Phylogenetics ja dating

Introduction. Molecular phylogenetics has greatly improved our understanding of the evolution of monocotyledoneous plants. Nearly all studies have found support for monocots as a monophyletic group (e.g. Chase et al., 1993), and one found them well supported as sister to Ceratophyllum L. and eudicots (Saarela et al., 2007).APG III recognized 77 monocot families in 11 orders; Dasypogonaceae ... Author summary HIV-1 infected individuals rarely know when they became infected but knowing when an infection occurred provides critical information regarding HIV-1 pathogenesis and epidemiology. Using a unique cohort in which infection was known to have occurred in a narrow interval, we investigated methods to estimate the timing of infections. Several methods suggested that HIV-1 infection ... An exciting recent development is the merging of phylogenetics and genomics. Phylogenetic hypotheses have become the framework for the choice of organisms in genomic analyses, and more and more molecular biologists are using phylogenetic trees to guide their sampling of taxa for comparative research. This trend will continue. iii Chapter 1. Mating System Evolution in the Southern South American Radiation of Valeriana (Valerianaceae) 1 Chapter 2. Exploring the Utility of Next-generation Genomic Sequence Data on Inferring Relationships Among the Southern South American Valerians 21 Works Cited 40 Vita 47 The evolutionary analysis of molecular sequence variation is a statistical enterprise. This is reflected in the increased use of probabilistic models for phylogenetic inference, multiple sequence alignment, and molecular population genetics. Here we present BEAST: a fast, flexible software architecture for Bayesian analysis of molecular sequences related by an evolutionary tree. Bayesian tip-dating methods used frequently in phylogenetics are employed to resolve this debate. Bayes factors are used to compare the results of analyses incorporating tip age priors based on different stratigraphic hypotheses, to show which stratigraphic scheme best fits the morphological data and phylogeny. Bayesian tip-dating approaches allow for the uncertainty in phylogenetic placement of fossil taxa to be accounted for by simultaneously inferring the placement of fossil taxa and using them to calibrate the phylogeny (Pyron, 2011; Ronquist et al., 2012a). Butterflies of the subtribe Mycalesina (Nymphalidae: Satyrinae) are important model organisms in ecology and evolution. This group has radiated spectacularly in the Old World tropics and presents an exciting opportunity to better understand processes of invertebrate rapid radiations. However, the generic-level taxonomy of the subtribe has been in a constant state of flux, and relationships ... Dating the human-ape. ... Sullivan J, Markert JA, Kilpatrick CW. 1997. ... and review methods that have been applied to model selection in phylogenetics: likelihood-ratio tests, AIC, BIC, and ... Doyle JA, Sauquet H, Scharaschkin T, Le Thomas A: Phylogeny, molecular and fossil dating, and biogeographic history of Annonaceae and Myristicaceae (Magnoliales). Int J Plant Sci. 2004, 165: S55-S67. 10.1086/421068. Article; CAS; Google Scholar

BEAST: Bayesian evolutionary analysis by sampling trees ...