic Activities ◽  
Prototype Implementation ◽  
Policies And Measures ◽  
Private Data ◽  
Public Data ◽  
Rapid Spread

The COVID-19 pandemic has caused many countries around the globe to put strict policies and measures in place in an attempt to control the rapid spread of the virus. These measures have affected economic activities and have impacted a broad range of businesses, such as international traveling, restaurants, and shopping malls. As COVID-19 vaccination efforts progress, countries are starting to relax international travel constraints and permit passengers from certain destinations to cross the border. Moreover, travelers from those destinations are likely required to provide certificates of vaccination results or negative COVID-19 tests before crossing the borders. Implementing these travel guidelines requires sharing information between countries, such as the number of COVID-19 cases and vaccination certificates for travelers. In this paper, we introduce SPIN, a framework leveraging a permissioned blockchain for sharing COVID-19 information between countries. This includes public data, such as the number of vaccinated people, and private data, such as vaccination certificates for individuals. Additionally, we employ cancelable fingerprint templates to authenticate private information about travelers. We analyze the framework from scalability, efficiency, security, and privacy perspectives. To validate our framework, we provide a prototype implementation using the Hyperledger Fabric platform.

scholarly journals Taxonomic review of the Dichotomius (Luederwaldtinia) agenor species group (Coleoptera: Scarabaeidae: Scarabaeinae)

2021 ◽  
Vol 734 ◽  
pp. 1-64 ◽  
Author(s):  
Santiago Montoya-Molina ◽  
Fernando Z. Vaz-de-Mello
Keyword(s):  
New Species ◽  
Costa Rica ◽  
Male Genitalia ◽  
Species Group ◽  
External Morphology ◽  
Type Specimens ◽  
Mato Grosso ◽  
New Synonym ◽  
Species Descriptions ◽  
Group D

The Neotropical D. agenor species group of the subgenus Luederwaldtinia Martínez, 1951 is taxonomically reviewed. After examination of specimens in collections, the D. agenor species group will consist of seventeen species, a leap from the former nine species: D. agenor (Harold, 1869), D. amplicollis (Harold, 1869), D. belus (Harold, 1880), D. centralis (Harold, 1869), D. deyrollei (Harold, 1869), D. sagittarius (Harold, 1869) stat. rev., D. tristis (Luederwaldt, 1923), D. triquetrus (Luederwaldt, 1923), D. validipilosus (Luederwaldt, 1931), D. fornicatus (Luederwaldt, 1931) [transferred to D. lucasi species group and to which D. bosqi (Pereira, 1941) is considered to be a new synonym], D. inachoides (Felsche, 1901) [transferred from the group fisus (Selenocopris)], D. simplicicornis (Luederwaldt, 1935) [transferred from the group fisus (Selenocopris)], D. subaeneus (Castelnau, 1840) [transferred from the D. carbonarius species group], D. rafanunezi sp. nov. from Mato Grosso, D. henripittieri sp. nov. from Venezuela and D. enioi sp. nov. from Guatemala and Costa Rica. This review was based on external morphology and characters of the male genitalia (aedeagus and internal sac). Descriptions of new species and redescriptions were made after examining the type-specimens of the already described species. Lectotype designations, species revalidations, redescriptions and new species descriptions are provided.

scholarly journals Food security: underpin with public and private data sharing

Nature ◽  
2020 ◽  
Vol 578 (7796) ◽  
pp. 515-515 ◽  
Author(s):  
Sylvain Coutu ◽  
Inbal Becker-Reshef ◽  
Alyssa K. Whitcraft ◽  
Chris Justice
Keyword(s):  
Food Security ◽  
Data Sharing ◽  
Public And Private ◽  
Private Data

No Humans Here

2022 ◽  
Vol 6 (GROUP) ◽  
pp. 1-13
Author(s):  
Jessica Pater ◽  
Casey Fiesler ◽  
Michael Zimmer
Keyword(s):  
Data Privacy ◽  
Ethical Decision Making ◽  
Human Subjects ◽  
Open Science ◽  
Unintended Consequences ◽  
Institutional Review Boards ◽  
Research Communities ◽  
Institutional Review ◽  
Public Data ◽  
Regulatory Bodies

Many research communities routinely conduct activities that fall outside the bounds of traditional human subjects research, yet still frequently rely on the determinations of institutional review boards (IRBs) or similar regulatory bodies to scope ethical decision-making. Presented as a U.S. university-based fictional memo describing a post-hoc IRB review of a research study about social media and public health, this design fiction draws inspiration from current debates and uncertainties in the HCI and social computing communities around issues such as the use of public data, privacy, open science, and unintended consequences, in order to highlight the limitations of regulatory bodies as arbiters of ethics and the importance of forward-thinking ethical considerations from researchers and research communities.

Sign in / Sign up

Export Citation Format

Share Document