Results 11 to 20 of about 209,245 (257)
BMC Bioinformatics, 2019 Background Reconciliation methods are widely used to explain incongruence between a gene tree and species tree. However, the common approach of inferring maximum parsimony reconciliations (MPRs) relies on user-defined costs for each type of event, which ...
Ross Mawhorter +3 more
doaj +2 more sources
Genome-scale phylogenetic analysis finds extensive gene transfer among Fungi [PDF]
Philosophical Transactions of the Royal Society B: Biological Sciences, 2015 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.
Boussau, Bastien +4 more
core +6 more sources
Efficient Exploration of the Space of Reconciled Gene Trees [PDF]
Systematic Biology, 2013 Gene trees record the combination of gene level events, such as duplication, transfer and loss, and species level events, such as speciation and extinction.
Boussau, Bastien +4 more
core +8 more sources
Host-symbiont-gene phylogenetic reconciliation
Peer Community Journal, 2023 Motivation Biological systems are made of entities organized at different scales (e.g. macro-organisms, symbionts, genes…) which evolve in interaction. These interactions range from independence or conflict to cooperation and coevolution, which results ...
Menet, Hugo +3 more
doaj +2 more sources
Reconstruction of the evolution of microbial defense systems
BMC Evolutionary Biology, 2017 Background Evolution of bacterial and archaeal genomes is a highly dynamic process that involves intensive loss of genes as well as gene gain via horizontal transfer, with a lesser contribution from gene duplication.
Pere Puigbò +4 more
doaj +2 more sources
AleRax: a tool for gene and species tree co-estimation and reconciliation under a probabilistic model of gene duplication, transfer, and loss [PDF]
bioRxiv, 2023 Motivation Genomes are a rich source of information on the pattern and process of evolution across biological scales. How best to make use of that information is an active area of research in phylogenetics.
Benoît Morel +3 more
openalex +2 more sources
SimPhy: Phylogenomic Simulation of Gene, Locus, and Species Trees
bioRxiv, 2015 We present a fast and flexible software package--SimPhy--for the simulation of multiple gene families evolving under incomplete lineage sorting, gene duplication and loss, horizontal gene transfer--all three potentially leading to species tree/gene tree ...
De Oliveira Martins, L +2 more
core +3 more sources
Hierarchical clustering of maximum parsimony reconciliations
BMC Bioinformatics, 2019 Background Maximum parsimony reconciliation in the duplication-transfer-loss model is a widely-used method for analyzing the evolutionary histories of pairs of entities such as hosts and parasites, symbiont species, and species and genes. While efficient
Ross Mawhorter, Ran Libeskind-Hadas
doaj +1 more source
BMC Genomics, 2017 Background Insect mitochondrial genomes (mitogenomes) exhibit high diversity in some lineages. The gene rearrangement and large intergenic spacer (IGS) have been reported in several Coleopteran species, although very little is known about mitogenomes of ...
Chao Du +6 more
doaj +1 more source
Magnetosome Gene Duplication as an Important Driver in the Evolution of Magnetotaxis in the Alphaproteobacteria [PDF]
, 2019 The evolution of microbial magnetoreception (or magnetotaxis) is of great interest in the fields of microbiology, evolutionary biology, biophysics, geomicrobiology, and geochemistry.
Bazylinski, Dennis A. +9 more
core +4 more sources