1 Cladistics Reading for this topic: Worobey et al. 2004. Contaminated polio vaccine theory refuted. Nature 428: 820. [note: when requesting this, request a color copy] I. Terms & Concepts A. Phylogeny vs. Cladogram I. Terms & Concepts B. Phylogeny vs. Tokogeny
This document is posted to help you gain knowledge. Please leave a comment to let me know what you think about it! Share it to your friends and learn new things together.
Transcript
1
Cladistics
Reading for this topic: Worobey et al. 2004. Contaminated polio vaccine theory refuted. Nature 428: 820.
[note: when requesting this, request a color copy]
I. Terms & ConceptsA. Phylogeny vs. Cladogram
I. Terms & ConceptsB. Phylogeny vs. Tokogeny
2
I. Terms & ConceptsC. Clades & Monophyletic groups
e.g., Carpel Presence: 0 = absent; 1 = present.g p p
3
I. Terms & ConceptsE. Phylogenetic Evidence
1. Characters & Character states
Molecular Characters(e.g., DNA sequence characters)
Protein coding genes (e g cox1 or rbcL)Protein coding genes (e.g., cox1 or rbcL)Structural RNA genes (e.g., 18S or 26S rDNA)
I. Terms & ConceptsE. Phylogenetic Evidence
1. Characters & Character states
Molecular Characters(e.g., DNA sequence characters)
Protein coding genes (e g cox1 or rbcL)Protein coding genes (e.g., cox1 or rbcL)Structural RNA genes (e.g., 18S or 26S rDNA)
e.g., Position 36 in rbcL gene: 0 = A; 1 = G; 2 = C; 3 = T.
or
e.g., Position 36 in rbcL gene: A; G; C; T.
I. Terms & ConceptsE. Phylogenetic Evidence
1. Characters & Character states
Molecular Characters
(e.g., amino acid sequence characters)
P iti 5 i bi 0 l t i 1 li te.g., Position 5 in rubisco: 0 = glutamine; 1 = proline; etc.
4
I. Terms & ConceptsE. Phylogenetic Evidence
2. Apomorphies vs. plesiomorphies
a. autapomophy vs. synapomorphy
b synapomorphy vs symplesiomorphyb. synapomorphy vs. symplesiomorphy
c. hashmarks
I. Terms & ConceptsE. Phylogenetic Evidence
3. Homology, analogy, and homoplasy
I. Terms & ConceptsE. Phylogenetic Evidence
3. Homology, analogy, and homoplasy
Homology = similarity due to common descent
e.g., plicate leaves in Cocos and Serenoae g petals in Magnolia and Liriodendrone.g., petals in Magnolia and Liriodendrone.g., 5 stamens in Solanum and Capsicume.g., flippers in whales and arms (forelimbs)
in terrestrial mammals.e.g., lack of vertebrae in bacteria, plants,
snails
5
I. Terms & ConceptsE. Phylogenetic Evidence
3. Homology, analogy, and homoplasy
Analogy = similarity due to similar function(usually only superficial)
e g wings in birds and bats and insectse.g., wings in birds and bats and insectse.g., reduced to absence petals in
Poaceae and Fagaceaee.g., succulence in Aloe and Crassula leavese.g., tendrils in grapes and bean plants
I. Terms & ConceptsE. Phylogenetic Evidence
3. Homology, analogy, and homoplasy
Homoplasy = confounds phylogenetic inference b/c it creates similarity that is not homologous
e g reversalse.g., reversalse.g., convergence
I. Terms & ConceptsE. Phylogenetic Evidence
3. Homology, analogy, and homoplasy
Primary Homology Assessment(during character coding and scoring)
e.g., PETAL COLOR: 0 = red; 1 = blue
6
I. Terms & ConceptsE. Phylogenetic Evidence
3. Homology, analogy, and homoplasy
Secondary Homology Assessment(read from cladogram)
Sp. A Red
Sp. B Red
Sp. D Blue
Sp. E Blue
Sp. F Blue
Sp. C Red
I. Terms & ConceptsE. Phylogenetic Evidence
3. Homology, analogy, and homoplasy
Secondary Homology Assessment(read from cladogram)
Sp. A Red
Sp. B Red
Sp. C Red
Sp. D Blue
Sp. E Blue
Sp. F Blue
II. Cladogram ConstructionA. Scope
Ingroup vs. outgroup
Leaf shapeIG Sp. A cordateIG Sp. B cordate
C
B
A
DIG Sp. B cordateIG Sp. C ellipticIG Sp. D elliptic
B
1 step on this unrooted network
7
II. Cladogram ConstructionA. Scope
Ingroup vs. outgroup
Leaf shapeIG Sp. A cordateIG Sp. B cordate
C
B
A
D
Root here?
IG Sp. B cordateIG Sp. C ellipticIG Sp. D elliptic
B
Root here?
II. Cladogram Construction
DBA
1 step on this rooted network
C
A. Scope
Ingroup vs. outgroup
Leaf shapeIG Sp. A cordateIG Sp. B cordate
1 step on this rooted networkProblem: These are equally
parsimonious
A C DB
IG Sp. B cordateIG Sp. C ellipticIG Sp. D elliptic
II. Cladogram Construction
1 step on this rooted network
A. Scope
Ingroup vs. outgroup
Leaf shapeIG Sp. A cordateIG Sp. B cordate
D A BC
1 step on this rooted network
A C DB
IG Sp. B cordateIG Sp. C ellipticIG Sp. D elliptic
Problem: These are equallyparsimonious
8
II. Cladogram Construction
1 step on this
A. Scope
Ingroup vs. outgroup
Leaf shapeIG Sp. A cordateIG Sp. B cordate
OG A BCD
2 steps on this rooted tree, either way…
1 step on this rooted network
OG C DB
IG Sp. B cordateIG Sp. C ellipticIG Sp. D ellipticOG Sp. elliptic
AOG C DBA
II. Cladogram ConstructionB. Data Matrix
II. Cladogram ConstructionC. Parsimony
to cladogram construction / phylogenetic inference
1. For one character at a time
9
How to infer a phylogenyOrHow to build a cladogram:Synapomorphies
Evidences for relationships? Shared derived character states.
10
How to infer a phylogenyOrHow to build a cladogram:Synapomorphies
Notochord; hollow dorsal nerve chord
How to infer a phylogenyOrHow to build a cladogram:Synapomorphies
Notochord; hollow dorsal nerve chord
How to infer a phylogenyOrHow to build a cladogram:Synapomorphies
Notochord; hollow dorsal nerve chord
vertebrae; jaws
11
How to infer a phylogenyOrHow to build a cladogram:Synapomorphies
vertebrae; jaws
Lungs, 4-legs
Notochord; hollow dorsal nerve chord
How to infer a phylogenyOrHow to build a cladogram:Synapomorphies
vertebrae; jaws
Claws or nails
Lungs, 4-legs
Notochord; hollow dorsal nerve chord
How to infer a phylogenyOrHow to build a cladogram:Synapomorphies
vertebrae; jaws
Claws or nails
Fur; mammary glands
Notochord; hollow dorsal nerve chord
Lungs, 4-legs
12
How to infer a phylogenyOrHow to build a cladogram:Synapomorphies
vertebrae; jaws
Claws or nails
Fur; mammary glands
Loss of tail
Notochord; hollow dorsal nerve chord
Lungs, 4-legs
II. Cladogram ConstructionC. Parsimony
to cladogram construction / phylogenetic inference
1. For one character at a time (e.g., Tutorial 1)
II. Cladogram ConstructionSimple when all characters yield compatible results i.e., no homoplasy, where one character does not contradict another
Examples of homoplasy: reversal and parallelism/convergence
13
II. Cladogram Constructione.g., adding snake would introduce a reversal regarding
absence of legs.
II. Cladogram Constructione.g., adding pedalism as a character would introduce a
parallelism / convergence regarding bipedalism.
II. Cladogram ConstructionC. Application of Parsimony
to cladogram construction / phylogenetic inference
2. For multiple characters at a time (e.g., Tutorial 2, but below is different)
a. Start with all possible ingroup topologies
14
II. Cladogram ConstructionC. Application of Parsimony
to cladogram construction / phylogenetic inference
2. For multiple characters at a time (e.g., Tutorial 2)
b. Use parsimony to map characters
II. Cladogram ConstructionC. Application of Parsimony
to cladogram construction / phylogenetic inference
2. For multiple characters at a time (e.g., Tutorial 2)
c. Choose cladogram with fewer steps
10 “steps”
vertebrae; jaws
Claws or nails
Fur; mammary glands
Loss of tail
Notochord; hollow dorsal nerve chord
Lungs, 4-legs
15
How to evaluate an alternative cladogram? Parsimony (number of steps)
How to evaluate an alternative cladogram? Parsimony (number of steps)
Notochord; hollow dorsal nerve chord
How to evaluate an alternative cladogram? Parsimony (number of steps)
vertebrae; jaws
vertebrae; jaws
Notochord; hollow dorsal nerve chord
16
How to evaluate an alternative cladogram? Parsimony (number of steps)
vertebrae; jaws
vertebrae; jaws
Notochord; hollow dorsal nerve chord
Lungs, 4-legs
Lungs, 4-legs
How to evaluate an alternative cladogram? Parsimony (number of steps)
vertebrae; jaws
vertebrae; jaws
Notochord; hollow dorsal nerve chord
Lungs, 4-legs
Lungs, 4-legs
Claws or nails
Claws or nails
How to evaluate an alternative cladogram? Parsimony (number of steps)
vertebrae; jaws
vertebrae; jaws
Notochord; hollow dorsal nerve chord
Lungs, 4-legs
Lungs, 4-legs
Claws or nails
Claws or nails
Fur; mamm
Fur; mammary glands
17
How to evaluate an alternative cladogram? Parsimony (number of steps)
vertebrae; jaws
vertebrae; jaws
Notochord; hollow dorsal nerve chord
Lungs, 4-legs
Lungs, 4-legs
Claws or nails
Claws or nails
Fur; mamm
Fur; mammary glands
tail
How to evaluate an alternative cladogram? Parsimony (number of steps)
17 “steps”
vertebrae; jaws
vertebrae; jaws
Notochord; hollow dorsal nerve chord
Lungs, 4-legs
Lungs, 4-legs
Claws or nails
Claws or nails
Fur; mamm
Fur; mammary glands
tail
How to evaluate an alternative cladogram? Parsimony (number of steps)
18 “steps”
karate
http://www.youtube.com/watch?v=_kRb06w_XPo
vertebrae; jaws
vertebrae; jaws
Notochord; hollow dorsal nerve chord
Lungs, 4-legs
Lungs, 4-legs
Claws or nails
Claws or nails
Fur; mamm
Fur; mammary glands
tail
18
III. Uses of CladogramsA. Taxonomies (Classifications)
1. Revision of Existing Classification Schemes
(e.g., angiosperms)
III. Uses of CladogramsAngiosperms are monophyletic: therefore, we could
recognize as a taxon (e.g., Magnoliophyta or Magnoliopsida)
•Review synapomorphies from Taxonomic Overview lectures
magnoliids
nymphaeids(water-lilies & friends)
asteridscaryophyllids
rosids
monocotsRanunculids& other primitive eudicots
magnoliids
nymphaeids(water-lilies & friends)
But what about classic subdivision into “monocots” &“dicots?” e.g., Cronquist (1981) Which of Cronquist’s classes is not monophyletic (i.e., which is paraphyletic)?
But what about classic subdivision into “monocots” &“dicots?” e.g., Cronquist (1981) Which of Cronquist’s classes is not monophyletic (i.e., which is paraphyletic)?
Analogous to situation with birds, dinosaurs and reptiles:
Birds evolved from theropod dinosaurs and dinosaurs evolved from reptiles. Thus, the old classification of Reptilia and Aves as classes violates cladistic principles of classification.
More: Cronquist’s Magnoliidae included water-lilies, Magnoliids, and some primitive eudicots.
III. Uses of CladogramsA. Taxonomies (Classifications)
2. Construction of new classification schemes
(e.g., cycads)
21
1. Most parsimonious cladogram from Stevenson (1992).
2. Classification based on cladogram.
III. Uses of CladogramsA. Taxonomies (Classifications)
3. How to recognize new taxa within existing shemes
(e.g., spiderworts)
e.g., recognition of new genus, Plowmanianthus, in Commelinaceae (2004).
Timeline:
1. 1976 – Strange Commelinaceae discovered at Field Museum Herbarium- were misplaced in Gesneriaceae indet folders
2. Herbarium search turns up several more
3. Ca. 1980 - Tim Plowman returns from S America w/ living plant
4. C-some counts, flower point to relationship with Cochliostema...
22
Timeline (Continued):
5. 1995-2001: Fieldwork inS America reveals new discoveries that further support affinityw/ Cochliostema.
...
1 cm
Cochliostema1. NW South America.2. n = 19.3. Epiphytic in trees.4. Fringed petals.5. Reduction to 3 stamens.6. Filaments basally fused.7. Anthers concealed by
fused filament hairs.8. Anthers spirally coiled.
3. 4-7. 4-8.
Summary of Biogeography & character states uniting & differentiatingCochliostema and these new undescribed species.
8. Anthers spirally coiled.
Undescribed spp.1. NW South America.2. n=19.3. Semi-terrestrial: rooting
only in leaf litter. 4. Fringed petals.5. Reduction to 3 stamens.6. Filaments basally fused.7. Anthers concealed by
Cladistic analysis of Hardy (2001) provided support for the recognition of two genera, with the undescribed species comprising the second genus, Plowmanianthus.________________________________________
Which of the following three cladograms match the one obtained by Hardy?
Hint: remember Hennig’s principle that only monophyletic groups should be named.
Hint 2: Hennig said that clades (and taxa) are recognized based on synapomorphies, not symplesiomorphies.
A
B C
23
III. Uses of CladogramsB. Disease Origins & Disease Forensics
HIV origins
Species Virulence Transmittability Prevalence Purported origin
Table 1. A comparison of species (strains) of Human Immunodeficiency Virus (HIV).
HIV-1 High High Global Common Chimp
HIV-2 Lower Low West Africa Sooty Mangabey
1992: Rolling Stone, Tom Curtis:HIV-1 (human immunodeficiency virus type 1) may have jumped into humans via OPV
•Chimps have related Simian IV (SIVcpz) •Human HIV is clearly derived from SIVcpz•Certain population of chimps in DR Congo were allegedly used to prepare OPV by Hilary Koprowski in the 1950’s.•Rolling stone retracts story.
1999: “The River: A Journey to the
e.g., HIV origins
1999: The River: A Journey to the Source of HIV and AIDS” by Edward Hooper.
•7 yrs journalistic research. •His conclusion: “Good” evidence for OPV-origin.•http://www.aidsorigins.com/
Map of the Democratic Republic of the Congo
24
Worobey et al. 2004. Contaminated polio vaccine theory refuted. Nature428: 820. Map of chimp
subspecies Pan troglodytes troglodytes (green) and P. t. schweinfurthii (red)
Cladogram showing phylogenetic relation of HIV-1 types to SIV found in Ptt.
HIV transmission (disease forensics)
CDC Teams Up with Systematists:
•1990’s: Florida dentist was suspected of transmitting HIV to several of his patients.
•Several of his patients were indeed infected, but some had other risk factors as well.
•Conclusions?
Which patients were infected by dentist, which were not?
25
III. Uses of CladogramsC. Conservation Strategic Planning
1 2 3 4 5
Conservation Strategies / Prioritization
One park to be designated, two possible locations of equal area:
Area 1: includes 100 species from lineages 4 and 5
Area 2: includes 90 species from lineages 1 and 4.
III. Uses of CladogramsD. Ancestor Reconstruction
III. Uses of Cladograms
Hardy CR, HP Linder. 2007. Phylogeny and historical ecology of Rhodocoma (Restionaceae) from the Cape Floristic Region. Aliso 23: 213-226.
26
III. Uses of Cladograms
III. Uses of CladogramsE. Testing Adaptational Hypotheses
Euphorbia (Euphorbiaceae) Cereus (Cactaceae)
S (xeric)
NS (mesic)
NS (mesic)
NS (mesic)
NS (mesic)
NS (mesic)
Which cladogram provides the stronger evidence for succulence (s) as an adaptation to desert (xeric) environments?