Article
Evolutionary Biology
Yi Yu, Lingfeng Kong, Qi Li
Summary: In this study, the sequencing of 11 muricid mitochondrial genomes revealed the conservation of gene arrangement, genome size, and nucleotide composition within the family. Phylogenetic analysis supported the monophyly of each subfamily and redefined the relationships between subfamilies and genera. These findings provide new insights into the classification and evolutionary history of Muricidae.
Article
Fisheries
Giulia Fassio, Paolo Russo, Giuseppe Bonomolo, Alexander E. Fedosov, Maria Vittoria Modica, Elisa Nocella, Marco Oliverio
Summary: A high diversity of native small spindle-shells has been discovered in the Mediterranean Sea, with 23 species identified based on shell morphology. The researchers reconstructed a molecular phylogenetic framework to examine the classification of Mediterranean Fusininae species and found that they form a single monophyletic radiation. The results indicate that Fusinus s.s. should be restricted to large-shelled species from the Indo-West Pacific.
MEDITERRANEAN MARINE SCIENCE
(2022)
Article
Biochemistry & Molecular Biology
Nicolas Mongiardino Koch
Summary: Phylogenomic subsampling is a method of selecting small sets of loci from large genome-scale data sets for phylogenetic inference, often motivated by computational limitations or testing the robustness of phylogenetic results. This study reveals a predictability in the patterns of covariance of gene properties across different phylogenomic data sets and proposes a multivariate method to optimize phylogenetic signal while controlling for bias. Common subsampling approaches are found to introduce unintended effects in gene properties, and selecting loci at random is shown to be more effective than other methods.
MOLECULAR BIOLOGY AND EVOLUTION
(2021)
Article
Zoology
Yuri Kantor, Alexander E. Fedosov, Alisa R. Kosyan, Nicolas Puillandre, Pavel A. Sorokin, Yasunori Kano, Roger Clark, Philippe Bouchet
Summary: The superfamily Buccinoidea is widely distributed across different depths of the oceans, with 3351 recent species in 337 genera. Through molecular data and anatomical and radula data, the monophyly of the superfamily and the relationships among the families have been confirmed. The classification of the superfamily has been revised and new families and subfamilies have been proposed.
ZOOLOGICAL JOURNAL OF THE LINNEAN SOCIETY
(2022)
Article
Immunology
Colleen M. Bianco, Ahmed M. Moustafa, Kelsey O'Brien, Michael A. Martin, Timothy D. Read, Barry N. Kreiswirth, Paul J. Planet
Summary: USA300 has been the dominant MRSA clone in the United States and Northern South America for over 20 years. This study utilizes sequencing data and newly sequenced isolates to investigate the pre-epidemic evolution of USA300. The results confirm the divergence of NAE and SAE lineages around 1970 and identify independent acquisition events of ACME and COMER loci. The study also reveals a new USA300 clade (PEB1) that predates the establishment of South and North American epidemics.
FRONTIERS IN CELLULAR AND INFECTION MICROBIOLOGY
(2023)
Article
Genetics & Heredity
Zongxing Wang, Jingxi Liu, Yuanjin Liu, Zongjun Xu, Fengrong Zheng, Wei Chen
Summary: The complete mitochondrial genome of Sydaphera spengleriana was characterized for the first time. It has a total length of 16,336 bp and consists of 13 protein-coding genes, 22 tRNA genes, and 2 rRNA genes. Phylogenetic analysis shows that S. spengleriana is closely related to Bivetiella cancellata within the family Cancellariidae.
MITOCHONDRIAL DNA PART B-RESOURCES
(2022)
Article
Marine & Freshwater Biology
Natan C. Pedro, Luiz Ricardo L. Simone
Summary: This study describes a new species of genus Thaisella, Thaisella ovalis, found in the estuarine environment of Maraca Island in northern Brazil. The new species shows distinct morphological and anatomical differences from its previously misidentified species, Thaisella coronata, which is native to West Africa. Comparison with other related species, particularly the recently discovered Thaisella guatemalteca from Guatemala, is also discussed.
ARCHIV FUR MOLLUSKENKUNDE
(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
Genetics & Heredity
Yanling Liao, Jinxing Fu, Bingmiao Gao, Tianle Tang
Summary: The complete mitochondrial genome of the tubular cone snail Conus betulinus was characterized, revealing its genetic composition and close relationship with other cone snail species. The high A+T content and phylogenetic analysis based on protein-coding genes provided insights into the evolution of cone snails according to their dietary type.
MITOCHONDRIAL DNA PART B-RESOURCES
(2021)
Article
Microbiology
Alberto Pascual-Garcia
Summary: The comment analyzes the novel concept of PCG proposed by Aguirre de Carcer, identifying logical and methodological flaws and proposing methodological refinements. These refinements help to determine PCGs more consistently, promoting PCGs as a valuable tool in microbial ecology.
Article
Biotechnology & Applied Microbiology
Yicen Xu, Bo Fang, Jingling Li, Yuanwei Wang, Jingting Liu, Chang Liu, Jie Yu
Summary: The plastomes of twelve plum cultivars were sequenced, assembled, and analyzed in this study. Molecular markers were developed for their differentiation. The results provide valuable information for molecular identification and phylogenetic analysis of plum cultivars, contributing to the study of genetic basis for agronomic and adaptive differentiation in Prunus species.
Article
Biochemistry & Molecular Biology
Besian Sejdiu, D. Peter Tieleman
Summary: ProLint is a webserver that automates the analysis of MD generated files and visualization of lipid-protein interactions, offering modular analysis methods and interactive visualization tools for detailed qualitative and quantitative exploration. Additionally, it includes a database of published MD results that can be accessed by anyone.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Biology
Alma Rubi Castrejon-Rios, Jesus G. Padilla-Serrato, Maria del Pilar Torres-Garcia, Erika Samantha Palacios-Avila, Carmina Torreblanca-Ramirez, Pedro Flores-Rodriguez, Rafael Flores-Garza
Summary: This study assessed fishery data for Hexaplex princeps in Guerrero. The results showed that the reproductive activity of this species mainly occurred from December to July, related to sea surface temperatures. The study also found a high percentage of juvenile organisms in the catches.
REVISTA DE BIOLOGIA TROPICAL
(2022)
Article
Biochemistry & Molecular Biology
Sarah Nadeau, Christian W. Thorball, Roger Kouyos, Huldrych F. Guenthard, Juerg Boeni, Sabine Yerly, Matthieu Perreau, Thomas Klimkait, Andri Rauch, Hans H. Hirsch, Matthias Cavassini, Pietro Vernazza, Enos Bernasconi, Jacques Fellay, Venelin Mitov, Tanja Stadler
Summary: Infectious diseases pose challenges for GWAS due to the influence of genetic effects from both pathogen and host. This research proposes a new method that estimates and removes heritable pathogen effects on a trait based on the pathogen phylogeny, restoring sample independence in GWAS. The method was tested in simulations and applied to data from two host-pathogen systems, showing its potential to increase GWAS power and provide insight into the evolutionary dynamics of traits in pathogen populations.
MOLECULAR BIOLOGY AND EVOLUTION
(2022)
Article
Chemistry, Medicinal
Jessica Lanini, Gianluca Santarossa, Finton Sirockin, Richard Lewis, Nikolas Fechner, Hubert Misztela, Sarah Lewis, Krzysztof Maziarz, Megan Stanley, Marwin Segler, Nikolaus Stiefl, Nadine Schneider
Summary: Machine-learning and deep-learning models are widely used in cheminformatics to predict molecular properties and accelerate compound prioritization. However, evaluating and comparing these models is challenging due to different setups, frameworks, and molecular representations. In this study, we present a new framework called PREFER, based on Python and AutoSklearn, that allows comparison between different representations and machine-learning models. We provide an overview, examples, and discuss the use of PREFER on small data sets. The framework's code is freely available on GitHub.
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2023)
Article
Marine & Freshwater Biology
Juan E. Uribe, Suzanne T. Williams, Jose Templado, Samuel Abalde, Rafael Zardoya
JOURNAL OF MOLLUSCAN STUDIES
(2017)
Article
Evolutionary Biology
John D. Taylor, Emily A. Glover, Elizabeth M. Harper, J. Alistair Crame, Chiho Ikebe, Suzanne T. Williams
BIOLOGICAL JOURNAL OF THE LINNEAN SOCIETY
(2018)
Article
Evolutionary Biology
Heather E. Grant, Suzanne T. Williams
BIOLOGICAL JOURNAL OF THE LINNEAN SOCIETY
(2018)
Article
Ecology
Edward J. G. Wort, Mark A. Chapman, Stephen J. Hawkins, Lucy Henshall, Alfonso Pita, Marc Rius, Suzanne T. Williams, Phillip B. Fenberg
JOURNAL OF BIOGEOGRAPHY
(2019)
Article
Spectroscopy
Jessica Wade, Hazel Pugh, James Nightingale, Ji-Seon Kim, Suzanne T. Williams
JOURNAL OF RAMAN SPECTROSCOPY
(2019)
Article
Multidisciplinary Sciences
Lauren Sumner-Rooney, Nathan J. Kenny, Farah Ahmed, Suzanne T. Williams
SCIENTIFIC REPORTS
(2019)
Article
Zoology
Claude Vilvens, Suzanne T. Williams
Article
Marine & Freshwater Biology
S. T. Williams, Y. Kano, A. Waren, D. G. Herbert
JOURNAL OF MOLLUSCAN STUDIES
(2020)
Article
Biology
Nathan J. Kenny, Shane A. McCarthy, Olga Dudchenko, Katherine James, Emma Betteridge, Craig Corton, Jale Dolucan, Dan Mead, Karen Oliver, Arina D. Omer, Sarah Pelan, Yan Ryan, Ying Sims, Jason Skelton, Michelle Smith, James Torrance, David Weisz, Anil Wipat, Erez L. Aiden, Kerstin Howe, Suzanne T. Williams
Article
Biochemistry & Molecular Biology
Alison R. Irwin, Ellen E. Strong, Yasunori Kano, Elizabeth M. Harper, Suzanne T. Williams
Summary: This study reports seven new stromboid mitogenomes, including the first mitogenomes for some Recent families, and investigates the relationships among these groups. All analyses support the monophyly of Stromboidea as redefined to include Xenophoridae, but reject the monophyly of Littorinimorpha, consistent with previous studies.
MOLECULAR PHYLOGENETICS AND EVOLUTION
(2021)
Article
Multidisciplinary Sciences
Emel Cakmak, Behlul Koc-Bilican, Omar Hernando Avila-Poveda, Tugce Karaduman, Demet Cansaran-Duman, Suzanne T. Williams, Murat Kaya
Summary: This article describes the isolation and characterization of a natural hydrogel obtained from the girdle of a chiton species through a gentle acid treatment. The natural hydrogel shows non-toxicity, proliferative effect, and good swelling properties, making it an important discovery in material sciences with potential industrial applications.
Article
Biology
Alison R. Irwin, Suzanne T. Williams, Daniel Speiser, Nicholas W. Roberts
Summary: Species within the Strombidae family have well-developed camera-type eyes, showing sensitivity to spatial resolution and contrast. Conch snails may use spatial vision for early predator detection. An integration of behavioral and morphological approaches in animal vision studies is beneficial, as supported by anatomical data and behavioral measures.
JOURNAL OF EXPERIMENTAL BIOLOGY
(2022)
Article
Ecology
Suzanne T. Williams, Emily S. Noone, Lisa Marie Smith, Lauren Sumner-Rooney
Summary: This study investigates the evolutionary loss of shell pigmentation, pattern, and eye structure in deep-sea gastropods. The results show that the loss of these traits is irreversible, occurs at different rates, and is correlated with increasing depth. It is also found that species with better vision have poor spatial acuity and contrast sensitivity, indicating relatively weak visual abilities in deep-sea gastropods.
Article
Ecology
Karolina M. Zarzyczny, Michael E. Hellberg, Elena B. Lugli, Moira MacLean, David A. Paz-Garcia, Marc Rius, Ethan G. Ross, Erick X. Trevino Balandra, James Vanstone, Suzanne T. Williams, Phillip B. Fenberg
Summary: This study investigates the consequences of tropicalisation in rocky shore gastropods using distributional and genetic data. The findings show range contraction in temperate species and range expansion in tropical species. Additionally, population subdivision and phylogeographic breaks are observed in temperate species.
JOURNAL OF BIOGEOGRAPHY
(2023)
Review
Environmental Sciences
Alex David Rogers, Hannah Appiah-Madson, Jeff A. Ardron, Nicholas J. Bax, Punyasloke Bhadury, Angelika Brandt, Pier-Luigi Buttigieg, Olivier De Clerck, Claudia Delgado, Daniel L. Distel, Adrian Glover, Judith Gobin, Maila Guilhon, Shannon Hampton, Harriet Harden-Davies, Paul Hebert, Lisa Hynes, Miranda Lowe, Sandy MacIntyre, Hawis Madduppa, Ana Carolina de Azevedo Mazzuco, Anna McCallum, Chris McOwen, Tim Wilhelm Nattkemper, Mika Odido, Tim O'Hara, Karen Osborn, Angelique Pouponneau, Pieter Provoost, Muriel Rabone, Eva Ramirez-Llodra, Lucy Scott, Kerry Jennifer Sink, Daniela Turk, Hiromi Kayama Watanabe, Lauren V. Weatherdon, Thomas Wernberg, Suzanne Williams, Lucy Woodall, Dawn J. Wright, Daniela Zeppilli, Oliver Steeds
Summary: Ocean Census is a strategic science mission aimed at accelerating the discovery and description of marine species. It addresses the knowledge gap of marine biodiversity and the need to protect marine life and ecosystems.
FRONTIERS IN MARINE SCIENCE
(2023)