PPT-Gene-tree reconciliation with MUL-trees for

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 . 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. 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. 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. . 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. 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). 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..