26 papers · ranked by Valyu relevance
Fabio Scarpa, Marco Casu, Daria Sanna
Genetic variation, evolution, and conservation are three strictly interconnected words, but none of them exist without the others, unless wanting to waive a complete and operational sense. These terms are considered the key concepts in evolutionary biology and represent the essence of life on our planet. It must be…
Jun Kitano, Asano Ishikawa, Mark Ravinet, Virginie Courtier-Orgogozo
Does evolution proceed in small steps or large leaps? How repeatable is evolution? How constrained is the evolutionary process? Answering these long-standing questions in evolutionary biology is indispensable for both understanding how extant biodiversity has evolved and predicting how organisms and ecosystems will…
Maria-Anna Kyrgiafini, Zissis Mamuris
Theodosius Dobzhansky famously wrote in 1973 that “nothing in biology makes sense except in the light of evolution” [1], laying the foundations for the Modern Synthesis that combined population genetics with evolutionary biology and bridged the gap between geneticists and naturalists. Population genetics study the…
Mauricio González-Forero
Mathematically integrating genetics, development, and evolution is a longstanding challenge. Here I develop general mathematical theory that integrates sexual, discrete, multilocus genetics, development, and evolution. This yields an exact method to describe the evolutionary dynamics of allele frequencies and linkage…
Nicholas H. Barton
When Mendel’s work was rediscovered in 1900, and extended to establish classical genetics, it was initially seen in opposition to Darwin’s theory of evolution by natural selection on continuous variation, as represented by the biometric research program that was the foundation of quantitative genetics. As Fisher…
Xiaoqiu Huang
This theory seeks to define species and to explore evolutionary forces and genetic elements in speciation and species maintenance. The theory explains how speciation and species maintenance are caused by natural selection acting on non-Mendelian and Mendelian variation, respectively. The emergence and maintenance of…
Mauricio González-Forero, Andy Gardner
Natural selection acts on developmentally constructed phenotypes, raising the question of how development affects evolution. A mathematical framework that explicitly integrates development into evolution has recently been derived. Here we use this framework to analyse how development affects evolution. We show that…
Ádám Kun
It is often claimed that humanity has stopped evolving because modern medicine erased all selection on survival. Even if that would be true, and it is not, there would be other mechanisms of evolution which could still led to changes in allelic frequencies. Here I show, by applying basic evolutionary genetics…
Nathan W. Anderson, Lloyd Kirk, Joshua G. Schraiber, Aaron P. Ragsdale
Many phenotypic traits have a polygenic genetic basis, making it challenging to learn their genetic architectures and predict individual phenotypes. One promising avenue to resolve the genetic basis of complex traits is through evolve-and-resequence experiments, in which laboratory populations are exposed to some…
Aedan Brown, Sarah Datta, Pankaj Mehta, Brian Cleary
Population genetics has been successful in explaining how drift, selection, and mutation shape allele frequencies. However, we still lack an understanding of how biological and evolutionary constraints arising from genotype-phenotype maps shape evolutionary dynamics. To explore this question, we developed a new…
Susan E. Johnston, Nancy Chen, Emily B. Josephs
A key goal in studies of ecology and evolution is understanding the causes of phenotypic diversity in nature. Most traits of interest, such as those relating to morphology, life-history, immunity and behaviour are quantitative, and phenotypic variation is driven by the cumulative effects of genetic and environmental…
Andrea Iglesias-Ramas, Samuele Pio Lipani, Rosalind J. Allen
Population genetics lies at the heart of evolutionary theory. This topic forms part of many biological science curricula but is rarely taught to physics students. Since physicists are becoming increasingly interested in biological evolution, we aim to provide a brief introduction to population genetics, written for…
Francisco Berkemeier, Karen M. Page
Within the expansive landscape of evolutionary dynamics, symmetry features embedded in well-established models significantly influence the interpretation of individual interaction patterns. Such symmetries are determined through interaction kernel functions, which serve as mathematical models for characterizing the…
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…
Álvaro Soto, David Rodríguez-Martínez, Unai López de Heredia
Practical approaches have become a standard in many scientific disciplines, including population genetics. By analyzing properly selected datasets, the students can calculate parameters and draw conclusions about genetic diversity, differentiation and evolution of populations with higher efficiency than if based…
Claudia Bank
Epistasis occurs when the effect of a mutation depends on its carrier's genetic background. Despite increasing evidence that epistasis for fitness is common, its role during evolution is contentious. Fitness landscapes, mappings of genotype or phenotype to fitness, capture the full extent and complexity of epistasis.…
Tetsuhiro S. Hatakeyama
Phenotypic plasticity and genetic assimilation play key roles in adaptive evolution, yet their underlying mechanism has lacked a unified physical description. A major theoretical difficulty lies in the fundamental difference in timescales, as phenotypic plasticity occurs rapidly within a generation whereas genetic…
Tyler Clark
The evolution of altruistic behavior, which confers benefits to others at a cost to the individual, remains a fundamental question in evolutionary biology. While previous models have investigated the conditions favoring the emergence and stability of altruism, they have often employed simplifying assumptions, such as…
Maurice HT Ling
Genetic algorithm (GA) is inspired by biological evolution of genetic organisms by optimizing the genotypic combinations encoded within each individual with the help of evolutionary operators, suggesting that GA may be a suitable model for studying real-life evolutionary processes. This paper describes the design of a…
Diethard Tautz, Luisa F Pallares, Leif Andersson, Neda Barghi + 20 more
The long-standing notion that genotypes map to phenotypes through simple one gene-one trait relationships continues to shape both research in the life sciences and public understanding, with implications for policy and funding priorities. Yet this paradigm is increasingly recognized as inadequate for explaining…
Joshua Meyers, Nathan Brown
De novo molecular design is effective for optimizing compounds with desirable properties in drug discovery. In the realm of chemoinformatics, population-based evolutionary approaches have been known for over a decade including those that use retrosynthetically inspired fragment-based workflows to to balance the…
Jonas Verhellen
Computer-assisted design of small molecules has experienced a resurgence in academic and indus- trial interest due to the widespread use of data-driven techniques such as deep generative models. While the ability to generate molecules that fulfill required chemical properties is encouraging, the use of deep learning…
Authors not listed
Genetic Algorithms are a powerful method to solve optimization problems with complex cost functions over vast search spaces that rely in particular on recombining parts of previous solutions. Crossover operators play a crucial role in this context. Here, we describe a large class of these operators designed for…
Pavel Kohout, Michal Vasina, Marika Majerova, Veronika Novakova + 5 more
Enzymes play a crucial role in sustainable industrial applications, with their optimization posing a formidable challenge due to the intricate interplay among residues. Computational methodologies predominantly rely on evolutionary insights, leveraging homologous sequences to pinpoint conserved and functionally…
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…
Dariia Yehorova, Rory Crean, Peter Kasson, Shina Caroline Lynn Kamerlin
Protein structure (and thus function) is dictated by non-covalent interaction networks. These can be highly evolutionarily conserved across protein families, the members of which can diverge in sequence and evolutionary history. Here we present KIN, a tool to identify and analyze conserved non-covalent interaction…