Related papers: Observations and perspectives on the diversificati…

A central and long-standing issue in evolutionary theory is the origin of the biological variation upon which natural selection acts1. Some hypotheses suggest that evolutionary change represents an adaptation to the surrounding environment…

We studied a relations between the triplet frequency composition of mitochondria genomes, and the phylogeny of their bearers. First, the clusters in 63dimensional space were developed due to $K$-means. Second, the clade composition of those…

The continuity of life and its evolution, we proposed, emerge from an interactive group process manifested in networks of interaction. We term this process \textit{survival-of-the-fitted}. Here, we reason that survival of the fitted results…

We present a statistical model of bacterial evolution based on the coupling between codon usage and tRNA abundance. Such a model interprets this aspect of the evolutionary process as a balance between the codon homogenization effect due to…

We have presented the basic knowledge on the structure of molecules coding the genetic information, mechanisms of transfer of this information from DNA to proteins and phenomena connected with replication of DNA. In particular, we have…

The genetic code structure into distinct multiplet-classes as well as the numeric degeneracies of the latter are revealed by a two-step process. First, an empirical inventory of the degeneracies (of the shuffled multiplets) in two specific…

In special coordinates (codon position--specific nucleotide frequencies) bacterial genomes form two straight lines in 9-dimensional space: one line for eubacterial genomes, another for archaeal genomes. All the 348 distinct bacterial…

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…

Degeneracy is a salient feature of genetic codes, because there are more codons than amino acids. The conventional table for genetic codes suffers from an inability of illustrating a symmetrical nature among genetic base codes. In fact,…

By unifying three foundational principles of modern biology, we develop a mathematical framework to analyze the growing tree of life. Contrary to the static case, where the analogy between phylogenetic trees and the tree that grows in soil…

The coding space of protein sequences is shaped by evolutionary constraints set by requirements of function and stability. We show that the coding space of a given protein family--the total number of sequences in that family--can be…

Most amino acids are encoded by multiple synonymous codons. For an amino acid, some of its synonymous codons are used much more rarely than others. Analyses of positions of such rare codons in protein sequences revealed that rare codons can…

The persistence of life requires populations to adapt at a rate commensurate with the dynamics of their environment. Successful populations that inhabit highly variable environments have evolved mechanisms to increase the likelihood of…

The interactions between DNA, RNA, and proteins are fundamental to biological processes, as illustrated by the central dogma of molecular biology. Although modern biological pre-trained models have achieved great success in analyzing these…

Given a set of species whose evolution is represented by a species tree, a gene family is a group of genes having evolved from a single ancestral gene. A gene family evolves along the branches of a species tree through various mechanisms,…

Evolution consists of distinct stages: cosmological, biological, linguistic. Since biology verges on natural sciences and linguistics, we expect that it shares structures and features from both forms of knowledge. Indeed, in DNA we…

During the course of evolution, an organism's genome can undergo changes that affect the large-scale structure of the genome. These changes include gene gain, loss, duplication, chromosome fusion, fission, and rearrangement. When gene gain…

Protein evolution involves mutations occurring across a wide range of time scales. In analogy with disordered systems in statistical physics, this dynamical heterogeneity suggests strong correlations between mutations happening at distinct…

Diversity is an important factor in evolutionary algorithms to prevent premature convergence towards a single local optimum. In order to maintain diversity throughout the process of evolution, various means exist in literature. We analyze…

Speciation is of fundamental importance to understanding the huge diversity of life on Earth. In contrast to current phenomenological models, we develop a biophysically motivated approach to study speciation involving the co-evolution of…