Article
Biochemistry & Molecular Biology
Nhan Ly-Trong, Suha Naser-Khdour, Robert Lanfear, Bui Quang Minh
Summary: Sequence simulators are important in phylogenetics for evaluating methods, hypothesis testing, and generating data. AliSim is a new tool that efficiently simulates biologically realistic alignments, outperforming popular software in terms of speed and efficiency.
MOLECULAR BIOLOGY AND EVOLUTION
(2022)
Article
Public, Environmental & Occupational Health
Jordan E. Sealey, Ashley Hammond, Kristen K. Reyher, Matthew B. Avison
Summary: This study investigated the excretion of fluoroquinolone-resistant E. coli by dogs in rural and urban environments and found that rural dogs tend to excrete bacteria types commonly found in cattle, while urban dogs carry plasmid-mediated quinolone resistance genes similar to those found in human E. coli. Feeding dogs uncooked meat was identified as a potential transmission link for fluoroquinolone-resistant E. coli, emphasizing the importance of enhanced hygiene practices for handling and housing such dogs.
Article
Biotechnology & Applied Microbiology
Haftom Baraki Abraha, Jae-Won Lee, Gayeong Kim, Mokhammad Khoiron Ferdiansyah, Rathnayaka Mudiyanselage Ramesha, Kwang-Pyo Kim
Summary: In this study, the genomic diversity of 61 BSPs was analyzed, and a comprehensive classification scheme was proposed. The identification of orthologs taxonomic signature genes contributed to phage taxonomy.
Article
Biodiversity Conservation
Heriberto Barbosa-Moyano, Gisela Sobral, Claudio Alvarenga de Oliveira
Summary: This study validated an enzyme immunoassay for quantification of glucocorticoid metabolites (MGC) in Megascops choliba and found that MGC levels varied between individuals based on the time of day but not on sex. Additionally, higher levels of MGC were associated with increased active behaviors. The results suggest that the secretion of glucocorticoids in birds is plastic and can impact their physiology and behavior in natural or artificial environments.
CONSERVATION PHYSIOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Han Yan, Zhirui Hu, Gregg W. C. Thomas, Scott Edwards, Timothy B. Sackton, Jun S. Liu
Summary: The paper introduces PhyloAcc-GT, a method that extends PhyloAcc by modeling gene tree heterogeneity, to effectively identify lineage-specific accelerations in substitution rate while accounting for incomplete lineage sorting. The method outperforms other methods in detecting complex patterns of rate shifts and is robust to population size parameter specification.
MOLECULAR BIOLOGY AND EVOLUTION
(2023)
Article
Biochemistry & Molecular Biology
Joel O. Wertheim, Reilly Hostager, Diane Ryu, Kevin Merkel, Samuel Angedakin, Mimi Arandjelovic, Emmanuel Ayuk Ayimisin, Fred Babweteera, Mattia Bessone, Kathryn J. Brun-Jeffery, Paula Dieguez, Winnie Eckardt, Barbara Fruth, Ilka Herbinger, Sorrel Jones, Hjalmar Kuehl, Kevin E. Langergraber, Kevin Lee, Nadege F. Madinda, Sonja Metzger, Lucy Jayne Ormsby, Martha M. Robbins, Volker Sommer, Tara Stoinski, Erin G. Wessling, Roman M. Wittig, Yisa Ginath Yuh, Fabian H. Leendertz, Sebastien Calvignac-Spencer
Summary: Research discovered that herpes simplexviruses from African apes are more closely related to HSV-2, indicating a potential shared evolutionary event between humans and gorillas. Through molecular clock-based hypothesis testing, multiple cross-species transmission events were identified, with the most recent one occurring between humans and bonobos.
MOLECULAR BIOLOGY AND EVOLUTION
(2021)
Article
Agriculture, Dairy & Animal Science
Lucas M. Leveau, Isis Ibanez
Summary: This study aimed to determine the responses of different bird species to urbanization using ordination analysis and to describe their life history traits by combining information on diet, habitat, and plumage color. The results showed that certain bird species, termed "urban exploiters," tend to nest in buildings and have uniform plumage, while others, termed "urban avoiders," tend to be ground-nesting species with variable plumage. A third type, called "urban adapters," tend to be tree-nesting species with specific traits such as a low diet breadth, intermediate plumage lightness, low presence of sexual dimorphism, and high presence of iridescence. This study suggests that nest predation and habitat loss may lead to exclusion of ground nesting birds from urban areas, and the high density of pedestrians and domestic animals in urban centers may favor uniform plumages in birds to enhance camouflage.
Article
Evolutionary Biology
Alessandra Riccieri, Emiliano Mancini, Monica Pitzalis, Daniele Salvi, Marco A. Bologna
Summary: This study investigates the phylogeny of the tribe Lyttini in the beetle family Meloidae and tests for its monophyly. The study uses a comprehensive molecular dataset and finds 11 phylogenetically distinct lineages within Lyttini. The boundaries of this tribe prove to be hard to define. Based on the results, the tribe is restricted to specific genera and new nomenclatural acts are proposed.
SYSTEMATIC ENTOMOLOGY
(2022)
Article
Virology
Gladys Atim, Titus Tugume, Qouilazoni A. Ukuli, Bernard Erima, Andrew Mubiru, Hannah Kibuuka, Edison Mworozi, Pamela McKenzie, Jasmine C. M. Turner, David Walker, Trushar Jeevan, Robert G. Webster, Jeremy Jones, Richard J. Webby, Mariette F. Ducatez, Fred Wabwire-Mangen, Denis K. Byarugaba
Summary: The H9N2 avian influenza A viruses in Uganda have undergone genetic evolution with nucleotide substitutions and reassortments, leading to variations in phylogeny. The viruses carry several mutations associated with mammalian host adaptation, increased virulence, replication, drug resistance, and resistance to the endonuclease inhibitor Baloxavir acid. The viruses pose a zoonotic threat due to poor biosecurity practices in live bird markets.
Article
Biochemistry & Molecular Biology
Frank E. Anderson, Annie R. Lindgren
Summary: Despite decades of research, the phylogenetic relationships among squids and cuttlefishes have remained unclear. This study re-evaluates these relationships using higher-quality genome and transcriptome data, and identifies key clade relationships such as the grouping of closed-eye squid, cuttlefishes, and open-eye squid, as well as the position of pygmy squids as the sister group to all sampled decapodiform lineages. Further research with improved taxon sampling and additional genomic data is needed to rigorously test these novel hypotheses.
MOLECULAR PHYLOGENETICS AND EVOLUTION
(2021)
Article
Genetics & Heredity
Yuqi Huang, Minghao Sun, Lenan Zhuang, Jin He
Summary: This study provides a comprehensive molecular phylogenetic analysis of vertebrate AIGs, revealing loss or gain of AIG members in different species during evolution. The findings can be used for future functional characterization of AIGs.
Article
Biochemistry & Molecular Biology
Sudhir Kumar
Summary: Molecular evolutionary analysis requires computationally intensive steps that have a significant environmental impact. However, innovative methods and heuristics can reduce the carbon footprint, lower environmental costs, and promote green evolutionary computing.
MOLECULAR BIOLOGY AND EVOLUTION
(2022)
Article
Zoology
Sergio Jimenez Pinadero, Daniel Fernandez Marchan, Marta Novo, Dolores Trigo, Jorge Dominguez, Dario J. Diaz Cosin
Summary: Molecular phylogenetics has made significant contributions to earthworm taxonomy, particularly in studying the Lumbricidae genus. This study investigated Zophoscolex species and found that they do not belong to a single clade. Z. atlanticus was closely related to several other species, while other species belong to different genera.
ZOOLOGICAL JOURNAL OF THE LINNEAN SOCIETY
(2022)
Article
Immunology
Sandra E. Chaudron, Christine Leemann, Katharina Kusejko, Huyen Nguyen, Nadine Tschumi, Alex Marzel, Michael Huber, Juerg Boeni, Matthieu Perreau, Thomas Klimkait, Sabine Yerly, Alban Ramette, Hans H. Hirsch, Andri Rauch, Alexandra Calmy, Pietro Vernazza, Enos Bernasconi, Matthias Cavassini, Karin J. Metzner, Roger D. Kouyos, Huldrych F. Guenthard
Summary: Studying HIV-1 superinfection is crucial for understanding virus transmission, disease progression, and vaccine development. This study developed a molecular epidemiology screening method using the Swiss HIV Cohort Study, which identified 325 potential HIV-1 superinfections based on phylogenetic reconstruction and distance criteria. Among the tested samples, 52 cases of superinfection were confirmed.
JOURNAL OF INFECTIOUS DISEASES
(2022)
Article
Virology
Adriano Mendes, Olivia Lentsoane, Mushal Allam, Zamantungwaka Khumalo, Arshad Ismail, Jacobus A. W. Coetzer, Marietjie Venter
Summary: This study isolated and sequenced the Bagaza virus, described its genome and mutations, and investigated its phylogenetic relationship with other related viruses. The results showed that there is consistent exchange of Bagaza virus and Israel turkey meningoencephalomyelitis virus (ITV) between Europe and Africa.
Article
Multidisciplinary Sciences
Christophe Dufresnes, Nadege Remollino, Celine Stoffel, Ralph Manz, Jean-Marc Weber, Luca Fumagalli
SCIENTIFIC REPORTS
(2019)
Article
Zoology
Christophe Dufresnes, Christian Miquel, Pierre Taberlet, Luca Fumagalli
Editorial Material
Biochemistry & Molecular Biology
Lucie Zinger, Aurelie Bonin, Inger G. Alsos, Miklos Balint, Holly Bik, Frederic Boyer, Anthony A. Chariton, Simon Creer, Eric Coissac, Bruce E. Deagle, Marta De Barba, Ian A. Dickie, Alex J. Dumbrell, Gentile Francesco Ficetola, Noah Fierer, Luca Fumagalli, M. Thomas P. Gilbert, Simon Jarman, Ari Jumpponen, Havard Kauserud, Ludovic Orlando, Johan Pansu, Jan Pawlowski, Leho Tedersoo, Philip Francis Thomsen, Eske Willerslev, Pierre Taberlet
Article
Biochemistry & Molecular Biology
Christophe Dufresenes, Menad Beddek, Dmitriy Skorinov, Luca Fumagalli, Nicolas Perrin, Pierre-Andre Crochet, Spartak N. Litvinchuk
MOLECULAR PHYLOGENETICS AND EVOLUTION
(2019)
Article
Biochemistry & Molecular Biology
Arnaud Gaigher, Reto Burri, Luis M. San-Jose, Alexandre Roulin, Luca Fumagalli
Article
Ecology
Christophe Dufresnes, Manon Pribille, Berenice Alard, Helena Goncalves, Felix Amat, Pierre-Andre Crochet, Sylvain Dubey, Nicolas Perrin, Luca Fumagalli, Miguel Vences, Inigo Martinez-Solano
Article
Biodiversity Conservation
Stefanie Roder, Francois Biollaz, Stephane Mettaz, Fridolin Zimmermann, Ralph Manz, Marc Kery, Sergio Vignali, Luca Fumagalli, Raphael Arlettaz, Veronika Braunisch
JOURNAL OF APPLIED ECOLOGY
(2020)
Article
Biodiversity Conservation
G. Yannic, V Helfer, R. Sermier, B. R. Schmidt, L. Fumagalli
Summary: Delineating population boundaries in anthropogenic landscapes is crucial for biology domains focusing on ecology, evolution, and conservation. This task is particularly challenging for amphibian species reproducing in aquatic habitats but living in terrestrial habitats, highlighting the difficulty of defining management units in open systems.
CONSERVATION GENETICS
(2021)
Article
Multidisciplinary Sciences
Judith Schneider, Eduard Mas-Carrio, Catherine Jan, Christian Miquel, Pierre Taberlet, Katarzyna Michaud, Luca Fumagalli
Summary: Stomach content analyses are a valuable tool in human forensic science to interpret perimortem events. DNA metabarcoding has the potential to increase sensitivity and taxonomic resolution in identifying food components. This pilot study applied DNA metabarcoding to assess plant and vertebrate components of human stomach content samples, showing promising perspectives for biomedical dietary surveys.
SCIENTIFIC REPORTS
(2021)
Article
Multidisciplinary Sciences
Christophe Dufresnes, Alan Brelsford, Daniel L. Jeffries, Glib Mazepa, Tomasz Suchan, Daniele Canestrelli, Alfredo Nicieza, Luca Fumagalli, Sylvain Dubey, Inigo Martinez-Solano, Spartak N. Litvinchuk, Miguel Vences, Nicolas Perrin, Pierre-Andre Crochet
Summary: Research on frog and toad hybrid zones suggests that as lineages diverge, parts of the genome resist introgression, indicating that anuran speciation involves the gradual accumulation of multiple barrier loci scattered across the genome. This highly polygenic nature of reproductive isolation, along with the lack of hemizygous sex chromosomes, may explain the slower speciation clock in amphibians compared to other vertebrates.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Multidisciplinary Sciences
Guangpeng Ren, Xu Zhang, Ying Li, Kate Ridout, Martha L. Serrano-Serrano, Yongzhi Yang, Ai Liu, Gudasalamani Ravikanth, Muhammad Ali Nawaz, Abdul Samad Mumtaz, Nicolas Salamin, Luca Fumagalli
Summary: The study reveals the domestication history of Cannabis sativa, indicating that it was first domesticated in early Neolithic times in East Asia, and that both hemp and drug cultivars diverged from an ancestral gene pool in China. Candidate genes associated with traits differentiating hemp and drug cultivars were identified, as well as evidence for loss of function of genes involved in cannabinoid synthesis during selection.
Article
Ecology
Loic Brun, Judith Schneider, Eduard Mas Carrio, Pooja Dongre, Pierre Taberlet, Erica van de Waal, Luca Fumagalli
Summary: Assessing the diet of wild animals is crucial for understanding their ecology and trophic relationships. This study compares two methods (environmental DNA and observations) and finds that DNA metabarcoding has higher taxonomic coverage and resolution. Seasonality has a significant effect on plant and arthropod consumption, and vervet monkeys adapt their diet according to available resources.
ECOLOGY AND EVOLUTION
(2022)
Review
Biodiversity Conservation
P. J. Stephenson, Maria Cecilia Londono-Murcia, Paulo A. Borges, Louw Claassens, Heidrun Frisch-Nwakanma, Nicholas Ling, Sapphire McMullan-Fisher, Jessica J. Meeuwig, Kerrigan Marie Machado Unter, Judith L. Walls, Ian J. Burfield, Danilo do Carmo Vieira Correa, Gary N. Geller, Irina Montenegro Paredes, Leonard K. Mubalama, Yaa Ntiamoa-Baidu, Ignacio Roesler, Francesco Rovero, Yash Pal Sharma, Nara Wisesa Wiwardhana, Jun Yang, Luca Fumagalli
Summary: This article reviews the importance of enhancing biodiversity monitoring, assesses the challenges involved, and identifies potential solutions. It highlights the urgent need to strengthen capacity for biodiversity monitoring, especially in poorer, high-biodiversity countries where data gaps are significant. The article also emphasizes the use of modern tools and technologies to fill taxonomic and geographic data gaps, and the importance of stakeholders adopting best monitoring practices, making data openly available, and companies investing in collecting necessary data for sustainability.
Article
Biodiversity Conservation
Ines Moreno, Jerome Marcel Walter Gippet, Luca Fumagalli, P. J. Stephenson
Summary: Understanding the availability and biases of species data is crucial for effective conservation decision-making. This study conducted a case study in East Africa to evaluate data biases, factors influencing data availability, and the consequences for conservation. The results showed that data on vertebrates were more available than invertebrates, and countries with higher tourism income had more priority species and more species with data. The main challenges to data accessibility were high expenses, technological challenges, and a lack of resources for data processing and analysis.
BIODIVERSITY AND CONSERVATION
(2023)
Article
Biodiversity Conservation
Christophe Dufresnes, Tony Dejean, Silvia Zumbach, Benedikt R. Schmidt, Luca Fumagalli, Petra Ramseier, Sylvain Dubey
CONSERVATION SCIENCE AND PRACTICE
(2019)
Article
Biochemistry & Molecular Biology
Markus Osaland Fjelde, Einar Timdal, Reidar Haugan, Mika Bendiksby
Summary: This study investigated the taxonomy of the crustose lichen genus Calvitimela using molecular phylogenetics and morphological observations. The results revealed evolutionarily old and deeply divergent lineages within Calvitimela, with overlapping morphological characters between different subgenera. Chemical characters were informative at the level of subgenera but often homoplastic at the species level. A practical taxonomy of Calvitimela was proposed based on these findings.
MOLECULAR PHYLOGENETICS AND EVOLUTION
(2024)
Article
Biochemistry & Molecular Biology
Bo-Yang Shi, Da Pan, Kang-Qin Zhang, Tian-Yu Gu, Darren C. J. Yeo, Peter K. L. Ng, Neil Cumberlidge, Hong-Ying Sun
Summary: This study investigates the evolutionary history and speciation mechanisms of montane potamids in the Hengduan Mountains Region. The results suggest that the vicariance events of these crabs are correlated with the emergence of sky islands due to the uplift of the mountains. The mountain ridges provided corridors for their dispersal and past climatic conditions played a crucial role in their evolutionary history. The mechanisms isolating sky islands are reinforced by the climatic features of dry-hot valleys and continue to affect local diversification.
MOLECULAR PHYLOGENETICS AND EVOLUTION
(2024)
Article
Biochemistry & Molecular Biology
Attila Nemeth, Edvard Mizsei, Levente Laczko, David Czaban, Zsolt Hegyeli, Szabolcs Lengyel, Gabor Csorba, Gabor Sramko
Summary: Species delimitation of European blind mole rats is challenging due to their small morphological differences and complex chromosomal evolution. This study provides a comprehensive framework to improve understanding of their evolutionary history and revise their taxonomy. The results reveal the presence of multiple superspecies and species, with distinct geographic patterns and rapid chromosomal evolution.
MOLECULAR PHYLOGENETICS AND EVOLUTION
(2024)
Article
Biochemistry & Molecular Biology
Ying Qi, Zhaoyan Zhong, Xu Liu, Xing He, Yadong Zhou, Lili Zhang, Chong Chen, Katrin Linse, Jian-Wen Qiu, Jin Sun
Summary: This study investigates the phylogenetic relationships among patellogastropod families using mitochondrial and phylogenomic data. The results show that the mitochondrial phylogeny recovers monophyly of most families, but the relationships among families are still contentious. However, a more robust family-level topology consistent with morphology is achieved by phylogenomics. Additionally, the mainly deep-water families are found to be monophyletic, suggesting a single colonization of the deep water during the Jurassic.
MOLECULAR PHYLOGENETICS AND EVOLUTION
(2024)
Article
Biochemistry & Molecular Biology
Yu-Jie Shi, Jin -Liang Huang, Jia-Xuan Mi, Jing Li, Fan-Yu Meng, Yu Zhong, Fang He, Fei -Fei Tian, Fan Zhang, Liang-Hua Chen, Han-Bo Yang, Hong-Lin Hu, Xue-Qin Wan
Summary: Despite numerous studies on hybrid speciation, our understanding of this process remains limited. In this study, we conducted an 18-year systematic investigation on Populus taxa on the Qinghai-Tibet Plateau and discovered three new taxa that originated from distant hybridization between two different sections. These hybrid taxa demonstrate greater ecological adaptability than their ancestral species due to heterosis. We propose a hybrid speciation process model that can explain important evolutionary concerns.
MOLECULAR PHYLOGENETICS AND EVOLUTION
(2024)
Article
Biochemistry & Molecular Biology
Anna Cho, Denis Tikhonenkov, Gordon Lax, Kristina I. Prokina, Patrick J. Keeling
Summary: Unlike conspicuous ochrophytes, many small and overlooked flagellates belonging to basally branching stramenopiles remain poorly characterized at the cellular or genomic level. This study describes four new species, including two new genera, of sediment-dwelling MAST-6 and provides updated phylogenomic tree of stramenopiles. The characterization of these flagellates is important due to their phylogenetic diversity and abundance in various environments.
MOLECULAR PHYLOGENETICS AND EVOLUTION
(2024)
Article
Biochemistry & Molecular Biology
Tian-Tian Xue, Steven B. Janssens, Bin-Bin Liu, Sheng-Xiang Yu
Summary: Phylogenomic conflicts are widespread among genomic data, with most previous studies primarily focusing on nuclear datasets instead of organellar genomes. In this study, we investigated the phylogenetic conflicts within and between plastid and mitochondrial genomes using Potentilla as a case study. We found that both plastid and mitochondrial genomes divided Potentilla into eight highly supported clades, with two newly identified clades. Our results demonstrate that mitochondrial genes can fully resolve phylogenetic relationships among major clades of Potentilla and are not always linked with plastomes in evolutionary history.
MOLECULAR PHYLOGENETICS AND EVOLUTION
(2024)
Article
Biochemistry & Molecular Biology
Alexandra A. Grossi, Chunpo Tian, Mengjiao Ren, Fasheng Zou, Daniel R. Gustafsson
Summary: This study suggests that the coevolutionary relationships between chewing lice, endosymbiotic bacteria, and birds are not independent, but the patterns vary depending on the analysis method used. Additionally, louse host-switching does not seem to affect bacterial strains.
MOLECULAR PHYLOGENETICS AND EVOLUTION
(2024)
Article
Biochemistry & Molecular Biology
Ingrid Olivares, Sergio Tusso, Maria Jose Sanin, Marylaure de La Harpe, Oriane Loiseau, Jonathan Rolland, Nicolas Salamin, Michael Kessler, Kentaro K. Shimizu, Margot Paris
Summary: Traditionally, differences between species have been associated with morphological variation. However, the discovery of cryptic diversity suggests that the evolution of distinct lineages can occur without morphological differences. Through genetic analysis, we found that a tropical montane plant lineage is composed of numerous unrecognized genetic groups that are not morphologically distinct. Geographic distance and topography play a crucial role in determining the genetic divergence of these groups.
MOLECULAR PHYLOGENETICS AND EVOLUTION
(2024)