Related papers: DNA Replication Timing, Genome Stability and Non-a…
Most non-synonymous mutations are thought to be deleterious because of their effect on protein sequence. These polymorphisms are expected to be removed or kept at low frequency by the action of natural selection, and rare deleterious…
Mutational robustness quantifies the effect of random mutations on fitness. When mutational robustness is high, most mutations do not change fitness or have only a minor effect on it. From the point of view of fitness landscapes, robust…
Within the framework of population genetics we consider the evolution of an asexual haploid population under the effect of a rapidly varying natural selection (microevolution). We focus on the case in which the environment exerting…
We introduce a family of models incorporating random segmental substitutions and point mutations and demonstrate that such models reproduce algebraic length distributions of exact matches with the slope $-4$ observed earlier in pairwise…
The ratio of non-synonymous to synonymous substitutions $\omega(=d_{N}/d_{S})$ has been widely used as a measure of adaptive evolution in protein coding genes. Omega can be defined in terms of population genetics parameters as the fixation…
How mutations accumulate in genomes is the central question of molecular evolution theories, however our understanding of this process is far from complete. Drake's rule is a notoriously universal property of genomes from microbes to…
Gene expression levels exhibit stochastic variations among genetically identical organisms under the same environmental conditions (called gene expression "noise" or phenotype "fluctuation"). In yeast and Escherichia coli, positive…
Many biological populations exhibit diversity in their strategy for survival and reproduction in a given environment, and microbes are an example. We explore the fate of different strategies under sustained environmental change by…
The relationship between sequences and secondary structures or shapes in RNA exhibits robust statistical properties summarized by three notions: (1) the notion of a typical shape (that among all sequences of fixed length certain shapes are…
We consider the accumulation of beneficial and deleterious mutations in large asexual populations. The rate of adaptation is affected by the total mutation rate, proportion of beneficial mutations and population size $N$. We show that…
Evolution on neutral networks of genotypes has been found in models to concentrate on genotypes with high mutational robustness, to a degree determined by the topology of the network. Here analysis is generalized beyond neutral networks to…
Selection in a time-periodic environment is modeled via the continuous-time two-player replicator dynamics, which for symmetric pay-offs reduces to the Fisher equation of mathematical genetics. For a sufficiently rapid and cyclic…
DNA is emerging as an increasingly attractive medium for data storage due to a number of important and unique advantages it offers, most notably the unprecedented durability and density. While the technology is evolving rapidly, the…
This study presents the first global, 1 Mbp level analysis of patterns of nucleotide substitutions along the human lineage. The study is based on the analysis of a large amount of repetitive elements deposited into the human genome since…
The origin and organizing principles of the genetic code remain fundamental puzzles in life science. The vanishingly low probability of the natural codon-to-amino acid mapping arising by chance has spurred the hypothesis that its structure…
The PHASE software package allows phylogenetic tree construction with a number of evolutionary models designed specifically for use with RNA sequences that have conserved secondary structure. Evolution in the paired regions of RNAs occurs…
Cell reproduction involves replication of diverse molecule species, in contrast to simple replication system with fewer components. Here, we address why such diversity is sustained despite the efficiency of simple replication systems, using…
This theory seeks to define species and to explore evolutionary forces and genetic elements in speciation and species maintenance. The theory explains how speciation and species maintenance are caused by natural selection acting on…
Background: Acceleration of adaptation dynamics by stress-induced hypermutation has been found experimentally. Evolved evolvability is a prominent explanation. We investigate a more generally applicable explanation by a physical constraint.…
Gene gains and losses have shaped the gene repertoire of species since the universal last common ancestor to species today. Genes in extant species were gained at different historical times via de novo creation of new genes, duplication of…