Related papers: Two Major Paths of Gene-Duplicates Evolution
Maintaining genetic diversity as a means to avoid premature convergence is critical in Genetic Programming. Several approaches have been proposed to achieve this, with some focusing on the mating phase from coupling dissimilar solutions to…
This work illustrates potentials for recognition within {\em ad hoc} sensor networks if their nodes possess individual inter-related biologically inspired genetic codes. The work takes ideas from natural immune systems protecting organisms…
Our understanding of the evolutionary process has gone a long way since the publication, 150 years ago, of "On the origin of species" by Charles R. Darwin. The XXth Century witnessed great efforts to embrace replication, mutation, and…
In eukaryotes, DNA replication is initiated along each chromosome at multiple sites called replication origins. Locally, each replication origin is "licensed", or specified, at the end of the M and the beginning of G1 phases of the cell…
Despite the greater functional importance of protein levels, our knowledge of gene expression evolution is based almost entirely on studies of mRNA levels. In contrast, our understanding of how translational regulation evolves has lagged…
Cells often exhibit different and stable phenotypes from the same DNA sequence. Robustness and plasticity of such cellular states are controlled by diverse transcriptional and epigenetic mechanisms, among them the modification of…
Genetic redundancy is ubiquitous and can be found in any organism. However, it has been argued that genetic redundancy reduces total population fitness, and therefore, redundancy is unlikely to evolve. In this letter, we study an…
The evolution of the full repertoire of proteins encoded in a given genome is mostly driven by gene duplications, deletions, and sequence modifications of existing proteins. Indirect information about relative rates and other intrinsic…
Different evolutionary models are known to make disparate predictions for the success of an invading mutant in some situations. For example, some evolutionary mechanics lead to amplification of selection in structured populations, while…
Recurrent mutations are a common phenomenon in population genetics. They may be at the origin of the fixation of a new genotype, if they give a phenotypic advantage to the carriers of the new mutation. In this paper, we are interested in…
When mutation rates are low, natural selection remains effective, and increasing the mutation rate can give rise to an increase in adaptation rate. When mutation rates are high to begin with, however, increasing the mutation rate may have a…
Stronger selection implies faster evolution---that is, the greater the force, the faster the change. This apparently self-evident proposition, however, is derived under the assumption that genetic variation within a population is primarily…
Segmental duplications (SDs), or low-copy repeats (LCR), are segments of DNA greater than 1 Kbp with high sequence identity that are copied to other regions of the genome. SDs are among the most important sources of evolution, a common…
Models of codon evolution are commonly used to identify positive selection. Positive selection is typically a heterogeneous process, i.e., it acts on some branches of the evolutionary tree and not others. Previous work on DNA models showed…
Although the role of lateral gene transfer is well recognized in the evolution of bacteria, it is generally assumed that it has had less influence among eukaryotes. To explore this hypothesis we compare the dynamics of genome evolution in…
Most living systems rely on double-stranded DNA (dsDNA) to store their genetic information and perpetuate themselves. This biological information has been considered the main target of evolution. However, here we show that symmetries and…
Unraveling the evolutionary forces shaping bacterial diversity can today be tackled using a growing amount of genomic data. While the genome of eukaryotes is highly stable, bacterial genomes from cells of the same species highly vary in…
The relationship between genotype and phenotype plays a crucial role in determining the function and robustness of biological systems. Here the evolution progresses through the change in genotype, whereas the selection is based on the…
A major goal of molecular evolutionary biology is to identify loci or regions of the genome under selection versus those evolving in a neutral manner. Correct identification allows accurate inference of the evolutionary process and thus…
Genomic duplication-divergence events, which are the primary source of new protein functions, occur stochastically at a wide range of genomic scales, from single gene to whole genome duplications. Clearly, this fundamental evolutionary…