CORRECTION article Front. Ecol. Evol., 05 September 2023Sec. Phylogenetics, Phylogenomics, and Systematics Volume 11 - 2023 | https://doi.org/10.3389/fevo.2023.1279696

Differential coexistence among species underlies geographical patterns of biodiversity. Understanding such patterns has relied either on ecological or historical approaches applied separately. Recently, macroecology and community phylogenetics have tried to integrate both ecological and historical approaches. However, macroecology is mostly non-phylogenetic, whereas community phylogenetics is l...

It is possible to consider stochastic models of sequence evolution in phylogenetics in the context of a dynamical tensor description inspired from physics. Approaching the problem in this framework allows for the well developed methods of mathematical physics to be exploited in the biological arena. We present the tensor description of the homogeneous continuous time Markov chain model of phylo...

Maximum parsimony distance is a measure used to quantify the dissimilarity of two unrooted phylogenetic trees. It NP-hard compute, and very few positive algorithmic results are known due its complex combinatorial structure. Here we address this shortcoming by showing that problem fixed parameter tractable. We do establishing linear kernel i.e., after applying certain reduction rules resulting i...

Evaluating phylogenetics trees is an endeavor fundamental to comparative genomics and a core discipline of Bioinformatics. However, with single trees taking up to a week on the fastest processor under general models of evolution and the number of trees growing exponentially with the number of sequences analyzed, this is an exceptionally computationally intensive endeavor. There has been much wo...

A common assumption in multiple scientific applications is that the distribution of observed data can be modeled by a latent tree graphical model. An important example phylogenetics, where t...

Model selection is a topic of special relevance in molecular phylogenetics that affects many, if not all, stages of phylogenetic inference. Here we discuss some fundamental concepts and techniques of model selection in the context of phylogenetics. We start by reviewing different aspects of the selection of substitution models in phylogenetics from a theoretical, philosophical and practical poi...