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
Biochemistry & Molecular Biology
Chaowei Zhang, Kerry Reid, Arthur F. Sands, Antoine Fraimout, Mikkel Heide Schierup, Juha Merila
Summary: Mutation rate is a critical parameter in population genetics, but accurate estimates for wild organisms are limited. This study estimated mutation rates in two marine populations of nine-spined stickleback using pedigrees, whole-genome resequencing, and a high-quality reference genome. The results showed high levels of parental mosaicism and increased estimated divergence times after recalibration with the mutation rate.
MOLECULAR BIOLOGY AND EVOLUTION
(2023)
Article
Biochemistry & Molecular Biology
Haoling Xie, Wen Li, Yuqiong Hu, Cheng Yang, Jiansen Lu, Yuqing Guo, Lu Wen, Fuchou Tang
Summary: This study achieved high continuity human genome assembly using single-cell genome long-read sequencing technology and explored the impact of different assemblers and sequencing strategies on genome assembly. It is of great significance for the practice of single-cell genome de novo assembly.
NUCLEIC ACIDS RESEARCH
(2022)
Review
Genetics & Heredity
Mohiuddin Mohiuddin, R. Frank Kooy, Christopher E. Pearson
Summary: Mosaicism, the existence of genetically distinct populations of cells, is a significant cause of genetic diseases. Neurodevelopmental or neuropsychiatric disorders, such as autism, often arise from de novo mutations that are not present in either parent. The timing and mode of mutations can affect the burden and distribution of mutations.
FRONTIERS IN GENETICS
(2022)
Article
Biochemistry & Molecular Biology
Richard J. Wang, Muthuswamy Raveendran, R. Alan Harris, William J. Murphy, Leslie A. Lyons, Jeffrey Rogers, Matthew W. Hahn
Summary: The mutation rate is a fundamental evolutionary parameter that affects the health and function of individuals. A study on domestic cats found that their mutation rate is 28% lower than that of humans, but consistent with their shorter generation time. Older sires were found to transmit more mutations.
MOLECULAR BIOLOGY AND EVOLUTION
(2022)
Article
Biochemistry & Molecular Biology
Fernando S. Goes, Mehdi Pirooznia, Martin Tehan, Peter P. Zandi, John McGrath, Paula Wolyniec, Gerald Nestadt, Ann E. Pulver
Summary: This study identified numerous de novo variants in BD patients, including loss-of-function and damaging missense variants associated with BD. These variants were enriched in constrained genes, genes located in the postsynaptic density, and the Phosphoinositides pathway. Interestingly, trios with loss-of-function variants did not show evidence of polygenic transmission of common variant risk for BD.
MOLECULAR PSYCHIATRY
(2021)
Article
Psychology, Developmental
Julie C. Chow, Fereydoun Hormozdiari
Summary: Early detection of neurodevelopmental disorders (NDDs) is crucial for improving patient outcomes. By analyzing the differential burden of genetic mutations, a subset of NDD cases can be accurately predicted and prioritized for further clinical study.
JOURNAL OF AUTISM AND DEVELOPMENTAL DISORDERS
(2023)
Article
Genetics & Heredity
Mingpeng Zhang, Qiang Yang, Huashui Ai, Lusheng Huang
Summary: This study estimated the de novo mutation rate of pigs and reinvestigated their evolutionary history. The results showed that the divergence events in pig evolution were not as ancient as previously thought, and the most recent divergence between Chinese wild and domesticated pigs occurred in northern China.
GENOMICS PROTEOMICS & BIOINFORMATICS
(2022)
Article
Genetics & Heredity
Amanda K. Broz, Gus Waneka, Zhiqiang Wu, Matheus Fernandes Gyorfy, Daniel B. Sloan
Summary: The study used high-fidelity Duplex Sequencing technique to analyze mitochondrial mutations in multiple angiosperms from the genus Silene, revealing extreme variations in rates of mitochondrial sequence evolution among different species. While Silene latifolia maintained low variant frequencies, Silene conica showed higher variant frequencies and a biased mutational spectrum. This suggests historical fluctuations in mutation rates drive the extreme variation in plant mitochondrial sequence evolution.
Article
Biochemistry & Molecular Biology
Yannick Mahlich, Maximillian Miller, Zishuo Zeng, Yana Bromberg
Summary: Research shows that while humans carry a large number of SAVs in their genomes, many have little impact on protein function. Some unobserved SAVs may have significant functional effects, but most only have mild effects. Common variants are more likely to occur in less conserved protein positions and have mild to moderate effects, while rare variants are more likely to have severe effects.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2021)
Article
Biochemistry & Molecular Biology
Anne D. Yoder, George P. Tiley
Summary: Germline mutations are crucial for natural selection and species evolution, but excessive mutations can have detrimental effects on fitness and population viability. Molecular ecology faces the challenge of determining the rate and mechanisms of mutation accrual across the tree of life. Despite the high potential of pedigree-based genome comparisons for detecting germline mutations, technical challenges remain significant in this emerging field.
Article
Biochemical Research Methods
Aojie Lian, James Guevara, Kun Xia, Jonathan Sebat
Summary: SynthDNM is a random-forest based classifier that can adapt to new sequencing or variant-calling pipelines by constructing simulated training examples from real data using a flexible approach. The optimized SynthDNM classifiers accurately predict de novo SNPs and indels across multiple variant calling methods.
Article
Genetics & Heredity
Shan Liu, Kunlin Pei, Lu Chen, Jing Wu, Qiuling Chen, Jinyan Zhang, Hui Zhang, Chengyi Wang
Summary: This is a case report of a 5-year-old boy with anemia of unknown etiology. Whole-exome sequencing revealed a de novo GATA1 c.220 + 1G>C mutation. Reporter gene assay showed that this mutation did not affect GATA1 transcriptional activity. However, normal GATA1 transcription was disturbed with increased expression of the shorter isoform. RDDS prediction analysis suggested that abnormal GATA1 splicing might be the underlying mechanism disrupting GATA1 transcription, leading to impaired erythropoiesis. Prednisone treatment significantly improved erythropoiesis, as evidenced by increased hemoglobin and reticulocyte counts.
FRONTIERS IN GENETICS
(2023)
Article
Engineering, Environmental
Selina B. I. Schmidt, Alexandro Rodriguez-Rojas, Jens Rolff, Frank Schreiber
Summary: Antimicrobial resistance (AMR) is a global health problem and the environment plays a significant role in the evolution and transmission of AMR. This study shows that active substances used in material preservatives can increase mutation and conjugation rates in a species- and substance-dependent manner. The RpoS-mediated general stress and RecA-linked SOS response are also found to be associated with increased rates of mutation and conjugation.
JOURNAL OF HAZARDOUS MATERIALS
(2022)
Article
Biology
David Berger, Josefine Stangberg, Julian Baur, Richard J. Walters
Summary: Research suggests that rising global temperatures will intensify natural selection throughout the genome. While environmental stress per se did not increase mean selection on de novo mutation, elevated temperature increased the mean strength of selection on genome-wide polymorphism.
PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES
(2021)
Letter
Obstetrics & Gynecology
Adam Eyre-Walker
HUMAN REPRODUCTION UPDATE
(2019)
Article
Biochemistry & Molecular Biology
Juraj Bergman, Adam Eyre-Walker
MOLECULAR BIOLOGY AND EVOLUTION
(2019)
Editorial Material
Evolutionary Biology
Laura A. Katz, Adam Eyre-Walker
GENOME BIOLOGY AND EVOLUTION
(2019)
Article
Multidisciplinary Sciences
Lucile Vigue, Adam Eyre-Walker
Article
Biochemistry & Molecular Biology
Beth Gibson, Adam Eyre-Walker
JOURNAL OF MOLECULAR EVOLUTION
(2019)
Article
Evolutionary Biology
Jennifer James, Adam Eyre-Walker
GENOME BIOLOGY AND EVOLUTION
(2020)
Review
Ecology
Walter Bodmer, R. A. Bailey, Brian Charlesworth, Adam Eyre-Walker, Vernon Farewell, Andrew Mead, Stephen Senn
Article
Evolutionary Biology
Vivak Soni, Adam Eyre-Walker
Summary: This study investigates the correlations between adaptive and nonadaptive evolution and various factors such as recombination rate, gene age, protein length, gene expression level, and gene function. The results show significant positive correlations between adaptive evolution and recombination rate, protein length, and gene expression level, while negative correlation is observed with gene age. In contrast, nonadaptive evolution shows negative correlations with all these factors. Furthermore, gene function is found to have a significant effect on both adaptive and nonadaptive evolution rates.
GENOME BIOLOGY AND EVOLUTION
(2022)
Article
Evolutionary Biology
Vivak Soni, Ana Filipa Moutinho, Adam Eyre-Walker
Summary: In the divergence of humans and chimpanzees, the rate of adaptive evolution is found to be negatively correlated with the dissimilarity of amino acid pairs in terms of polarity and volume, as well as the strength of purifying selection. These correlations are not affected by population size contraction.
GENOME BIOLOGY AND EVOLUTION
(2022)
Editorial Material
Evolutionary Biology
Adam Eyre-Walker, Laura A. Katz
GENOME BIOLOGY AND EVOLUTION
(2022)
Article
Genetics & Heredity
Julie Dazeniere, Alexandros Bousios, Adam Eyre-Walker
Summary: This study presents a new approach to study natural selection patterns in the evolution of transposable elements over short time scales. By analyzing intact elements from a single genome of a specific transposable element family, the study shows that the ratio of nonsynonymous to synonymous variants decreases as variant frequency increases, indicating strong negative selection acting on the transposable element genome.
G3-GENES GENOMES GENETICS
(2022)
Article
Biochemistry & Molecular Biology
Vivak Soni, Michiel Vos, Adam Eyre-Walker
Summary: This study introduces a new test to examine the role of balancing selection in maintaining genetic diversity and provides some evidence that hundreds of nonsynonymous polymorphisms in humans are subject to balancing selection.
Article
Evolutionary Biology
David L. J. Vendrami, Toni Gossmann, Nayden Chakarov, Anneke J. Paijmans, Vivienne Litzke, Adam Eyre-Walker, Jaume Forcada, Joseph Hoffman
Summary: Nuclear copies of mitochondrial genes (numts) are common in vertebrate genomes. This study characterizes 25 numts in the Antarctic fur seal genome and identifies two recent numts that have multiple substitutions due to noncanonical insertions.
GENOME BIOLOGY AND EVOLUTION
(2022)
Article
Evolutionary Biology
Parul Johri, Adam Eyre-Walker, Ryan N. Gutenkunst, Kirk E. Lohmueller, Jeffrey D. Jensen
Summary: This article discusses the challenges of disentangling the effects of natural selection and population history on genome-wide variation in population genetics. It highlights the theoretical and computational challenges that still need to be addressed, as well as the difficulties in dealing with model complexity and violations, and offers thoughts on potentially fruitful next steps.
GENOME BIOLOGY AND EVOLUTION
(2022)
Article
Evolutionary Biology
Alice Clark, Gizem Koc, Ying Eyre-Walker, Adam Eyre-Walker
Summary: We examined the factors influencing synonymous diversity of mitochondrial DNA in over 300 bird species. We found that diversity was significantly associated with clutch and range size, but not with other variables such as body mass, latitude, and longevity. The correlation between diversity and range size seems to be a result of the relationship between range size and effective population size, as a measure of the effectiveness of natural selection, which is expected to be correlated with effective population size, is also correlated with range size. The slope of the relationship between diversity and range size is shallow, consistent with Lewontin's paradox, and similar to the pattern found in mammals.
GENOME BIOLOGY AND EVOLUTION
(2023)
