Results 1 to 10 of about 103,658 (45)
The Theory of Gene Family Histories [PDF]
arXiv, 2023 Most genes are part of larger families of evolutionary related genes. The history of gene families typically involves duplications and losses of genes as well as horizontal transfers into other organisms. The reconstruction of detailed gene family histories, i.e., the precise dating of evolutionary events relative to phylogenetic tree of the underlying
arxiv
Orientation of Fitch Graphs and Detection of Horizontal Gene Transfer in Gene Trees [PDF]
arXiv, 2021 Horizontal gene transfer events partition a gene tree $T$ and thus, its leaf set into subsets of genes whose evolutionary history is described by speciation and duplication events alone. Indirect phylogenetic methods can be used to infer such partitions $\mathcal{P}$ from sequence similarity or evolutionary distances without any a priory knowledge ...
arxiv
A probabilistic model for gene content evolution with duplication, loss, and horizontal transfer [PDF]
, 2005 We introduce a Markov model for the evolution of a gene family along a phylogeny. The model includes parameters for the rates of horizontal gene transfer, gene duplication, and gene loss, in addition to branch lengths in the phylogeny. The likelihood for the changes in the size of a gene family across different organisms can be calculated in O(N+hM^2 ...
arxiv +1 more source
Impact of the horizontal gene transfer on the evolutionary equilibria of a population [PDF]
arXiv, 2023 How does the interplay between selection, mutation and horizontal gene transfer modify the phenotypic distribution of a bacterial or cell population? While horizontal gene transfer, which corresponds to the exchange of genetic material between individuals, has a major role in the adaptation of many organisms, its impact on the phenotypic density of ...
arxiv
Adaptive evolution of hybrid bacteria by horizontal gene transfer [PDF]
, 2020 Horizontal gene transfer is an important factor in bacterial evolution that can act across species boundaries. Yet, we know little about rate and genomic targets of cross-lineage gene transfer, and about its effects on the recipient organism's physiology and fitness.
arxiv +1 more source
Inferring multiple consensus trees and supertrees using clustering: a review [PDF]
arXiv, 2023 Phylogenetic trees (i.e. evolutionary trees, additive trees or X-trees) play a key role in the processes of modeling and representing species evolution. Genome evolution of a given group of species is usually modeled by a species phylogenetic tree that represents the main patterns of vertical descent. However, the evolution of each gene is unique.
arxiv
Quasispecies Theory for Horizontal Gene Transfer and Recombination [PDF]
, 2008 We introduce a generalization of the parallel, or Crow-Kimura, and Eigen models of molecular evolution to represent the exchange of genetic information between individuals in a population. We study the effect of different schemes of genetic recombination on the steady-state mean fitness and distribution of individuals in the population, through an ...
arxiv +1 more source
Gene cluster analysis method reliably identifies horizontally transferred genes and reveals their involvement in operon formation [PDF]
arXiv, 2006 The formation mechanism of operons remains controversial despite the proposal of many models. Although acquisition of genes from other species, horizontal gene transfer, is considered to occur, definitive concrete cases have been unavailable. It is desirable to select horizontally transferred genes reliably and examine their relationship to operons. We
arxiv
The infinitely many genes model with horizontal gene transfer [PDF]
arXiv, 2013 The genome of bacterial species is much more flexible than that of eukaryotes. Moreover, the distributed genome hypothesis for bacteria states that the total number of genes present in a bacterial population is greater than the genome of every single individual. The pangenome, i.e.
arxiv
Supra-operonic clusters of functionally related genes (SOCs) are a source of horizontal gene co-transfers [PDF]
arXiv, 2016 Adaptation of bacteria occurs predominantly via horizontal gene transfer (HGT). While it is widely recognized that horizontal acquisitions frequently encompass multiple genes, it is unclear what the size distribution of successfully transferred DNA segments looks like and what evolutionary forces shape this distribution.
arxiv