Results 11 to 20 of about 155,453 (213)

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

Efficient Exploration of the Space of Reconciled Gene Trees [PDF]

, 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, Daubin, Vincent, Rosikiewicz, Wojciech, Szöllősi, Gergely J., Tannier, Eric   +4 more
core   +6 more sources

Genome-scale phylogenetic analysis finds extensive gene transfer among Fungi [PDF]

, 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, Daubin, Vincent, Davín, Adrián Arellano, Szöllősi, Gergely J., Tannier, Eric   +4 more
core   +4 more sources

Plasmid copy number underlies adaptive mutability in bacteria. [PDF]

, 2014
The origin of mutations under selection has been intensively studied using the Cairns-Foster system, in which cells of an Escherichia coli lac mutant are plated on lactose and give rise to 100 Lac+ revertants over several days. These revertants have been
Aboubechara, John Paul, Maisnier-Patin, Sophie, Quiñones-Soto, Semarhy, Roth, John R, Sano, Emiko   +4 more
core   +1 more source

Inferring Species Trees from Incongruent Multi-Copy Gene Trees Using the Robinson-Foulds Distance [PDF]

, 2012
We present a new method for inferring species trees from multi-copy gene trees. Our method is based on a generalization of the Robinson-Foulds (RF) distance to multi-labeled trees (mul-trees), i.e., gene trees in which multiple leaves can have the same ...
Burleigh, J. Gordon, Chaudhary, Ruchi, Fernández-Baca, David   +2 more
core   +2 more sources

Inferring Pareto-optimal reconciliations across multiple event costs under the duplication-loss-coalescence model

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, Nuo Liu, Ran Libeskind-Hadas, Yi-Chieh Wu   +3 more
doaj   +1 more source

Mitochondrial genomes of blister beetles (Coleoptera, Meloidae) and two large intergenic spacers in Hycleus genera

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, Lifang Zhang, Ting Lu, Jingnan Ma, Chenjuan Zeng, Bisong Yue, Xiuyue Zhang   +6 more
doaj   +1 more source

Integrated pipeline for inferring the evolutionary history of a gene family embedded in the species tree: a case study on the STIMATE gene family

BMC Bioinformatics, 2017
Background Because phylogenetic inference is an important basis for answering many evolutionary problems, a large number of algorithms have been developed.
Jia Song, Sisi Zheng, Nhung Nguyen, Youjun Wang, Yubin Zhou, Kui Lin   +5 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., Du, Haijian, Lin, Wei, Pan, Hongmiao, Pan, Yongxin, Wu, Long-Fei, Xiao, Tian, Zhang, Weijia, Zhang, Wensi, Zhang, Wenyan   +9 more
core   +4 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, Kira S. Makarova, David M. Kristensen, Yuri I. Wolf, Eugene V. Koonin   +4 more
doaj   +1 more source