PPT-New methods for inferring species trees in the presence of incomplete lineage sorting

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. 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.. 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. SUM 2013. Batya. . Kenig. Avigdor. Gal. Ofer. . Strichman. Probabilistic Databases for managing uncertain data. A variety of data sources generate incomplete, noisy and uncertain data (sensor networks, information extraction, data integration…). . 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. 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 . Area Based Methods. Tree Based Methods. Area Based Methods. Main Types. Strip Cruise. Fixed Plot. Point Sampling. Remote Sensing. Varieties for specific applications. Fixed Count. Fixed Count Measure. Bhargav Kanagal. Amol Deshpande. University of Maryland. Motivation: Information Extraction/Integration. [Gupta&Sarawagi’2006, . Jayram et al. 2006. ]. Structured entities extracted from text in the internet. 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. . Dr. EP de Villiers. Adapted from: http://. viralzone.expasy.org. / . Tree basics. The . Concept of . Phylogenetic Tree. . Trees . Capture Major Events in a Species' Existence . A tree . is composed of Leaves, Branches, and Inner Nodes .