Biological systems are modular, and this modularity affects the evolution of biological systems over time and in different environments. We here develop a theory for the dynamics of evolution in a rugged, modular fitness landscape. We show analytically how horizontal gene transfer couples to the modularity in the system and leads to more rapid rates of evolution at short times. The model, in general, analytically demonstrates a selective pressure for the prevalence of modularity in biology. We use this model to show how the evolution of the influenza virus is affected by the modularity of the proteins that are recognized by the human immune system. Approximately 25% of the observed rate of fitness increase of the virus could be ascribed to a modular viral landscape.
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http://dx.doi.org/10.1088/1478-3975/12/2/025001 | DOI Listing |
Proc Natl Acad Sci U S A
January 2025
Department of Physics and Astronomy, University of California, Los Angeles, CA 90095.
The course of evolution is strongly shaped by interaction between mutations. Such epistasis can yield rugged sequence-function maps and constrain the availability of adaptive paths. While theoretical intuition is often built on global statistics of large, homogeneous model landscapes, mutagenesis measurements necessarily probe a limited neighborhood of a reference genotype.
View Article and Find Full Text PDFNat Commun
December 2024
Department of Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstrasse 190, Zurich, CH-8057, Switzerland.
Transcription factor binding sites (TFBSs) are important sources of evolutionary innovations. Understanding how evolution navigates the sequence space of such sites can be achieved by mapping TFBS adaptive landscapes. In such a landscape, an individual location corresponds to a TFBS bound by a transcription factor.
View Article and Find Full Text PDFAm J Primatol
January 2025
School of Resources and Environmental Engineering, Anhui University, Hefei, Anhui, China.
Many animals face significant challenges in locating and acquiring resources that are unevenly distributed in space and time. In the case of nonhuman primates, it remains unclear how individuals remember goal locations and whether they navigate using a route-based or a coordinate-based mental representation when moving between out-of-sight feeding and resting sites (i.e.
View Article and Find Full Text PDFCommun Biol
December 2024
The Institute of Medical Science, The University of Tokyo, Minato-ku, Tokyo, 1088639, Japan.
One of the major age-related declines in female reproductive function is the reduced quantity and quality of oocytes. Here we demonstrate that structural changes in the zona pellucida (ZP) were associated with decreased fertilization rates from 34- to 38-week-old female mice, equivalent to the mid-reproductive of human females. In middle-aged mouse ovaries, the decline in the number of transzonal projections was accompanied by a decrease in cumulus cell-oocyte interactions, resulting in a deterioration of the oocyte quality.
View Article and Find Full Text PDFPhys Rev E
November 2024
Université Grenoble Alpes, CEA List, 38000 Grenoble, France.
Models for viral populations with high replication error rates (such as RNA viruses) rely on the quasispecies concept, in which mutational pressure beyond the so-called "error threshold" leads to a loss of essential genetic information and population collapse, an effect known as the "error catastrophe." We explain how crossing this threshold, as a result of increasing mutation rates, can be understood as a second-order phase transition, even in the presence of lethal mutations. In particular, we show that, in fitness landscapes with a single peak, this collapse is equivalent to a ferroparamagnetic transition, where the back-mutation rate plays the role of the external magnetic field.
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