Finding Order in Diversity

Classification

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?

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

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

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

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 (1)biochemical and genetic information (DNA, proteins),(2) embryological development, (3)fossil record – (1)+(2)+(3)=evolutionary relationships,

(4) in addition to their body structure

Early Classification and naming systems

• Aristotle – Greek philosopher– Invented the first classification system– He classified organisms into two major groups plants and

animals

Land

WaterShrubsHerbs

Plants Animals

AirTrees

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

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

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?

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…..

Photo CreditsSea Lion: Bill LimAnt Lion: AmphioxusLion: law_keven

Sea Lion?

Ant lion?

Lion?

Which one of these is NOT actually a bear?

Photo CreditsPanda: Chi KingKoala: BelgianchocolateBlack Bear: SparkyLeigh

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

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.

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

To help you remember the list

KING PHILIP CAME OVER FOR GREAT SOUP

Kingdom, Phylum, Class, Order, Family, Genus, Species

Kingdom AnimaliaPhylum Chordata

Class Mammalia

Order Primate

Family Hominidae

Genus Homo

Species sapiens

The scientific name is always the genus + speciesHumans = Homo sapiens

Photo by atomicshark

Lion Tiger Pintail DuckKingdom Animalia Animalia Animalia

Phylum Chordata Chordata Chordata

Class Mammalia Mammalia Aves

Order Carnivora Carnivora Anseriformes

Family Felidae Felidae Anatidae

Genus Panthera Panthera Anas

Species Leo Tigris acouta

What are the scientific names of each of these organisms?

What is a species?

Defined as organisms that can interbreed with one another, and produce fertile offspring

When two organisms of different species interbreed, the offspring is

called a HYBRID

Example:  ligers and mules

Is offspring fertile?

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

Tree of Life

Shared characteristics or evolutionary relationships?

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

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

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.

What's in a Clade

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)

How are we related to Chimps?

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

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

What characteristics did you use to classify the chips and candy?

Did all the teams use the same characteristics?

Could you use different ones?

Molecular Phylogenetics

and what it all means......

Chips and Candy vs. Living things

Using only physical characteristics or evolutionary relationships?

How would you group these?

How would you group these?

• They are both Mammals – have a common ancestor

BUT• Have markedly different physical

characteristics

Fossil Records and DNA comparison

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

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

(1)similarities, (2)differences, (3)gaps in alignment

Allignment

Adding time to a tree

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

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.

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

Videohttp://archive.peabody.yale.edu/exhibits/treeoflife/film_study.html

Investigating Alleged crimesDespite 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.

Investigating Alleged crimes

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

'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:

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

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

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

The KingdomsThere are currently 6 kingdoms

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)

Kingdom Animalia

•Multicellular

•Heterotrophic

•Most can move

•Examples: birds, insects, worms, mammals, reptiles, humans, anemones

Photo by Eduardo Amorim

Photo by Tambako the Jaguar

Kingdom Plantae

•Multicellular

•Autotrophic

•Eukaryotic

•Cannot move

(due to cell walls)

Kingdom Fungae•Multicellular (most)

•Heterotrophic (mainly decomposers)

•Eukaryotic

Photos by nutmeg66

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

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

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)