Article
Biochemistry & Molecular Biology
Cameron M. Nugent, Tyler A. Elliott, Sujeevan Ratnasingham, Paul D. N. Hebert, Sarah J. Adamowicz
Summary: DNA barcoding and metabarcoding are widely used for species discovery and biodiversity assessments, but high error rates can inflate estimates. The debar package utilizes a hidden Markov model to denoise COI sequences, reducing indel errors and being sensitive to true COI variation in the animal kingdom. This results in more accurate sequences and aids in characterizing species diversity.
MOLECULAR ECOLOGY RESOURCES
(2021)
Review
Biochemistry & Molecular Biology
Natalia Lima Lira, Sandro Tonello, Roberto Laridondo Lui, Josiane Baccarin Traldi, Heleno Brandao, Claudio Oliveira, Daniel Rodrigues Blanco
Summary: Studies on fish eggs and larvae have been conducted since the late 19th century and have provided important information for understanding fish fauna and environmental inventory. The use of molecular identification techniques, particularly DNA barcoding, has greatly improved taxonomic precision in studying ichthyoplankton. Recent research shows a significant increase in the use of DNA barcoding, with high accuracy compared to traditional taxonomic identification methods.
MOLECULAR BIOLOGY REPORTS
(2023)
Article
Zoology
Kari Nupponen, Pasi Sihvonen
Summary: This article acknowledges various individuals and organizations for their assistance and support in field work, specimen photography, DNA analysis, comments and criticism, as well as funding. The acknowledgements highlight the collaborative nature of research and the importance of various contributions to its success.
Article
Agriculture, Multidisciplinary
Chengtong Chen, Yanfei Ding, Yi Wang, Qiong Jiang, Feijuan Wang, Chenze Lu, Leilei Zhang, Cheng Zhu
Summary: The study focused on authenticating four species of pufferfish using the high-resolution melting (HRM) method, with DNA barcoding coupled with HRM analysis identified as a rapid and efficient tool to prevent consumer fraud or mislabeling of fish products. The findings revealed the potential of COI as the optimal DNA barcode for pufferfish authentication.
JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY
(2021)
Article
Environmental Sciences
Jinxia Zhang, Lei Xu, Feiyan Du, Quehui Tang, Lianggen Wang, Jiajia Ning, Delian Huang, Yafang Li, Shuangshuang Liu, Xuehui Wang
Summary: This study employed DNA barcoding and molecular identification approaches to explore the species diversity and distribution pattern of marine fish in both the northern and southern sea areas of Hainan Island in the northern South China Sea. A total of 186 sequences were obtained, representing 56 species, 47 genera, 34 families, and 17 orders.
FRONTIERS IN MARINE SCIENCE
(2023)
Article
Agriculture, Multidisciplinary
J-C Huang, X-Y Li, Y-P Li, R-S Zhang, D-B Chen, R-X Xia, Y-Q Liu
Summary: This study analyzed the mitochondrial COI gene sequences from 13 Samia species and provided a DNA barcode-based phylogenetic framework for species identification. The results showed a close relationship between S. ricini and S. canningi, but a distant relationship between S. ricini and S. cynthia.
JOURNAL OF INSECTS AS FOOD AND FEED
(2022)
Article
Entomology
Karin Kirchgatter, Lilian de Oliveira Guimaraes, Eliana Ferreira Monteiro, Vanessa Christe Helfstein, Juliana Telles-de-Deus, Regiane Maria Tironi de Menezes, Simone Liuchetta Reginato, Carolina Romeiro Fernandes Chagas, Vera Lucia Fonseca de Camargo-Neves
Summary: This study aimed to provide genetic data of Mansonia, a mosquito species that is an important vector of viruses and other parasites. The morphological identification of this species is difficult, and the DNA sequences obtained in this study can be used for molecular identification. The cytochrome c oxidase subunit I (COI) DNA barcode region is considered a valuable and reliable tool for mosquito species recognition. This research provides tools for the genetic identification of species that play a significant role in pathogen transmission.
Review
Green & Sustainable Science & Technology
Chiranjib Chakraborty, Ashish Ranjan Sharma, Garima Sharma, Manojit Bhattacharya, Sang-Soo Lee
Summary: This article reviews the current status of global microbial diversity, focusing on microbial biodiversity in marine and terrestrial ecosystems. The study demonstrates how 'Biodiversity Informatics' can assist scientists in mapping the diversity of recorded microbial species in different habitats. Additionally, it highlights the use of databases to explore microbial biodiversity and other species of fauna and flora.
ENVIRONMENT DEVELOPMENT AND SUSTAINABILITY
(2023)
Article
Zoology
Michael J. Sharkey, Austin Baker, Ramya Manjunath, Paul D. N. Hebert
Summary: This article discusses the transfer of Neotropical members from Earinus to the new genus Chilearinus, as well as the transfer of some species. The status of certain species and the description of new species are also discussed.
Article
Agriculture, Multidisciplinary
Xinying Yin, Hao Yang, Yongzhe Piao, Yulin Zhu, Qiuyue Zheng, Mohammad Rizwan Khan, Yong Zhang, Rosa Busquets, Bing Hu, Ruijie Deng, Jijuan Cao
Summary: In this study, a label-free and colorimetric nucleic acid assay was developed for detecting DNA barcodes and determining food authenticity with the naked eye. The method, called the CRISPR-based colorimetric DNA barcoding (Cricba) assay, utilized CRISPR/Cas12a to recognize PCR products and trans-cleave the G-quadruplex DNAzyme, resulting in a color change that could be observed without any instruments. The assay demonstrated high sensitivity and versatility, and could be a competitive method for food authenticity testing.
JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY
(2022)
Article
Biodiversity Conservation
Natalia Petit-Marty, Maite Vazquez-Luis, Iris E. Hendriks
Summary: Threatened species exhibit reduced genetic diversity, as shown by analysis of COI nucleotide diversities in this study, indicating higher extinction risks. A comparative frame was established to evaluate conservation status using COI nucleotide diversity in nonthreatened species. The study concluded that COI nucleotide diversity serves as a good proxy for assessing conservation status when knowledge is limited.
CONSERVATION LETTERS
(2021)
Article
Biotechnology & Applied Microbiology
Ben A. Parslow, Michael P. Schwarz, Mark Stevens
Summary: Gasteruptiidae Ashmead is a family of wasps with 589 described species worldwide. The lack of molecular data and phylogenetic research has made species-level identification difficult, but incorporating molecular species delimitation techniques can assist in resolving taxonomic uncertainty in the family.
Article
Multidisciplinary Sciences
Martin Schwentner, Reza Zahiri, Satoshi Yamamoto, Martin Husemann, Bjoern Kullmann, Ralf Thiel
Summary: The study utilized a COI-based eDNA approach to assess the biodiversity within the Elbe, revealing poor representation of fish species likely due to universal COI primers. Tidal influence was strong on the recovered taxa, with downstream sites resembling upstream during low tide and showing significant differences during high and early tide.
Article
Biodiversity Conservation
Mali Guo, Chaohai Yuan, Leyan Tao, Yafei Cai, Wei Zhang
Summary: DNA barcoding is a modern method for cataloguing biodiversity, which allows for fast, reliable, and inexpensive assessment of species composition across all forms of life. Global DNA barcoding campaigns have led to the development of online workbenches and databases, such as the BOLD system, serving as barcode references. This article provides an overview of the characteristics and features of barcode markers and major reference libraries, as well as addresses the limitations and opportunities of DNA barcoding in the scientific and societal communities.
CONSERVATION GENETICS RESOURCES
(2022)
Article
Ecology
Xin Peng, Qiang Li, Zhentao Cheng, Xiaolei Huang
Summary: The growth and implementation of genetic data in the field of biogeography has significantly benefited the discipline. Scientists have perceived an imbalance of genetic data among different regions and taxonomic groups, but lack empirical evidence to understand the current situation. By constructing a dataset consisting of millions of nucleotide sequences and specific sequences from different kingdoms and taxonomic groups, this study provides evidence of the geographical and taxonomical imbalance of genetic data. It also identifies major gaps and inappropriate practices in the production, application, and sharing of genetic data, and discusses perspectives on improving the quantity and quality of genetic data.
FRONTIERS IN ECOLOGY AND EVOLUTION
(2023)
Article
Plant Sciences
Olga N. Selivanova, Galina G. Zhigadlova, Gary W. Saunders
Article
Plant Sciences
Manuela Parente, Robert L. Fletcher, Filipe O. Costa, Gary W. Saunders
Summary: This study identified 11 independent genetic lineages of Ralfsia-like taxa, leading to the proposal of a new classification unit, Pseudoralfsiaceae, and two new genera, Pseudoralfsia and Nuchella. Additionally, species of Pseudoralfsiaceae can be distinguished from Ralfsia sensu stricto (Ralfsiaceae) mainly by DNA sequences and by consistently having frequent hair pits, and typically unsymmetrical thalli.
EUROPEAN JOURNAL OF PHYCOLOGY
(2021)
Article
Plant Sciences
Trevor T. Bringloe, Cody Brooks, Meghann Bruce, Gary W. Saunders
Summary: The research confirms the presence of Eisenia arborea in Haida Gwaii, Canada, with potential scattered populations throughout the western portions of the archipelago. The populations in Haida Gwaii could serve as potential monitoring sites for ecological and evolutionary investigations of E. arborea.
Article
Plant Sciences
Craig W. Schneider, Michael J. Wynne, Gary W. Saunders
Summary: Specimens of Spyridia 'filamentosa' from Southern New England and New York were sequenced for mitochondrial COI-5P and chloroplastic rbcL genes, showing distinct differences from Mediterranean specimens. As a result, a little-known species name, Spyridia americana Durant, was assigned to specimens collected from the northeastern coast of the United States.
Article
Plant Sciences
Joseph L. Richards, Gary W. Saunders, Jeffery R. Hughey, Paul W. Gabrielson
Summary: Partial rbcL sequences were obtained from type specimens of Lithophyllum coarctatum and L. gardineri. Despite morpho-anatomical similarities, phylogenetic analyses confirmed that both species belong in Porolithon. A novel epiphytic species, P. epiphyticum sp. nov., from Cocos-Keeling Islands was also identified.
Article
Plant Sciences
Viviana Pena, David Belanger, Patrick Gagnon, Joseph L. Richards, Line Le Gall, Jeffery R. Hughey, Gary W. Saunders, Sandra C. Lindstrom, Eli Rinde, Vivian Husa, Hartvig Christie, Stein Fredriksen, Jason M. Hall-Spencer, Robert S. Steneck, Kathryn M. Schoenrock, Janne Gitmark, Ellen Sofie Grefsrud, Marc B. Angles D'Auriac, Erwann Legrand, Jacques Grall, Thomas F. Mumford, Nicholas A. Kamenos, Paul W. Gabrielson
Summary: The study analyzed DNA sequences of Arctic and Subarctic coralline red algae, confirming the existence of four Lithothamnion species and correcting previous taxonomical errors based on morpho-anatomy. The importance of sequencing historical type specimens was demonstrated, and the distributions and ecology of these species were updated based on sequenced specimens.
EUROPEAN JOURNAL OF PHYCOLOGY
(2021)
Article
Plant Sciences
Craig W. Schneider, Margaret M. Cassidy, Gary W. Saunders
Summary: The newly discovered red alga Dasya sylviae sp. nov. was found at mesophotic depths of 60-90 m off Bermuda. Genetic sequences and morphological characteristics distinguish it as a distinct pseudodichotomous species within the genus Dasya.
EUROPEAN JOURNAL OF TAXONOMY
(2021)
Article
Plant Sciences
John M. Huisman, Gary W. Saunders
Summary: Molecular analyses have revealed discrepancies in Australian taxa previously classified as Plocamium cartilagineum with the species from its northern hemisphere type locality. After examining and designating a lectotype for Plocamium pusillum, it has been resurrected as a distinct species genetically and morphologically, differing from authentic P. cartilagineum.
CRYPTOGAMIE ALGOLOGIE
(2021)
Article
Plant Sciences
Thea R. Popolizio, Craig W. Schneider, Walter M. Jongbloed, Gary W. Saunders, Christopher E. Lane
Summary: In the last decade, molecular tools have revealed previously unrecognized taxa in Bermuda's marine flora, especially among the Rhodophyta. Misidentified species have been reclassified and many novel species have been discovered. The `Laurencia complex' has also been modified globally, with five of the eight recognized genera found in Bermuda. The study presents new species and revises the classification of existing ones using genetic sequencing.
CRYPTOGAMIE ALGOLOGIE
(2022)
Article
Ecology
Marlene Elias, Matt Kandel, Stephanie Mansourian, Ruth Meinzen-Dick, Mary Crossland, Deepa Joshi, Juliet Kariuki, Lynn C. Lee, Pamela McElwee, Amrita Sen, Emily Sigman, Ruchika Singh, Emily M. Adamczyk, Thomas Addoah, Genevieve Agaba, Rahinatu S. Alare, Will Anderson, Indika Arulingam, SGiids Kung Vanessa Bellis, Regina Birner, Sanjiv De Silva, Mark Dubois, Marie Duraisami, Mike Featherstone, Bryce Gallant, Arunima Hakhu, Robyn Irvine, Esther Kiura, Christine Magaju, Cynthia McDougall, Gwiisihlgaa Daniel McNeill, Harini Nagendra, Tran Huu Nghi, Daniel K. Okamoto, Ana Maria Paez Valencia, Tim Pagella, Ondine Pontier, Miranda Post, Gary W. Saunders, Kate Schreckenberg, Karishma Shelar, Fergus Sinclair, Rajendra S. Gautam, Nathan B. Spindel, Hita Unnikrishnan, Gulxa Taaa Gaagii Ngaang Nadine Wilson, Leigh Winowiecki
Summary: The importance of considering human and social dimensions in ecosystem restoration is emphasized, with a set of ten people-centered rules proposed to achieve ecological and social goals. These rules provide actionable ways for stakeholders to center humans and social dimensions in restoration initiatives, aiming to generate fair and sustainable outcomes. The integration of socio-political issues throughout the restoration process is crucial for successful and impactful restoration efforts.
RESTORATION ECOLOGY
(2022)
Article
Plant Sciences
John M. Huisman, Gary W. Saunders
Summary: Three new species of the red algal genus Asteromenia were described in this study, with one being a previously misidentified undescribed species and the other two from different islands. These new species showed morphological overlap and required accurate species recognition through DNA sequencing. The study highlights the importance of sequence analysis.
Article
Plant Sciences
Margaret M. Cassidy, Craig W. Schneider, Gary W. Saunders
Summary: Molecular studies of Dasya genus in Bermuda revealed two new species and reclassified known species. The study also uncovered the relationship between Dasya and Dasysiphonia.
JOURNAL OF PHYCOLOGY
(2022)
Article
Biodiversity Conservation
Gary W. Saunders, Cody M. Brooks
Summary: By screening DNA from 285 coralline crusts in Canada and adjacent waters, the distribution range of Porphyra corallicola was found to be far beyond previous knowledge. In addition, it was found that other species also exist only in the Conchocelis stage. The further development of this method will facilitate the study of Conchocelis stages in nature, greatly enhancing ecological knowledge of bangialean species.
Meeting Abstract
Plant Sciences
Viviana Pena, David Belanger, Patrick Gagnon, Joseph L. Richards, Line Le Gall, Jeffery R. Hughey, Gary W. Saunders, Sandra C. Lindstrom, Eli Rinde, Vivian Husa, Hartvig Christie, Stein Fredriksen, Jason M. Hall-Spencer, Robert S. Steneck, Kathryn M. Schoenrock, Janne Gitmark, Ellen Sofie Grefsrud, Marc B. Angles d'Auriac, Erwann Legrand, Jacques Grall, Thomas M. Mumford, Nicholas A. Kamenos, Paul W. Gabrielson
Article
Plant Sciences
Gerald T. Kraft, Gary W. Saunders
Summary: The Acrotylaceae, a red-algal family composed of six genera, lacks common habits and vegetative features among them, with cystocarps being the most unifying characteristic. Molecular studies reveal that the family consists of two subfamilies, Acrotylaceae and the newly proposed Clavicloniaceae. The South African genus Reinboldia, previously included in Acrotylaceae, is now considered questionable for inclusion in the family.
AUSTRALIAN SYSTEMATIC BOTANY
(2021)