PPT-Estimating species trees from multiple gene trees in the presence of ILS

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. 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.. 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. 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. Algorithmic Computational Genomics. Tandy Warnow. Departments of Bioengineering and Computer Science. http://. tandy.cs.illinois.edu. Course Details. Office hours: . To be determined. Course webpage: . 1. ILS Approach Nomenclature. ILS. Converging ILS. The ILS "converges. " with another . approach . and thus has higher minimums. . Usually . if there are two converging . approaches . the ATIS will broadcast that converging . 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. . 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. MAIS – ils ne font pas partie des groupes algonquiennes comme les Beothuk, les Mi’kmaq, et les Innu.. Ils ne sont pas membres des Premières Nations du Canada – ils font un groupe unique.. Ils ne sont pas uniques au Labrador ou au Canada – ils se trouvent mondialement au nord du cercle polaire arctique.. 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 . According to the . PMBOK. ®. Guide, . Project Cost Management knowledge area includes the processes involved in planning, estimating, budgeting, financing, funding, managing, and controlling costs to complete the project within the approved budget. OpSpec C061. ILS Classification System. Reference Documents:. ICAO Annex 10, . Aeronautical Communications. FAAO 6750.24, . Instrument . Landing System and Ancillary Electronic Component Configuration and Performance Requirements . Marshall Breeding. Director for Innovative Technology and Research. Vanderbilt University Library. Founder and Publisher, Library Technology Guides. http://www.librarytechnology.org/. http://twitter.com/mbreeding. Zaho Divis