Related papers: Universal pacemaker of genome evolution
Centromeres are essential for chromosome segregation, yet their DNA sequences evolve rapidly. In most animals and plants that have been studied, centromeres contain megabase-scale arrays of tandem repeats. Despite their importance, very…
Estimation of molecular evolutionary divergence times requires models of rate change. These vary with regard to the assumption of what quantity is penalized. The possibilities considered are the rate of evolution, the log of the rate of…
The genetic blueprint for the essential functions of life is encoded in DNA, which is translated into proteins -- the engines driving most of our metabolic processes. Recent advancements in genome sequencing have unveiled a vast diversity…
The Central Dogma of molecular biology, as originally proposed by Crick, asserts that information passed into protein cannot flow back out. This principle has been interpreted as underpinning modern understandings of heredity and evolution,…
Molecular phylogeny has focused mainly on improving models for the reconstruction of gene trees based on sequence alignments. Yet, most phylogeneticists seek to reveal the history of species. Although the histories of genes and species are…
Well protected human and laboratory animal populations with abundant resources are evolutionary unprecedented, and their survival far beyond reproductive age may be a byproduct rather than tool of evolution. Physical approach, which takes…
Scientific and technological frontiers advance through punctuated dynamics, yet the principles governing these dynamics remain poorly understood. Here we collect and analyze datasets tracking the evolution of frontiers across 9 different…
Many organisms possess both a cell cycle to control DNA replication and a circadian clock to anticipate changes between day and night. In some cases, these two rhythmic systems are known to be coupled by specific, cross-regulatory…
Phylogenetic comparative methods (PCMs) are widely used to study trait evolution. However, many evolutionary histories involve reticulate evolutionary scenarios, such as hybridization, that violate core assumptions of these methods. In this…
Evolving biomolecular networks have to combine the stability against perturbations with flexibility allowing their constituents to assume new roles in the cell. Gene duplication followed by functional divergence of associated proteins is a…
In this work we propose a physical model of organismal evolution, where phenotype, organism life expectancy, is directly related to genotype i.e. the stability of its proteins which can be determined exactly in the model. Simulating the…
Background. The large-scale pattern of distribution of genes on the chromosomes in the known animal genomes is not well characterized. We hypothesized that individual genes will be distributed on chromosomes in a mathematically ordered…
It is suggested that the degree distribution for networks of the cell-metabolism for simple organisms reflects an ubiquitous randomness. This implies that natural selection has exerted no or very little pressure on the network degree…
Evolution has fascinated quantitative and physical scientists for decades: how can the random process of mutation, recombination, and duplication of genetic information generate the diversity of life? What determines the rate of evolution?…
Textual analysis of typical microbial genomes reveals that they have the statistical characteristics of a DNA sequence of a much shorter length. This peculiar property supports an evolutionary model in which a genome evolves by random…
Rhythmic and sequential subdivision of the elongating vertebrate embryonic body axis into morphological somites is controlled by an oscillating multicellular genetic network termed the segmentation clock. This clock operates in the…
Naturally evolving proteins gradually accumulate mutations while continuing to fold to thermodynamically stable native structures. This process of neutral protein evolution is an important mode of genetic change, and forms the basis for the…
Inference of evolutionary trees and rates from biological sequences is commonly performed using continuous-time Markov models of character change. The Markov process evolves along an unknown tree while observations arise only from the tips…
Molecular generation and molecular property prediction are both crucial for drug discovery, but they are often developed independently. Inspired by recent studies, which demonstrate that diffusion model, a prominent generative approach, can…
Statistical analysis of distributions of occurrence frequencies of short words in 108 microbial complete genomes reveals the existence of a set of universal "root-sequence lengths" shared by all microbial genomes. These lengths and their…