Article
Evolutionary Biology
Debora Princepe, Marcus A. M. de Aguiar
Summary: This study explores how interactions between mitochondrial and nuclear DNA affect species identification accuracy and the speciation process. The findings suggest that mito-nuclear compatibility plays a crucial role in speciation and genetic data reconstruction.
SYSTEMATIC BIOLOGY
(2021)
Article
Parasitology
Aneta Trefancova, Jana Kvicerova, Anna Macova, Michal Stanko, Lada Hofmannova, Vaclav Hypsa
Summary: Research shows that rodent-associated Eimeria parasites form a complex system of genetic lineages with different host specificities, and these lineages retain their specificities while spreading across large geographic areas. Additionally, the study demonstrates that genetic structure is only partially reflected by morphological traits.
INTERNATIONAL JOURNAL FOR PARASITOLOGY
(2021)
Article
Multidisciplinary Sciences
Elena Dembech, Marco Malatesta, Carlo De Rito, Giulia Mori, Davide Cavazzini, Andrea Secchi, Francesco Morandin, Riccardo Percudani
Summary: Coevolution at the gene level can be revealed by analyzing correlated events of gene loss or gain through phylogenetic profile analysis. We describe a suitable procedure for large-scale analysis that assesses the statistical significance of correlated presence/absence transitions between gene pairs to reveal coevolution. Using this method, we identified coevolutionary modules linking known and unknown genes in protein complexes and biological pathways. Furthermore, we demonstrated the ability of the method to predict hidden gene associations through experimental validation.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Article
Ecology
Renate Radek, Katja Platt, Deniz Oztas, Jan Sobotnik, David Sillam-Dusses, Robert Hanus, Andreas Brune
Summary: Lower termites carry diverse symbiotic gut flagellates, and this study identified a new lineage called Retractinymphidae. The new genus Retractinympha glossotermitis is closely related to Teranymphidae, but its rostrum is longer than the body, and its anterior end is retractable. In addition, the presence of Heliconympha and Retractinympha and the absence of Pseudotrichonympha in Serritermitidae support the hypothesis of horizontal transmission.
FRONTIERS IN ECOLOGY AND EVOLUTION
(2023)
Review
Genetics & Heredity
Lilian Motta Cantanhede, Carlos Mata-Somarribas, Khaled Chourabi, Gabriela Pereira da Silva, Bruna Dias das Chagas, Luiza de Oliveira R. Pereira, Mariana Cortes Boite, Elisa Cupolillo
Summary: The genus Leishmania, responsible for leishmaniasis, likely originated in the Mesozoic era and has globally dispersed prior to the breakup of the Gondwana supercontinent through evolutionary processes. Various species of Leishmania have been reported to be infected by Leishmania RNA viruses and Leishbunyaviruses, with different genomic structures assigned to different parasite species. There is strong evidence suggesting that these viruses can enhance the parasitic survival through complex mechanisms, potentially contributing to the worldwide dispersion of Leishmania.
Article
Microbiology
Mayara Cristhine de Oliveira Santana, Khaled Chourabi, Lilian Motta Cantanhede, Elisa Cupolillo
Summary: This study investigates the specificity of Leishmania RNA Virus 1 (LRV1) in relation to Leishmania (Viannia) species hosts. LRV1 was found to be associated with increased severity of Tegumentary Leishmaniasis (TL) symptoms and unfavorable clinical outcomes. The presence of LRV1 in various Leishmania species suggests host specificity, and phylogenetic analysis supports the coevolution of LRV1 and Leishmania.
Article
Multidisciplinary Sciences
Joseph W. Schafer, Lauren L. Porter
Summary: This study reveals the widespread phenomenon of dual-fold coevolution, demonstrating that some proteins can switch between two stable structures. The researchers developed a method to predict multiple protein structures from a single sequence using this coevolution information, providing important insights into the function and evolution of proteins.
NATURE COMMUNICATIONS
(2023)
Article
Plant Sciences
Matthieu Chabannes, Marc Gabriel, Abderrahmane Aksa, Serge Galzi, Jean-Francois Dufayard, Marie-Line Iskra-Caruana, Emmanuelle Muller
Summary: Badnaviruses, double-stranded DNA pararetroviruses of the family Caulimoviridae, exhibit wide genetic diversity in banana. The coevolution between badnaviral sequences of different clades and banana suggests primary viral integrations occurred millions of years ago in banana genomes. Endogenous badnaviral sequences can be used as powerful markers to characterize the Musa phylogeny more accurately.
MOLECULAR PLANT PATHOLOGY
(2021)
Article
Engineering, Chemical
Seshu K. Damarla, Xi Sun, Fangwei Xu, Ashish Shah, Biao Huang
Summary: Control valve, affected by stiction, causes oscillations in closed-loop signals, leading to reduced product quality, plant throughput, and increased environmental impact. Therefore, it is crucial to detect and quantify stiction in control valves. In this study, four noninvasive and practical methods are developed using statistical tests such as F-test, t-test, modified Hotelling T2-test, and reverse arrangement test. These methods are applied to benchmark control loops from various industries and compared with existing methods. The results show that the proposed methods perform equally well or better than existing methods, with the t-test-based method and the modified Hotelling T2-test-based method being particularly effective. The proposed methods not only detect stiction but also quantify its severity, providing timely notifications to operators and assisting maintenance engineers in scheduling plant shutdowns. These methods are applicable to all control loops except for level loops.
INDUSTRIAL & ENGINEERING CHEMISTRY RESEARCH
(2023)
Article
Neurosciences
Giancarlo Valente, Agustin Lage Castellanos, Lars Hausfeld, Federico De Martino, Elia Formisano
Summary: The study focuses on the false positive control of different permutation strategies and the statistical power of different cross-validation schemes. Simulations demonstrate that estimating the entire cross-validation error on each permuted dataset is the only statistically valid permutation strategy. Among different cross-validation schemes, a repeated split-half cross-validation is the most powerful.
Article
Biology
Andrea Mazzolini, Thierry Mora, Aleksandra M. Walczak
Summary: Chronic HIV infections involve a complex coevolutionary process between the virus and the host immune system. In this study, longitudinal data from ten HIV-infected individuals were analyzed to explore the turnover rates of viral strains and immune repertoires. While there was no significant correlation at the individual level, an anti-correlation was observed when aggregating the data across patients. The findings suggest that large changes in the viral pool composition are associated with small changes in the B-cell receptor repertoire.
PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES
(2023)
Article
Chemistry, Multidisciplinary
Jintao Su, Zhaoxiang Deng
Summary: This paper provides a reference for the application of the hybrid FE-SEA model in complex structures. By establishing the hybrid FE-SEA commercial vehicle model using an experimental statistical energy parameter modeling and modification method, various modeling problems have been effectively addressed.
APPLIED SCIENCES-BASEL
(2021)
Article
Entomology
Jekaterina Havelka, Jurij Danilov, Rimantas Rakauskas
Summary: By analyzing genetic sequences of aphids and their endosymbiotic bacteria, this study revealed co-evolutionary relationships and confirmed the influence of host aphid species relatedness on symbiont communities. New gamma-proteobacterial endosymbionts were also discovered in two species of adelgid aphids in Lithuania.
BULLETIN OF INSECTOLOGY
(2021)
Review
Microbiology
Shusuke Kawakubo, Hangil Kim, Minoru Takeshita, Chikara Masuta
Summary: This study investigates the host-adaptive evolution of leek yellow stripe virus (LYSV) through Bayesian phylogenetic comparative methods and a functional assay of viral RNA silencing suppressor (RSS) activity. It reveals that LYSV has evolved in response to different Allium plant hosts, with distinct evolutionary backgrounds between leek and garlic isolates. The research also demonstrates that viral RSS activity may play a crucial role in the host-specific adaptation of LYSV, specifically in leek.
MICROBIOLOGY SPECTRUM
(2023)
Article
Neurosciences
Satoshi Hirose
Summary: In decoding studies, a second-level group statistical test is often conducted after individual analyses to test the information about labels in brain activation. However, these tests may not provide conclusive evidence on the typical effect in the population. Therefore, a novel information prevalence inference method using the i-th order statistic is proposed, which improves the inference of typical effect in the population.
Article
Statistics & Probability
Amaury Lambert, Emmanuel Schertzer
PROBABILITY THEORY AND RELATED FIELDS
(2020)
Review
Biochemistry & Molecular Biology
Remi Denise, Sophie S. Abby, Eduardo P. C. Rocha
TRENDS IN MICROBIOLOGY
(2020)
Article
Ecology
Elise Kerdoncuff, Amaury Lambert, Guillaume Achaz
THEORETICAL POPULATION BIOLOGY
(2020)
Article
Ecology
Carolina Reyes, Logan H. Hodgskiss, Melina Kerou, Thomas Pribasnig, Sophie S. Abby, Barbara Bayer, Stephan M. Kraemer, Christa Schleper
Article
Ecology
Julie Marin, Guillaume Achaz, Anton Crombach, Amaury Lambert
JOURNAL OF EVOLUTIONARY BIOLOGY
(2020)
Article
Biochemistry & Molecular Biology
Marc Manceau, Julie Marin, Helene Morlon, Amaury Lambert
MOLECULAR BIOLOGY AND EVOLUTION
(2020)
Article
Biology
Guilhem Doulcier, Amaury Lambert, Silvia De Monte, Paul B. Rainey
Article
Microbiology
Sophie S. Abby, Melina Kerou, Christa Schleper
Article
Statistics & Probability
Amaury Lambert, Veronica Miro Pina, Emmanuel Schertzer
Summary: The study focuses on the evolution of chromosome color partition in a Moran model with recombination in a large population, by tracing back the ancestry of chromosomes to investigate the distribution of chromosome colors. An approximation of the stationary distribution of the partition can be provided when the value of rho is large, and the length distribution of the leftmost block of the partition converges to an exponential distribution.
ANNALS OF APPLIED PROBABILITY
(2021)
Article
Ecology
Melina Kerou, Rafael I. Ponce-Toledo, Rui Zhao, Sophie S. Abby, Miho Hirai, Hidetaka Nomaki, Yoshihiro Takaki, Takuro Nunoura, Steffen L. Jorgensen, Christa Schleper
Summary: The study presents 11 metagenome-assembled genomes of the most abundant AOA clades from sediment cores obtained from the Atlantic Mid-Ocean ridge flanks and Pacific abyssal plains, revealing their adapted features such as ammonia oxidation, carbon fixation, and conversion of fermentation products. The phylogenomic placement of these AOA suggests that they have independently evolved adaptations to the high-pressure environment of marine sediments, with distinctive features like ATPase and DNA repair systems.
Article
Computer Science, Software Engineering
Francois Bienvenu, Amaury Lambert, Mike Steel
Summary: This paper investigates tree-child networks and their derived ranked tree-child networks (RTCNs), finding that introducing biologically relevant ranking structure can make some mathematical questions tractable in the networks. The properties of uniform RTCNs are studied, including the lengths of random walks in the network, distribution of cherry numbers, etc.
RANDOM STRUCTURES & ALGORITHMS
(2022)
Article
Mathematical & Computational Biology
Amaury Lambert
Summary: In a model of the COVID-19 epidemic, it was found that digital interventions can reduce the average number of secondary infections, but are not enough to bring it below 1 without non-digital interventions. The study highlights the importance of a combination of digital and non-digital interventions to control the epidemic.
MATHEMATICAL MODELLING OF NATURAL PHENOMENA
(2021)
Article
Infectious Diseases
Celia P. F. Domingues, Joao S. Rebelo, Joel Pothier, Francisca Monteiro, Teresa Nogueira, Francisco Dionisio
Summary: There is a positive correlation between the diversity of virulence genes and antibiotic-resistance genes in human metagenomes. This correlation becomes stronger when the transmission probability between individuals is higher than the probability of losing resistance genes. The leading causes for this positive correlation are the transmission between people and antibiotic usage.
Article
Statistics & Probability
Felix Foutel-Rodier, Amaury Lambert, Emmanuel Schertzer
Summary: The study shows that any exchangeable coalescent process can be represented as a paintbox based on a random nondecreasing process, and demonstrates that a Lambda-coalescent can be obtained from a unique random nested interval partition. It also explores the weak isometry between ultrametric measure spaces and nested interval-partitions, providing a theoretical basis for understanding and describing coalescent phenomena.
ANNALS OF APPLIED PROBABILITY
(2021)
Article
Biology
Nicolas Cluzel, Amaury Lambert, Yvon Maday, Gabriel Turinici, Antoine Danchin
COMPTES RENDUS BIOLOGIES
(2020)