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Introduction to Alignment and Basic Tree Building

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Learn to construct phylogenetic trees using aligned amino acid sequences, understand evolutionary relationships, and interpret phylogenetic data.

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Introduction to Alignment and Basic Tree Building

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  1. Introduction to Alignment and Basic Tree Building Julie Noor, Monnie McGee, and Kurt Regner

  2. Project Outline • Provide students with Amino Acid sequences from 7 organisms for a gene that is present in all vertebrates • We chose hemoglobin zeta/alpha 2 • Assignment • Perform basic alignment using http://www.phylogeny.fr • Use aligned sequences to construct phylogenetic tree

  3. Objectives • Students will understand that molecular data can be used to illustrate evolutionary relationships • Students will learn to interpret a phylogenetic tree • Students will use the tree to test a hypothesis • Variations • Students will learn how different multiple alignment algorithms affect the topology of the tree

  4. Organisms • Leiostomus xanthurus • Mus musculus • Taeniopygia guttata • Hynobius retardatus • Geocelone chilenis • Homo sapiens • Riftia pachyptila

  5. Aligned Sequences • Using Robust Phylogeny for NonSpecialists • Perform alignment using MUSCLE • Use Gblocks to curate • PhyML for Phylogeny Dereeper A., Guignon V., Blanc G., Audic S., Buffet S., Chevenet F., Dufayard J.-F., Guindon S., Lefort V., Lescot M., Claverie J.-M., Gascuel O. Phylogeny.fr: robust phylogenetic analysis for the non-specialist Nucleic Acids Research. 2008 Jul 1; 36 (Web Server Issue):W465-9. Epub 2008 Apr 19

  6. The Tree

  7. Hmmmm…. • Placement of the salamander introduced more questions than our students should have to deal with • Replaced Hynobius retardatus with Bufo gargarizans and Leiostomus xanthurus with Danio rerio • Also wanted to illustrate birds’ relationship to lizards and snakes • Added Naja naja

  8. Re-Aligned Sequences Dereeper A., Guignon V., Blanc G., Audic S., Buffet S., Chevenet F., Dufayard J.-F., Guindon S., Lefort V., Lescot M., Claverie J.-M., Gascuel O. Phylogeny.fr: robust phylogenetic analysis for the non-specialist Nucleic Acids Research. 2008 Jul 1; 36 (Web Server Issue):W465-9. Epub 2008 Apr 19 Using Robust Phylogeny for NonSpecialists Perform alignment using MUSCLE Use Gblocks to curate PhyML for Phylogeny

  9. Re-drew the Tree

  10. Still have problems… • Placement of amphibian still a problem and now placement of snake a problem, too • Retrieved new amino acid sequences for the 8 species by starting from globin domain in PFAM (and added Alligator mississippiensis to (hopefully) better demonstrate reptile/bird relationship)

  11. Re-drew the Tree again!

  12. And still got hard to explain relationships! • Choose different protein? • Check alignments? • Try nucleotide sequence? • Checked this quickly this morning with a different protein for good measure

  13. Re-drew the Tree yetagain!

  14. And still got hard to explain relationships! • Find way to make sure we have orthologous sequences • Choose different protein? • Check alignments?

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