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Final project – intermediate stage:

Final project – intermediate stage:. By 9/26 you should: - Choose the ingroup species. - Download the mitochondrial protein-coding genes. - Identify an outgroup.

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Final project – intermediate stage:

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  1. Final project – intermediate stage: • By 9/26 you should: - Choose the ingroup species. - Download the mitochondrial protein-coding genes.- Identify an outgroup. • Submit a short report with:- Question number.- List of scientific names of ingroup species.- Table with all mitochondrial genes in each species.- The outgroup species with an explanation on how you identified it.

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  3. 10/17 & 10/24: Oral Presentation 1. Describe the taxa in the assignment. 2. Outline the current phylogenetic views pertaining to the taxa in the assignment. 3. Describe the methods that have been used in these studies. 4. Present open questions (if any).

  4. Final project - example Are Artiodactyla monophyletic? The study should include: 1 species belonging to the Mysticeti, 1 species belonging to the Odontoceti, 1 species belonging to the Suina, 1 species belonging to the Tylopoda, 2 species belonging to the Cervidae, 1 species belonging to the Bovidae, 1 species belonging to the Hippopotamidae + the closest outgroup to all these taxa that you can find.

  5. Display Protein FASTA to retrieve the protein sequences

  6. others Mysticeti Cetacea Odontoceti others Tylopoda Suiformes Ancodonta Suina Cervidae Artiodactyla Bovidae Ruminantia

  7. + Odontoceti Mysticeti = Cetacea

  8. Antilocapra americana Pronghorn Bos taurus Cow Ruminantia = Cervidae +Bovidae

  9. Pecari tajacu Collared peccary Sus barbatus Bearded pig Suina Pigs

  10. Hippopotamus amphibius Hippopotamus Ancodonta

  11. + Ancodonta Suina = Suiformes

  12. Camelus bactrianus Bactrian camel Lama glama Llama Tylopoda Camelids

  13. Suiformes + + Tylopoda Ruminantia = Artiodactyla Even-toed ungulates

  14. Choosing an outgroup • Use tBLASTn to BLAST cytochrome c oxidase subunit I from all the species in the ingroup taxa against refseq_genomics which is a database of complete genomes only • Use an Entrez Query of: “animalia[orgn] NOT XXX[orgn]” where XXX = the ingroup taxon name

  15. Clouded leopard Northern raccoon • Repeat this process for each of the proteins. • Compile the first 5 results in each of your searches. • Chose the most abundant result as your outgroup

  16. Examine NJ trees – cytochrome b Artiodactyla Not Artiodactyla

  17. Examine NJ trees - cytochrome c oxidase subunit I Artiodactyla Not Artiodactyla

  18. Examine NJ trees - ATP synthase Artiodactyla Not Artiodactyla

  19. Examine NJ trees - NADH dehydrogenase subunit 1 Artiodactyla Not Artiodactyla

  20. Artiodactyla is not monophyletic!!!

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