Diversity of Life: Introduction to Biological Classification
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Transcript of Diversity of Life: Introduction to Biological Classification
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Diversity of Life:
Introduction to Biological
Classification
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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
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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
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Carolus von Linnaeus(1707-1778)
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
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Hierarchical Classification
Taxonomic categories Kingdom King Phylum Philip Class Came Order Over Family For Genus Green Species Soup
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Kingdoms and Domains
Bacteria Archaea Eukarya
Bacteria Archaea Protista Plantae Fungi Animalia
Monera Protista Plantae Fungi Animalia
The three-domain system
The six-kingdom system
The traditional five-kingdom system
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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
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Taxonomic Diagrams
CladogramPhylogeneticTree
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Table of Acquired Characteristics
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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?
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One possible tree…
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Taxonomic Diagrams
Mammals Turtles Lizards and Snakes
Crocodiles Birds Mammals Turtles Lizards and Snakes
Crocodiles Birds
CladogramPhylogeneticTree
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Tree of Life (cladogram style)
Yeast
Jellyfish
Squid
Nematode
Fruit fly
Starfish
Sharks
Bony Fish
Amphibians
Snakes
Birds
Turtles
Kangaroo
Mice
Bats
Humans
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Tree of Life (pedigree style)
Yeast
Jellyfish
Squid
Nematode
Fruit fly
Starfish
Sharks
Bony Fish
Amphibians
Snakes
Birds
Turtles
Kangaroo
Mice
Bats
Humans
multicellularanimals chordates
bilateria
deuterostomes
vertebrates
bony skeleton
tetrapods
amniotes
mammalsplacenta
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Phylogenetics!
Open your laptops
Go to http://www.tolweb.org/ Learn about phylogenetics
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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
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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
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CytB BLAST Tree (local alignment)
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Multiple Sequence Alignment
Go to align.genome.jp
Copy and paste the Cytochrome B sequences
Make a dendrogram with distances
Answer questions on sheet
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CytB ClustalW Tree (global alignment)
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Primate Tree of LifeGallus 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 monkeysprimates
hominids
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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
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Primate Mitochondrial Phylogeny (cladogram style)
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Primate Mitochondrial Phylogeny (pedigree style)