Article
Biology
Maria Vasilarou, Nikolaos Alachiotis, Joanna Garefalaki, Apostolos Beloukas, Pavlos Pavlidis
Summary: Computational analyses of SARS-CoV-2 genomes revealed evidence of positive selection regions co-localized with regions from recombination events with nonhuman hosts, suggesting the involvement of pangolin coronavirus in the evolution of SARS-CoV-2. Additionally, there were indications of recombination events with coronavirus genomes from other hosts like hedgehogs and sparrows, and even within human hosts. The study also estimated a demographic scenario involving exponential growth of SARS-CoV-2 populations in European, Asian, and Northern American cohorts, supporting observed polymorphism patterns in the genomes.
Article
Biochemistry & Molecular Biology
Leo Speidel, Lara Cassidy, Robert W. Davies, Garrett Hellenthal, Pontus Skoglund, Simon R. Myers
Summary: The study introduces a fast and scalable approach, Colate, for inferring ancestral relationships between low-coverage genomes without requiring phasing or imputation. The method leverages sharing patterns of mutations dated using a genealogy to infer coalescence rates. By applying this approach to modern and ancient DNA samples, the research identifies dynamic population structure and gene flow between early farmers and European hunter-gatherer groups.
MOLECULAR BIOLOGY AND EVOLUTION
(2021)
Article
Biochemistry & Molecular Biology
Emma L. Berdan, Alexandre Blanckaert, Tanja Slotte, Alexander Suh, Anja M. Westram, Ines Fragata
Summary: The proposed research framework uses the population genetic effects of mutations to determine their relative evolutionary significance in a given scenario. Further study on population genetic effects of different mutation types and their connection to different evolutionary outcomes is needed. Linking experimental and theoretical approaches to examine different mutation types simultaneously is crucial for understanding their evolutionary significance.
Article
Plant Sciences
Nikita Gambhir, Zhian N. Kamvar, Rebecca Higgins, B. Sajeewa Amaradasa, Sydney E. Everhart
Summary: Exposure to sublethal fungicide doses can increase the frequency of insertions/deletions in certain strains of Sclerotinia sclerotiorum, while transposable element insertions are generally repressed. The frequency and distribution of mutations vary with genomic background.
Article
Biochemistry & Molecular Biology
Eugenio Lopez-Cortegano, Rory J. Craig, Jobran Chebib, Toby Samuels, Andrew D. Morgan, Susanne A. Kraemer, Katharina B. Boendel, Rob W. Ness, Nick Colegrave, Peter D. Keightley
Summary: De novo mutations play a crucial role in evolution by providing genetic variation, but studying them is challenging and often limited to model species, leading to a restricted understanding of mutation rate evolution among closely related species. Through a mutation accumulation experiment and comparative analysis between Chlamydomonas incerta and Chlamydomonas reinhardtii, researchers found variability in the mutation rate and differing mutation spectra, indicating similarities in genomic factors influencing mutation rate but a greater divergence in mutation spectra between the two species.
MOLECULAR BIOLOGY AND EVOLUTION
(2021)
Article
Genetics & Heredity
Hui Dong, Khyati Chandratre, Yue Qin, Jing Zhang, Xiaoqing Tian, Ce Rong, Ning Wang, Maoni Guo, Guoping Zhao, San Ming Wang
Summary: This study identified a prevalence of 0.38% for pathogenic BRCA variants in the Chinese Han population, with one carrier out of every 265 individuals and 5.1 million carriers among the total population of 1.3 billion Chinese Hans. This information will be valuable for cancer prevention and treatment related to BRCA in this population.
JOURNAL OF MEDICAL GENETICS
(2021)
Article
Multidisciplinary Sciences
Adrian Gonzalo, Pablo Parra-Nunez, Andreas L. Bachmann, Eugenio Sanchez-Moran, Kirsten Bomblies
Summary: Polyploids, which result from genome duplication events, play an important role in genome evolution in eukaryotes and offer potential benefits for crop improvement. This study investigates the hypothesis that reducing meiotic cross-over rates can limit the formation of abnormal chromosomal associations, called multivalents, in polyploids. The researchers developed Arabidopsis thaliana lines with low cross-over rates and found that the reduction in cross-overs decreased multivalent formation in polyploids, but also resulted in increased univalent frequency and did not improve polyploid fertility. These findings highlight the complexity of factors affecting meiotic stability and fertility in polyploids.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Article
Biochemical Research Methods
Corentin Molitor, Tomasz J. Kurowski, Pedro M. Fidalgo de Almeida, Pramod Eerolla, Daniel J. Spindlow, Sarvesh P. Kashyap, Bijendra Singh, H. C. Prasanna, Andrew J. Thompson, Fady R. Mohareb
Summary: Solanum sitiens, a self-incompatible wild relative of tomato, has salt and drought-resistance traits and its high-quality de novo genome and transcriptome assembly have been successfully developed. Compared to other stress resistant wild tomato relatives, it has distinct morphology, classification, and ecotype, with identified genes related to drought resistance.
Article
Biochemical Research Methods
Haoliang Fan, Ying Zeng, Weiwei Wu, Hong Liu, Quyi Xu, Weian Du, Honglei Hao, Changhui Liu, Wenyan Ren, Weibin Wu, Ling Chen, Chao Liu
Summary: The study investigated the Y-STR landscape of Coastal Southeastern Han (CSEH) in southeast China, revealing a high level of variability and mutations. The findings suggest different strategies for familial searching and individual identification based on the Y-STR mutability of different populations.
Article
Biotechnology & Applied Microbiology
Federico Casale, Delphine Van Inghelandt, Marius Weisweiler, Jinquan Li, Benjamin Stich
Summary: Meiotic recombination is crucial for adaptation and breeding in sexually reproducing eukaryotes. This study assessed recombination rate variation in cultivated barley, highlighting differences in general and specific recombination effects. The research demonstrated the potential of genomic selection to predict recombination rate and manipulate it through natural variation.
PLANT BIOTECHNOLOGY JOURNAL
(2022)
Review
Biology
Roberta Bergero, Peter Ellis, Wilfried Haerty, Lee Larcombe, Iain Macaulay, Tarang Mehta, Mette Mogensen, David Murray, Will Nash, Matthew J. Neale, Rebecca O'Connor, Christian Ottolini, Ned Peel, Luke Ramsey, Ben Skinner, Alexander Suh, Michael Summers, Yu Sun, Alison Tidy, Raheleh Rahbari, Claudia Rathje, Simone Immler
Summary: The separation of germ cell populations from the soma plays a crucial role in genetic inheritance and evolutionary transition to multicellularity. Molecular processes affecting the germline genome, such as segregation, recombination, mutation, and selection, can alter allele frequencies and potentially deviate from Mendelian inheritance. The use of new sequencing technologies has opened up opportunities to delve into the micro-evolutionary processes occurring at the germline genome level.
BIOLOGICAL REVIEWS
(2021)
Article
Genetics & Heredity
William R. Milligan, Guy Amster, Guy Sella
Summary: Different mutation rates and spectra are observed among human populations, which could be explained by evolution at mutation modifiers. Through analytical models and simulations, it was found that the evolution at modifier sites could significantly impact variation in mutation rates within and among populations, with weakly selected modifier sites contributing most to within-population variation and strongly selected modifier sites contributing most to between-population variation. Additionally, a modest number of modifier sites subject to moderate to strong selection could account for the observed variation in mutation rates among human populations.
Article
Biochemistry & Molecular Biology
Brian Charlesworth, Jeffrey D. Jensen
Summary: It has been proposed that lower mutation rates in gene bodies in Arabidopsis thaliana are an adaptive modification related to the rate of beneficial and deleterious mutations. However, the assumptions made in the population genomics analyses for this claim were questionable. Specifically, the difference in Tajima's D between gene bodies and less selectively constrained sequences can be explained by purifying selection rather than lower mutation rates.
MOLECULAR BIOLOGY AND EVOLUTION
(2023)
Article
Virology
Parastoo Pouraziz, Milad Yousefi, Adyatma Irawan Santosa, Davoud Koolivand
Summary: Viral symptoms were observed in cucurbits in Iran, and the main suspected causal agent, cucurbit aphid-borne yellows virus (CABYV), was detected and analyzed for genetic diversity. Phylogenetic analysis revealed that Iranian isolates belonged to two major clades, Asian and Mediterranean.
Article
Biochemistry & Molecular Biology
Kaichi Huang, Kate L. Ostevik, Cassandra Elphinstone, Marco Todesco, Natalia Bercovich, Gregory L. Owens, Loren H. Rieseberg
Summary: In this study, the patterns of recombination, transposable element abundance, and coding sequence evolution were investigated in sunflower species. The results showed significant negative correlations between recombination rates and retrotransposon abundance with deleterious mutations. However, there was no increase in these features in inversions, except for a modest increase in stop codon mutations in some inversions. Additionally, inversions had a greater load in polymorphic populations compared to monomorphic populations.
MOLECULAR BIOLOGY AND EVOLUTION
(2022)
Review
Physics, Multidisciplinary
Uri Obolski, Yoav Ram, Lilach Hadany
REPORTS ON PROGRESS IN PHYSICS
(2018)
Article
Ecology
Yoav Ram, Uri Liberman, Marcus W. Feldman
THEORETICAL POPULATION BIOLOGY
(2019)
Article
Multidisciplinary Sciences
Yoav Ram, Eynat Dellus-Gur, Maayan Bibi, Kedar Karkare, Uri Obolski, Marcus W. Feldman, Tim F. Cooper, Judith Berman, Lilach Hadany
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2019)
Article
Multidisciplinary Sciences
Eyal Zinger, Ariel Gueijman, Uri Obolski, Yoav Ram, Eliya Ruby, Mor Binder, Nivi Yechieli, Nir Ohad, Lilach Hadany
SCIENTIFIC REPORTS
(2019)
Letter
Multidisciplinary Sciences
Yoav Ram, Uri Obolski, Marcus W. Feldman, Judith Berman, Lilach Hadany
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2020)
Article
Ecology
Uri Liberman, Yoav Ram, Lee Altenberg, Marcus W. Feldman
THEORETICAL POPULATION BIOLOGY
(2020)
Article
Multidisciplinary Sciences
Kaleda Krebs Denton, Yoav Ram, Uri Liberman, Marcus W. Feldman
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2020)
Article
Biochemistry & Molecular Biology
Oren Kolodny, Michael Berger, Marcus W. Feldman, Yoav Ram
Article
Biochemical Research Methods
Ronan F. Arthur, James H. Jones, Matthew H. Bonds, Yoav Ram, Marcus W. Feldman
Summary: Epidemics pose challenging dilemmas for governments and individuals, requiring a delicate balance between economic and personal health considerations. Adaptive social contact plays a key role in epidemic outcomes, yet the complexity of human-nature epidemic systems remains poorly understood.
PLOS COMPUTATIONAL BIOLOGY
(2021)
Article
Biology
Dor Cohen, Ohad Lewin-Epstein, Marcus W. Feldman, Yoav Ram
Summary: The study examines the cultural evolution of cooperation under vertical and non-vertical cultural transmission, finding conditions for fixation and coexistence of cooperation and defection. Cooperation evolution is facilitated by horizontal transmission and an association between social interactions and horizontal transmission. When stable polymorphism occurs, reduced association between social interactions and horizontal transmission leads to lower cooperation frequency and population mean fitness.
PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES
(2021)
Article
Infectious Diseases
Ilia Kohanovski, Uri Obolski, Yoav Ram
Summary: This study analyzes the differences between the official and effective start dates of non-pharmaceutical interventions (NPIs) and finds that neglecting these differences can lead to underestimation of the impact of NPIs. The study reveals that the effective start dates of NPIs are often later than the official dates in various regions.
INTERNATIONAL JOURNAL OF INFECTIOUS DISEASES
(2022)
Article
Ecology
Kaleda K. Denton, Yoav Ram, Marcus W. Feldman
Summary: The evolution of altruism has been extensively studied under genetic transmission, but less is known about its dynamics under cultural transmission. Previous research has shown that cultural transmission can facilitate the evolution of altruism by increasing the probability of adopting altruistic behavior and promoting assortment among altruists. This study incorporates vertical and oblique transmission, and explores the effects of conformist and anti-conformist transmission on the evolution of altruism in different scenarios. It also investigates the invasion of an allele that increases individuals' content bias for altruism in the absence of other forms of cultural transmission.
THEORETICAL POPULATION BIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Grace Avecilla, Julie N. Chuong, Fangfei Li, Gavin Sherlock, David Gresham, Yoav Ram
Summary: The rate of adaptive evolution depends on the rate at which beneficial mutations are introduced into a population and their fitness effects. This study estimates the rate at which beneficial copy number variants (CNVs) are introduced and their fitness effects using CNV adaptation dynamics and simulation-based likelihood-free inference approaches. The results demonstrate the importance of CNVs in rapid adaptive evolution and validate the use of neural network-based likelihood-free inference methods for inferring evolutionary rates and effects.
Correction
Multidisciplinary Sciences
Yoav Ram, Eynat Dellus-Gur, Maayan Bibi, Kedar Karkare, Uri Obolski, Marcus W. Feldman, Tim F. Cooper, Judith Berman, Lilach Hadany
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2020)