Article
Plant Sciences
Zhi-Fang Liu, Hui Ma, Xiao-Yan Zhang, Xiu-Qin Ci, Lang Li, Jian-Lin Hu, Can-Yu Zhang, Jian-Hua Xiao, His-Wen Li, John G. Conran, Alex D. Twyford, Peter M. Hollingsworth, Jie Li
Summary: The aim of DNA barcoding is to accurately identify species. However, universal barcodes often fail to discriminate species in taxonomically complex groups. The development of assays that allow low-cost access to large numbers of nuclear markers is a major challenge in plant DNA barcoding.
BOTANICAL JOURNAL OF THE LINNEAN SOCIETY
(2022)
Article
Virology
Alexandre Hassanin, Opale Rambaud, Dylan Klein
Summary: Recombination generates mosaic genomes with mixed ancestry, complicating evolutionary inference. Researchers developed a sliding window bootstrap method to identify regions supporting phylogenetic relationships in bat coronaviruses, including SARS-CoV and SARS-CoV-2. Results revealed that most relationships were supported by a few genomic regions, confirming the presence of three distinct lineages in bats from Yunnan.
Review
Ecology
Xueni Bian, Beulah H. Garner, Huaxi Liu, Alfried P. Vogler
Summary: Most insect communities are composed of diverse lineages, but there is a lack of detailed phylogenetic analysis of whole communities, especially in species-rich tropical ecosystems. The SITE-100 program aims to construct the Tree-of-Life by sampling high-biodiversity sites globally. The study uses large-scale high-resolution cameras for specimen imaging, DNA extraction, sequencing, and phylogenetic analysis. To overcome limitations and challenges, the research combines nuclear shotgun data, site-based mitochondrial genomes, and DNA barcodes in a hierarchical approach.
FRONTIERS IN ECOLOGY AND EVOLUTION
(2022)
Article
Biodiversity Conservation
Arnaud Goulpeau, Benoit Penel, Marie-Eugenie Maggia, Daniel Fernandez Marchan, Dirk Steinke, Mickael Hedde, Thibaud Decaens
Summary: This study compared different methods for delimiting operational taxonomic units (OTUs) using DNA barcodes of earthworms. Phylogenetic methods were found to be less suitable for this purpose, while distance-based methods such as ASAP showed efficient results with shorter computation times and fewer mismatches.
Article
Multidisciplinary Sciences
Huili Li, Wenjun Xiao, Tie Tong, Yongliang Li, Meng Zhang, Xiaoxia Lin, Xiaoxiao Zou, Qun Wu, Xinhong Guo
Summary: DNA barcoding is used as an effective tool for rapid and accurate identification of plant species, including Orchidaceae which is the second largest family of flowering plants globally. By analyzing chloroplast genes, this study provides a theoretical basis for species identification, germplasm conservation and innovative utilization of orchids.
SCIENTIFIC REPORTS
(2021)
Article
Forestry
Benno Eberhard, Natascia Magagnotti, Rodolfo Picchio, Raffaele Spinelli
Summary: Coppice management is becoming more popular due to its ability to meet multiple demands in modern forestry. Mechanization is needed to improve profitability, and this study found that there were no significant differences in the resprouting ability of stumps between using an excavator mounted disc saw and an excavator mounted hydraulic shear.
FOREST ECOLOGY AND MANAGEMENT
(2023)
Article
Multidisciplinary Sciences
Elise Parey, Alexandra Louis, Jerome Montfort, Olivier Bouchez, Celine Roques, Carole Iampietro, Jerome Lluch, Adrien Castinel, Cecile Donnadieu, Thomas Desvignes, Christabel Floi Bucao, Elodie Jouanno, Ming Wen, Sahar Mejri, Ron Dirks, Hans Jansen, Christiaan Henkel, Wei-Jen Chen, Margot Zahm, Cedric Cabau, Christophe Klopp, Andrew Thompson, Marc Robinson-Rechavi, Ingo Braasch, Guillaume Lecointre, Julien Bobe, John H. Postlethwait, Camille Berthelot, Hugues Roest Crollius, Yann Guiguen
Summary: Through the study of gene sequence and chromosomal rearrangement in teleosts, it was found that Elopomorpha and Osteoglossomorpha are sister groups to all other teleosts, resolving over 50 years of controversy on their evolutionary relationships.
Article
Engineering, Multidisciplinary
Sophia B. Coban, William R. B. Lionheart, Philip J. Withers
Summary: The paper discusses the performance assessment of CT reconstruction algorithms and introduces a evaluation technique called physical quantification, which measures the features of the test object to assess the reconstruction efficacy. The study highlights the importance of choosing the optimal reconstruction strategy based on the features extracted from the scan.
MEASUREMENT SCIENCE AND TECHNOLOGY
(2021)
Article
Biology
Stefan Moestl, Fabian Hoffmann, Jan-Niklas Hoenemann, Jose Ramon Alvero-Cruz, Jorn Rittweger, Jens Tank, Jens Jordan
Summary: This study investigates the application and accuracy of pulse wave velocity (PWV) in master athletes. The results show that estimated PWV is mainly correlated with age and does not accurately reflect the true vascular condition, thus unable to detect the beneficial effects of lifelong exercise on vascular health.
Article
Ecology
Fabio Laurindo da Silva, Luiz Carlos Pinho, Elisabeth Stur, Silvio Shigueo Nihei, Torbjorn Ekrem
Summary: This study investigates the performance of DNA-based species delimitation methods in rapidly estimating the diversity of Polypedilum in South America. The results suggest that the sGMYC method is the most suitable for estimating putative species in the dataset, identifying 75 species. Additionally, the study finds higher species richness in South America compared to the Palearctic and Oriental realms, as well as potential differences in species composition between South America and neighboring regions.
ECOLOGY AND EVOLUTION
(2023)
Article
Plant Sciences
Sarah A. Herzog, Maribeth Latvis
Summary: The study found that DNA barcoding is generally successful in identifying genera and families in tallgrass prairies, but has limited effectiveness in species-level identifications. Database size is a key factor in successful plant identification.
APPLICATIONS IN PLANT SCIENCES
(2021)
Article
Forestry
M. C. A. Torbenson, U. Buntgen, P. Roemen, O. Urban, M. Trnka, A. Ac, F. Reinig, M. Rybnicek, T. Kolar, T. Arosio, E. Martinez del Castillo, E. Konasova, N. Pernicova, J. Caslavsky, J. Esper
Summary: This study analyzes the potential influence of changing earlywood and latewood components of individual tree rings on stable carbon and oxygen records. The results show that the variation in earlywood and latewood does not significantly affect the isotopic composition in oak and pine tree rings. Therefore, this simple approach can be applied to reduce potential biases caused by intra-annual variability in long-term tree-ring stable isotope records.
Article
Biochemistry & Molecular Biology
Kyle R. Piller, Elyse Parker, Alan R. Lemmon, Emily Moriarty Lemmon
Summary: This study investigated the phylogenetic relationships among families within the Cyprinodontiformes using the anchored hybrid enrichment method. The results revealed new sets of relationships and confirmed the monophyly of two well-established clades. The assessment of gene tree discordance provided support for alternative topological hypotheses. This study provides a robust framework for further investigation in biogeography, taxonomy, ecology, and physiology of these fishes.
MOLECULAR PHYLOGENETICS AND EVOLUTION
(2022)
Article
Virology
Alexandre Hassanin, Opale Rambaud
Summary: A new method called coloured genomic bootstrap (CGB) barcodes is proposed to study the origins of coronaviruses and understand their host and geographic origins. The study reveals that SARS-CoV and SARS-CoV-2 contain genomic regions of mixed ancestry from horseshoe bat viruses. Different regions of the viruses share exclusive ancestry with various Rhinolophus viruses from different regions of China and Southeast Asia, supporting their emergence in these bat species. However, further research is needed to investigate the diversity of coronaviruses in bats from other Southeast Asian countries.
Article
Zoology
David H. Kavanaugh, David R. Maddison, W. Brian Simison, Sean D. Schoville, Joachim Schmidt, Arnaud Faille, Wendy Moore, James M. Pflug, Sophie L. Archambeault, Tinya Hoang, Jei-Ying Chen
Summary: The phylogeny of the carabid beetle supertribe Nebriitae was inferred from DNA sequence data, resulting in a well-resolved tree with most nodes strongly supported. Relationships within Nebriitae were not well resolved, and a revised classification was proposed based on the inferred phylogeny, highlighting some evident vicariance patterns. Expanding DNA sequence data sampling is recommended for a better understanding of relationships within this supertribe.