相关论文: Recovering the tree-like trend of evolution despit…

In phylogenetic studies, the evolution of molecular sequences is assumed to have taken place along the phylogeny traced by the ancestors of extant species. In the presence of lateral gene transfer (LGT), however, this may not be the case,…

A major problem for inferring species trees from gene trees is that evolutionary processes can sometimes favour gene tree topologies that conflict with an underlying species tree. In the case of incomplete lineage sorting, this phenomenon…

Reconstructing the tree of life from molecular sequences is a fundamental problem in computational biology. Modern data sets often contain a large number of genes, which can complicate the reconstruction problem due to the fact that…

The complex pattern of presence and absence of many genes across different species provides tantalising clues as to how genes evolved through the processes of gene genesis, gene loss and lateral gene transfer (LGT). The extent of LGT,…

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…

Hybrid evolution and horizontal gene transfer (HGT) are processes where evolutionary relationships may more accurately be described by a reticulated network than by a tree. In such a network, there will often be several paths between any…

Horizontal gene transfer (HGT) is an important process in bacterial evolution. Current phylogeny-based approaches to capture it cannot however appropriately account for the fact that HGT can occur between bacteria living in different…

Phylogenetic trees illustrate the evolutionary history of genes and species. In most cases, although genes evolve along with the species they belong to, a species tree and gene tree are not identical, because of evolutionary events at the…

The transfer of genetic materials across species (lateral genetic transfer, LGT) contributes to genomic and physiological innovation in prokaryotes. The extent of LGT in prokaryotes has been examined in a number of studies, but the unit of…

Background. Models of ancestral gene order reconstruction have progressively integrated different evolutionary patterns and processes such as unequal gene content, gene duplications, and implicitly sequence evolution via reconciled gene…

Evolutionary events such as incomplete lineage sorting and lateral gene transfer constitute major problems for inferring species trees from gene trees, as they can sometimes lead to gene trees which conflict with the underlying species…

Lateral transfer, a process whereby species exchange evolutionary traits through non-ancestral relationships, is a frequent source of model misspecification in phylogenetic inference. Lateral transfer obscures the phylogenetic signal in the…

Phylogenetic trees are simple models of evolutionary processes. They describe conditionally independent divergent evolution of taxa from common ancestors. Phylogenetic trees commonly do not have enough flexibility to adequately model all…

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…

Orthology and paralogy relations are often inferred by methods based on gene similarity, which usually yield a graph depicting the relationships between gene pairs. Such relation graphs are known to frequently contain errors, as they cannot…

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…

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,…

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 widespread presence of antibiotic resistance and virulence among Staphylococcus isolates has been attributed to lateral genetic transfer (LGT) between different strains or species. However, there has been very little study of the extent…

Several implicit methods to infer Horizontal Gene Transfer (HGT) focus on pairs of genes that have diverged only after the divergence of the two species in which the genes reside. This situation defines the edge set of a graph, the…