PPT-Full modeling versus summarizing gene-tree uncertainty: Met

LL Knowles et al Molecular Phylogenetics and Evolution 65 2012 501509 Full modeling versus summarizing genetree uncertainty Method choice and speciestree accuracy a Estimate . All these partitioned analyses of concatenated data sets make the assumption . t. hat all the genes share a common gene tree.. However there are several important reasons that phylogeny estimates from separate genes might be incongruent.. Horizontal Gene Transfer. Fan Ge, Li-San Wang, . Junhyong. Kim. Mourya Vardhan. Outline . Controversy : The extent of HGT affecting the core genealogical history. Examination of this controversy by assessing the extent among core orthologous genes . Consider a strictly asexual group.. Must . the true tree for all positions in the genome be concordant? Why? . Yes, because they are physically linked to one another. Yes, because inheritance is uniparental. s. tudent evaluations. Please follow this link to the on-line surveys . that . are open for you this semester.. . the gradualist point of view. Evolution occurs within populations where the fittest organisms have a selective advantage. Over time the advantages genes become fixed in a population and the population gradually changes. . Master Thesis . By. Ashu Gupta. 1. Phylogenetic Pipeline . Most common pipeline using summary method. Step 1: Get gene alignments from sequence data (e.g. . Prank. , . MAFFT. , etc.). Step 2: Get gene trees from gene alignments (e.g. . US Forest Service, Pacific Northwest Research Station. Building a Common Vocabulary. model. model. L. . modus. : mode, measure. model. conceptual. diagrammatic. mathematical. computational. Hall, C. A. S., and J. W. Day. 1977. Systems and models: terms and basic principles. . Tandy Warnow. Joint work with . Siavash. . Mirarab. , . Md. S. . Bayzid. , and others. Orangutan. Gorilla. Chimpanzee. Human. From the Tree of the Life Website. ,. . University . of . Arizona. Dates from Lock et al. Nature, 2011. Tandy Warnow. The University of Texas at Austin. Orangutan. Gorilla. Chimpanzee. Human. From the Tree of the Life Website,. University of Arizona. Phylogeny. (evolutionary tree). Applications. . of Phylogeny Estimation . Structure dictates function . Prokaryotic transcription is simpler. DNA exists in one chromosome . Less non-coding sequence. RNA polymerase binds the promoter directly. Genes are clustered into functional groups called operons. cenancestor. is . neither a single cell nor a single genome. , but is instead an entangle bank of heterogeneous genomes with relatively free flow of genetic information. Out of this entangled bank of frolicking genomes arose probably many evolutionary lineages with horizontal gene transfer gradually reduced and confined within individual lineages. Only three (Archaea, Eubacteria, and Eukarya) of these early lineages have representatives survived to this day.. : . Case Study of. . Residential Wood Combustion . Rabab . Mashayekhi, . Shunliu. . Zhao, . Sahar . Saeednooran. , . Amir . Hakami. Department of Civil and Environmental Engineering, Carleton University, . program . Kostadin. . Ivanov. Kaiyue. . Zeng, Jason . Hou, Maria . Avramova. . Multiphysics . Model . Validation Workshop. NCSU, . Raleigh. June. . 27 - 29, 2017. 2. OECD/NEA LWR Uncertainty Analysis in Modeling (UAM) Benchmark. All these partitioned analyses of concatenated data sets make the assumption . that all the genes share a common gene tree.. However there are several important reasons that phylogeny estimates from separate genes might be incongruent.. Figure 26.1 Some major episodes in the history of life. Figure 26.15 Whittaker’s five-kingdom system. Figure 26.16 Our changing view of biological diversity. Figure 27.2 The three domains of life.