Maximum parsimony reconciliation in the DTLOR model [PDF]
BMC Bioinformatics, 2021 Background Analyses of microbial evolution often use reconciliation methods. However, the standard duplication-transfer-loss (DTL) model does not account for the fact that species trees are often not fully sampled and thus, from the perspective of ...
Jingyi Liu +5 more
doaj +5 more sources
Hierarchical clustering of maximum parsimony reconciliations [PDF]
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 +5 more sources
On the computational complexity of the maximum parsimony reconciliation problem in the duplication-loss-coalescence model [PDF]
Algorithms for Molecular Biology, 2017 Phylogenetic tree reconciliation is a widely-used method for inferring the evolutionary histories of genes and species. In the duplication-loss-coalescence (DLC) model, we seek a reconciliation that explains the incongruence between a gene and species tree using gene duplication, loss, and deep coalescence events.
Daniel Bork +4 more
europepmc +5 more sources
Phylogenetic analysis of seven WRKY genes across the palm subtribe Attaleinae (Arecaceae) [corrected] identifies Syagrus as sister group of the coconut. [PDF]
PLoS ONE, 2009 BACKGROUND:The Cocoseae is one of 13 tribes of Arecaceae subfam. Arecoideae, and contains a number of palms with significant economic importance, including the monotypic and pantropical Cocos nucifera L., the coconut, the origins of which have been one ...
Alan W Meerow +9 more
doaj +1 more source
Feasibility of nuclear ribosomal region ITS1 over ITS2 in barcoding taxonomically challenging genera of subtribe Cassiinae (Fabaceae) [PDF]
PeerJ, 2016 Premise of the Study The internal transcribed spacer (ITS) region is situated between 18S and 26S in a polycistronic rRNA precursor transcript. It had been proved to be the most commonly sequenced region across plant species to resolve phylogenetic ...
Priyanka Mishra +4 more
doaj +2 more sources
Bacterial microevolution and the Pangenome [PDF]
, 2020 The comparison of multiple genome sequences sampled from a bacterial population reveals considerable diversity in both the core and the accessory parts of the pangenome.
A Bankevich +68 more
core +1 more source
The inference of gene trees with species trees [PDF]
, 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,
Bastien Boussau +4 more
core +6 more sources
Assessing the robustness of parsimonious predictions for gene neighborhoods from reconciled phylogenies [PDF]
, 2015 The availability of a large number of assembled genomes opens the way to study the evolution of syntenic character within a phylogenetic context. The DeCo algorithm, recently introduced by B{\'e}rard et al.
Chauve, Cedric +2 more
core +5 more sources
On the origin of Halipeurus heraldicus on Round Island petrels: cophylogenetic relationships between petrels and their chewing lice [PDF]
, 2010 Lice phylogenetic relationships have often been used to elucidate host relationships and vice versa. In this study, we investigate the louse genus Halipeurus which parasitizes bird hosts in the families Procellariidae, Hydrobatidae and Pelecanoididae ...
Brown, R. +4 more
core +1 more source
Pareto-optimal phylogenetic tree reconciliation [PDF]
, 2014 Motivation: Phylogenetic tree reconciliation is a widely used method for reconstructing the evolutionary histories of gene families and species, hosts and parasites and other dependent pairs of entities.
Bansal, Mukul S. +4 more
core +1 more source