Looking Back at Prerequisites

1
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
truethen the dependent variable will
respondwhen I manipulate the independent
variable. Experiment Manipulate the independent
variabletreatmentCompare the response to an
unmanipulated control Analysis Use statistical
test and allow for statistical errorType 1
rejecting a true H -- Type2 failing to reject
false H Decision Reject hypothesis or Cannot
reject hypothesis
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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 Reproductionfailure extinction Acclimatiza
tion-short term responses behavior Adaptation-lo
ng term responses evolution
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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
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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
Common MED4 Sea lettuce Wild Rose
5
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
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Cabbage Brassica oleracea capitata
http//www.blueoniondesign.com/blog/cabbage.jpg
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Kale Brassica oleracea acephala
http//www.hilltopfarms.org/images/kale.jpg
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Brussels sprouts Brassica oleracea gemmifera
http//www.vegetables.pe.kr/vegetablesgallery/leaf
_vegetables/images/brussels20sprouts_prince20mar
vel.jpg
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Kohlrabi Brassica oleracea caulorapa
http//www.hrt.msu.edu/course/HRT204L/VEG_ID/kohlr
abi.jpg
10
Broccoli Brassica oleracea italica
http//www.cloverseed.com.hk/web_clover_c/broccoli
/broccoli_monterey.jpg
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Cauliflower Brassica oleracea botrytis
http//green-acres.org/images/products/cauliflower
.jpg
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Brassica oleracea capitata
cultivar names in home language and in single
quotes
King Slaw
Two Seasons Hybrid
Earliana
Salad Delight
http//www.burpee.com/jump.jsp?itemID219itemType
CATEGORYiMainCat13iSubCat219
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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

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Shifting Kingdoms
Lumpers
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
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How Many Kingdoms?
Extant
Extinct
Long Time with Prokaryotes only
Original Cell
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How Long Ago?
Extant
Plants
Land!
Multicellular
First Eukaryotes
Extinct
Cyanobacterial Oxygen
Long Time with Prokaryotes only
Origin of Life
Original Cell
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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

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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

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Typical Cladogram
Extant A
Present
This branching of evolution is called
cladogenesis.
Extinct Transitional Forms
A is the common ancestor of extant A and extant B
Time
This straight line of evolution is called
anagenesis.
Common Ancestor
Ancient
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Typical Cladogram
Extant A
Extant B
Present
A
A A B constitute a clade
A C are a grade (is paraphyletic)
A
Time
A C A A B are a clade
A
A A B is the sister group of C
Common Ancestor
Ancient
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Typical Cladogram
Present
A
D A E are a ? clade
Common ancestor A D E are a ? grade
A
Time
A
The ABC clade may be, say, a genus. The DE clade
may be another genus in the
same family
Common Ancestor
Ancient
The ABCDE clade would be the family
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Typical Cladogram
Extant A
Extant C
Extant D
Extant E
Extant B
Present
A
On the other hand
A
AB are a genus C is a monotypic
genus DE are a genus
Extinct!
A
Time
A
A
ABC might be one family DE are in another family
Common Ancestor
Ancient
ABCDE might constitute an order
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Protists are polyphyletic (unnatural taxon)
Extant
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
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Character Number Taxon 1 2 3 4 5 6 7 8 9 10
OG 0 0 0 0 0 0 0 0 0 0 A 0 0 1 1 1 0 0 1 0 1
B 1 0 0 1 0 0 1 1 0 0 C 0 1 1 1 0 1 0 1 1 1
D 0 0 1 1 0 1 0 1 1 1 E 1 0 0 1 0 0 0 1 0 0
OG
ABCDE
8
4
25
Character Number Taxon 1 2 3 4 5 6 7 8 9 10
OG 0 0 0 0 0 0 0 0 0 0 A 0 0 1 1 1 0 0 1 0 1
B 1 0 0 1 0 0 1 1 0 0 C 0 1 1 1 0 1 0 1 1 1
D 0 0 1 1 0 1 0 1 1 1 E 1 0 0 1 0 0 0 1 0 0
OG
ABCDE
ACD
8
4
26
Character Number Taxon 1 2 3 4 5 6 7 8 9 10
OG 0 0 0 0 0 0 0 0 0 0 A 0 0 1 1 1 0 0 1 0 1
B 1 0 0 1 0 0 1 1 0 0 C 0 1 1 1 0 1 0 1 1 1
D 0 0 1 1 0 1 0 1 1 1 E 1 0 0 1 0 0 0 1 0 0
OG
ACD
BE
10
3
8
4
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Character Number Taxon 1 2 3 4 5 6 7 8 9 10
OG 0 0 0 0 0 0 0 0 0 0 A 0 0 1 1 1 0 0 1 0 1
B 1 0 0 1 0 0 1 1 0 0 C 0 1 1 1 0 1 0 1 1 1
D 0 0 1 1 0 1 0 1 1 1 E 1 0 0 1 0 0 0 1 0 0
autapomorphies
OG
A
CD
BE
1
9
6
10
3
8
4
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How do you DO classification?
Warmup!

• Get with a partner to form a team
• Look over the cards you are given for your team
• Every group gets the same set of 8 cards
• Bob
• Sue
• Deb
• Lou
• Jen
• Cal
• Hal
• Val
• Sort the cards into what you believe may be
  natural groups
• Names do not count, use only shapes shown on card
• Decide who will tell the class how you sorted
  your groups
• What theme unites/defines each group

29
How do you DO classification?

• Sharing our Results

30
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
• Along the trail straightaways are check-in
  stations
• At each check-in station, a worker has a unique
  stamp
• Each runner has a card that is stamped as s/he
  passes a station
• Runners are not allowed to retrace a path
• All runners must finish the race
• 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

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The Forest Meet

• Sharing our Results

Bob Sue Deb Lou Jen Cal Hal Val
? x x x x x x x x
? x x x x x
? x x
? x
? x x x x
? x x
? x
? x x
? x
? x x x
? x
? x
32
The Forest Meet

• Sharing our Results

Bob Sue Deb Lou Jen Cal Hal Val Total
? x x x x x x x x 8
? x x x x x 5
? x x 2
? x 1
? x x x x 4
? x x 2
? x 1
? x x 2
? x 1
? x x x 3
? x 1
? x 1
33
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
34
The Forest Meet

• Sharing our Results

Bob Sue Deb Lou Jen Cal Hal Val Total
? x x x x x x x x 8
? x x x x x 5
? x x 2
? x 1
? x x x x 4
? x x 2
? x 1
? x x 2
? x 1
? x x x 3
? x 1
? x 1
35
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
Sue, Lou, Jen, Hal, Val
Bob, Deb, Cal
?
?
Start
36
The Forest Meet

• Sharing our Results

Bob Sue Deb Lou Jen Cal Hal Val Total
? x x x x x x x x 8
? x x x x x 5
? x x 2
? x 1
? x x x x 4
? x x 2
? x 1
? x x 2
? x 1
? x x x 3
? x 1
? x 1
37
The Forest Meet

• Sharing our Results

Hal
Runners can finish anywhere along this northern
edge
Because paths do not rejoin, Hal is separated and
thus we can draw him at the finish line
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
38
The Forest Meet

• Sharing our Results

Bob Sue Deb Lou Jen Cal Hal Val Total
? x x x x x x x x 8
? x x x x x 5
? x x 2
? x 1
? x x x x 4
? x x 2
? x 1
? x x 2
? x 1
? x x x 3
? x 1
? x 1
39
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
Sue, Lou, Jen, Val
Bob, Deb, Cal
?
?
?
?
Start
40
The Forest Meet

• Sharing our Results

Bob Sue Deb Lou Jen Cal Hal Val Total
? x x x x x x x x 8
? x x x x x 5
? x x 2
? x 1
? x x x x 4
? x x 2
? x 1
? x x 2
? x 1
? x x x 3
? x 1
? x 1
41
The Forest Meet

• Sharing our Results

Hal
Bob
Finish Line
Jen and Lou passed the heart station, but Sue and
Val passed the spade station, so the group of
four divided
Deb, and Cal passed the star station, but Bob did
not, so the group divided
Sue, Val
Jen, Lou
Deb, Cal
?
?
Sue, Lou, Jen, Val
?
Bob, Deb, Cal
?
?
?
?
Start
42
The Forest Meet

• The rest are autapomorphies

Bob Sue Deb Lou Jen Cal Hal Val Total
? x x x x x x x x 8
? x x x x x 5
? x x 2
? x 1
? x x x x 4
? x x 2
? x 1
? x x 2
? x 1
? x x x 3
? x 1
? x 1
43
The Forest Meet

• Autapomorphies!

Hal
Bob
Cal
Deb
Jen
Lou
Sue
Val
?
?
?
Jen, Lou
Sue, Val
Deb, Cal
?
?
?
?
?
?
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
44
The Forest Meet!
But Wait! We have one really-slow runner just
exiting! Here is his cardfigure out his pathway
45
The Forest Meet

• Sharing our Results

Bob Sue Deb Lou Jen Cal Hal Val Ross
? x x x x x x x x x
? x x x x x x
? x x
? x
? x x x x
? x x
? x x
? x x
? x
? x x x
? x
? x x
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The Forest Meet
Hal
Bob
Cal
Deb
Jen
Lou
Sue
Val
Ross
?
?
?
?
?
?
?
?
?
?
What did Ross do? What is parsimonious? Are our
ideas wrong?
?
?
Maybe Ross followed Hal.. Then hit a rougue
station?
?
Start
47
The Clade Race!

• 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
• Along the trail straightaways are check-in
  stations
• At each check-in station, a worker has a unique
  stamp
• Each runner has a card that is stamped as s/he
  passes a station
• Runners are not allowed to retrace a path
• All runners must finish the race
• 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

1. This game represents the evolution of some
related organisms
2. The organisms are believed to be a clade
(w/common ancestor)
3. The organisms we are using are all extant
(none are fossils)
4. We make no assumptions about possible
phenotypes observed
5. We make few assumptions about the evolution
pathway
Cladogenesis divides one species into two
species
We assume there is no convergent or parallel
evolution
6. Anagenesis is expected to occur between
generations
7. Evolution shows its record of changes in the
genotype
8. The record of evolution in genotype is shown
in the phenotype
9. Evolution is permanent we assume no reversals
of states
10. In this study, we are using no fossils of
extinct clade members
11. Using the phenotypes observed in the extant
organisms
Sketch the cladogram
Show the location of character state
transitions
Show the relationships among the taxa
48
How do you DO cladistics?

• Look at a group of organisms that you think are
  related
• Find a not-too-distantly related (primitive?)
  out-group
• Select characters that will help to distinguish
  the organisms
• Polarize the character states by
• Stratigraphic sequence (fossil sequence)
• Developmental sequence (ontogeny recaps
  phylogeny)
• Outgroup comparison
• Build a data matrix
• Group by number of synapomorphies (shared
  derived)
• Sketch possible cladograms
• Seek simplest (most parsimonious) cladogram