26 papers · ranked by Valyu relevance
Michael J McDonald
Microbial experimental evolution uses controlled laboratory populations to study the mechanisms of evolution. The molecular analysis of evolved populations enables empirical tests that can confirm the predictions of evolutionary theory, but can also lead to surprising discoveries. As with other fields in the life…
Karissa Plum, Jason Tarkington, Rebecca A. Zufall, Cristina Miceli + 2 more
'Adriana Vallesi' 'Ronald Edward Pearlman'] Experimental evolution has provided novel insight into a wide array of biological processes. Species in the genus Tetrahymena are proving to be a highly useful system for studying a range of questions using experimental evolution. Their unusual genomic architecture, diversity…
Leah Anderson, Jasmine Schoch, Eleftheria Anastasia, Virginia Wang + 3 more
Experimental evolution is a powerful method for studying the relationship between genotype and phenotype by observing how populations genetically adapt to controlled selective pressures. In educational settings, this approach also offers a dynamic way for students to engage with molecular genetics. One such educational…
Leah Anderson, Jasmine Schoch, Eleftheria Anastasia, Faheem Azeemi + 7 more
Experimental evolution is a powerful method for studying the relationship between genotype and phenotype by observing how populations genetically adapt to controlled selective pressures. In educational settings, this approach also offers a dynamic way for students to engage with molecular genetics. One such educational…
Richard E. Lenski, W. Ford Doolittle
Ever since Darwin, the role of natural selection in shaping the morphological, physiological, and behavioral adaptations of animals and plants across generations has been central to understanding life and its diversity. New discoveries have shown with increasing precision how genetic, molecular, and biochemical…
Sivan Kaminski Strauss, Dvir Schirman, Ghil Jona, Aaron N. Brooks + 60 more
In experimental evolution, scientists evolve organisms in the lab, typically by challenging them to new environmental conditions. How best to evolve a desired trait? Should the challenge be applied abruptly, gradually, periodically, sporadically? Should one apply chemical mutagenesis, and do strains with high innate…
Donghui Xu, Haoyuan Wu, Yonghua Wu
The process of evolutionary change remains poorly understood. By analyzing genomic data from 12 populations in Lenski’s long-term evolution experiment (LTEE) over 60,000 generations, we identified a clear sequence in gene adaptation: growth-related genes evolved early, while survival-related genes evolved later.…
Margarida Matos, Pedro Simões, Marta A. Santos, Sofia G. Seabra + 4 more
'Gonçalo S. Faria' 'Filipa Vala' 'Josiane Santos' 'Inês Fragata'] Ever since Darwin, understanding evolutionary processes and patterns have been major scientific quests. In the Origin of Species, Darwin explained both adaptation and diversity, and most of his arguments were based on indirect evidence, including…
Lee F. Greer
Biology as a science is beginning its third century with new genomic foundations. The challenge of combining experimental evolution with genomics, is being met by a growing number of researchers, including the contributors to the current Frontier Topics Issue volume on the Genomics of Experimental Evolution, who in…
Diogo P. Godinho, Miguel A. Cruz, Maud Charlery de la Masselière, Jéssica Teodoro-Paulo + 5 more
Laboratory studies are often criticized for not being representative of processes occurring in natural populations. This can be partially mitigated by using lab populations that capture large amounts of variation. Additionally, many studies addressing adaptation of organisms to their environment are done with…
Michelle Hays, Katja Schwartz, Danica T. Schmidtke, Dimitra Aggeli + 1 more
There are many mechanisms that give rise to genomic change: while point mutations are often emphasized in genomic analyses, evolution acts upon many other types of genetic changes that can result in less subtle perturbations. Changes in chromosome structure, DNA copy number, and novel transposon insertions all create…
Mila Tost, Cathy Westhues, Ginnie Morrison, Dietrich Kaufmann + 1 more
Experimental evolution studies are common in agricultural research, where they are often deemed “long term selection”. These are often used to perform selection mapping, which involves identifying markers which were putatively under selection based on finding signals of selection left in the genome. A challenge of…
Sinéad Collins, Andrew Rambaut, Stephen Bridgett
We introduce a system for experimental evolution consisting of populations of short oligonucleotides (Oli populations) evolving in a modified quantitative Polymerase Chain Reaction (qPCR). It is tractable at the genetic, genomic, phenotypic and fitness levels. The Oli system uses DNA hairpins designed to form…
Tian Wu, Shifeng Cheng
Evolutionary experiments provide a unique lens through which to observe the impacts of natural selection on crop evolution, domestication, and adaptation through empirical evidence. Enabled by modern technologies-such as the development of large-scale, structured evolving populations, high-throughput phenotyping, and…
Betül K. Arslan, Eric A. Gaucher
One way to understand the role history plays on evolutionary trajectories is by giving ancient life a second opportunity to evolve. Our ability to empirically perform such an experiment, however, is limited by current experimental designs. Combining ancestral sequence reconstruction with synthetic biology allows us to…
Hande Topa, Ágnes Jónás, Robert Kofler, Carolin Kosiol + 1 more
'Antti Honkela'] Motivation: Recent advances in high-throughput sequencing (HTS) have made it possible to monitor genomes in great detail. New experiments not only use HTS to measure genomic features at one time point but to monitor them changing over time with the aim of identifying significant changes in their…
Rohan Maddamsetti, Jacob S. Bower‐Bir
Experimental evolution has yielded surprising insights into human history and evolution by shedding light on the roles of chance and contingency in history and evolution, and on the deep evolutionary roots of cooperation, conflict and kin discrimination. We argue that an interesting research direction would be to…
Nathan Partlan, Luis Antonio Cruz Soto, Jim Howe, Sarthak Shrivastava + 2 more
'Sarthak Shrivastava' 'Magy Seif El‐Nasr' 'Stacy Marsella'] We should consider, then, whether it is possible to make an AI-enabled, computationally co-creative tool that could aid and collaborate with game developers in crafting and refining NPC behavior. As a prerequisite, however, such a tool must be able to produce…
Hong-Yan Shih, Harry Mickalide, David T. Fraebel, Nigel Goldenfeld + 1 more
'Seppe Kuehn'] Abstract. Phenotypes of individuals in a population of organisms are not fixed. Phenotypic fluctuations, which describe temporal variation of the phenotype of an individual or individual-to-individual variation across a population, are present in populations from microbes to higher animals. Phenotypic…
Authors not listed
Designing molecules with specific target properties remains a fundamental challenge in computational chemistry. While existing approaches show promise, most rely on simplified representations like SMILES strings or 2D graphs that lack essential three-dimensional geometric information. We present EvoDiffMol, a…
Justin Villard, Murat Kılıç, Ursula Rothlisberger
Identification of the most stable structure(s) of a system is a prerequisite for the calculation of any of its properties from first-principles. However, even for relatively small molecules, exhaustive explorations of the potential energy surface (PES) are severely hampered by the dimensionality bottleneck. In this…
Brianna Greenstein, Danielle Elsey, Geoffrey Hutchison
Genetic algorithms (GAs) are a powerful tool to search large chemical spaces for inverse molecular design. However, GAs have multiple hyperparameters that have not been thoroughly investigated for chemical space searches. In this work, we examine the general effects of a number of hyperparameters, such as population…
Jan H. Jensen
This paper presents a comparison of a graph-based genetic algorithm (GB-GA) and machine learning (ML) results for the optimisation of logP values with a constraint for synthetic accessibility and shows that GA is as good or better than the ML approaches for this particular property. The molecules found by GB-GA bear…
J. Davila-Velderrain, E. R. Alvarez-Buylla
Understanding the mapping of genotypes into phenotypes is a central challenge of current biological research. Such mapping, conceptually represents a developmental mechanism through which phenotypic variation can be generated. Given the nongenetic character of developmental dynamics, phenotypic variation to a great…
Authors not listed
Free energy calculations have become invaluable in protein design, offering a powerful means to rapidly and accurately screen potential variants. Here, we provide a step-by-step protocol that combines molecular dynamics simulations with non-equilibrium alchemical free energy methods to tackle open questions in protein…
Authors not listed
The $a-m$ model governed by the equation $ay^3+y=mx$ with $a>0$, traces S-curves on an $xy-$ plane. Their superposition has been used to model the protease kinetic activity on various substrates as well as growth of yeast cultures, bacterial colonies, plants, and animals. Enzyme kinetics and growth are dynamic…