Relative evolutionary rate inference in HyPhy with LEISR. The results provided by the new method can be used to represent the inferred conflicting signals by means of explicit and easy-to-interpret phylogenetic networks. Conclusions Our weighted consensus network inference method allows one to infer, visualize and validate statistically major conflicting signals induced by the mechanisms of reticulate evolution. We successfully tested our method on some synthetic and real datasets to infer the above-mentioned evolutionary events which may have influenced the evolution of many species. Results We provide a way of building a weighted phylogenetic network for each of the following reticulation mechanisms: diploid hybridization, intragenic recombination and complete or partial horizontal gene transfer. Methods To tackle this problem, we hereby describe a new method for inferring and representing alternative (reticulate) evolutionary histories of species as an explicit weighted consensus network which can be constructed from a collection of gene trees with or without prior knowledge of the species phylogeny. However, several reticulate evolution processes, such as horizontal gene transfer and hybridization, have been shown to blur the species evolutionary history by causing discordance among phylogenies inferred from different genes. Inferring explicit weighted consensus networks to represent alternative evolutionary historiesīackground The advent of molecular biology techniques and constant increase in availability of genetic material have triggered the development of many phylogenetic tree inference methods. Copyright © 2011 Cognitive Science Society, Inc. Implications for introducing tree thinking into biology curricula are discussed. The results illuminate students' misconceptions concerning common taxa and constraints on their willingness to override faulty knowledge when given appropriate evolutionary evidence. The effect of providing cladograms depended on students' background in biology. Some subjects received cladograms (hierarchical diagrams) depicting the evolutionary relationships among the taxa. Experiment 2, with 10th graders, also included triads involving mammals, birds, and snakes/crocodilians (birds and snakes/crocodilians are most closely related). Experiment 1 and its follow-up, with college students, used triads involving amphibians, reptiles, and mammals (reptiles and mammals are most closely related evolutionarily) and plants, fungi, and animals (fungi are more closely related to animals than to plants). Subjects were told that different enzymes help regulate cell function in two taxa and asked which enzyme a third taxon most likely uses.
Three experiments, adopting an evolutionary biology perspective, investigated subjects' inferences about living things.
Novick, Laura R Catley, Kefyn M Funk, Daniel J Inference is bliss: using evolutionary relationship to guide categorical inferences.
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