Isoprenyl diphosphate synthases: Protein sequence comparisons, a phylogenetic tree, and predictions of secondary structure [PDF]
, 1994 Anjun Chen +2 more
openalex +1 more source
Endosymbiotic ratchet accelerates divergence after organelle origin
BioEssays, Volume 45, Issue 1, January 2023., 2023 Primary endosymbiosis gave rise to mitochondria and plastids. The proximate impacts of organelle origin on lineage evolution have not been addressed at the population level. Using data from the photosynthetic amoeba Paulinella, we hypothesize that primary endosymbiosis accelerates lineage divergence, a process we refer to as the endosymbiotic ratchet ...
Debashish Bhattacharya +3 more
wiley +1 more source
Nonbinary tree-based phylogenetic networks [PDF]
arXiv, 2016 Rooted phylogenetic networks are used to describe evolutionary histories that contain non-treelike evolutionary events such as hybridization and horizontal gene transfer. In some cases, such histories can be described by a phylogenetic base-tree with additional linking arcs, which can for example represent gene transfer events.
arxiv
A randomisation test of the null hypothesis that two cladograms are sample estimates of a parametric phylogenetic tree [PDF]
, 1993 Allen G. Rodrigo +3 more
openalex +1 more source
Taxonomic colouring of phylogenetic trees of protein sequences
BMC Bioinformatics, 2006 Background Phylogenetic analyses of protein families are used to define the evolutionary relationships between homologous proteins. The interpretation of protein-sequence phylogenetic trees requires the examination of the taxonomic properties of the ...
Andrade-Navarro Miguel A +2 more
doaj +1 more source
Syntactic Phylogenetic Trees [PDF]
arXiv, 2016 In this paper we identify several serious problems that arise in the use of syntactic data from the SSWL database for the purpose of computational phylogenetic reconstruction. We show that the most naive approach fails to produce reliable linguistic phylogenetic trees. We identify some of the sources of the observed problems and we discuss how they may
arxiv
Reliable estimation of tree branch lengths using deep neural networks.
PLoS Computational BiologyA phylogenetic tree represents hypothesized evolutionary history for a set of taxa. Besides the branching patterns (i.e., tree topology), phylogenies contain information about the evolutionary distances (i.e. branch lengths) between all taxa in the tree,
Anton Suvorov, Daniel R Schrider
doaj +1 more source
Bridging the gap between rooted and unrooted phylogenetic networks [PDF]
arXiv, 2015 The need for structures capable of accommodating complex evolutionary signals such as those found in, for example, wheat has fueled research into phylogenetic networks. Such structures generalize the standard phylogenetic tree model by also allowing cycles and have been introduced in rooted and unrooted form. In contrast to phylogenetic trees, however,
arxiv
Rapid Evaluation of Least-Squares and Minimum-Evolution Criteria on Phylogenetic Trees [PDF]
, 1998 David Bryant, Peter J. Waddell
openalex +1 more source
Multiple local maxima for likelihoods of phylogenetic trees: a simulation study [PDF]
, 1999 James S. Rogers, David L. Swofford
openalex +1 more source