22 papers · ranked by Valyu relevance
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…
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…
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…
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…
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…
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…
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…
Luis Pedro García-Pintos
This paper focuses on the maximum speed at which biological evolution can occur. I derive inequalities that limit the rate of evolutionary processes driven by natural selection, mutations, or genetic drift. These rate limits link the variability in a population to evolutionary rates. In particular, high variances in…
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…
Vivak Soni, Ana Filipa Moutinho, Adam Eyre-Walker, David Enard
It is known that methods to estimate the rate of adaptive evolution, which are based on the McDonald-Kreitman test, can be biased by changes in effective population size. Here, we demonstrate theoretically that changes in population size can also generate an artifactual correlation between the rate of adaptive…
Mark Pagel, Jacob D. Gardner, Andrew Meade
What rates of directional change are species likely to be capable of sustaining indefinitely such as in response to a warming climate? We derive estimates of the maximum rates of phenotypic change that populations can sustain in response to a directionally changing environment, using a quantitative genetics simulation…
Brian Mintz, Feng Fu
Under constant selection, each trait has a fixed fitness, and small mutation rates allow populations to efficiently exploit the optimal trait. Therefore it is reasonable to expect mutation rates will evolve downwards. However, we find this need not be the case, examining several models of mutation. While upwards…
Atsushi Shibai, Minako Izutsu, Hazuki Kotani, Chikara Furusawa
The mutation is a fundamental source of biological evolution that create genetic variation in populations. Mutations can create new advantageous traits, but also potentially interfere with pre-existing organismal functions. Therefore, organisms may have evolved their mutation rates to appropriate levels to maintain or…
Bhaskar Kumawat, Alexander Lalejini, Monica M. Acosta, Luis Zaman
Title: Significance That all the diversity of life constitutes what Erasmus Darwin called “a single living filament”-an unbroken chain of descent from the last universal common ancestor-is evidence of life’s fundamental adaptability. However, the evolutionary processes that shape this ability to adapt (evolvability)…
Stephan Baehr, Cooper Call
DNA mutation on average is deleterious, and evolution generally acts to reduce mutation rates to the limit of natural selection. The limit of natural selection is set by multiple factors, of which effective population size is only one. We consider lethal mutagenesis as an upper bound to mutation rates for any organism…
Mateusz Krukowski
The paper is devoted to the study of Darwinian evolution in two mathematical models. The first one is a variation on the Malthusian population growth model with Verhulst's environmental capacity. The second model is grounded in the theory of Markov chains and their stationary distributions. We prove preliminary results…
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…
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…
Jonas Verhellen
In recent years, there have been considerable academic and industrial research efforts to develop novel generative models for high-performing, small molecules. Traditional, rules-based algorithms such as genetic algorithms [Jensen, Chem. Sci., 2019, 12, 3567-3572] have, however, been shown to rival deep learning…
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…