Article
Biochemistry & Molecular Biology
Kavitha Uthanumallian, Cintia Iha, Sonja Repetti, Cheong Xin Chan, Debashish Bhattacharya, Sebastian Duchene, Heroen Verbruggen
Summary: This study investigates the genomic signature of secondary plastid endosymbiosis, revealing an increase in gene loss associated with this process while showing that essential genes for plastid function are retained. The data also demonstrate a temporary relaxation of purifying selection during secondary endosymbiosis, with selection intensity rebounding to pre-endosymbiosis levels afterwards. Independent endosymbiosis events in different lineages highlight evolutionary contexts and the interplay between selection and drift during organellogenesis.
MOLECULAR BIOLOGY AND EVOLUTION
(2022)
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
Genetics & Heredity
Chuan Ma, Ruoyang Hu, Cecilia Costa, Jianke Li
Summary: This study sequenced the mitochondrial genomes of genetically selected high royal jelly-producing bees (RJBs) and unselected Italian bees (ITBs). The results showed that RJBs had lower genetic diversity levels and were mainly influenced by genetic drift and purifying selection.
FRONTIERS IN GENETICS
(2022)
Article
Virology
Jiazheng Xie, Bowen Tan, Yi Zhang
Summary: Bats have unique biological features and the TRIM family of proteins play important roles in various cellular functions in bats. The study analyzed the composition, evolution, and expression of bat TRIM genes and found potential links to antiviral immunity, longevity, and DNA damage tolerance. These findings provide a theoretical basis for further research on bat TRIM in these areas.
Article
Evolutionary Biology
Gilles Dupouy, Ronan Cashell, Galina Brychkova, Reetu Tuteja, Peter C. McKeown, Charles Spillane
Summary: The evolution and diversification of proteins play a critical role in cell fate determination. This study demonstrates that duplication of genes encoding CHD3 proteins led to distinct evolutionary trajectories and antagonistic impacts on seed development. The results provide insights into the selective pressures on transcriptomes during plant reproduction and the diversification of the CHD3 family.
GENOME BIOLOGY AND EVOLUTION
(2023)
Article
Cell Biology
Hussain Bahbahani, Sanaa Al-Zoubi, Fatima Ali, Arwa Afana, Mohammed Dashti, Abdulaziz Al-Ateeqi, David Wragg, Suzanne Al-Bustan, Faisal Almathen
Summary: This study investigates the natural selection signatures in the mitochondrial DNA of different dromedary camel populations. The findings reveal adaptive divergence between Old World and New World camels, with evidence of purifying selection among Old World camel species. A total of 89 codons, known to impact the physiochemical properties of proteins, were found to be under positive selection in the Camelidae family.
Article
Evolutionary Biology
Rebekka Muller, Ingemar Kaj, Carina F. Mugal
Summary: The nearly neutral theory is a common framework for describing natural selection at the molecular level by emphasizing the importance of slightly deleterious mutations. However, this theory was formulated under equilibrium conditions and may not be applicable to non-equilibrium natural populations. In this study, a modeling approach is developed to investigate the effects of population size changes on natural selection and effective population size, revealing substantial deviations from the equilibrium selection-drift balance after a change in population size.
GENOME BIOLOGY AND EVOLUTION
(2022)
Article
Biology
Chun Wu, Nicholas J. Paradis, Phillip M. Lakernick, Mariya Hryb
Summary: The genomic substitution rate of SARS-CoV-2 exhibits a molecular clock feature and is not affected by environmental factors. Existing evolution theories fail to explain the evolutionary nature of this virus. A new model called near-neutral balanced selection theory is proposed and supported by empirical evidence.
COMPUTERS IN BIOLOGY AND MEDICINE
(2023)
Article
Ecology
Zhuoyu Chen, Xiaojun Wang, Yu Song, Qinglu Zeng, Yao Zhang, Haiwei Luo
Summary: The authors found that the effective population size of Prochlorococcus is smaller than that of many free-living bacteria, indicating the important role of drift in their evolution. Despite sharing characteristics with endosymbiotic bacteria, Prochlorococcus have a different evolutionary mechanism, where genetic drift plays a key role.
NATURE ECOLOGY & EVOLUTION
(2022)
Article
Genetics & Heredity
Siliang Song, Jianzhi Zhang
Summary: The natural environment fluctuates, affecting the fitness of organisms. The commonly used measure of geometric mean fitness may be misleading due to genetic drift. In this study, a new measure called effective fitness is proposed, which captures the overall effect of fluctuating selection more accurately by considering average expected allele frequency change caused by selection.
G3-GENES GENOMES GENETICS
(2023)
Article
Business, Finance
Kazuhiro Takino, Yoshikazu Ishinagi
Summary: This study verifies the construction of utility maximization problem for banks in their asset allocation. It considers both risk-averse and risk-neutral utility maximization problems, determining optimal lending ratios as the representation of banks' optimal asset allocation. The mean-variance utility is applied to the risk-averse problem and a risk constraint is imposed on the risk-neutral problem to obtain the optimal solution. Through calibration, the study investigates the fitting of the optimal lending ratios derived from the models to the actual bank lending ratio. The statistical tests indicate no significant difference in model fitting between the risk-averse and risk-neutral models, enabling the use of both models to describe banks' asset allocation.
JOURNAL OF BEHAVIORAL AND EXPERIMENTAL FINANCE
(2023)
Article
Multidisciplinary Sciences
D. Noll, F. Leon, D. Brandt, P. Pistorius, C. Le Bohec, F. Bonadonna, P. N. Trathan, A. Barbosa, A. Raya Rey, G. P. M. Dantas, R. C. K. Bowie, E. Poulin, J. A. Vianna
Summary: This study reveals that environmental factors can influence the diversity of mitochondrial genomes in penguins, promoting the adaptation of certain genotypes in response to local environments. This adaptation is likely to have played a role in the diversification and survival of penguins in extreme environments.
SCIENTIFIC REPORTS
(2022)
Article
Ecology
T. Latrille, N. Lartillot
Summary: Molecular sequences are shaped by selection and drift, where populations with high effective population size undergo stronger purifying selection leading to a lower substitution rate for selected mutations. Increase in protein expression level decreases the substitution rate for selected mutations, but selection for protein stability may not fully explain the observed variation in substitution rate across species.
THEORETICAL POPULATION BIOLOGY
(2021)
Article
Microbiology
Yizhak Hershko, Amos Adler, Daniel Barkan
Summary: The current study evaluated the feasibility of using the aph(2'') gene as a positive selection marker in various Mycobacteria and Nocardia. The gene showed good selectability against Tobramycin and can improve the efficiency of genetic manipulation processes in these organisms.
Article
Ecology
Claus Vogl, Lynette Caitlin Mikula
Summary: This article analyzes a biallelic reversible mutation model with linear and quadratic selection, which can lead to patterns of polymorphism and substitution rates. By using a boundary-mutation Moran model, the equilibrium distribution for polymorphic and monomorphic variants in populations is derived.
THEORETICAL POPULATION BIOLOGY
(2021)