The Closest Unicellular Relatives of Animals

1. The Closest Unicellular Relatives of Animals B.F. Lang, C. O’Kelly, T. Nerad, M.W. Gray, and G. Burger Current Biology (2002) 12, 1773–1778 Presented by Tan Wang in June 15

2. Outline of Presentation • Introduction of Mitochondria. • Questions about the evolutionary relationships of animal (metazoa) and protists. • Previous study using phylogenetic analysis approach to resolve the above evolutionary relationships. • Dr. Lang’s approach: using mitochondrial genome to carry out the Phylogenetics analysis. • Results and analysis. • Conclusion.

3. Introduction of Mitochondria

4. Introduction of Mitochondria The human mitochondrial genome probably originated following endocytosis of a prokaryotic cell by a eukaryotic precursor cell.

5. Introduction of Mitochondria

6. Origin of life: the three kingdoms of life and the origin of eukaryotes by endosymbiosis

7. metazoan choanoflagellate fungi Sarcophyton Schizophyllum ichthyosporean amoebidium Questions about the evolutionary relationships of animal (metazoa) and protists ? ? ?

8. Kumar S, Rzhetsky A. J Mol Evol (1996) 42:183–193 Based on nuclear small subunit (SSU) rDNA sequences

9. Based on small subunit (SSU) rDNA sequences Yves Van de Peer, Rupert De Wachter. J Mol Evol (1997) 45:619–630

10. Based on 18S small-subunit ribosomal DNA Herr, R.A., Ajello, L., Taylor, J.W., Arseculeratne, S.N., and Mendoza, L. (1999) J. Clin. Microbiol. 37, 2750–2754.

11. Dr. Lang’ approach: mitochondrial genome for Phylogenetic analysis. -present in all cellular organisms. -evolve at fast enough rate to separate taxa into monophyletic groups. -each has same function in all taxa. -a single set of gene, so that homologous genes are being compared. -easily isolated in large quantities.

12. Dr. Lang’ approach: (Which Sequences ?) • DNA Very sensitive, non-uniform mutation rates • Protein Sequences Useful for most remote homologies, deep phylogenies, more uniform mutation rates, more character states. • In this study, the protein sequences of 11 well-conserved proteins (Cox1,2,3, Cob, Atp6,9, and Nad1,3,4,4L,5) were used. Also the above proteins from a-proteobacteria used as outgroup.

13. The five steps in phylogenetic analysis 1 Sequence data 2 Align Sequences Phylogenetic signal?evolutionary processes? 3 Distances methods Characters based methods Distance calculation (which model?) 4 Choose a method ML MP Wheighting? (sites, changes)? Model? Calculate or estimate best fit tree 5 Test phylogenetic reliability Modified from Hillis et al., (1993). Methods in Enzymology 224, 456-487

14. Maximum Likelihood Tree of Concatenated Proteins Encoded by mtDNA (ichthyosporean) (choanoflagellate) (metazoan)

15. Distance Method Tree of Concatenated Proteins Encoded by mtDNA

16. Test phylogenetic reliability All phylogenetic trees represent hypotheses about the evolutionary history of the sequences. Like any good hypothesis, it is reasonable to ask two questions about how well it describes the underlying data: • How much confidence can be attached to the overall tree and its branches ? Bootstrapping. • How much more likely is one tree to be correct than a particular or randomly chosen alternative tree ? Comparing tree topologies using log likelihood difference (T), standard approximately unbiased test (AU), bootstrap probility (BP), weighted Kishino-Hasegawa test (WKH test), weighted Shimodaira-Hasegawa test(WSH test), these tests can tell us whether sub-optimal trees are significantly worse than the ML tree.

17. Likelihood Tests of Alternative Tree Topologies

18. Conclusion • The evidence that Choanoflagellata, Ichthyosporea, and Metazoa constitute a monophyletic assemblage: the Holozoa. • A total of five major eukaryotic clades that encompass both unicellular and multicellular members: the Fungi, Streptophyta (charophyte algae land plants), Rhodophyta (red algae), Phaeophyta (brown algae), and the Holozoa defined here. Such relationships cannot be discerned by single-gene analyses.

19. Thank you Question ?

20. Monophyletic taxon : A group composed of a collection of organisms, including the most recent common ancestor of all those organisms and all the descendants of that most recent common ancestor. A monophyletic taxon is also called a clade. Examples : Mammalia, Aves (birds), angiosperms, insects, fungi, etc. Paraphyletic taxon : A group composed of a collection of organisms, including the most recent common ancestor of all those organisms. Unlike a monophyletic group, a paraphyletic taxon does not include all the descendants of the most recent common ancestor. Examples : Traditionally defined Dinosauria, fish, gymnosperms, invertebrates, protists, etc. Polyphyletic taxon : A group composed of a collection of organisms in which the most recent common ancestor of all the included organisms is not included, usually because the common ancestor lacks the characteristics of the group. Polyphyletic taxa are considered "unnatural", and usually are reclassified once they are discovered to be polyphyletic. Examples : marine mammals, bipedal mammals, flying vertebrates, trees, algae, etc.

21. Multiple Sequence Alignment • Align sequences so that corresponding positions are in same columns. • Trim the sequences so that gaps are removed and only conservative regions are kept. • Each “column” then becomes a single character in the phylogeny computation. • Each gene from each species alone can be used to construct phylogenetic trees or each gene is concatenated for each species. Then use concatenated gene to construct tree. • In this study, 11 well-conserved proteins (Cox1,2,3, Cob, Atp6,9, and Nad1,3,4,4L,5) were concatenated and used.