Article
Biology
Kenneth B. Hoehn, Jackson S. Turner, Frederick Miller, Ruoyi Jiang, Oliver G. Pybus, Ali H. Ellebedy, Steven H. Kleinstein
Summary: The study found that after seasonal influenza vaccination, GC B cell lineages often exhibit measurable evolution, suggesting that the poor efficacy of seasonal influenza vaccines is not solely due to the inhibition of vaccine-specific B cell evolution.
Article
Ecology
William A. Freyman, Matthew G. Johnson, Carl J. Rothfels
Summary: In this paper, we introduce homologizer, a flexible Bayesian method that uses a phylogenetic framework to infer the separation of gene copies into their respective subgenomes across different loci. Through simulation tests, we demonstrate the robustness of homologizer to factors such as incomplete lineage sorting and the phylogenetic informativeness of loci. Furthermore, we establish the utility of homologizer on real data by analyzing a multilocus dataset from the fern family Cystopteridaceae. Lastly, we discuss the potential use of homologizer beyond its core phasing functionality to identify non-homologous sequences.
METHODS IN ECOLOGY AND EVOLUTION
(2023)
Article
Biochemistry & Molecular Biology
Matthew A. Spence, Matthew D. Mortimer, Ashley M. Buckle, Bui Quang Minh, Colin J. Jackson
Summary: This study used a structural alignment of diverse serpins to generate a comprehensive 6,000-sequence phylogeny, showing extensive diversification of the superfamily into many novel functional clades. Analysis indicated that the hub proteins are ancient and similar due to convergent evolution, rather than horizontal gene transfer as previously speculated. This work clarifies longstanding questions in the evolution of serpins and provides new directions for research in the field of serpin biology.
MOLECULAR BIOLOGY AND EVOLUTION
(2021)
Review
Biology
Gad Degani, Isana Veksler-Lublinsky, Ari Meerson
Summary: This review summarizes recent studies on genes, many of them involved in growth and reproduction, which can be used to differentiate between species in the Anabantoidei suborder of fish, with a focus on the Blue Gourami as a model species. Genetic markers in the Blue Gourami differ from those in other bony fishes, with the mitochondrial cytochrome c oxidase subunit 1 (COI) gene often used for studying the Anabantoidei suborder. The most suitable genetic markers for distinguishing between Anabantoidei species are related to genes involved in controlling growth and reproduction in the hypothalamic-pituitary-somatotropic axis.
Article
Evolutionary Biology
M. Angel Leon-Tapia
Summary: The study examined the DNA barcoding identification of the Yucatan deer mouse Peromyscus yucatanicus and its intraspecific relationships, revealing that it is monophyletic and showing signs of demographic stability and growth. Three genetic haplogroups were identified within the species. This research provides insights into the evolutionary history and genetic differentiation of P. yucatanicus.
JOURNAL OF MAMMALIAN EVOLUTION
(2021)
Review
Medicine, General & Internal
Laurens D'hoore, Guy T'Sjoen
Summary: With increasing demand for hormone treatment among transgender and gender nonbinary individuals, more research data is becoming available. A recent literature review found that gender-affirming hormone treatment can lead to increased life satisfaction and reduced psychological difficulties for those who feel it is necessary. The use of hormones can also change body composition and contours. Studies on bone health have shown reassuring results, but special attention is needed for adolescent and adult trans women in terms of hormone dosage and treatment compliance. The use of certain estrogens in trans women may increase the risk of myocardial infarction and stroke, highlighting the importance of lifestyle management in trans healthcare.
JOURNAL OF INTERNAL MEDICINE
(2022)
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
Zoology
Eva Ladurner, Paolo Colangelo, Gianni Amori, Federica Lazzeri, Elisa Colonna, Petra Kranebitter
Summary: The study used molecular markers to revise the specimens of the Sorex araneus group in South Tyrol, Italy, detecting the presence of both S. antinorii and S. araneus in the region. This finding underscores the importance of revising museum collections using modern technologies to accurately assess the diversity of small mammal fauna at regional and national levels.
HYSTRIX-ITALIAN JOURNAL OF MAMMALOGY
(2021)
Article
Immunology
A. Chaillon, D. M. Smith
Summary: The study suggests that the rapid rise of the B.1.1.7 Variant of Concern most likely occurred through global dispersal rather than convergent evolution from multiple sources.
CLINICAL INFECTIOUS DISEASES
(2021)
Article
Multidisciplinary Sciences
Tyler Funnell, Ciara H. O'Flanagan, Marc J. Williams, Andrew McPherson, Steven McKinney, Farhia Kabeer, Hakwoo Lee, Sohrab Salehi, Ignacio Vazquez-Garcia, Hongyu Shi, Emily Leventhal, Tehmina Masud, Peter Eirew, Damian Yap, Allen W. Zhang, Jamie L. P. Lim, Beixi Wang, Jazmine Brimhall, Justina Biele, Jerome Ting, Vinci Au, Michael Van Vliet, Yi Fei Liu, Sean Beatty, Daniel Lai, Jenifer Pham, Diljot Grewal, Douglas Abrams, Eliyahu Havasov, Samantha Leung, Viktoria Bojilova, Richard A. Moore, Nicole Rusk, Florian Uhlitz, Nicholas Ceglia, Adam C. Weiner, Elena Zaikova, J. Maxwell Douglas, Dmitriy Zamarin, Britta Weigelt, Sarah H. Kim, Arnaud Da Cruz Paula, Jorge S. Reis-Filho, Spencer D. Martin, Yangguang Li, Hong Xu, Teresa Ruiz de Algara, So Ra Lee, Viviana Cerda Llanos, David G. Huntsman, Jessica N. McAlpine, Sohrab P. Shah, Samuel Aparicio
Summary: This study reveals the contribution of cell-to-cell structural variation to the phenotypic and evolutionary diversity in human breast cancer and ovarian cancer, and provides insights into the genomic and mutational states of individual cancer cells.
Article
Multidisciplinary Sciences
Ningping Gong, Diogo Ferreira-Martins, Jessica L. Norstog, Stephen D. McCormick, Mark A. Sheridan
Summary: This study investigated the early evolution and function of the growth hormone (GH)/prolactin (PRL) family using a representative of one of the oldest vertebrate lineages. A second member of the GH/PRL family, prolactin-like (PRL-L), was identified in the sea lamprey. The findings provide insights into the origin and divergence of GH/PRL family genes in early vertebrates. The lamprey PRL-L plays a role in osmoregulation and is comparable to the function of PRLs in jawed vertebrates.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Evolutionary Biology
Michele Rossini, Vasily Grebennikov, Thomas Merrien, Andreia Miraldo, Heidi Viljanen, Sergei Tarasov
Summary: The phylogenetic relationships of the Paleotropical dung beetle clades (Grebennikovius, Epactoides, and Ochicanthon) were reconstructed using morphology and molecular data. The study reveals the divergence and dispersal patterns of these clades in relation to geological changes and climate conditions between Africa, Madagascar, and Reunion island.
SYSTEMATIC ENTOMOLOGY
(2022)
Review
Pediatrics
Michael Hermanussen, Sergei Erofeev, Christiane Scheffler
Summary: This research explores the impact of social competition and status on human growth and development, linking it to the evolutionary conserved endocrine signaling system. It suggests a connection between size and status in social structures, with height being favored in upper social classes. The study also highlights the competitive nature of Western societies and the importance of striving for status and prestige in shaping human growth patterns.
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
Fisheries
Lucija Raguz, Ivana Buj, Zoran Marcic, Vatroslav Veble, Lucija Ivic, Davor Zanella, Sven Horvatic, Perica Mustafic, Marko Caleta, Marija Sabolic
Summary: This study investigated the phylogenetic reconstruction of the Danube barbel using cytochrome b as a genetic marker, revealing the divergence of three Barbus balcanicus lineages in Croatian watercourses. The Croatian lineage displayed a high reproductive potential, but habitat degradation and fragmentation have led to reduced population sizes in some populations.
KNOWLEDGE AND MANAGEMENT OF AQUATIC ECOSYSTEMS
(2021)
Article
Biochemistry & Molecular Biology
Ray C. Schmidt, Henry L. Bart, Frank Pezoid
MOLECULAR PHYLOGENETICS AND EVOLUTION
(2016)
Article
Evolutionary Biology
Ryan E. Chabarria, Christopher M. Murray, Paul E. Moler, Henry L. Bart, Brian I. Crother, Craig Guyer
JOURNAL OF ZOOLOGICAL SYSTEMATICS AND EVOLUTIONARY RESEARCH
(2018)
Article
Biochemistry & Molecular Biology
Ray C. Schmidt, Henry L. Bart, Wanja Dorothy Nyingi
MOLECULAR PHYLOGENETICS AND EVOLUTION
(2017)
Article
Anatomy & Morphology
John S. S. Denton, John G. Maisey, Mark Grace, Alan Pradel, Michael H. Doosey, Henry L. Bart, Gavin J. P. Naylor
JOURNAL OF ANATOMY
(2018)
Article
Biodiversity Conservation
Mollie F. Cashner, Henry L. Bart
SOUTHEASTERN NATURALIST
(2018)
Article
Zoology
Ray C. Schmidt, Henry L. Bart, Wanja Dorothy Nyingi
Article
Evolutionary Biology
Ray C. Schmidt, Megan N. Dillon, Natalie M. Kuhn, Henry L. Bart, Frank Pezold
Article
Zoology
Mark A. Grace, Michael H. Doosey, John S. S. Denton, Gavin J. P. Naylor, Henry L. Bart, John G. Maisey
Article
Zoology
Henry L. Bart, Ray C. Schmidt, Wanja Dorothy Nyingi, Joseph Gathua
Article
Ecology
Mohannad Elhamod, Kelly M. Diamond, A. Murat Maga, Yasin Bakis, Henry L. Bart, Paula Mabee, Wasila Dahdul, Jeremy Leipzig, Jane Greenberg, Brian Avants, Anuj Karpatne
Summary: Species classification is a crucial task laying the groundwork for various applications involving species studies. The proposed hierarchy-guided neural network (HGNN) method outperforms traditional ConvNet models in terms of classification accuracy and robustness, especially in scenarios with limited training data.
METHODS IN ECOLOGY AND EVOLUTION
(2022)
Article
Information Science & Library Science
Kevin Karnani, Joel Pepper, Yasin Bakis, Xiaojun Wang, Henry Bart, David E. Breen, Jane Greenberg
Summary: Metadata is crucial for applying machine learning to digitized biological specimens. This research extends previous work and improves computational methods to generate accurate metadata for fish specimens, demonstrating the ability of computational methods to enhance digital library services worldwide.
INTERNATIONAL JOURNAL ON DIGITAL LIBRARIES
(2022)
Article
Biology
Thomas F. Turner, Henry L. Bart Jr, Frank McCormick, Alexi C. Besser, Rachel E. Bowes, Krista A. Capps, Emily S. DeArmon, Casey B. Dillman, Katelyn P. Driscoll, Aubrey Dugger, Gregor L. Hamilton, Phillip M. Harris, Dean A. Hendrickson, Joel Hoffman, Jason H. Knouft, Ryan F. Lepak, Hernan Lopez-Fernandez, Carmen G. Montana, Seth D. Newsome, Allison A. Pease, W. Leo Smith, Christopher A. Taylor, Rachel L. Welicky
Summary: This article explores the potential for transformative research in ecology by integrating biodiversity collections, stable isotope analysis (SIA), and environmental informatics. Integration of SIA data allows for evaluation of long-term ecological change. Challenges such as sparse samples and lack of baseline information can be overcome. Collections and SIA provide historical context and quantitative assessment for freshwater ecological research.
Proceedings Paper
Computer Science, Information Systems
Joel Pepper, Jane Greenberg, Yasin Bakis, Xiaojun Wang, Henry Bart, David Breen
Summary: This research focuses on using machine-driven approaches to analyze digitized fish images and extract crucial features, providing key metadata for Biology Guided Neural Networks (BGNN). Results demonstrate the importance of automatically generated metadata for predictive analytics of neural networks, outperforming humans in terms of time and accuracy in the automated process.
2021 ACM/IEEE JOINT CONFERENCE ON DIGITAL LIBRARIES (JCDL 2021)
(2021)
Article
Zoology
Ray C. Schmidt, Henry L. Bart, Frank Pezold, John P. Friel
Article
Zoology
Kyle R. Piller, Henry L. Bart
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)