Article
Biochemistry & Molecular Biology
Mahan Ghafari, Louis du Plessis, Jayna Raghwani, Samir Bhatt, Bo Xu, Oliver G. Pybus, Aris Katzourakis
Summary: High-throughput sequencing allows rapid genome sequencing during outbreaks, providing insight into pathogen evolution dynamics. Evolutionary analyses over short timescales are challenging due to the time-dependent nature of evolutionary rate estimates. The study on SARS-CoV-2 and pH1N1 influenza found that inferred evolutionary parameters decline over time, with growth rates and emergence dates stable after 4 months. Terminal branches exhibit elevated substitution rates, correlated with purifying selection generating time dependency in evolutionary parameters.
MOLECULAR BIOLOGY AND EVOLUTION
(2022)
Article
Biochemistry & Molecular Biology
Balan Ramesh, Thomas J. Firneno, Jeffery P. Demuth
Summary: The red flour beetle is one of the most well-studied eukaryotic genetic model organisms, providing insights into the tempo and mode of evolutionary innovation through comparative analysis with other species. Recent research using Bayesian methods has estimated the relationships and divergence times among Tribolium species, shedding light on their evolutionary history.
MOLECULAR PHYLOGENETICS AND EVOLUTION
(2021)
Article
Evolutionary Biology
Jose Barba-Montoya, Qiqing Tao, Sudhir Kumar
Summary: This study compared the accuracy, bias, and coverage probabilities of different rapid relaxed-clock dating methods. Among the methods tested, RelTime showed more accurate estimates, especially when evolutionary rates were autocorrelated or shifted convergently among lineages.
GENOME BIOLOGY AND EVOLUTION
(2021)
Article
Evolutionary Biology
Jose Barba-Montoya, Qiqing Tao, Sudhir Kumar
Summary: We compared the accuracy, bias, and coverage probabilities of three rapid dating methods, and found that RelTime was consistently more accurate, particularly in cases of autocorrelated or convergent evolutionary rates. The 95% confidence intervals around RelTime dates showed appropriate coverage probabilities, whereas other methods produced rather low coverage probabilities due to overly narrow CIs of time estimates. Overall, RelTime appears to be a more efficient method for estimating divergence times for large phylogenies.
GENOME BIOLOGY AND EVOLUTION
(2021)
Article
Biochemistry & Molecular Biology
Yuval Nov
Summary: We introduce a novel statistical learning method to analyze context dependent error rates in error-prone PCR experiments. By applying this method to PCR sequencing data, we demonstrate its potential for enhancing the evolvability of genes in protein engineering.
Article
Environmental Sciences
Irene Albarran Lozano, Pablo J. Alonso-Gonzalez, Jose Javier Nunez-Velazquez
Summary: Population statistics indicate an increase in life expectancy, but not all groups benefit equally. The lack of specific statistics makes measuring this increase challenging. Using multistate models to calculate life expectancy, results show that dependent populations have lower life expectancies than the general population, varying by gender and intensity of dependency.
INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH
(2021)
Article
Biochemical Research Methods
Feng Chen, Yubo Bai, Chunhe Li
Summary: In this study, we proposed a data-driven approach to estimate non-equilibrium transition rate, combining kernel density estimation and non-equilibrium transition rate theory. Our approach showed superior performance in estimating transition rate from data compared to previous methods, due to the introduction of a nonparametric density estimation method and consideration of flux effects in determining the new saddle point. We demonstrated the practical validity of our approach by applying it to a simplified cell fate decision model and a high-dimensional stem cell differentiation model. Our approach can be applied to other biological and physical systems.
BRIEFINGS IN BIOINFORMATICS
(2023)
Article
Biochemistry & Molecular Biology
Artem N. Bondaryuk, Nina V. Kulakova, Olga I. Belykh, Yurij S. Bukin
Summary: The study evaluated the temporal signal and substitution rate of different subtypes of tick-borne encephalitis virus (TBEV). The analysis showed that the TBEV Siberian subtype lacked temporal structure and could not be used for substitution rate estimation without other TBEV subtypes. The common clade of TBEV had the lowest substitution rate among tick-borne flaviviruses, and the European subtype had the lowest rate within the common clade.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Ornithology
Angel Arcones, Raquel Ponti, David R. Vieites
Summary: Research indicates that there is variation in mtDNA molecular clock substitution rates among bird lineages and markers, casting doubt on the universality of the standard molecular clock. Specific substitution rates have been provided for each mtDNA marker in avian orders sampled, serving as a valuable tool for molecular clock analysis in the absence of fossil calibrations.
Article
Virology
Iris S. Molina, Victor Jimenez-Vasquez, Wendy Lizarraga, Nieves Sevilla, Veronica Hurtado, Carlos Padilla-Rojas
Summary: During the 2022 COVID-19 pandemic, the human monkeypox virus (hMPXV) underwent various genetic changes, resulting in the emergence of multiple sub-lineages. This study investigated the epidemiological and phylogenetic characteristics of the B.1.6 sub-lineage of hMPXV in Peru and compared it with other circulating sub-lineages during the global outbreak. The B.1.6 sub-lineage was mainly found in Peru, with predominantly male cases and a higher prevalence among individuals with HIV.
JOURNAL OF MEDICAL VIROLOGY
(2023)
Article
Computer Science, Artificial Intelligence
Allam Shehata, Yasushi Makihara, Daigo Muramatsu, Md Atiqur Rahman Ahad, Yasushi Yagi
Summary: In this paper, an uncertainty-aware estimation framework for gait relative attributes is proposed. The framework includes a two-stream network model that takes a pair of gait videos as input and outputs Gaussian distributions of gait absolute attribute scores and annotator-dependent gait relative attribute label distributions. Two uncertainty layers are introduced to estimate the gait relative attribute score distribution and the uncertainty on the gait relative attribute labels. Experiments on two gait relative attribute datasets demonstrate the effectiveness of the proposed method.
PATTERN RECOGNITION
(2023)
Article
Chemistry, Inorganic & Nuclear
Qinghuan Bian, Huanxi Liao, Changcun Tang, Kunjiao Li, Jiabao Wan, Yanhe Xiao, Baochang Cheng, Shuijin Lei
Summary: This work presents the controlled synthesis of quinary Cu3NiInSnS6 nanocrystals and the selective preparation of two metastable phases by tuning the sulfur source. The nanocrystals exhibit superparamagnetic behavior and have direct band gaps. The study is significant for the development of novel multifunctional materials based on metastable multinary metal chalcogenide phases.
DALTON TRANSACTIONS
(2022)
Article
Ecology
Peng-Cheng Fu, Shan-Shan Sun, Alex D. Twyford, Bei-Bei Li, Rui-Qi Zhou, Shi-Long Chen, Qing-Bo Gao, Adrien Favre
Summary: The structure and sequence of plastid genomes are highly conserved in most land plants, but independent gene losses, particularly of the ndh complex, have occurred in multiple clades within the subtribe Gentianinae of the Gentianaceae family. These losses are associated with shifts in substitution rates and species' habitats, demonstrating diverse degradation patterns shaping the evolution of plastids in this species-rich plant group.
ECOLOGY AND EVOLUTION
(2021)
Article
Business, Finance
Paola Stolfi, Mauro Bernardi, Davide Vergni
Summary: Most financial signals show time dependency, causing challenges in parameter estimations. This paper introduces a robust method to handle extreme events and time-dependency in financial time series, along with an algorithm for parameter estimations using the maximization-minimization approach.
FINANCIAL INNOVATION
(2022)
Review
Cell Biology
Louise Richardson, Scott G. Wilcockson, Luca Guglielmi, Caroline S. Hill
Summary: The TGFβ family of cytokines regulate cell fate decisions in development and homeostasis. Recent studies suggest that stable cell fate specification can arise from a noisy combination of signaling inputs and a broad range of signaling levels. Additionally, TGFβ family signaling plays critical roles in tissue maintenance and homeostasis in the skeletal, hematopoietic, and immune systems. However, small perturbations in TGFβ signaling during development can lead to aberrant cell fate specification and disease later in life.
NATURE REVIEWS MOLECULAR CELL BIOLOGY
(2023)
Article
Genetics & Heredity
Yue Hao, Jonathon Fleming, Joanna Petterson, Eric Lyons, Patrick P. Edger, J. Chris Pires, Jeffrey L. Thorne, Gavin C. Conant
Summary: The study finds that the evolutionary forces acting on polyploids are remarkably similar regardless of the species they occur in. The rate of duplicate gene loss is relatively high in the early stages of polyploid evolution, suggesting that most selectively neutral duplicate gene losses occur during this period. There is strong evidence of biases in the duplicate losses, indicating that allopolyploidies with distinct progenitors are common. Additionally, reciprocal gene losses are ongoing and extensive between these polyploid genomes, making the formation of viable diploid hybrid species highly unlikely. The ability of new polyploidies to bypass reciprocal gene loss barriers may explain the relatively high frequency of recurrent polyploidy in certain lineages.
G3-GENES GENOMES GENETICS
(2022)
Article
Multidisciplinary Sciences
Tae-Kun Seo, Benjamin D. Redelings, Jeffrey L. Thorne
Summary: This paper proposes a simple nonparametric test to assess the conventional treatment of alignment gaps as missing data in evolutionary inference. The test results show that there is a correlation between the locations of alignment gaps and the nucleotide substitution or amino acid replacement process. Further simulations and analyses suggest that relying solely on individual optimal alignments may lead to biased evolutionary inferences.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
