Article
Food Science & Technology
Meng-Yue Zhou, Ran -Ran Xing, Ke-Han Liu, Yi-Qiang Ge, Ying Chen
Summary: This study aimed to develop a DNA barcoding method for the species identification of culinary spices. Five barcodes were evaluated to detect 19 culinary spices, but they could not definitively identify all the species. The combination of ITS2 and psbA-trnH barcodes improved the identification ability, successfully identifying all tested spices except for Cambodian cardamom. The method can be used to standardize labels on commercial culinary spices.
Article
Ecology
Jacopo D'Ercole, Roger Vila, Leonardo Dapporto, Mikko Pentinsaari, Gerard Talavera, Vlad Dinca, Paul D. N. Hebert
Summary: This study examined mitochondrial DNA sequence variation in introduced insect species and found that genetic variation is significantly lower in introduced populations compared to native populations. The study suggests that these genetic patterns are likely a result of general processes. Understanding the molecular evolution of introduced species is crucial for managing their impact on ecosystems.
FRONTIERS IN ECOLOGY AND EVOLUTION
(2023)
Article
Plant Sciences
Ria Cahyaningsih, Lindsey Jane Compton, Sri Rahayu, Joana Magos Brehm, Nigel Maxted
Summary: DNA barcoding has emerged as a scientific breakthrough in plant identification and conservation, especially in the field of medicinal plants. This study focused on analyzing the effectiveness of different DNA barcoding regions for Indonesian medicinal plant identification, with matK being recommended as the main region. Findings from this study have implications for forensic studies and the conservation of medicinal plants on a national and global scale.
Article
Biology
Maria Pia Miglietta, Sarah Pruski
Summary: Sampling in multiple localities and molecular barcoding reveal the presence of local cryptic species in allopatry in wide-ranging nominal species. However, cryptic species in sympatry can easily be missed if they have different seasonality and require long-term frequent sampling for identification. This study investigates the presence of cryptic species within a temporal gradient and on a spatial scale in Hydrozoa using mitochondrial sequencing and finds a high number of sympatric cryptic species. The bi-dimensional cryptic diversity highlighted in this study is crucial for understanding evolution processes, biogeography, and biodiversity assessments in the sea.
PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES
(2023)
Article
Microbiology
Vanessa Nascimento Brito, Janaina Lana Alves, Kaliane Sirio Araujo, Tiago de Souza Leite, Casley Borges de Queiroz, Olinto Liparini Pereira, Marisa Vieira de Queiroz
Summary: In this study, 30 endophytic Trichoderma isolates obtained from wild Hevea spp. in the Brazilian Amazon were analyzed. The analysis revealed known Trichoderma species as well as four new species. This study contributes to our understanding of the diversity of endophytic Trichoderma species in Neotropical forests and identifies potential biocontrol agents for plant disease management.
FRONTIERS IN MICROBIOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Sebastian Kvist, Ismay Earl, Ester Kink, Alejandro Oceguera-Figueroa, Peter Trontelj
Summary: The Holarctic leech genus Haemopis is composed of 11 macrophagous species, which are important fish food and predators. However, there is a lack of data on morphology and genetic variation, hindering species identification and natural history inference. To address this, we conducted genetic analysis and morphological investigations, producing a phylogenetic hypothesis and DNA barcodes for the genus. Our study highlights species delimitation and evolutionary history of this neglected group of leeches.
MOLECULAR PHYLOGENETICS AND EVOLUTION
(2023)
Article
Plant Sciences
Irene Bosmali, Georgios Lagiotis, Nadia Haider, Maslin Osathanunkul, Costas Biliaderis, Panagiotis Madesis
Summary: By analyzing DNA barcoding regions, this study identified 71 Vicia specimens of Eurasian descent. The trnL and ITS2 regions were effective in discriminating the analyzed species, while the rpoC1 region could not identify all selected species due to sequence conservation or missing sequences in GenBank. The combination of DNA barcoding regions is essential for accurate species discrimination within the Vicia genus.
Article
Plant Sciences
Mengying Chen, Jian Sun, Hui Yao, Fuyu Gong, Long Cai, Chanyan Wang, Qingsong Shao, Zhian Wang
Summary: This study examined the genetic and chemical variability among five Curcuma species using ITS2 and trnK intron gene fragment. The results showed that these gene fragments were able to distinguish the five species clearly. Additionally, there were significant differences in chemical composition, with C. longa showing the largest variation. These findings are important for selecting the original plants of Curcuma medicinal materials and discovering new medicinal plant resources.
FRONTIERS IN PLANT SCIENCE
(2023)
Article
Biochemistry & Molecular Biology
Nicolas Puillandre, Sophie Brouillet, Guillaume Achaz
Summary: ASAP is a fast and efficient method for constructing species partitions from single locus sequence alignments. It offers a new scoring system without prior biological insight, and can be used through a graphical web interface or downloaded for local usage.
MOLECULAR ECOLOGY RESOURCES
(2021)
Article
Plant Sciences
Mohammed Al-Dakhil, Salem Alghamdi, Hussein Migdadi, Muhammad Afzal, Ahmed Abdelrahim Ali
Summary: This study investigated ten duckweed isolates from different regions in Saudi Arabia and identified Lemna gibba as a dominant species in many regions, with L. gibba, L. minor, and L. punctata being the most widely distributed species in the country. Variations in morphological traits were observed among the clones, suggesting potential diversity within the duckweed species in the studied areas. Further research on adaptability, molecular genetics, and functional genomics is needed for the commercial utilization of these species in Saudi Arabia.
Article
Food Science & Technology
Jiahleen B. Roungchun, Amanda M. Tabb, Rosalee S. Hellberg
Summary: Accurate species identification of tuna products is crucial for combating fraud, improving stock regulation, and reducing health risks. This study utilized a DNA mini-barcoding system to successfully identify tuna species in raw and processed samples, with potential for further optimization in future research for canned tuna samples.
Article
Plant Sciences
Girme Aoudumbar Ramesh, Deepu Mathew, K. Joseph John, V Ravisankar
Summary: This study utilized DNA barcoding to identify seven species of Momordica and determine their relationships. Analysis of matK gene sequences resulted in distinct barcodes that could differentiate the species. The study also confirmed M. cymbalaria as a member of the Momordica genus.
HORTICULTURAL PLANT JOURNAL
(2022)
Article
Genetics & Heredity
Mariano Martinez, Lars Harms, Doris Abele, Christoph Held
Summary: The species delimitation of Aequiyoldia eightsii in South America and Antarctica is complicated by mitochondrial heteroplasmy and amplification bias in molecular barcoding. Different data sources suggest that cross-Drake populations belong to different species, but the situation is not clear within Antarctic populations. Standard barcoding procedures lead to amplification bias and overestimate the species richness. Nuclear SNPs show no differentiation, suggesting that the Antarctic populations represent a single species. Multiple data sources and quality control measures are important to increase the accuracy of species delimitation.
Article
Plant Sciences
Jianli Wang, Zhenfei Yan, Peng Zhong, Zhongbao Shen, Guofeng Yang, Lichao Ma
Summary: This study evaluated the utility of four candidate DNA barcoding regions in seven genera of Gramineae. It found that matK and ITS showed the highest discriminatory power, while rbcL and trnL-F were less effective. The study also demonstrated the feasibility of establishing a technical system for rapid and reliable identification of these seven genera, and provided crucial reference for analyzing the genetic diversity of grass germplasm resources.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Evolutionary Biology
Rafael Henrique da Rocha, Carlos Alexandre Fernandes, Thais Souto Bignotto, Vladimir Pavan Margarido, Luiz Fernando Caserta Tencatt, Weferson Junio da Graca, Eder Andre Gubiani
Summary: This study characterized Corydoras carlae and Corydoras sp. through cytogenetic, morphometric, and molecular analyses, revealing distinct evolutionary lineages and a recent speciation process. Mitochondrial and nuclear sequences were effective in discriminating between the two species, suggesting the absence of gene flow between them. The study also identified differences in morphometric proportions and suggested two Molecular Operational Taxonomic Units (MOTUs) for Corydoras specimens from the Iguassu River.
ORGANISMS DIVERSITY & EVOLUTION
(2022)
Article
Biodiversity Conservation
Robin Leppitt, Luke Einoder, Peter M. Kyne, John C. Z. Woinarski, Stephen Garnett
Summary: A survey conducted in northern Australia on the Endangered Alligator Rivers Yellow Chat found that the bird's habitat selection is influenced by fire and feral animals. The study provides recommendations for future monitoring.
BIRD CONSERVATION INTERNATIONAL
(2022)
Article
Fisheries
Robin S. Waples, Pierre Feutry
Summary: Research has found that genetic methods and close-kin mark-recapture methods differ in estimating population size, but combining the two can provide a better assessment of both ecological and evolutionary processes.
FISH AND FISHERIES
(2022)
Article
Genetics & Heredity
Chen Wang, Tinghe Lai, Peiyuan Ye, Yunrong Yan, Pierre Feutry, Binyuan He, Zhongjian Huang, Ting Zhu, Junjie Wang, Xiao Chen
Summary: In this study, the complete mitogenome of the Japanese topeshark was determined for the first time, revealing a novel non-coding region and gene rearrangements. Phylogenetic analysis based on mitogenomic data provided further insights into the evolution and phylogeny of shark mitogenomes.
Article
Fisheries
Brendan S. Talwar, Brooke Anderson, Cristopher G. Avalos-Castillo, Maria del Pilar Blanco-Parra, Alejandra Briones, Diego Cardenosa, John K. Carlson, Patricia Charvet, Charles F. Cotton, Zoe Crysler, Danielle H. Derrick, Michael R. Heithaus, Katelyn B. Herman, Olga Koubrak, David W. Kulka, Peter M. Kyne, Oscar M. Lasso-Alcala, Paola A. Mejia-Falla, Jorge Manuel Morales-Saldana, Beatriz Naranjo-Elizondo, Andres F. Navia, Nathan Pacoureau, Juan C. Perez-Jimenez, Riley A. Pollom, Cassandra L. Rigby, Eric V. C. Schneider, Nikola Simpson, Nicholas K. Dulvy
Summary: Chondrichthyan fishes in the Western Central Atlantic Ocean are at risk of extinction due to intense fishing. Catches in the region peaked in 1992 and have since declined. The United States, Venezuela, and Mexico have the highest catches and host most of the threatened species.
FISH AND FISHERIES
(2022)
Article
Ecology
Robin Leppitt, Alea Rose, Wayne A. Houston, Peter M. Kyne, Sam C. Banks, John C. Z. Woinarski, Stephen T. Garnett
Summary: The delineation of subspecies is important in biodiversity evaluation and protection, but inconsistent criteria and lack of agreement cause challenges. By using mitochondrial DNA, the study evaluated the genetic variation of the endemic Yellow Chat in Australia and found low levels of genetic variation, indicating vulnerability to environmental change.
ECOLOGY AND EVOLUTION
(2022)
Article
Environmental Sciences
Ciaran A. Hyde, Giuseppe Notarbartolo di Sciara, Lynn Sorrentino, Charlotte Boyd, Brittany Finucci, Sarah L. Fowler, Peter M. Kyne, Guido Leurs, Colin A. Simpfendorfer, Michael J. Tetley, Freya Womersley, Rima W. Jabado
Summary: Area-based conservation is crucial for safeguarding declining biodiversity. The Important Shark and Ray Area (ISRA) approach provides standardized criteria for identifying and managing discrete portions of habitat important for shark, ray, and chimaera species. This approach aims to address the global biodiversity crisis faced by these species and contribute to their recovery.
FRONTIERS IN MARINE SCIENCE
(2022)
Article
Fisheries
Giulia Anderson, Jed Macdonald, Joanne Potts, Pierre Feutry, Peter M. Grewe, Marion Boutigny, Campbell R. Davies, Jeff A. Muir, Francois Roupsard, Caroline Sanchez, Simon J. Nicol
Summary: Cross-contamination is a widespread issue in genetics and genomics, especially in the context of managing marine resources using molecular methods. An experiment on wild-caught bigeye tuna was conducted to assess cross-contamination risk under different tissue sampling treatments. Adjustments to current tissue sampling protocols were shown to significantly reduce cross-contamination risk for downstream genetic analyses on tunas and potentially on other species and fisheries.
ICES JOURNAL OF MARINE SCIENCE
(2023)
Article
Biochemistry & Molecular Biology
Natacha Nikolic, Floriaan Devloo-Delva, Diane Bailleul, Ekaterina Noskova, Clement Rougeux, Chrystelle Delord, Philippe Borsa, Cathy Liautard-Haag, Mohamad Hassan, Amandine D. Marie, Pierre Feutry, Peter Grewe, Campbell Davies, Jessica Farley, Daniel Fernando, Sebastian Biton-Porsmoguer, Francois Poisson, Denham Parker, Agostino Leone, Jorden Aulich, Matt Lansdell, Francis Marsac, Sophie Arnaud-Haond
Summary: The blue shark is a widely distributed top predator, classified as Critically Endangered in the Mediterranean Sea and Near Threatened globally. Genetic studies have previously suggested a single global population. However, this study used a genome-wide approach and revealed two main groups, the Mediterranean Sea and northern Atlantic samples differentiated from Indo-west Pacific samples. Within the Atlantic Ocean, further genetic differentiation was observed, as well as between the Atlantic Ocean and the Mediterranean Sea. The results highlight the importance of considering genetic population structure and demographic history in the management and conservation strategies of the blue shark.
Article
Multidisciplinary Sciences
Toby A. Patterson, Richard M. Hillary, Peter M. Kyne, Richard D. Pillans, Rasanthi M. Gunasekera, James R. Marthick, Grant J. Johnson, Pierre Feutry
Summary: By using sibling pairs, the abundance and connectivity of adult sharks in two river systems in Australia were estimated. The results showed male philopatry in the Adelaide River and high connectivity of males in the Alligator Rivers with the Adelaide River. This method allows simultaneous assessment of abundance and connectivity in rare and threatened species.
Article
Evolutionary Biology
Luke R. Lloyd-Jones, Matthew L. Brien, Pierre Feutry, Emma Lawrence, Paul Beri, Simon Booth, Steven Coulson, Shane M. Baylis, Kira Villiers, Laurence E. Taplin, David A. Westcott
Summary: Effective management of protected species requires understanding of appropriate evolutionary and geographic population boundaries, as well as knowledge of how the physical environment and life-history traits shape population structure and connectivity. A study on saltwater crocodiles in Queensland, Australia revealed significant genetic structure with six broad populations correlated with geographical location. Gene flow was found to be higher along the east coast compared to the west, indicating limited dispersal and reproductive philopatry. Management and conservation interventions should be considered at regional and state-wide scales due to limited dispersal, lack of suitable habitat, low crocodile densities, and a high proportion of immature individuals.
EVOLUTIONARY APPLICATIONS
(2023)
Article
Ecology
Floriaan Devloo-Delva, Christopher P. Burridge, Peter M. Kyne, Juerg M. Brunnschweiler, Demian D. Chapman, Patricia Charvet, Xiao Chen, Geremy Cliff, Ryan Daly, J. Marcus Drymon, Mario Espinoza, Daniel Fernando, Laura Garcia Barcia, Kerstin Glaus, Blanca I. Gonzalez-Garza, Michael I. Grant, Rasanthi M. Gunasekera, Sebastian Hernandez, Susumu Hyodo, Rima W. Jabado, Sebastien Jaquemet, Grant Johnson, James T. Ketchum, Helene Magalon, James R. Marthick, Frederik H. Mollen, Stefano Mona, Gavin J. P. Naylor, John E. G. Nevill, Nicole M. Phillips, Richard D. Pillans, Bautisse D. Postaire, Amy F. Smoothey, Katsunori Tachihara, Bree J. Tillet, Jorge A. Valerio-Vargas, Pierre Feutry
Summary: In this study, the population structure of the Bull Shark was assessed globally for the first time. The results revealed reproductive isolation between and across ocean basins, with distinct island populations in Japan and Fiji. The Bull Sharks maintain gene flow through shallow coastal waters as dispersal corridors, but large oceanic distances and historical land-bridges act as barriers. Protecting these insular populations of Bull Sharks is crucial for ecosystem stability and functioning.
ECOLOGY AND EVOLUTION
(2023)
Article
Forestry
Robin Leppitt, Jay Evans, Luke Einoder, Peter M. Kyne, John C. Z. Woinarski, Stephen T. Garnett
Summary: This study aimed to characterize the fire history of floodplains in coastal Northern Territory, Australia. It was found that floodplains in conservation reserves experienced more frequent fires compared to those on pastoral lands, and floodplain fire regimes differed from savanna fire regimes. Further research is needed to establish floodplain-specific fire management thresholds.
INTERNATIONAL JOURNAL OF WILDLAND FIRE
(2023)
Article
Fisheries
Michael I. Grant, Peter M. Kyne, Julie James, Yi Hu, Sushmita Mukherji, Yolarnie Amepou, Leontine Baje, Andrew Chin, Grant Johnson, Tegan Lee, Brandon Mahan, Christopher Wurster, William T. White, Colin A. Simpfendorfer
Summary: By analyzing the elemental ratios in vertebrae, it was found that barium (Ba) can indicate freshwater use, while lithium (Li) and strontium (Sr) can indicate marine water use. The results showed that the northern river shark and speartooth shark mainly inhabit upper-estuarine environments, while the narrow sawfish primarily uses freshwater environments. This study demonstrates the applicability of in situ LA-ICP-MS elemental characterization for understanding elasmobranch movements across salinity gradients.
JOURNAL OF FISH BIOLOGY
(2023)
Article
Multidisciplinary Sciences
Luke R. R. Lloyd-Jones, Mark V. V. Bravington, Kyle N. N. Armstrong, Emma Lawrence, Pierre Feutry, Christopher M. M. Todd, Annabel Dorrestein, Justin A. A. Welbergen, John M. M. Martin, Karrie Rose, Jane Hall, David N. N. Phalen, Isabel Peters, Shane M. M. Baylis, Nicholas A. A. Macgregor, David A. A. Westcott
Summary: Reliable population size information is crucial for managing threatened species. In this study, we applied the close-kin mark-recapture method to estimate the abundance of the critically endangered Christmas Island flying-fox (CIFF). Our findings provide the most robust understanding of the CIFF population status and have important implications for conservation initiatives.
SCIENTIFIC REPORTS
(2023)