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. 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. 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. Departments of Computer Science and Bioengineering. University of Illinois at Urbana-Champaign. Large-scale statistical phylogeny estimation. Ultra-large multiple-sequence alignment. Estimating species trees from incongruent gene trees. 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. 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). 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.. University of Illinois at Urbana-Champaign. http://. tandy.cs.Illinois.edu. Orangutan. Gorilla. Chimpanzee. Human. From the Tree of the Life Website,. University of Arizona. Species 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 .