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.
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)
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.
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
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
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
Diana Sanchez-Bernal, Jose Gregorio Martinez, Izeni Pires Farias, Tomas Hrbek, Susana Caballero
Summary: The Neotropics are home to a diverse range of freshwater fish species, including the cardinal tetra, which is widely traded in the ornamental fish market. This study investigated the phylogeography and population structure of the cardinal tetra, as well as potential migration routes between the Orinoco and Negro basins. The results suggest that river capture, physical barriers, and ecological factors may have played a role in shaping the distribution and genetic patterns of the cardinal tetra.
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
Zoology
Zhentao Cheng, Xiaolei Huang
Summary: Two new species of aphids were described, Aphis (Toxoptera) fafuensis and Aphis (Toxoptera) sennae, which feed on Adinandra millettii and Senna bicapsularis, respectively, in China. Morphological and molecular data supported the taxonomic classification of these new species within the subgenus Aphis (Toxoptera). A key for identifying apterous viviparous females of this subgenus was provided.
Article
Genetics & Heredity
Yanan Zhang, Shaolin Xu, Chenghe Sun, Henri Dumont, Bo-Ping Han
Summary: The development of new primers 30 F and 885 R for amplifying the COI gene of rotifers shows higher efficiency compared to universal primers, contributing to a better understanding of the species diversity and phylogeny of rotifers.
MITOCHONDRIAL DNA PART B-RESOURCES
(2021)
Article
Biodiversity Conservation
Ana S. Lavrador, Joao T. Fontes, Pedro E. Vieira, Filipe O. Costa, Sofia Duarte
Summary: The introduction of non-indigenous species is a major threat to European coastal ecosystems. DNA-based assessments are increasingly used for monitoring these species, but their accuracy depends on the reliability of DNA barcode reference libraries. This study aimed to compile and audit a DNA barcode reference library for marine invertebrate non-indigenous species in Europe.
Article
Parasitology
Chihiro Kitajima, Toshihiro Ichijo, Madoka Ichikawa-Seki
Summary: This study described the morphology of Setaria marshalli and established a reliable DNA barcode using the COI region. The COI region can be a useful marker for species discrimination in the case of S. marshalli, although the phylogenetic relationship with its congeners remains unclear.
Article
Ecology
David S. Green, Marie E. Martin, Roger A. Powell, Eric L. McGregor, Mourad W. Gabriel, Kristine L. Pilgrim, Michael K. Schwartz, Sean M. Matthews
Summary: The historical suppression of forest fires and increasing droughts due to climate change are predicted to result in larger and more intense wildfires in western North America and other regions. Understanding the impact of wildfires on forest-dependent species and species interactions is crucial for conservation and management decisions.
Article
Biodiversity Conservation
Kellie J. Carim, Lisa A. Eby, Loren M. Miller, Holly McLellan, Virgil Dupuis, Michael K. Schwartz
Summary: The spread of aquatic invasive species is typically a result of both natural and human mediated dispersal. This study used genetic information to understand the invasion history and dynamics of northern pike in the Columbia River basin. The results showed that the initial introduction of northern pike was due to human transport, and subsequent reproduction and natural dispersal led to the downstream expansion of the species. These findings emphasize the importance of a holistic approach to invasive species suppression.
MANAGEMENT OF BIOLOGICAL INVASIONS
(2022)
Article
Ecology
Daniel J. Isaak, Michael K. Young, Dona L. Horan, David Nagel, Michael K. Schwartz, Kevin S. McKelvey
Summary: Mountain headwater streams are crucial climate refuges for native cold-water species due to their extreme physical conditions and slow climate velocities. Persistent species in these refuges often exist as fragmented populations from broader historical distributions, facing ongoing habitat reductions and increasing isolation. Conservation planning should focus on identifying where remaining populations will persist and developing habitat restoration strategies to enhance species resilience. A case study on bull trout revealed that regional improvements in their status were challenging due to climate change and limited restoration actions. However, targeted investments for responsive populations near strongholds could enhance resilience and contribute to local enclaves that enhance dispersal among populations.
ECOLOGICAL APPLICATIONS
(2022)
Article
Agriculture, Dairy & Animal Science
Francesca Marucco, Kristine L. Pilgrim, Elisa Avanzinelli, Michael K. Schwartz, Luca Rossi
Summary: Wildlife dispersal has direct influence on population expansion patterns and indirect effects on the spread of wildlife diseases. This study documents the natural dispersal processes of an expanding wolf population in the Italian Alps, aiming to understand population dynamics and identify diseases associated with the recolonization pattern.
Article
Biochemistry & Molecular Biology
John A. Kronenberger, Taylor M. Wilcox, Daniel H. Mason, Thomas W. Franklin, Kevin S. McKelvey, Michael K. Young, Michael K. Schwartz
Summary: Environmental DNA (eDNA) sampling is a sensitive and cost-effective technique for wildlife monitoring. This study used SYBR Green and TaqMan hydrolysis probes to test 10 qPCR assays and trained random forest classifiers to predict amplification. The models achieved high accuracy in cross-validation and independent tests, making it easier for practitioners to develop specific assays.
MOLECULAR ECOLOGY RESOURCES
(2022)
Article
Fisheries
Michael K. Young, Daniel J. Isaak, David Nagel, Dona L. Horan, Kellie J. Carim, Thomas W. Franklin, Victoria A. Zeller, Brett Roper, Michael K. Schwartz
Summary: One of the most challenging tasks for aquatic ecologists is to precisely delineate the range of species, especially those that are broadly distributed, require specialized sampling methods, and may be simultaneously declining and increasing in different portions of their range. In this study, the distribution of Pacific lamprey in the upper Snake River basin was determined through a two-stage environmental DNA survey. The results showed that Pacific lamprey mainly occupied river main stems and stocked tributaries, with weaker detections in downstream and warm channels and near their headwaters. Furthermore, there was no evidence of indigenous populations in natural habitats.
JOURNAL OF FISH BIOLOGY
(2022)
Article
Ecology
Andrew J. Shirk, Gavin M. Jones, Zhiqiang Yang, Raymond J. Davis, Joseph L. Ganey, R. J. Gutierrez, Sean P. Healey, Shaula J. Hedwall, Serra J. Hoagland, Ron Maes, Karl Malcolm, Kevin S. McKelvey, Carly Vynne, Jamie S. Sanderlin, Michael K. Schwartz, Mark E. Seamans, Ho Yi Wan, Samuel A. Cushman
Summary: This study introduces a framework for automatically monitoring and assessing species habitats. Using this framework, an automated habitat monitoring system for the Mexican spotted owl was developed and linked to federal agency adaptive management plans. The system demonstrated high accuracy in monitoring the owl's habitat over a 35-year period. It highlights the necessity for continuous monitoring and the benefits of an automated workflow in managing species in dynamic landscapes.
Correction
Ecology
Gavin M. Jones, Andrew J. Shirk, Zhiqiang Yang, Raymond J. Davis, Joseph L. Ganey, R. J. Gutierrez, Sean P. Healey, Shaula J. Hedwall, Serra J. Hoagland, Ron Maes, Karl Malcolm, Kevin S. McKelvey, Jamie S. Sanderlin, Michael K. Schwartz, Mark E. Seamans, Ho Yi Wan, Samuel A. Cushman
Article
Ecology
Gavin M. Jones, Andrew J. Shirk, Zhiqiang Yang, Raymond J. Davis, Joseph L. Ganey, R. J. Gutierrez, Sean P. Healey, Shaula J. Hedwall, Serra J. Hoagland, Ron Maes, Karl Malcolm, Kevin S. McKelvey, Jamie S. Sanderlin, Michael K. Schwartz, Mark E. Seamans, Ho Yi Wan, Samuel A. Cushman
Summary: Understanding habitat dynamics is crucial for effective conservation. This study developed a dynamic model of Mexican spotted owl habitat using an automated habitat monitoring system. The study explored environmental correlates, spatial non-stationarity in habitat selection, long-term trends, and the impact of wildfires on habitat changes. The results showed that topography and climate had a significant influence on the owl's habitat, with a decline in total habitat area over the past 35 years, and wildfires accounting for a portion of the habitat loss.
Article
Ecology
Gretchen H. Roffler, Kristine L. Pilgrim, Katherine E. Zarn, Michael K. Schwartz, Taal Levi
Summary: Wolves focus on natal den sites during the pup-rearing season, where the survival of their pups depends on food provided by adult pack members. The availability of prey is influenced by habitat quality within the wolves' home range. A study conducted in Southeast Alaska's Prince of Wales Island examined the relationship between prey species, habitat characteristics, wolf diet, and litter size.
ECOLOGY AND EVOLUTION
(2023)
Article
Biodiversity Conservation
Kristine L. Pilgrim, Rebecca E. Green, Kathryn L. Purcell, Taylor M. Wilcox, Eric L. McGregor, Larissa E. Gleason, Samuel K. Wasser, Michael K. Schwartz
Summary: A recent climate-induced tree mortality in California has resulted in significant landscape changes in the southern Sierra Nevada. The mortality event has affected the habitat of the fisher, a species of concern in the region. Analysis of fisher scats showed changes in diet composition, with a decrease in mammalian prey and an increase in Ribes plants following the tree mortality event.
JOURNAL FOR NATURE CONSERVATION
(2023)
Article
Multidisciplinary Sciences
Todd B. Cross, Jason D. Tack, David E. Naugle, Michael K. Schwartz, Kevin E. Doherty, Sara J. Oyler-McCance, Ronald D. Pritchert, Bradley C. Fedy
Summary: Conserving genetic connectivity is crucial for species survival, especially for imperilled species. This study integrates network and functional connectivity models to identify population centres and pathways important for maintaining genetic connectivity in the greater sage-grouse population. The spatial action maps generated from this process prioritize areas important for range-wide genetic connectivity. Comparing these maps to impedances such as cultivation and woodland expansion provides valuable information for future management and tracking conservation efforts.
ROYAL SOCIETY OPEN SCIENCE
(2023)
Article
Biodiversity Conservation
L. M. Elbroch, S. H. Williams, O. Ohrens, K. Pilgrim, A. Moeller, S. Arroyo-Arce, M. Parker, D. Goic, H. Robinson, M. K. Schwartz
Summary: Determining the abundance of cryptic carnivores is essential for conservation management and coexistence strategies. This study compares two methods, one using camera traps and the other using genetic data extracted from scats, to estimate the population of pumas in a UNESCO Biosphere Reserve in Chile. The results show the variation in estimates depending on the analysis start time and length of the sampling window, and present a refined iterative sampling approach to stabilize density estimates.
ANIMAL CONSERVATION
(2023)
Article
Evolutionary Biology
Joanna W. Elmore, Taylor M. Wilcox, Alex E. Dutcher, Yuki Reiss, Michael K. Schwartz
Summary: Predation is a crucial factor to consider when studying the impact of invasive species on ecosystems. However, observing and understanding predation can be challenging. This study used DNA metabarcoding to analyze the digestive tracts of invasive Barn Owls and identified multiple species of seabirds as their prey. Traditional morphological assessment detected only a small proportion of seabirds in owl stomach contents, highlighting the effectiveness of molecular methods.
JOURNAL OF HEREDITY
(2023)
Article
Biodiversity Conservation
Michael K. Young, Rebecca Smith, Kristine L. Pilgrim, Daniel J. Isaak, Kevin S. McKelvey, Sharon Parkes, Jacob Egge, Michael K. Schwartz
Summary: The taxonomy of sculpins in western North America remains unresolved. This study used molecular approaches to identify candidate species and assess their distribution. Results indicated the presence of 43 candidate species and established a benchmark for understanding sculpin diversity in the region.
WESTERN NORTH AMERICAN NATURALIST
(2022)