1. Finding Order in Diversity
Classification

2. Why do we need to classify?
Imagine a store…..how do you know where to find the milk or the cereal? Are they in the same aisle? How is the store “organized”? Are all stores similar?
Imagine your computer or mp3 player…..are all of your songs and files in a single folder or do you have them grouped in some way?

3. Evolution overview
All life on earth began about 3.5 billion years ago with organisms that were a single cell
Then one billion years ago organisms that are made of many cells appeared as a result of evolution
During evolution traits that do not help organisms survive disappear while good traits that help with survival remain

4. Classification
As a result of evolution earth is populated by many different organisms with different traits.
We group these organisms according to their similar characteristics
Classification – grouping and naming of organisms according to their evolutionary relationships and shared characteristics

5. Taxonomy
Branch of biology that deals with classification of life forms
Taxonomist – use the tools of classification to identify and find relationships among organisms
Taxonomists classify organisms based on their biochemical and genetic information, embryological development, fossil record, and evolutionary relationships, in addition to their body structure

6. Early Classification and naming systems
Aristotle – Greek philosopher
Invented the first classification system
He classified organisms into two major groups plants and animals
Plants
Animals
Land
Water
Shrubs
Herbs
Air
Trees

7. Early Classification and naming systems continued . . .
Carolus Linnaeus – Swedish botanist
In the 18th century developed a new classification system
He also grouped them into plants and animals
He classified animals based on their similar body structures and not where they lived
Example: bats were grouped with mammals not with birds

8. Binomial Nomenclature
Linnaeus also gave each organism a two-word, Latin scientific name
This is called binomial nomenclature – still used today
Binomial – consisting of two terms
Nomenclature – a system of names

9. Bi-Nominal – two terms, two names
How many names do you use to identify yourself?
Example: Karen Wood
But why do we need this? Can we just call her Karen or simply that girl over there?

10. ….this is why we CLASSIFY
When you have a lot of information, it is best to organize and group items so that you can find them easier or easily see their relationship to other items
….this is why we CLASSIFY
Even websites must  organize their products

11. Scientists also need a way to *NAME* organisms
The “common names” used by people  can sometimes be misleading or confusing
In order to communicate effectively, biologists need a CONSISTENT naming protocol.
*Check out these slides of confusing names…..

12. Sea Lion? Ant lion? Lion? Photo Credits Sea Lion: Bill Lim
Ant Lion: Amphioxus Lion: law_keven
Sea Lion?
Ant lion?
Lion?

13. Which one of these is NOT actually a bear?
Photo Credits
Panda: Chi King
Koala: Belgianchocolate
Black Bear: SparkyLeigh

14. Bi-Nominal – two terms, two names: Genus and Species
The first word in binomial nomenclature is called the genus which is a group that has one or more different species classified within it
Closely related species that come from a common ancestor
The second word is species or a group of similar organisms that are capable of producing fertile offspring with each other

15. Genus and Species Example:
Panthera leo – lion and Panthera tigris – tiger
Both species are classified in the same genus Panthera along with other big cats however they are each a different species because they can’t reproduce with each other
Genus and species names are always italicized.
First letter of the genus is always capitalized and the first letter of the species is always lower case.

16. Taxonomic Groupings
Taxonomists classify things into seven major groups or taxa
They are:
Kingdom – largest group of living things (broadest)
Phylum – largest group within a kingdom
Class – largest group within a phylum
Order – largest group within a class
Family – largest group within an order
Genus – largest group within a family
Species – smallest group of living thing (most specific)
HINT for remembering the order of the levels of classification:
King Phillip Came Over For Great Spaghetti
King Phillip Cried Out For Great Soup

17. Grouping Kingdom Phylum Class Order Family Genus Species
Each group gets smaller and more specific – just think of the way you file things on your computer into folders and subfolders
Kingdom
Phylum
Class
Order
Family
Genus
Species

18. To help you remember the list
KING PHILIP CAME OVER FOR GREAT SOUP
Kingdom, Phylum, Class, Order, Family, Genus, Species

19. Phylogenetic Taxonomy
Taxonomists use two different approaches to place an organism into the correct taxonomic category:
Systematics: a phylogenetic tree or family tree is used to show the evolutionary relationships between different groups of organisms
This process stresses common ancestors and relies on the amount of differences within a group to construct the tree
Tree is based on evidence from the fossil record, morphology, embryological development, biochemistry and genetic studies

20. Phylogenetic Taxonomy Continued . . .
Second approach used to place an organism into the correct taxonomic category is called cladistics
Scientists construct a diagram based on specific characteristics of an organism
This is called a cladogram and its used to show evolutionary relationships among the different groups based on traits called shared derived characteristics
Derived characteristics – a trait that evolved only within the specific group under study
Example: Feathers in birds

21. The scientific name is always the genus + species
Kingdom
Animalia
Phylum
Chordata
Class
Mammalia
Order
Primate
Family
Hominidae
Genus
Homo
Species
sapiens
The scientific name is always the genus + species
Humans = Homo sapiens
Photo by atomicshark

22. The scientific name is always the genus + species
Kingdom
Animalia
Phylum
Chordata
Class
Mammalia
Order
Primate
Family
Hominidae
Genus
Homo
Species
sapiens
The scientific name is always the genus + species
Humans = Homo sapiens
Photo by atomicshark

23. What are the scientific names of each of these organisms?
Lion
Tiger
Pintail Duck
Kingdom
Animalia
Phylum
Chordata
Class
Mammalia
Aves
Order
Carnivora
Anseriformes
Family
Felidae
Anatidae
Genus
Panthera
Anas
Species
Leo
Tigris
acouta
What are the scientific names of each of these organisms?

24. What is a species?
Defined as organisms that can interbreed with one another, and produce fertile offspring

25. When two organisms of different species interbreed, the offspring is called a HYBRID
Is offspring fertile?
Example:  ligers and mules

27. Phylogenetic Taxonomy
Taxonomists use two different approaches to place an organism into the correct taxonomic category:
Systematics: a phylogenetic tree or family tree is used to show the evolutionary relationships between different groups of organisms
This process stresses common ancestors and relies on the amount of differences within a group to construct the tree
Tree is based on evidence from the fossil record, morphology, embryological development, biochemistry and genetic studies

28. Phylogenetic Taxonomy Continued . . .
Second approach used to place an organism into the correct taxonomic category is called cladistics
Scientists construct a diagram based on specific characteristics of an organism
This is called a cladogram and its used to show evolutionary relationships among the different groups based on traits called shared derived characteristics
Derived characteristics – a trait that evolved only within the specific group under study
Example: Feathers in birds

29. Phylogenetics A cladogram has CLADES
Clade – a monophylletic group - a grouping that includes a common ancestor and all the descendants (living and extinct) of that ancestor
Using a phylogeny, it is easy to tell if a group of lineages forms a clade. Imagine clipping a single branch off the phylogeny — all of the organisms on that pruned branch make up a clade.

31. The Kingdoms
There are currently 6 kingdoms

32. Classification into a kingdom is based on certain criteria
- Number of cells (unicellular or multicellular)
- How it obtains energy
(heterotroph or autotroph)
- Type of cell (eukaryote or prokaryote)

33. Kingdom Animalia Multicellular Heterotrophic Most can move
Photo by Tambako the Jaguar
Multicellular
Heterotrophic
Most can move
Examples: birds, insects, worms, mammals, reptiles, humans, anemones
Photo by Eduardo Amorim

34. Kingdom Plantae Multicellular Autotrophic Eukaryotic Cannot move
(due to cell walls)

35. Kingdom Fungae Multicellular (most) Heterotrophic (mainly decomposers)
Eukaryotic
Photos by nutmeg66

36. Kingdom Protista Most are unicellular
Can be heterotrophic or autotrophic
Eukaryotes (all have nucleus)
Examples: Ameba, paramecium, euglena, algae
Most live in water
Photo of Ameba by PROYECTO AGUA **/** WATER PROJECT

37. Kingdom Eubacteria & Kingdom Archaebacteria
Unicellular
Can be autotrophic or heterotrophic
Prokaryotes (do not have a nucleus)
Eubacteria = common bacteria (E. coli, Salmonella)
Archaebacteria = “ancient bacteria”, exist in extreme environments

38. Three Domain System    
Recently, scientists have added a group above Kingdom.  Three groups, called DOMAINS, contain each of the six kingdoms.
Domain Eukarya - includes organisms composed of eukaryotic cells (plants, animals, fungi, protists – 4 kingdoms)
Domain Bacteria - includes all prokaryotic cells, Kingdom Eubacteria
Domain Archaea - includes only "ancient" bacteria, Archaebacteria (1 kingdom)

39. Dichotomous Key
Precise method that helps taxonomists classify and identify unknown organisms
Made up of a list of observable, alternative characteristics, that leads, step by step, to the correct identification of an organism
Dichotomous means dividing in two because there are always two choices at each step
At each step the organism will have only one of the traits described and that is the path you follow

40. Example:
A dichotomous key for a plant would have one step where you chose between spores and seeds as a method of reproduction
Then it might ask for seeds if its cones or flowers
There would also be steps asking about leave structure and the stem

42. Molecular Phylogenetics
and what it all means......

43. Chips and Candy vs. Living things
Using only physical characteristics or evolutionary relationships?

44. Molecular Phylogenetics
Constructing trees based on DNA sequence comparisons
In certain stretches of DNA mutations occur at reliable rates - the more mutations the DNA has accumulated, the longer since it split off from its ancestral sequence
May use RNA (for RNA viruses) or protein sequences

45. Molecular Phylogenetics
Made possible by the availability of whole genome sequencing; new technologies make this faster – more organisms genomes sequenced
Many species genomes have been sequenced
Requires "Bioinformatics" – computer algorithms that compare sequences from multiple organisms
Comparison – align sequences, determine similarities, differences, gaps in alignment

46. Genomes sequenced

47. What's in a Clade

49. Clades are nested within one another — they form a nested hierarchy
Clades are nested within one another — they form a nested hierarchy. A clade may include many thousands of species or just a few. A clade may include species that are no longer living (extinct)

51. How are we related to Chimps?

52. Adding time to a tree

53. How do we know the time?
Life began 3.8 billion years ago, and insects diversified 290 million years ago, but the human and chimpanzee lineages diverged only five million years ago.
How have scientists figured out the dates of long past evolutionary events?
Here are some of the methods and evidence that scientists use to put dates on events: Radiometric dating; stratigraphy; molecular clocks

55. Molecular Clocks
Evolutionary changes may occur in a clock-like fashion
Changes in DNA sequence can build up over the course of million years at a reliable rate
Example: Alpha-globin gene experiences base changes at a rate of .56 changes per base pair per billion years - IF this rate is reliable, the gene could be used as a molecular clock.

56. Evolution and Trees beyond Taxonomy
Phylogenetics can be used to build NEW scientific knowledge:
Identifying the source of new human diseases;
Setting Conservation priorities
Agriculture
Investigating alleged crimes
Use of 'model' organisms in biomedical science

57. Video

58. Investigating Alleged crimes
Despite overwhelming evidence attesting to their innocence, last month six medical workers were sentenced to death in a Libyan trial.
The crime with which the five Bulgarian nurses and one Palestinian doctor are charged is indeed horrifying. After an outbreak of HIV at the Al-Fateh hospital, the Libyan government accused the defendants of committing an act of bioterrorism by deliberately injecting 426 hospitalized children with HIV-tainted blood.
The HIV strain is particularly virulent and has already contributed to the deaths of more than 50 of the infected children.

59. Investigating Alleged crimes
The children had been infected and their viruses had begun diverging several years before the medics even arrived on the scene!

60. 'Model' Organisms
Common ancestor – common morphology, common processes; common development
Can be used to study human development in the laboratory using 'model' organisms
Model human processes on studies performed in other organisms
Some examples:

61. Use of Model Organisms
Study of common cellular processes – cell division, glycolysis studied in bakers yeast
Study of common developmental process – human limb development in chicken
Screen for new drugs – which chemicals activate or block common/similar cellular pathways altered in human disease (e.g. cancer)
Toxicology – determine safety of compounds before human use

62. Think about it!
The development and safety of all modern medicines, cosmetic products, etc. is based on the Theory of Evolution and Modern Phylogenetics
The development of new Crops is based on the Theory of Evolution and Modern Phylogenetics
Conservation Biology is based on the Theory of Evolution and Modern Phylogenetics

63. Evolution is an inseparable part of ALL Life Science – Medicine -Agriculture

64. ENSEMBLE