Diversity of Life: Introduction to Biological Classification

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Diversity of Life:

Introduction to Biological

Classification

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www.BioEdOnline.orgBioEd 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

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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

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

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

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

Phylogenetics!

Open your laptops

Go to http://www.tolweb.org/ Learn about phylogenetics

http://www.tolweb.org/



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

http://www.ncbi.nlm.nih.gov/



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

http://www.ncbi.nlm.nih.gov/blast/

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 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


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

http://www.ncbi.nlm.nih.gov/blast/

Primate Mitochondrial Phylogeny (cladogram style)

Primate Mitochondrial Phylogeny (pedigree style)

Diversity of Life: Introduction to Biological Classification

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