Transcript Welcome to Biology 122 - Home Page for Ross Koning

Looking Back at Prerequisites
Science: a methodical approach to
the acquisition of knowledge
Observation: Use the metric (SI) units to measure your world!
Question: Be curious-the bad question is the one you fail to ask!
Hypothesis: Make falsifiable educated guess to answer question
Prediction: If the hypothesis is true…
then the dependent variable will respond…
when I manipulate the independent variable.
Experiment: Manipulate the independent variable=treatment
Compare the response to an unmanipulated control
Analysis: Use statistical test and allow % for statistical error
Type 1: rejecting a true H -- Type2: failing to reject false H
Decision: Reject hypothesis or Cannot reject hypothesis
Looking Back at Prerequisites
Biology: the Study of Life
What are the fundamental properties of life?
Cellular Structure (cell = unit of life)
Metabolism = Homeostasis (PSN, Resp, N2fix, ferment, etc.)
Growth = irreversible change in size
Reproduction…failure = extinction
Acclimatization-short term responses = behavior
Adaptation-long term responses = evolution
Looking Back at Prerequisites
Biology is multidimensional
Cell
Tissue
Organ
Organ System
Organism
Population
Community
Ecosystem
This array is an example of what dimension?
Levels of Organization
What fields of biology are at each extreme?
Biochemistry and Biophysics
In this course our focus will be upon…
These levels but only
in reference to plants
Looking Back at Prerequisites
Classification
Domain
Bacteria
Eukarya
Eukarya
Kingdom
Eubacteria
Protista
Or Plantae
Plantae
Phylum
Cyanophyta
Chlorophyta
Anthophyta
Magnoliophyta
Class
Prochlorophyceae
Chlorophyceae
Dicotyledonae
Order
Prochlorales
Ulvales
Rosales
Family
Prochlorococcaceae
Ulvaceae
Rosaceae
Genus
Prochlorococcus
Ulva
Rosa
Species
P. marinus
U. lactuca
R. multiflora
MED4
Sea lettuce
Wild Rose
Common
The species name is a Latin binomial
Dead Language
Universally known
The Genus name and a specific epithet
Example: Brassica oleracea
mustard of the garden
Sometimes the binomial is not good enough!
So we add a Latin variety name as well
(also known as subspecies)
Several examples of members of species Brassica oleracea
Cabbage:
Brassica oleracea capitata
QuickTime™ and a
TIFF (Uncompressed) decompressor
are needed to see this picture.
http://www.blueoniondesign.com/blog/cabbage.jpg
Kale:
Brassica oleracea acephala
http://www.hilltopfarms.org/images/kale.jpg
Brussels sprouts:
Brassica oleracea gemmifera
QuickTime™ and a
TIFF (Uncompressed) decompressor
are needed to see this picture.
http://www.vegetables.pe.kr/vegetablesgallery/leaf_vegetables/images/brussels%20sprouts_prince%20marvel.jpg
Kohlrabi:
Brassica oleracea caulorapa
QuickTime™ and a
TIFF (Uncompressed) decompressor
are needed to see this picture.
http://www.hrt.msu.edu/course/HRT204L/VEG_ID/kohlrabi.jpg
Broccoli:
Brassica oleracea italica
QuickTime™ and a
TIFF (Uncompressed) decompressor
are needed to see this picture.
http://www.cloverseed.com.hk/web_clover_c/broccoli/broccoli_monterey.jpg
Cauliflower:
Brassica oleracea botrytis
QuickTime™ and a
TIFF (Uncompressed) decompressor
are needed to see this picture.
http://green-acres.org/images/products/cauliflower.jpg
Brassica oleracea capitata
‘King Slaw’
QuickTime™ and a
TIFF (Uncompressed) decompressor
are needed to see this picture.
QuickTime™ and a
TIFF (Uncompressed) decompressor
are needed to see this picture.
QuickTime™ and a
TIFF (Uncompressed) decompressor
are needed to see this picture.
‘Earliana’
cultivar names in
home language and
in single quotes
‘Two Seasons Hybrid’
QuickTime™ and a
TIFF (Uncompressed) decompressor
are needed to see this picture.
‘Salad Delight’
http://www.burpee.com/jump.jsp?itemID=219&itemType=CATEGORY&iMainCat=13&iSubCat=219
How many species are there?
What is a species?
Animal species concept…
if offspring are fertile then same species…
does not apply among species of other kingdoms
Prokaryotes (no sex)
Algae (sex sometimes unknown)
Allopolyploidy in plants
Lumpers
Shifting Kingdoms
Splitters
2
3
5
6
8
Bacteria
Bacteria
Bacteria
Bacteria
Bacteria
Archaebacteria
Archaebacteria
Archaebacteria
Archaebacteria
Archaebacteria
Archezoans
Archezoans
Archezoans
Archezoans
Archezoans
Euglenoids
Euglenoids
Euglenoids
Euglenoids
Euglenoids
Chrysophytes
Chrysophytes
Chrysophytes
Chrysophytes
Chrysophytes
Green Algae
Green Algae
Green Algae
Green Algae
Green Algae
Brown Algae
Brown Algae
Brown Algae
Brown Algae
Brown Algae
Red algae
Red algae
Red algae
Red algae
Red algae
Slime Molds
Slime Molds
Slime Molds
Slime Molds
Slime Molds
True Fungi
True Fungi
True Fungi
True Fungi
True Fungi
Bryophytes
Bryophytes
Bryophytes
Bryophytes
Bryophytes
Tracheophytes
Tracheophytes
Tracheophytes
Tracheophytes
Tracheophytes
Protozoans
Protozoans
Protozoans
Protozoans
Protozoans
Myxozoans
Myxozoans
Myxozoans
Myxozoans
Myxozoans
Multicellular
Animals
Multicellular
Animals
Multicellular
Animals
Multicellular
Animals
Multicellular
Animals
Extant
How Many Kingdoms?
8
5
3
Extinct
2
1
Original Cell
Extant
How Long Ago?
Land!
Plants
0.5
Multicellular
Extinct
Original Cell
1
First Eukaryotes
2
Cyanobacterial Oxygen
3
Origin of Life
4 BYBP
Evidence Categories
•
•
•
•
•
•
History - clearer recently, more obscure anciently
Fossils - stratigraphic depth, isotope decay, etc.
Chemical - metabolic products such as O2, Ss
Molecular - DNA sequence alterations, etc.
Developmental sequences - onto- phylo- geny
Biogeography - Pangea, Gondwana & Laurasia
How do we know the Evolution Pathway?
Phylogenetic Systematics
Inferences from comparison of extant organisms
Characters-Attributes of the organism
»Anatomy
»Morphology
»Development
»Physiology
»Macromolecule Sequences
Polarizing Character States
•Plesiomorphies-Ancient, shared by descendants
•Apomorphies-More-recent derivatives
»Synapomorphy-Shared among related organisms
»Autapomorphy-Found only in one organism
•Use of outgroup to compare to ingroup
Typical Cladogram
Present Extant A Extant B
A’
Time
A”
A’”
Ancient Common
Ancestor
This branching of
evolution is called
cladogenesis.
Extinct
A’ is the common
Transitional ancestor of extant
Forms
A and extant B
This straight line of
evolution is called
anagenesis.
Typical Cladogram
Present Extant A Extant B Extant C
A’
Time
A”
A’”
A’ A B constitute a clade
A” C are a grade (is paraphyletic)
A” C A’ A B are a clade
A’ A B is the sister group of C
Ancient Common
Ancestor
Typical Cladogram
Present Extant A Extant B Extant C Extant D Extant E
A’
Time
A”
A’”
Ancient Common
Ancestor
D A””’ E are a ?
clade
Extinct!
A””
A””’
Common ancestor +
A””’ D E are a ?
grade
The ABC clade may be, say, a genus.
The DE clade may be another genus…
in the same family
The ABCDE clade would be the family
Typical Cladogram
Present Extant A Extant B Extant C Extant D Extant E
A’
Time
A”
A’”
Ancient Common
Ancestor
On the other
hand…
Extinct!
A””
A””’
AB are a genus
C is a monotypic
genus
DE are a genus
ABC might be one family
DE are in another family
ABCDE might constitute an order
Extant
Protists are polyphyletic (unnatural taxon)
Animals and
Fungi are a clade!
Plants are a clade (monophyletic)
Extinct
Eukaryotic organisms are a clade
Prokaryotic organisms are a grade (paraphyletic)
Living organisms are part of one clade
Original Cell
Character Number
Taxon 1
2
3
OG 0
0
0
A
0
0
1
B
1
0
0
C
0
1
1
D
0
0
1
E
1
0
0
4
0
1
1
1
1
1
5
0
1
0
0
0
0
6
0
0
0
1
1
0
7
0
0
1
0
0
0
8
0
1
1
1
1
1
9
0
0
0
1
1
0
10
0
1
0
1
1
0
OG
ABCDE
4
8
Character Number
Taxon 1
2
3
OG 0
0
0
A
0
0
1
B
1
0
0
C
0
1
1
D
0
0
1
E
1
0
0
4
0
1
1
1
1
1
5
0
1
0
0
0
0
6
0
0
0
1
1
0
7
0
0
1
0
0
0
8
0
1
1
1
1
1
9
0
0
0
1
1
0
10
0
1
0
1
1
0
OG
ABCDE
ACD
BE
3
4
8
10
Character Number
Taxon 1
2
3
OG 0
0
0
A
0
0
1
B
1
0
0
C
0
1
1
D
0
0
1
E
1
0
0
4
0
1
1
1
1
1
5
0
1
0
0
0
0
6
0
0
0
1
1
0
7
0
0
1
0
0
0
8
0
1
1
1
1
1
9
0
0
0
1
1
0
OG
10
0
1
0
1
1
0
A
ACD CD
BE
1
3
4
8
10
6
9
Character Number
Taxon 1
2
3
OG 0
0
0
A
0
0
1
B
1
0
0
C
0
1
1
D
0
0
1
E
1
0
0
OG
4
0
1
1
1
1
1
5
0
1
0
0
0
0
6
0
0
0
1
1
0
B
7
0
0
1
0
0
0
8
0
1
1
1
1
1
9
0
0
0
1
1
0
E
10
0
1
0
1
1
0
autapomorphies
A
D
C
5
7
CD
BE
2
1
3
4
8
10
6
9
How do you DO classification?
Warmup!
1. Get with a partner to form a team
2. Look over the cards you are given for your team
3. Every group gets the same set of 8 cards
•
•
•
•
•
•
•
•
Bob
Sue
Deb
Lou
Jen
Cal
Hal
Val
4. Sort the cards into what you believe may be natural groups
• Names do not count, use only shapes shown on card
5. Decide who will tell the class how you sorted your groups
• What theme unites/defines each group
How do you DO classification?
Sharing our Results
1.
2.
3.
4.
5.
The Forest Meet!
This game is a cross-country race in a forest
All runners enter the forest by a single south entrance
The finish line is the northern boundary of the forest
Runners need not exit at any particular place at the finish
There are many trails through the woods
• Trails only bifurcate (form two branches) at forks
• Trails never join together or rejoin after forking
6. Along the trail straightaways are check-in stations
7. At each check-in station, a worker has a unique stamp
8. Each runner has a card that is stamped as s/he passes a station
9. Runners are not allowed to retrace a path
10. All runners must finish the race
11. Using the punch cards handed in at the finish line:
• Sketch the trail map
• Show all station locations (on the straightaways)
• Mark the exit used by each runner
The Forest Meet


Bob
x
Sue
x
x

x


x


Deb
x

Lou
x
x
x
Jen
x
x
Cal
x
Hal
x
x
x
x
x
x
x
x
x
Val
x
x
x
x
x
x
x




Sharing our Results
x
x
x
The Forest Meet


Bob
x
Sue
x
x

x


x


Deb
x

Lou
x
x
x
Jen
x
x
Cal
x
Hal
x
x
x
x
x
x




Sharing our Results
x
x
x
x
x
x
x
x
Val
x
x
Total
8
5
x
x
x
2
1
4
2
1
2
1
3
1
1
The Forest Meet
Sharing our Results
Runners can finish anywhere along this northern edge
All of the runners passed the
circle station, so this station
must be near the start 
Start
The Forest Meet


Bob
x
Sue
x
x

x


x


Deb
x

Lou
x
x
x
Jen
x
x
Cal
x
Hal
x
x
x
x
x
x




Sharing our Results
x
x
x
x
x
x
x
x
Val
x
x
Total
8
5
x
x
x
2
1
4
2
1
2
1
3
1
1
The Forest Meet
Sharing our Results
Runners can finish anywhere along this northern edge
Five of the runners passed the
teardrop station, but three did
not, so our 8 runners must
have divided into two groups
Bob, Deb, Cal
Sue, Lou, Jen, Hal, Val


Start
The Forest Meet


Bob
x
Sue
x
x

x


x


Deb
x

Lou
x
x
x
Jen
x
x
Cal
x
Hal
x
x
x
x
x
x




Sharing our Results
x
x
x
x
x
x
x
x
Val
x
x
Total
8
5
x
x
x
2
1
4
2
1
2
1
3
1
1
The Forest Meet
Hal
Because paths do not
rejoin, Hal is separated
and thus we can draw
him at the finish line
Sharing our Results
Runners can finish anywhere along
this northern edge
Four runners of the group of
five passed the diamond
station, but Hal did not, so he
split away before this station
Sue, Lou, Jen, Val
Bob, Deb, Cal
Sue, Lou, Jen, Hal, Val



Start
The Forest Meet


Bob
x
Sue
x
x

x


x


Deb
x

Lou
x
x
x
Jen
x
x
Cal
x
Hal
x
x
x
x
x
x




Sharing our Results
x
x
x
x
x
x
x
x
Val
x
x
Total
8
5
x
x
x
2
1
4
2
1
2
1
3
1
1
The Forest Meet
Sharing our Results
Hal
Finish Line
Bob, Deb, and Cal all
passed the triangle
station so it was along
the path they shared
Bob, Deb, Cal
Sue, Lou, Jen, Val




Start
The Forest Meet


Bob
x
Sue
x
x

x


x


Deb
x

Lou
x
x
x
Jen
x
x
Cal
x
Hal
x
x
x
x
x
x




Sharing our Results
x
x
x
x
x
x
x
x
Val
x
x
Total
8
5
x
x
x
2
1
4
2
1
2
1
3
1
1
The Forest Meet
Bob
Sharing our Results
Hal
Finish Line
Jen and Lou passed the heart
station, but Sue and Val passed
the spade station, so the group
of four divided
Jen, Lou
Sue, Val
Deb, and Cal
passed the star
station, but Bob
did not, so the
group divided
Deb, Cal


Sue, Lou, Jen, Val
Bob, Deb, Cal 




Start
The Forest Meet


Bob
x
Sue
x
x

x


x


Deb
x

Lou
x
x
x
Jen
x
x
Cal
x
Hal
x
x
x
x
x
x




The rest are autapomorphies
x
x
x
x
x
x
x
x
Val
x
x
Total
8
5
x
x
x
2
1
4
2
1
2
1
3
1
1
The Forest Meet
Bob
Cal
Deb
Hal
Autapomorphies!
Jen
Lou
Sue



Jen, Lou
Deb, Cal

Val


Sue, Val


Notice the runners
are in alphabetical
order. But this is not
the only solution


All branches can be rotated:

e.g.: Lou before Jen

Sue-Val before Jen-Lou
Start
The Forest Meet!
But Wait!
We have one really-slow runner just exiting!
Here is his card…figure out his pathway
The Forest Meet


Bob
x
Sue
x
x

x


x


Deb
x

Lou
x
x
x
Jen
x
x
Cal
x
Hal
x
x
x
x
x
Ross
x
x
x
x
x
x
Val
x
x
x
x
x
x
x




Sharing our Results
x
x
x
x
x
The Forest Meet
Bob
Cal
Deb
Hal Ross Jen




Lou
Sue
Val






What did Ross do?

What is parsimonious?
Are our ideas wrong?
 Maybe Ross followed Hal..
Then hit a rougue station?

Start
The Clade Race!
1. This
the evolution
of asome
Thisgame
gamerepresents
is a cross-country
race in
forestrelated organisms
2. The
are the
believed
cladesouth
(w/common
Allorganisms
runners enter
foresttobybea asingle
entranceancestor)
3. The
are northern
using areboundary
all extant of
(none
are fossils)
Theorganisms
finish linewe
is the
the forest
4. We
make no
assumptions
possible place
phenotypes
observed
Runners
need
not exit at about
any particular
at the finish
5. We
make
assumptions
aboutthethewoods
evolution pathway
There
arefew
many
trails through
• Cladogenesis
divides one
species
two species
Trails only bifurcate
(form
two into
branches)
at forks
• WeTrails
assume
there
no convergent
or after
parallel
evolution
never
joinis together
or rejoin
forking
6. Anagenesis
is expected
to occurare
between
generations
Along the trail
straightaways
check-in
stations
shows itsstation,
recordaofworker
changes
genotype
7. Evolution
At each check-in
hasina the
unique
stamp
8. The
record
of has
evolution
genotype
is shown
the phenotype
Each
runner
a card in
that
is stamped
as s/heinpasses
a station
9. Evolution
is permanent;
reversals of states
Runners are
not allowedwe
toassume
retrace no
a path
In this
study,must
we are
using
fossils of extinct clade members
10. All
runners
finish
theno
race
11. Using the phenotypes
punch cardsobserved
handed ininatthe
theextant
finishorganisms:
line:
• Sketch
thethe
cladogram
Sketch
trail map
• Show
thealllocation
character
transitions
Show
station of
locations
(onstate
the straightaways)
• Show
thethe
relationships
the taxa
Mark
exit used byamong
each runner
How do you DO cladistics?
1. Look at a group of organisms that you think are related
2. Find a not-too-distantly related (primitive?) out-group
3. Select characters that will help to distinguish the organisms
4. Polarize the character states by:
• Stratigraphic sequence (fossil sequence)
• Developmental sequence (ontogeny recaps phylogeny)
• Outgroup comparison
5. Build a data matrix
6. Group by number of synapomorphies (shared derived)
7. Sketch possible cladograms
8. Seek simplest (most parsimonious) cladogram