Transcript Cactus Cladistics Lab Introduction for Bio 1B GSIs

Phylogenetics of Cacti
Lab Exercise Introduction
for
Teachers ONLY
Phylogenetics of Early-Diverging
Cacti
by
Ruth Kirkpatrick, Abby Moore, Bianca Knoll, Anna Larsen, Vicente Garcia,
Andy Murdock, and Michael Park
Phylogenetics of Cacti Lab Contents:
•
•
•
•
•
•
•
•
•
•
•
Introduction & Exercise Instructions and Forms
Glossary
Photo Library
Student Data Matrices
Answer Keys to Data Matrices and Cladograms
MacClade Files
Supplementary Exercises:
Green Plant Cladistics
Cactus Biogeography
Cactus large pruned molecular data matrix
Cactus Articles
Cactus Family Characteristics:
• SPINES !!!!!
– Please handle cautiously
• Long Shoots
– Stems with long
internodes
• Short Shoots
– Stems with short
internodes
• Areoles
– Extremely short shoots of
cacti.
– Produce spines, new
long shoots (=branches).
glochids, and flowers.
Classic Cactus Characters:
•
•
•
•
•
•
Photosynthetic stems
Succulent stems
CAM metabolism/photosynthesis
Vestigial or Ephemeral leaves
Glochids (only Opuntioideae)
Live in Hot & Dry Deserts
Two More (atypical) Cactus
Lineages:
• “Pereskias”
– Live in mesic forests
of Caribbean &
Central America
• “Maihuenias”
– Live in cold & dry
regions of Patagonia
and Chile
• Both use leaves
(not stems) for
photosynthesis
“Pereskia Model”
• Pereskia species are interpreted as
“relictual cacti” and used as a general
model for the “ancestral” condition from
which more highly derived cacti
evolved.
• Maihuenioideae & Pereskioideae
grouped together by shared “absence”
of “typical” cactus characteristics.
Is the Pereskia Model correct?
A.
Traditional view of all subfamilies monophyletic with Pereskia the
earliest diverging lineage and C. & O. most derived.
B.
M. C. and O. nested within a paraphyletic Pereskia with O. sister to C.
C.
M. C. and O. nested within a paraphyletic Pereskia with M. sister to C.
D.
Monophyletic O. M. & C. all nested within a polyphyletic Pereskia.
Your Goal: To test these
hypotheses of Cactus
relationships!
How?
Using Cladistic Analysis!!!
O UTGRO UP = close relative sof C actace ae
Portulacace ae(Purslan e Family)
Anacam pserostelephiastrum(ÒP an American Love PlantÓ)
Portulacapilosa (ÒPink P urslaneÓ)
INGRO UP = C actace ae(C actu s Fam ily)
T R A DI T I O N A L S U B F A M I L I E S
C actoide ae
O pu n tioide ae
Cereus sp. (ÒCereusÓ)
Austrocylindropuntia subulata
(ÒCane ChollaÓ)
Echinocactus sp
. (ÒHedgehog CactusÓ)
Opuntia longispina(ÒPrickly P earÓ)
Quiabentia verticillata
Tephrocactus glom eratus
(ÒP aperSpine CactusÓ)
Pereskiopsisporteri (ÒAlcajerÓ)
Maih u e n ioide ae
Pere skioide ae
Maihuenia poeppigii (ÒChupa SangreÓ) Pereskia aculeata(ÒBarbados GooseberryÓ)
Pereskia bleo (ÒWax RoseÓ)
Pereskia grandifolia (ÒRose CactusÓ)
Morphological Characters
Character 1: Succulent tissues
0 = absent
1 = present
succulent = having
thick, fleshy,
water-storing
tissue
http://aquiya.skr.jp/zukan/Opuntia_microdasys_var_albispina.jpg
QuickTime™ and a
TIFF (Uncompressed) decompressor
are needed to see this picture.
Character 1: Succulent tissues
0 = absent
1 = present {all ingroup and outgroup taxa}
Character 2: Spines
0 = absent
1 = present
fruit
flower
spines
areole
succulent
stem
glochids
Opuntia (prickly pear cactus) showing typical morphological
characteristics of the Opuntioideae.
leaves
spines
Maihuenia poeppigii
Character 2: Spines
0 = absent {outgroup}
1 = present {all Cactaceae}
Character 3: Ovary position
0 = superior
1 = inferior
2 = inferior and recessed
pistil
stigma
style
ovary
anther
filament
stamen
petal
sepal
ovule
stem
receptacle
Parts of a typical flower
superior
half-inferior
(=partially
inferior)
inferior
Ovary positions
tepals
stigma
stamens
style
stem
ovary
ovule
receptacle
Cross-section of Opuntia (prickly pear) flower
showing the ovary deeply recessed into the
inferior and recessed ovary
Opuntia macrorhiza
Character 3: Ovary position
0 = superior
{outgroup taxa}
1 = inferior
2 = inferior and recessed {all Cactaceae}
{given to students}
Character 4: Short & long shoots
0 = absent
1 = present
Example: Ginkgo biloba
QuickTime™ and a
TIFF (Uncompressed) decompressor
are needed to see this picture.
http://departments.bloomu.edu/biology/pics/botany/ginkgo_mega1.jpg
areole
Areoles are extremely short shoots
spine
glochid
areole
Opuntia sp.
areole on
fruit
Opuntia sp.
spines
areole
Tephrocactus sp.
Echinocactus
Character 4: Short & long shoots
0 = absent {outgroup}
1 = present {all Cactaceae}
Character 5: Areoles
0 = absent {outgroup}
1 = present {all Cactaceae}
Character 6: Leaves
0 = present
1 = reduced and/or ephemeral
2 = absent
leaves
Pereskia sp.
leaves
Opuntia macrorhiza
glochids
spine
ephemeral
leaves
areole
glochids
Austrocylindropuntia subulata
Character 6: Leaves
0 = present
1 = reduced and/or ephemeral
2 = absent
{given to students}
Character 7: Glochids
0 = absent
1 = present
spines
glochids
detail of
glochid
Areole with spines and tuft of glochids.
glochids
Opuntia sp.
Quiabentia verticillata
Character 7: Glochids
0 = absent
1 = present {Opuntioideae}
Character 8: Ribbed stems
0 = absent
1 = present
Ribbed stems
Cereus sp.
Echinocactus grusonii
Character 8: Ribbed stems
0 = absent
1 = present {Cactoideae}
Character 9: Stem stomata
0 = absent
1 = present
http://www.richmond.edu/~jhayden/croton_site/stem_surface/53_stem_stomates_KMO.JPG
QuickTime™ and a
TIFF (Uncompressed) decompressor
are needed to see this picture.
Character 9: Stem stomata
0 = absent
1 = present
{given to students}
Character 10: Delayed bark
0 = absent
1 = present
QuickTime™ and a
TIFF (Uncompressed) decompressor
are needed to see this picture.
http://www.terragalleria.com/images/np-desert/sagu32823.jpeg
Character 10: Delayed bark
0 = absent
1 = present
{given to students}
Character 11: Majority of
photosynthesis performed by…
0 = leaves {outgroup, Pereskioideae, Maihuenia}
1 = stem
{Note: Use Character 6 for help}
Character 12: Areoles with leaves
0 = yes
1 = no
{given to students}
Character 13: Habitat
0 = mesic and seasonally dry
1 = hot and dry
2 = cold and dry
{students to look up info in lab
introduction}
Cactus Lab Data Matrices
and Venn Diagrams
This Venn Diagram example uses nested boxes to group subclades and
clades to show taxa relationships. Branches are then drawn below the Venn Diagram
sets in order to reflect the ingroup relationships in the form of a cladogram.
ingroup
1
2
3
4
5
6 = outgroup
Cladistic Analysis Example of the 3 Domains of Life
1. Characters & States  2. Data Matrix  3. Venn Diagram  4. Cladogram
1. Characters & States:
1. Membrane bound organelles
0: absent, 1: present
3. Venn Diagram (= “nested boxes”)
2. Peptidoglycan in cell wall
2, 3, 4, 5
0: present, 1: absent
3. Protein synthesis initiator
0: formyl-methionine, 1: methionine
Bacteria
Archaea
Eukarya
4. Introns
0: absent
2: present
5. Histones w/DNA
7
0: absent
1. Present
6. Circular chromosome
0: yes
1: no
7. Grow in temps > 100oC
0: no
1. yes
4. Draw and label Cladogram
2. Data Matrix
Plant Example for characters & states --> data matrix --> Venn Diagram --> Tree
1. Terrestrial
0: no, aquatic
1: yes
2. Sporophyte dom.
0: no, gmpht. dom.
1: yes
3. Branching sphyt.
0: no
1: yes
4. cuticle
0: absent
1: present
5. Vascular tissue
0: absent
1: present
6. Non-motile sperm
0: absent
1: present
7. Indep. gmpt. & spht.
0: no
1: yes
8. pollen
0: no
1: yes
9. Secondary growth
0: no
1: yes
10. Seeds
0: no
1: yes
11. Flowers
0: no
1: yes
12. Fruit
0: no
1: yes
1, 4
2, 3, 5, 7
6, 8, 9, 10
Green algae
Moss
Fern
11, 12
Gymnosperm “Pine Tree”
Angiosperm “Flowering Plant
7
11, 12
6, 8, 9, 10
2, 3, 5
1, 4
Cactus Cladistics Lab
supplemental exercises and
documents
Biogeography Supplementary Exercise:
Molecular sequence “Nexus” file of pruned list of cactus taxa and sequence.
Questions to consider:
• 1. Are your three cladograms the same or different?
• 2. Is Pereskia monophyletic, paraphyletic, or polyphyletic?
• 3. Can you identify any homoplastic characters and/or any
paraphyletic or polyphyletic groups?
• 4. Can you suggest and describe any adaptive hypotheses based on
analogous (homoplastic) characters and/or any polyphyletic taxa?
• 5. Why do you think the morphology of Maihuenia poeppigii is so very
different from its closest relatives? What might the retention of leaves
suggest about possible functions and/or adaptive scenarios?
Cactus Cladistics Lab Student
Data Matrices
C ha racters = DNA sequenc e
position, C haracter s tates =
G =guanine, A =adenine,
C =cytocine, T=thymine
15
16 17 18
19
20
21
22
23
24
25 26
27
28 29
30
A
T
A
C
A
A
G
T
A
C
T
A
“Student form”
Molecular data
Taxa:
A
Portulaca sp.
G
T
T
C
B
Anacampseros telephi astrum
G
T
T
A
A
-
A
C
A
A
G
T
A
C
T
A
C
Pereskia bleo
G
T
T
C
G
C
A
A
A
A
G
T
A
C
T
A
D
Pereskia aculeata
G
T
C
C
A
T
C
A
A
A
T
C
A
A
G
A
E
Pereskia grandifolia
G
T
T
C
A
T
C
A
G
A
T
C
A
A
G
A
F
Opuntia sp.
G
A
T
C
A
T
C
A
A
A
T
T
A
C
A
A
G
Quiabentia verticillata
G
A
T
C
A
T
C
A
A
A
T
T
T
C
A
A
H
Pereskiopsis porteri
G
A
T
C
A
T
C
A
A
A
T
T
T
C
A
A
I
Tephroca ctus sp.
G
A
T
C
A
T
C
A
A
G
T
T
A
C
A
A
J
Austrocylindropu ntia subulata
G
A
T
C
A
T
C
A
A
G
T
T
A
C
A
A
K
Maihuenia sp.
A
T
T
C
A
T
C
A
A
A
T
A
A
C
A
G
L
Echinoc actus sp.
A
T
G
C
A
T
C
A
A
A
T
A
A
C
A
T
M
Cereus sp.
A
T
G
C
A
T
C
G
A
A
T
A
A
C
A
G
Answer Keys!
Cactus Cladistics Lab Data
Matrix Keys, Venn Diagrams,
and Trees
Characters = DNA sequenc e
position, Cha racter states =
G =guanine, A =adenine,
C =cytocine, T=thymine
15
16 17 18 19 20 21 22 23 24 25 26 27 28 29 30
G
G
G
G
G
G
G
G
G
G
A
A
A
T
T
T
T
T
A
A
A
A
A
T
T
T
“Student form”
Moleculardata
Taxa:
A
Portulaca pil osa (oleracea)
B
Anacampseros telephi astrum
C
Pereskia bleo
D
Pereskia aculeata
E
Pereskia grandifolia
F
Opuntia (longispina) di lleni
G
Quiabentia verticillata
H
Pereskiopsis porteri
I
Tephroca ctus (glomer atus) articulatus
J
Austrocylindropu ntia subul ata
K
Maihuenia (poeppigii) patagonica
L
Echinoc actus sp.
M
Cereus sp.
T
T
T
C
T
T
T
T
T
T
T
G
G
C
A
C
C
C
C
C
C
C
C
C
C
C
A
A
G
A
A
A
A
A
A
A
A
A
A
T
C
T
T
T
T
T
T
T
T
T
T
A
A
A
C
C
C
C
C
C
C
C
C
C
C
C
A
A
A
A
A
A
A
A
A
A
G
A
A
A
A
G
A
A
A
A
A
A
A
A
A
A
A
A
A
A
A
A
G
G
A
A
A
G
G
G
T
T
T
T
T
T
T
T
T
T
T
T
T
C
C
T
T
T
T
T
A
A
A
A
A
A
A
A
A
T
T
A
A
A
A
A
C
C
C
A
A
C
C
C
C
C
C
C
C
T
T
T
G
G
A
A
A
A
A
A
A
A
A
A
A
A
A
A
A
A
A
A
G
T
G
Venn diagram KEY for combined data
2, 3, 4, 5, 22
9, 10, 21, 25
11, 13(1), 29(A)
15, 26(A), 30
6(1), 7, 16
26(C),28,29(G)
A B
C
A B
D
C
27
E
D
F GH
E
24
29(G)
28
26(C)
16
7
6(1)
29(A)
2
3
4
5
IJ
27
9 10
6(2),8,12,17
24
K
F G H I J
-10
22
{-(9,10&11), +13(2)}
25
21
11
13(1)
L
K
-30
L
M
-30
-(9,10&11)
13(2)
6(2)
15
26(A)
30
8
12
17
M
B
A
C K
D
E
F G H I
13
45
3 (state 2)
2
3 (state 1)
A B
C
D
9
L
6(state 1)
7
(state 2)
J
8
M
12
6 (state 2)
13 11
10
(state 1)
Morphology Based Tree
E
F G H I J
27
-10
24
29(G)
28
26(C)
16
7
6(1)
K
L
-(9,10&11)
13(2)
6(2) 8
15
-30
M
12 17
26(A) 30
29(A)
9 10
2
A B
3
4
C
5
22
D
25
21
11
13(1)
Molecular Based Tree
E
F G H I J
27
-10
24
29(G)
28
26(C)
16
7
6(1)
K
L
-30
-(9,10&11)
13(2)
6(2) 8
15 26(A)
12
M
17
30
29(A)
9 10
2
3
4
5 22
25
21
11
13(1)
Morphology & Molecular Based Tree