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

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 BioEd Online

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

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

BioEd Online Hierarchical Classification Taxonomic categories KingdomKing PhylumPhilip ClassCame OrderOver FamilyFor GenusGreen SpeciesSoup BioEd Online

BioEd Online Kingdoms and Domains BacteriaArchaeaEukarya BacteriaArchaeaProtistaPlantaeFungiAnimalia MoneraProtistaPlantaeFungiAnimalia The three-domain system The six-kingdom system The traditional five-kingdom system BioEd Online

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 BioEd Online

BioEd Online Taxonomic Diagrams CladogramPhylogenetic Tree BioEd Online

Table of Acquired Characteristics

Now it’s your turn to make a tree! 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?

One possible tree…

Taxonomic Diagrams MammalsTurtlesLizards and Snakes CrocodilesBirdsMammalsTurtlesLizards and Snakes CrocodilesBirds CladogramPhylogenetic Tree BioEd Online

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

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

Phylogenetics! Open your laptops Go to Learn about phylogenetics

Phylogenetics and Bioinformatics! Open your laptops Go to Tour the website Learn about bioinformatics Download two files from Study Wiz Species accession numbers.txt CytB sequences.txt

Protein BLAST Instructions Go To BLAST website Click on “protein blast” Enter the accession number for human cytochrome B protein (NP_ ) 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

CytB BLAST Tree (local alignment)

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

CytB ClustalW Tree (global alignment)

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) old world monkeys new world monkeys primates hominids

BioEd Online Nucleotide BLAST Instructions Go To BLAST website 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

Primate Mitochondrial Phylogeny (cladogram style)

Primate Mitochondrial Phylogeny (pedigree style)