25 papers · ranked by Valyu relevance
John F. Y. Brookfield
Evolutionary genetics is a mature field of endeavour, and some of biology's greatest minds have contributed to the theory of population genetics. Initially, they faced a problem, in that following the rediscovery of Mendel's results in the early years of the 20th century, some saw an unbridgeable gulf between the…
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…
Michael K. Skinner
Environment has a critical role in the natural selection process for Darwinian evolution. The primary molecular component currently considered for neo-Darwinian evolution involves genetic alterations and random mutations that generate the phenotypic variation required for natural selection to act. The vast majority of…
Virginie Courtier-Orgogozo, Arnaud Martin
Repetitions in the mutations found to be responsible for independent evolution of similar phenotypes in various taxa have led some biologists to propose that for certain evolutionary changes the causal mutations are predictable. We examine here the nature of the predictions that have been made and their associated…
Joachim Krug
The mathematical theory of evolution is concerned with the changes in the genetic composition of populations that occur under the influence of the evolutionary forces of selection, mutation and demographic noise. In its focus on noisy, collective behavior in large ensembles of (relatively) simple constituents it…
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…
Annalise B. Paaby, Greg Gibson, John S. Torday, Jukka Finne
Evolutionary developmental genetics has traditionally been conducted by two groups: Molecular evolutionists who emphasize divergence between species or higher taxa, and quantitative geneticists who study variation within species. Neither approach really comes to grips with the complexities of evolutionary transitions…
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…
Lisandro Milocco, Isaac Salazar-Ciudad
A fundamental aim of post-genomic 21st century biology is to understand the genotype-phenotype map (GPM) or how specific genetic variation relates to specific phenotypic variation (1). Quantitative genetics approximates such maps using linear models, and has developed methods to predict the response to selection in a…
Richard A. Neher
To learn about the past from a sample of genomic sequences, one needs to understand how evolutionary processes shape genetic diversity. Most population genetic inference is based on frameworks assuming adaptive evolution is rare. But if positive selection operates on many loci simultaneously, as has recently been…
Gerd B. Müller
Since the last major theoretical integration in evolutionary biology-the modern synthesis (MS) of the 1940s-the biosciences have made significant advances. The rise of molecular biology and evolutionary developmental biology, the recognition of ecological development, niche construction and multiple inheritance…
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…
Eugene V. Koonin, Yuri I. Wolf
When Charles Darwin formulated the central principles of evolutionary biology in the Origin of Species in 1859 and the architects of the Modern Synthesis integrated these principles with population genetics almost a century later, the principal if not the sole objects of evolutionary biology were multicellular…
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…
Mauricio González-Forero, Andy Gardner
Natural selection acts on phenotypes constructed over development, which raises the question of how development affects evolution. Existing mathematical theory has considered either evolutionary dynamics while neglecting developmental dynamics, or developmental dynamics while neglecting evolutionary dynamics by…
Steven A. Frank
The theory of natural selection has two forms. Deductive theory describes how populations change over time. One starts with an initial population and some rules for change. From those assumptions, one calculates the future state of the population. Deductive theory predicts how populations adapt to environmental…
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…
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…
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…