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2. The Organism as a Unit of Life
Cellular Structure (cell = unit of life)…one or many!
Metabolism = Homeostasis (PSN, Resp, N2fix, ferment, etc.)
Growth = irreversible change in size
Movement…includes internal, limbs, locomotion
Reproduction…failure = extinction
Acclimatization-short term responses = behavior
Adaptation-long term responses = evolution

3. Biology is multidimensional
Ecosystem
Community
Population
Organism
Organ System
Organ
Tissue
Cell
This array is an example of what dimension?
Levels of Organization
What fields of biology are at each extreme?
Biophysics and Biochemistry
In this course our focus will be upon…
The Organism!
This level of organization is also…
Hierarchial / Multidimensional!

4. Swedish Botanist, Physician, and Zoologist
Carolus Linnaeus (aka Carl von Linné)
Swedish Botanist, Physician, and Zoologist
Developed a hierarchial classification scheme that we use to this day!

5. Taxonomy is also Hierarchial!
The Organisms are Diverse: Taxonomy
Domain
Bacteria
Archaea
Eukarya
Kingdom
Eubacteria
Gram +
Protista
(Chromista)
Plantae
Fungi
Animalia
Phylum
Proteobacteria
Eury-archaeota
Phaeophyta
Anthophyta
Magnolio-phyta
Basidio-mycota
Chordata
Class
Gamma-proteobacteria --
Phaeo-phyceae
Dicoty-ledonae
Hymeno-mycetes
Mammalia
Order
Entero-bacteriales
Halo-bacteriales
Fucales
Rosales
Agaricales
Primates
Family
Entero-bacteriaceae
Halo-bacteriaceae
Fucaceae
Rosaceae
Agaricaceae
Hominidae
Genus
Escherichia
Halo-bacterium
Fucus
Rosa
Agaricus
Homo
Species
E. coli
H. salinarum
F. distichus
R. multiflora
A. bisporus
H. sapiens
Common
DH5
Halophytic archaeon
Rockweed
Wild Rose
Mushroom
Human

6. Not chimps, gorillas, etc.
Figure 1-5 Page 7 of 3rd edition of your book (deleted from current edition)
KINGDOM
Not plants, fungi, etc.
(Animalia)
PHYLUM
Not invertebrates
(Chordata)
CLASS
Not birds, reptiles, etc.
(Mammalia)
ORDER
Not bison, etc.
(Primates)
FAMILY
Not lemurs, monkeys etc.
(Hominidae)
GENUS
Not chimps, gorillas, etc.
(Homo)
SPECIES
Not H. neanderthalensis, H. floresiensis, etc.
(Homo
sapiens)

7. √ Homo sapiens There are many Homo sapiens in class.
Learn your own Latin binomial.
Our genus means “self” not gender identity
Our epithet: we think that we think!
Our epithet always ends in ‘s’:
One Homo sapiens is the instructor.
There are many Homo sapiens in class.
Print in italics, underscore in manuscript.
I am a Homo sapiens. √

8. How many organisms are there?
Good Question! Let’s exclude extinct species!
Many extant are unknown so we estimate!
Bacteria: 10,000
Archaea: 1,000
Protista: 20,000
(includes Stramenopila and Rhodophyta)
Plantae: 285,000
(mostly flowering)
Fungi: 110,000
Animalia: 1,400,000
(mostly arthropods)

9. How many organisms are there?
What is a species?
Animal species concept…
if offspring are fertile then same species…
does not apply to species of other kingdoms:
Prokaryotes (no sex)
Allopolyploidy in plants

10. X Horse: Equus caballus Donkey: Equus asinus Mule: Sterile Hybrid
Mule: Sterile Hybrid

11. X X Fertile Hybrids! Coyote Canis latrans Wolf Canis lupus
German Shepherd Dog
Canis familiaris X X
Coydog
Wolfdog
Fertile Hybrids!

12. What is a Species? The Case of Bread Wheat
AA (diploid wheat) x DD (diploid grass)
Triticum urartu
Aegilops tauschii
AD (sterile diploid)
similar to mule!
colchicine
or spontaneous
AADD (fertile tetraploid)
BB (diploid grass)
Aegilops speltoides
BBAADD
Fertile hexaploid
Bread Wheat
Triticum aestivum
colchicine
or spontaneous
BAD (sterile triploid)
Bread Wheat Created 7500 BC with spontaneous doubling of DNA
Levy A. A. and M. Feldman The impact of polyploidy on grass genome evolution. Plant Physiol. 130:

13. How many kingdoms are there?
Good Question!
The relationships among known organisms are not completely understood.
Are you a lumper or a splitter?
Newer information appears to back up the taxonomic decisions of splitters!
Historical shifts from 2, to 3, to 4, to 5, to 6 and now to many more in just the last 40 years!

14. Multicellular Animals
Shifting Kingdoms
Lumpers
Splitters 2 3 5 6 8
Bacteria
Archaea
Archezoans
Euglenoids
Chrysophytes
Green Algae
Brown Algae
Red algae
Slime Molds
True Fungi
Bryophytes
Tracheophytes
Protozoans
Myxozoans
Multicellular Animals

15. Descent with Modification
Charles Darwin - British Naturalist
Formal Studies: Medicine and Theology
Descent with Modification
1880 The Power of Movement in Plants
1871 Descent of Man
1859 Origin of Species
Species evolved from generation to generation over time
HMS Beagle Voyage

16. Notice the very large number of extinctions!
Darwin’s Tree of Life (1859) the only figure in: On the Origin of Species
future time
present
The Roman numerals each represent 1000 generations
many more
many more
past time
The letters A-L represent hypothetical progenitor species within a single genus
Notice the very large number of extinctions!

17. DOMAIN BACTERIA DOMAIN ARCHAEA DOMAIN EUKARYA
Question 14 Page 15
before nucleus
true nucleus
Turn back to the tree of life shown in Figure 1.5. Note that Bacteria and
Archaea are prokaryotes, while Eukarya are eukaryotes. On the simplified
tree below, draw an arrow that points to the branch where the structure
called the nucleus originated. Explain your reasoning.
DOMAIN
BACTERIA
DOMAIN
ARCHAEA
DOMAIN
EUKARYA

18. How Many Kingdoms? Extant 8 5 3 First Eukaryote! Extinct 2 1
Multicellular Animals
Myxozoans
Protozoans
Tracheophytes
Bryophytes
True Fungi
Slime Molds
Red algae
Brown Algae
Green Algae
Chrysophytes
Euglenoids
Archezoans
Archaea
Bacteria 8 5 3
First Eukaryote!
Extinct 2 1
Long Time with
Prokaryotes only
Original Cell

19. How Many Kingdoms? Extant 8 5 3 First Eukaryote! Extinct 2 1
Multicellular Animals
Myxozoans
Protozoans
Tracheophytes
Bryophytes
True Fungi
Slime Molds
Red algae
Brown Algae
Green Algae
Chrysophytes
Euglenoids
Archezoans
Archaea
Bacteria 8 5 3
First Eukaryote!
Extinct 2 1
Long Time with
Prokaryotes only
Original Cell

20. Here is a phylogeny that covers some of the animals:

21. Figure 1-9 Page 10 of 3rd Edition
Plants, fungi, and
animals are small
branch tips on
the tree of life
This node represents the common
ancestor of archaea and eukaryotes
This node represents the common
ancestor of all organisms alive today

22. In which direction is the axis of time shown?
Page 7 Figure 1.5
In spite of this graphic image, and the highlighted point on the lower right, your book, like most others, is organized as if there were only two kingdoms (Plantae and Animalia), as if nothing happened since Linnaeus!
DOMAIN BACTERIA
Mycoplasma
How is this graphic from your book the same, and how is it different from the other depictions of the “Tree of Life” you have seen so far?
In which direction is the axis of time shown?
The long list of organisms down the right are?
Firmicutes
Cyanobacteria
Actinobacteria
Spirochaetes
Chlamydiae
Bacteriodetes
-Proteobacteria
-Proteobacteria
-Proteobacteria
This node
represents the
common ancestor
of all organisms
alive today
-Proteobacteria
-Proteobacteria
DOMAIN ARCHAEA
Thaumarchaeota
Crenarchaeota
Korarchaeota
This node
represents the
common ancestor
of archaea and
eukaryotes
Euryarchaeota
DOMAIN EUKARYA
Slime molds
Fungi
Animals
Choanoflagellates
Fungi,
animals,
and plants
are small
branch tips
on the
tree of life
Euglenids
Parabasilids
The three twigs highlighted on the tree are showing which level of modern Linnean taxonomy?
Diplomonads
Red algae
Green algae
Land plants
Foraminiferans
Ciliates
Dinoflagellates
Apicomplexans
Water molds
Diatoms
Brown algae

23. David Hillis’ tree of life based on total genome sequences (at the time)
Eukaryotes
Archaeons
How many twigs would be on this diagram if ALL the extant organisms were shown? ?
Prokaryotes
Time Dimension?

24. Because this analysis is easier/faster, more species can be included!
David Hillis’ tree of life based on rRNA sequence analysis (at press time)
Rhodophyta
Because this analysis is easier/faster, more species can be included!
origin
Stramenopila

25. Why did the five-kingdom system of classification fall out of favor?
It was too complex—the original two-kingdom system of Linnaeus was more useful.
Many organisms were difficult to classify because they had characteristics of more than one kingdom.
There were too many prokaryotes to be included in a single kingdom.
It did not reflect the actual evolutionary relationships among organisms very well.
Answer: D

26. Summary Points for Taxonomic/Phylogenetic Classification
Linnaean Classification is hierarchical: Kingdom, Phylum, Class, Order, Family, Genus, Species
Organisms have names: Common names are redundant and multiple, Latin binomials are universal and almost unique
Species of organisms have a recognized binomial: Genus name and specific epithet
There are more than a million species of organisms on our planet--most are arthropods
Many species on Earth are unknown or virtually unstudied
Organisms are grouped into a few kingdoms
The number of kingdoms has increased over time on the planet, and in biology over time too
Phylogenic Cladistics relates organisms based on evolutionary pathways rather than on taxa
All organisms on this planet evolved from a single ancestor and so are a clade
Most of the recognized Kingdoms are close to natural groupings based on shared ancestry
Kingdom Protista needs further dissection to become a natural grouping

27. For Figuring Biological Data This Week!
Bring your Biologist at Work Worksheet (completed?)
Bring your Figuring Biological Data Worksheet (read!)
Bring your Laptop with Excel installed…if you have one
Bring your Flash Drive if you do not have a laptop
Download the Course Data file from the course website:
To your Laptop with Excel…OR
To your Flash Drive