Complementary Theory of Evolutionary Genetics [PDF]
arXiv, 2021 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 non-Mendelian and Mendelian variation, respectively. The emergence and maintenance of species as groups of populations are
arxiv
Comparison of tRNA and rRNA Phylogenies in Proteobacteria: Implications for the Frequency of Horizontal Gene Transfer [PDF]
arXiv, 2004 The current picture of bacterial evolution is based largely on studies of 16S rRNA. However, this is just one gene. It is known that horizontal gene transfer can occur between bacterial species, although the frequency and implications of this are not fully understood.
arxiv
From gene trees to species trees II: Species tree inference in the deep coalescence model [PDF]
arXiv, 2010 When gene copies are sampled from various species, the resulting gene tree might disagree with the containing species tree. The primary causes of gene tree and species tree discord include lineage sorting, horizontal gene transfer, and gene duplication and loss.
arxiv
Evolution of bacterial genomes under horizontal gene transfer [PDF]
arXiv, 2011 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 gene content. This huge variation in gene content led to the concepts of the distributed genome of bacteria and their
arxiv
Counting and sampling gene family evolutionary histories in the duplication-loss and duplication-loss-transfer models [PDF]
arXiv, 2019 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, including - but not limited to - speciation, gene duplication, gene loss, horizontal gene transfer.
arxiv
Normalizing Kernels in the Billera-Holmes-Vogtmann Treespace [PDF]
arXiv, 2015 As costs of genome sequencing have dropped precipitously, development of efficient bioinformatic methods to analyze genome structure and evolution have become ever more urgent. For example, most published phylogenomic studies involve either massive concatenation of sequences, or informal comparisons of phylogenies inferred on a small subset of ...
arxiv
The Gossip Paradox: why do bacteria share genes? [PDF]
arXiv, 2020 Bacteria, in contrast to eukaryotic cells contain two types of genes: chromosomal genes that are fixed to the cell, and plasmids that are mobile genes, easily shared to other cells. The sharing of plasmid genes between individual bacteria and between bacterial lineages has contributed vastly to bacterial evolution, allowing specialized traits to `jump ...
arxiv
The inference of gene trees with species trees [PDF]
arXiv, 2013 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 tightly linked, they are seldom identical, because genes duplicate, are lost or horizontally transferred, and ...
arxiv
Novel gene cluster analysis method identifies horizontally transferred genes with high reliability and reveals their involvement in operon formation [PDF]
arXiv, 2005 This paper was withdrawn by the authors.
arxiv
kdetrees: Nonparametric Estimation of Phylogenetic Tree Distributions [PDF]
arXiv, 2013 Motivation: While the majority of gene histories found in a clade of organisms are expected to be generated by a common process (e.g. the coalescent process), it is well-known that numerous other coexisting processes (e.g. horizontal gene transfers, gene duplication and subsequent neofunctionalization) will cause some genes to exhibit a history quite ...
arxiv