PPT-Improving gene trees without more data

Master Thesis By Ashu Gupta 1 Phylogenetic Pipeline Most common pipeline using summary method Step 1 Get gene alignments from sequence data eg Prank MAFFT etc Step 2 Get gene trees from gene alignments eg . 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. trees (cont.). If we pick the adjacent nucleotide, what gene tree do we expect?. A. C. B. A-B coalescence. AB-C coalescence. Split 2. Split 1. If we pick a nucleotide from a distant part of the genome, what gene tree do we expect?. Phylogenomics. . (Phylogenetic estimation from whole genomes). Orangutan. Gorilla. Chimpanzee. Human. From the Tree of the Life Website,. University of Arizona. Species Tree. Large-scale statistical phylogeny estimation. Evolutionary History with Network Models in Population . Genomics: Challenges and Progress. Yufeng. Wu. Dept. of Computer Science and Engineering. University of Connecticut, USA. Dagstuhl. Seminar, 2010. BioE. 598 . Algorithmic Computational Biology. Phylogenomics. Genome-scale evolution. The multi-species coalescent, and gene tree incongruence due to incomplete lineage sorting (ILS). Estimating species trees in the presence of ILS. L.L. Knowles et al., Molecular . Phylogenetics. and Evolution 65 (2012): 501-509. Full modeling versus summarizing gene-tree uncertainty: . Method choice and species-tree accuracy. (a) . Estimate. . estimating . species trees . from genome-scale data. Tandy Warnow. The University of Illinois. Orangutan. Gorilla. Chimpanzee. Human. From the Tree of the Life Website,. University of Arizona. Phylogeny. Tandy Warnow. The University of Illinois at Urbana-Champaign. Orangutan. Gorilla. Chimpanzee. Human. From the Tree of the Life Website,. University of Arizona. Phylogeny. (evolutionary tree). DNA Sequence Evolution. 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 . Tandy Warnow. The University of Illinois. Avian . Phylogenomics. Project. G . Zhang, . BGI. . Approx. 50 species, whole genomes. 8000+ genes, . UCEs. MTP Gilbert,. Copenhagen. S. . Mirarab. Md. species trees . from genome-scale data. Tandy Warnow. The University of Illinois. Orangutan. Gorilla. Chimpanzee. Human. From the Tree of the Life Website,. University of Arizona. Phylogeny. (evolutionary tree). polyploid. analysis. Gregg Thomas, S. Hussain . Ather. , . and Matthew Hahn. Indiana University. Background: Polyploidy. The presence of additional . sets of chromosomes . in . an . organism due to .