Basic phylogenetics and associated "tree thinking" are often minimized or excluded in formal school curricula. Informal settings provide an opportunity to extend the K-12 school curriculum, introducing learners to new ideas, piquing interest in science, and fostering scientific literacy. Similarly, university researchers participating in science, technology, engineering, and mathematics (STEM) ...

Phylogenetics is the area of research concerned with finding the genetic relationships between species. The basic idea is to compare specific characters (features) of the species, under the natural assumption that similar species (i.e., species with similar characters) are genetically close. The term phylogeny refers to these relationships, usually presented as a phylogenetic tree (see Figures ...

A new species, Geastrum juliae, is described from Primorsky Krai in the Russian Far East. Based on analysis of sequences retrieved GenBank, this taxon also found China. The closest species G. rubellum based morphology and phylogenetics. We present with illustrated descriptions molecular data.

HIV continues to spread among vulnerable heterosexual (HET), Men-having-Sex with Men (MSM) and intravenous drug user (IDU) populations, influenced by a complex array of biological, behavioral and societal factors. Phylogenetics analyses of large sequence datasets from national drug resistance testing programs reveal the evolutionary interrelationships of viral strains implicated in the dynamic ...

UNLABELLED Analysis of Phylogenetics and Evolution (APE) is a package written in the R language for use in molecular evolution and phylogenetics. APE provides both utility functions for reading and writing data and manipulating phylogenetic trees, as well as several advanced methods for phylogenetic and evolutionary analysis (e.g. comparative and population genetic methods). APE takes advantage...

Phylogenetics has seen a steady increase in data set size and substitution model complexity, which require increasing amounts of computational power to compute likelihoods. This motivates strategies to approximate the likelihood functions for branch length optimization and Bayesian sampling. In this article, we develop an approximation to the 1D likelihood function as parametrized by a single b...

Recently we employed phylogenetics to predict that the cellular interpretation of TGF-β signals is modulated by monoubiquitylation cycles affecting the Smad4 signal transducer/tumor suppressor. This prediction was subsequently validated by experiments in flies, frogs and mammalian cells. Here we apply a phylogenetic approach to the Hippo pathway and predict that two of its signal transducers, S...

Phylogenetic reconstruction methods are subject to two types of limitations: our knowledge about the true history of organisms and the gross simplification implied in the numerical simulation models of the relationships between them. In such a situation, experimental phylogenetics provides a way to assess the accuracy of the phylogenetic reconstruction methods. Nonetheless, this capacity is onl...

Recent advances in the field of plant community phylogenetics and invasion phylogenetics are mostly based on plot-level data, which do not take into consideration the spatial arrangement of individual plants within the plot. Here we use within-plot plant coordinates to investigate the link between the physical distance separating plants, and their phylogenetic relatedness. We look at two vegeta...

Bayesian inference methods rely on numerical algorithms for both model selection and parameter inference. In general, these algorithms require a high computational effort to yield reliable inferences. One of the major challenges in phylogenetics regards the estimation of the marginal likelihood. This quantity is commonly used for comparing different evolutionary models, but its calculation, eve...