Related papers: Are there laws of genome evolution?
Scaling laws illuminate Nature's fundamental biological principles and guide bioinspired materials and structural designs. In simple cases they are based on the fundamental principle that all laws of nature remain unchanged (i.e.,…
The main statistical distributions applicable to the analysis of genome architecture and genome tracks are briefly discussed and critically assessed. Although the observed features in distributions of element lengths can be equally well…
We study the stochastic dynamics of sequences evolving by single site mutations, segmental duplications, deletions, and random insertions. These processes are relevant for the evolution of genomic DNA. They define a universality class of…
There is an intrinsic relationship between the molecular evolution in primordial period and the properties of genomes and proteomes of contemporary species. The genomic data may help us understand the driving force of evolution of life at…
Selection, the tendency of some traits to become more frequent than others in a population under the influence of some (natural or artificial) agency, is a key component of Darwinian evolution and countless other natural and social…
We found that models of evolving random networks exhibit dynamic scaling similar to scaling of growing surfaces. It is demonstrated by numerical simulations of two variants of the model in which nodes are added as well as removed [Phys.…
Just as physicists strive to develop a TOE (theory of everything), which explains and unifies the physical laws of the universe, the life-scientist wishes to uncover the TOE as it relates to cellular systems. This can only be achieved with…
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…
One of the most intriguing questions in evolution is how organisms exhibit suitable phenotypic variation to rapidly adapt in novel selective environments which is crucial for evolvability. Recent work showed that when selective environments…
We introduce a new model of evolution on a fitness landscape possessing a tunable degree of neutrality. The model allows us to study the general properties of molecular species undergoing neutral evolution. We find that a number of…
Based on statistical analysis of the complete genome sequences, a remote relationship has been observed between the evolution of the genetic code and the three domain tree of life. The existence of such a remote relationship need to be…
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…
Biologists have long sought a way to explain how statistical properties of genetic sequences emerged and are maintained through evolution. On the one hand, non-random structures at different scales indicate a complex genome organisation. On…
The formation of DNA loops by proteins and protein complexes is ubiquitous to many fundamental cellular processes, including transcription, recombination, and replication. Here we review recent advances in understanding the properties of…
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…
We propose a principle of consistency between different hierarchical levels of biological systems. Given a consistency between molecule replication and cell reproduction, universal statistical laws on cellular chemical abundances are…
In the present article the recent works to formulate laws in Darwinian evolutionary dynamics are discussed. Although there is a strong consensus that general laws in biology may exist, opinions opposing such suggestion are abundant. Based…
Protein domains are found on genomes with notable statistical distributions, which bear a high degree of similarity. Previous work has shown how these distributions can be accounted for by simple models, where the main ingredients are…
If a cultural feature is transmitted over generations and exposed to stochastic selection when spreading in a population, its evolution may be governed by statistical laws and be partly predictable, as in the case of genetic evolution.…
One of the basic questions of phylogenomics is how gene function evolves, whether among species or inside gene families. In this chapter, we provide a brief overview of the problems associated with defining gene function in a manner which…