26 papers · ranked by Valyu relevance
Ziyue Gao
Genome-wide scans for signals of selection have become a routine part of the analysis of population genomic variation datasets and have resulted in compelling evidence of selection during recent human evolution. This Essay spotlights methodological innovations that have enabled the detection of selection over very…
Elena Torres, Alfredo García-Fernández, Diana Iñigo, Carlos Lara-Romero + 5 more
'Carlos Lara-Romero' 'Javier Morente-López' 'Samuel Prieto-Benítez' 'María Luisa Rubio Teso' 'José M. Iriondo' 'Domenico Gargano'] Climate change poses a novel threat to biodiversity that urgently requires the development of adequate conservation strategies. Living organisms respond to environmental change by migrating…
Pim Edelaar, Jun Otsuka, Victor J. Luque
Evolutionary theory has made large impacts on our understanding and management of the world, in part because it has been able to incorporate new data and new insights successfully. Nonetheless, there is currently a tension between certain biological phenomena and mainstream evolutionary theory. For example, how does…
Anjali Gupta, Erik I. Svensson, Henrik Frietsch, Masahito Tsuboi
Following the development of regression-based methods to estimate natural and sexual selection, evolutionary biologists have quantified the strength, mode and direction of selection in natural populations. Although this approach has been successful, its limitations include lack of replication across species…
Kevin Frans, L. B. Soros, Olaf Witkowski
Inspired by natural evolution, evolutionary search algorithms have proven remarkably capable due to their dual abilities to radiantly explore through diverse populations and to converge to adaptive pressures. A large part of this behavior comes from the selection function of an evolutionary algorithm, which is a metric…
Alfredo Rago, Kostas Kouvaris, Tobias Uller, Richard Watson + 1 more
'Jessica C. Flack'] Adaptive plasticity allows organisms to cope with environmental change, thereby increasing the population’s long-term fitness. However, individual selection can only compare the fitness of individuals within each generation: if the environment changes more slowly than the generation time (i.e., a…
Joel W. McGlothlin, David N. Fisher
Evolution by natural selection is often viewed as a process that inevitably leads to adaptation, or an increase in population fitness over time. However, maladaptation, an evolved decrease in fitness, may also occur in response to natural selection under some conditions. Social effects on fitness (or social selection)…
Pedro Horta, Helena Raposeira, Javier Juste, Orly Razgour + 1 more
'Hugo Rebelo'] Title: ABSTRACT There is growing evidence for the role of introgressive hybridization in promoting species adaptation (i.e., adaptive introgression) owing to increasing genomic studies on a diversity of taxa over the past decades. However, introgressive hybridization was, and still is, regarded as a…
Marcela Vargas-Hernandez, Perla Valeria Munguia-Fragozo, Samantha de Jesus Rivero-Montejo, Diana Maria Amaya-Cruz + 4 more
Title: Simple Summary It is necessary to contextualize hormesis within an evolutionary framework that incorporates the advances developed from Neo-Darwinism to contemporary evolutionary biology. The central problem addressed in this review is the lack of a conceptual integration between hormesis and evolutionary…
Riccardo Rao, Stanislas Leibler
Any realistic evolutionary theory has to consider: (i) the dynamics of organisms that reproduce and possess heritable traits; (ii) the appearance of stochastic variations in these traits; and (iii) the selection of those organisms that better survive and reproduce. These elements shape the “evolutionary forces” that…
George Ellis
A conflict exists between field biologists and physiologists ("functional biologists" or "evolutionary ecologists") on the one hand and those working in molecular evolution ("evolutionary biologists" or "population geneticists") on the other concerns the relative importance of natural selection and genetic drift. This…
Finlay Clark, Graeme Robb, Daniel Cole, Julien Michel
Alchemical absolute binding free energy (ABFE) calculations have substantial potential in drug discovery, but are often prohibitively computationally expensive. To unlock their potential, efficient automated ABFE workflows are required to reduce both computational cost and human intervention. We present a…
Tom J. M. Van Dooren
Effects of climate change can be handled by means of mitigation and adaptation. In the biological sciences, adaptations are solutions which evolved when organisms needed to match an ecological challenge. Based on Adaptive Dynamics theory, a definition is proposed of adapted states and adaptational lags applicable…
Seth M. Rudman, Joshua J. Faber-Hammond, Ryan E. Sherman, René S. Shahmohamadloo + 4 more
Forecasting how populations adapt to changing environments is a central challenge in evolutionary biology. We tested the predictability of rapid adaptation by tracking both phenotypic and genomic trajectories of evolution in replicate outdoor populations of Drosophila melanogaster and comparing these data to…
Steven P. Brady, Daniel I. Bolnick, Amy L. Angert, Andrew Gonzalez + 14 more
'Rowan D.H. Barrett' 'Erika Crispo' 'Alison M. Derry' 'Christopher G. Eckert' 'Dylan J. Fraser' 'Gregor F. Fussmann' 'Frederic Guichard' 'Thomas Lamy' 'Andrew G. McAdam' 'Amy E.M. Newman' 'Antoine Paccard' 'Gregor Rolshausen' 'Andrew M. Simons' 'Andrew P. Hendry'] Title: Abstract Evolutionary biologists tend to…
Benjamin Patrick Evans, Bing Xue, Jun Zhang
A common claim of evolutionary computation methods is that they can achieve good results without the need for human intervention. However, one criticism of this is that there are still hyperparameters which must be tuned in order to achieve good performance. In this work, we propose a near "parameter-free" genetic…
Alexander Hendricks, Rachel Cohen, Gavin McEwen, Tony Tien + 4 more
: Glutathione Reductase-Like Metalloid Reductase (GRLMR) is an enzyme that reduces selenodiglutathione (GS-Se-SG), forming zerovalent Se nanoparticles (SeNPs). Error prone polymerase chain reaction was used to create a library of ~10,000 GRLMR variants. The library was expressed in BL21 Escherichia coli in liquid…
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…
Jose Guadalupe Hernandez, Alexander Lalejini, Charles Ofria
Parent selection algorithms (selection schemes) steer populations through a problem's search space, often trading off between exploitation and exploration. Understanding how selection schemes affect exploitation and exploration within a search space is crucial to tackling increasingly challenging problems. Here, we…
A. Carvajal-Rodríguez
Sexual selection plays a crucial role in modern evolutionary theory, offering valuable insight into evolutionary patterns and species diversity. Recently, a comprehensive definition of sexual selection has been proposed, defining it as any selection that arises from fitness differences associated with nonrandom success…
Authors not listed
Three-dimensional molecular generative models have emerged that produce de novo molecules both unconditionally and conditionally, e.g., within protein pockets. However, steering those models in a specific region of the chemical space that satisfies a set of desired properties remains challenging. In this study, we…
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…
Sarvesh Nikumbh, Shameek Ghosh, Vaidyanathan Jayaraman
—Microarray cancer gene expression data comprise of very high dimensions. Reducing the dimensions helps in improving the overall analysis and classification performance. We propose two hybrid techniques, Biogeography – based Optimization – Random Forests (BBO – RF) and BBO – SVM (Support Vector Machines) with gene…
Sterling Baird, Jason R. Hall, Taylor D. Sparks
Would you rather search for a line inside a cube or a point inside a square? Physics-based simulations and wet-lab experiments often have symmetries (degeneracies) that allow reducing problem dimensionality or search space, but constraining these degeneracies is often unsupported or difficult to implement in many…
Sterling Baird, Jason R. Hall, Taylor D. Sparks
Would you rather search for a line inside a cube or a point inside a square? This type of solution degeneracy often exists in physics-based simulations and wet-lab experiments, but constraining these degeneracies is often unsupported or difficult to implement in many optimization packages, requiring additional time and…
Jose Guadalupe Hernandez, Anil Kumar Saini, Jason H. Moore
Case Redundancy with Diagnostic Metrics Authors: ['Jose Guadalupe Hernandez' 'Anil Kumar Saini' 'Jason H. Moore'] Abstract Lexicase selection is a successful parent selection method in genetic programming that has outperformed other methods across multiple benchmark suites. Unlike other selection methods that require…