24 papers · ranked by Valyu relevance
Stephen De Lisle, Erik I. Svensson
Rates of molecular, phenotypic, and lineage diversification typically scale negatively with time interval of measurement, raising longstanding questions about time-dependency of evolutionary processes. These patterns and their potential meaning have recently re-entered evolutionary discussions. In this Perspective we…
Michael Kopp, Sebastian Matuszewski
An increasing number of studies demonstrate phenotypic and genetic changes in natural populations that are subject to climate change, and there is hope that some of these changes will contribute to avoiding species extinctions (‘evolutionary rescue’). Here, we review theoretical models of rapid evolution in…
Brian C. O’Meara, Jeremy M. Beaulieu, Iddo Friedberg
Across a variety of biological datasets, from genomes to conservation to the fossil record, evolutionary rates appear to increase toward the present or over short time scales. This has long been seen as an indication of processes operating differently at different time scales, even potentially as an indicator of a need…
Brian C. O’Meara, Jeremy M. Beaulieu
Interpretations of biodiversity patterns across timescales necessarily assume that fundamental processes of evolutionary change do not change over time. A recurring pattern across a variety of biological datasets, from genomes to the fossil record, has shown evolutionary rates increasing toward the present or over…
Yu Xia, Eric A. Franzosa, Mark B. Gerstein, Michael Levitt
Rates of evolution differ widely among proteins, but the causes and consequences of such differences remain under debate. With the advent of high-throughput functional genomics, it is now possible to rigorously assess the genomic correlates of protein evolutionary rate. However, dissecting the correlations among…
B. S. Martin, G. S. Bradburd, L. J. Harmon, M. G. Weber
Rates of phenotypic evolution vary markedly across the tree of life, from the accelerated evolution apparent in adaptive radiations to the remarkable evolutionary stasis exhibited by so-called “living fossils”. Such rate variation has important consequences for large-scale evolutionary dynamics, generating vast…
Luis Pedro García-Pintos
I derive uncertainty relations that bound the rate of evolutionary processes driven by natural selection, mutations, or by genetic drift. These rate limits imply that the variability –or statistical uncertainty– in a population allows for faster evolutionary rates. In particular, the variability of a given quantitative…
Emanuel A. Fronhofer, Dov Corenblit, Jhelam N. Deshpande, Lynn Govaert + 4 more
'Lynn Govaert' 'Philippe Huneman' 'Frédérique Viard' 'Philippe Jarne' 'Sara Puijalon'] - 1. ISEM, Universit´e de Montpellier, CNRS, IRD, EPHE, Montpellier, France - 2. Universit´e Clermont Auvergne, CNRS, GEOLAB F-63000 Clermont-Ferrand, France - 3. CNRS, Laboratoire ´ecologie fonctionnelle et environnement…
John P. DeLong, Valery E. Forbes, Nika Galic, Jean P. Gibert + 3 more
'Robert G. Laport' 'Joseph S. Phillips' 'Janna M. Vavra'] Title: Abstract It is increasingly recognized that evolution may occur in ecological time. It is not clear, however, how fast evolution - or phenotypic change more generally - may be in comparison with the associated ecology, or whether systems with fast…
Bruce S Martin, Gideon S Bradburd, Luke J Harmon, Marjorie G Weber + 1 more
'Hernán López-Fernández'] Title: Abstract Rates of phenotypic evolution vary markedly across the tree of life, from the accelerated evolution apparent in adaptive radiations to the remarkable evolutionary stasis exhibited by so-called “living fossils.” Such rate variation has important consequences for large-scale…
Kasper P. Kepp
Darwin's theory of evolution emphasized that positive selection of functional proficiency provides the fitness that ultimately determines the structure of life, a view that has dominated biochemical thinking of enzymes as perfectly optimized for their specific functions. The 20th -century modern synthesis, structural…
Sarah Sanderson, Marc-Olivier Beausoleil, Rose E. O’Dea, Zachary T. Wood + 13 more
Wild populations must continuously adapt to environmental changes or they risk extinction. Such adaptations can be measured as phenotypic rates of change and can allow us to predict patterns of contemporary evolutionary change. About two decades ago, a dataset of phenotypic rates of change in wild populations was…
Robert Worden
In 1995 I wrote a paper 'A Speed Limit for Evolution' – whose main result was that evolution must proceed rather slowly, in accordance with the earlier views and intuitions of many authors. The abstract of the paper said: 'An upper bound on the speed of evolution is derived. The bound concerns the amount of genetic…
Arlin Stoltzfus
Our understanding of evolution is shaped strongly by how we conceive of its fundamental causes. In the original Modern Synthesis, evolution was defined as a process of shifting the frequencies of available alleles at many loci affecting a trait under selection. Events of mutation that introduce novelty were not…
Victor P Shcherbakov
Consistent holistic view of sexual species as the highest form of biological existence is presented. The Weismann's idea that sex and recombination provide the variation for the natural selection to act upon is dominated in most discussions of the biological meaning of the sexual reproduction. Here, the idea is…
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…
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…
Amit Kahana, Lior Segev, Doron Lancet
The origin of life must have involved an unlikely transition from chaotic chemistry to reproducing supramolecular structures. Previous quantitative analyses of reproducing mutually catalytic networks made of simple molecules have led to increasing popularity of this pre-RNA scenario for life’s origin. Here, we…
Andres M. Bran, Peter F. Stadler, Juergen Jost, Guillermo Restrepo
The periodic system emerges by intertwining order and similarity relationships among chemical elements, which in turn arise from known substances at a given time that constitute the chemical space. Although the system has been adjusted to accommodate new elements, the connection with the chemical space has been largely…
Authors not listed
Organic molecular crystals offer a broad spectrum of potential applications. The vast number of possible molecules is both an opportunity and a challenge, because of the prohibitive expense of exhaustively searching chemical space to find novel molecules with promising solid-state properties. Computational methods can…
Nicolai M. Nürk, H. Peter Linder, Renske E. Onstein, Matthew J. Larcombe + 14 more
Understanding how and why rates of evolutionary diversification vary is a central issue in evolutionary biology and ecology. The concept of adaptive radiation has attracted much interest, but is metaphorical and verbal in nature, making it difficult to quantitatively compare different evolutionary lineages or…
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
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…
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…