Diversity of Life: Introduction to Biological Classification

1. BioEd Online Diversity of Life: Introduction to Biological Classification

2. BioEd Online Why Do We Classify Organisms? • Biologists group organisms to represent similarities and proposed relationships. • Classification systems change with expanding knowledge about new and well-known organisms. Tacitus bellus

3. BioEd Online Classification • Binomial Nomenclature • Two part name (Genus, species) • Hierarchical Classification • Seven Taxonomic Catagroies • Systematics • Study of the evolution of biological diversity Leucaena leucocephala Lead tree

4. BioEd Online Binomial Nomenclature • Carolus von Linnaeus • Two-word naming system • Genus • Noun, Capitalized, Underlined or Italicized • Species • Descriptive, Lower Case, Underlined or Italicized Carolus von Linnaeus(1707-1778) Swedish scientist who laid the foundation for modern taxonomy

5. BioEd Online Hierarchical Classification • Taxonomic categories • Kingdom King • Phylum Philip • Class Came • Order Over • Family For • Genus Green • Species Soup

6. BioEd Online Kingdoms and Domains The three-domain system Bacteria Archaea Eukarya The six-kingdom system Bacteria Archaea Protista Plantae Fungi Animalia The traditional five-kingdom system Monera Protista Plantae Fungi Animalia

7. BioEd Online Systematics:Evolutionary Classification of Organisms • Systematics is the study of the evolution of biological diversity, and combines data from the following areas. • Fossil record • Comparative homologies • Cladistics • Comparative sequencing of DNA/RNA among organisms • Molecular clocks

8. BioEd Online Taxonomic Diagrams PhylogeneticTree Cladogram

9. Table of Acquired Characteristics

10. Animals Drosophila melanogaster (fruit fly) Homo sapiens (you) Heterodontus francisci (horn shark) Chelonia mydas (green sea turtle) Xenopus laevis (african clawed frog) Gallus gallus (chicken) Mus musculus (house mouse) Danio rerio (zebrafish) Naja naja (Indian Cobra) Rousettus aegyptiacus (Egyptian fruit bat) Caenorhabditis elegans (roundworm nematode) Aurelia aurita (jellyfish) Asterias amurensis (northern Pacific sea star) Dosidicus gigas (giant squid) Saccharomyces cerevisiae (baker’s yeast) Macropus robustus (Eastern Wallaroo) Characters Homeothermy Warm vs cold blooded Appendages Fins, legs, wings Skin Smooth, scales, hair, feathers Skeleton Endo, exo, neither Amniotic sac Body plan Symmetry, # limbs, etc Can you think of others? Now it’s your turn to make a tree!

11. One possible tree…

12. BioEd Online Taxonomic Diagrams Mammals Turtles Lizards and Snakes Crocodiles Birds Mammals Turtles Lizards and Snakes Crocodiles Birds PhylogeneticTree Cladogram

13. Tree of Life (cladogram style) Yeast Jellyfish Squid Nematode Fruit fly Starfish Sharks Bony Fish Amphibians Snakes Birds Turtles Kangaroo Mice Bats Humans

14. Tree of Life (pedigree style) Yeast Jellyfish Squid Nematode Fruit fly Starfish Sharks Bony Fish Amphibians Snakes Birds Turtles Kangaroo Mice Bats Humans multicellular animals chordates bilateria deuterostomes vertebrates bony skeleton tetrapods amniotes mammals placenta

15. Phylogenetics! • Open your laptops • Go to http://www.tolweb.org/ • Learn about phylogenetics

16. Phylogenetics and Bioinformatics! • Open your laptops • Go to http://www.ncbi.nlm.nih.gov/ • Tour the website • Learn about bioinformatics • Download two files from Study Wiz • Species accession numbers.txt • CytB sequences.txt

17. Protein BLAST Instructions • Go To BLAST website • http://www.ncbi.nlm.nih.gov/blast/ • Click on “protein blast” • Enter the accession number for human cytochrome B protein (NP_536855.1) • Paste the other cytochrome B accession numbers into the “Entrez Query” box • This will limit our comparison to only the mitochondrial records we specify here • Click BLAST! • Click on “Distance tree of results” • Select “Taxonomic Name” under “Sequence Label” • Select the “Slanted” tab to view a cladogram style

18. CytB BLAST Tree (local alignment)

19. Multiple Sequence Alignment • Go to align.genome.jp • Copy and paste the Cytochrome B sequences • Make a dendrogram with distances • Answer questions on sheet

20. CytB ClustalW Tree (global alignment)

21. Primate Tree of Life Gallus gallus (chicken) Bardus aureus (Paris Hilton) Lemur catta (ring-tailed lemur) Tarsius bancanus (tarsier) Cebus albifrons (capuchin monkey) Macaca mulatta (rhesus monkey) Papio hamadryas (baboon) Nasalis larvatus (proboscis monkey) Hylobates lar (gibbon) Pongo pygmaeus (orangutan) Gorilla gorilla (gorilla) Pan troglodytes (chimp) Homo sapiens (you) new world monkeys primates old world monkeys hominids

22. Nucleotide BLAST Instructions • Go To BLAST website • http://www.ncbi.nlm.nih.gov/blast/ • Click on “nucleotide blast” • Enter the accession number for human mitochondrial genome (NC_001807) • Select database “Reference genomic sequences” • This will make sure we search within only genomic records • Paste the other mitochondrial accession numbers into the “Entrez Query” box • This will limit our comparison to only the mitochondrial records we specify here • Click BLAST! • Click on “Distance tree of results” • Select “Taxonomic Name” under “Sequence Label” • Select the “Slanted” tab to view a cladogram style

23. Primate Mitochondrial Phylogeny (cladogram style)

24. Primate Mitochondrial Phylogeny (pedigree style)