I. Terms & Concepts

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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

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I. Terms & ConceptsC. Clades & Monophyletic groups

I. Terms & ConceptsD. Sister groups

I. Terms & ConceptsE. Phylogenetic Evidence

1. Characters & Character states

Morphological Characters

e.g., Phyllotaxy: 0 = alternate; 1 = opposite; 2 = whorled.

e.g., Carpel Presence: 0 = absent; 1 = present.g p p

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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)



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.



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.

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2. Apomorphies vs. plesiomorphies

a. autapomophy vs. synapomorphy

b synapomorphy vs symplesiomorphyb. synapomorphy vs. symplesiomorphy

c. hashmarks


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

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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



Homoplasy = confounds phylogenetic inference b/c it creates similarity that is not homologous

e g reversalse.g., reversalse.g., convergence



Primary Homology Assessment(during character coding and scoring)

e.g., PETAL COLOR: 0 = red; 1 = blue

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Secondary Homology Assessment(read from cladogram)

Sp. A Red

Sp. B Red

Sp. D Blue

Sp. E Blue

Sp. F Blue

Sp. C Red



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

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II. Cladogram ConstructionA. Scope



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



1 step on this rooted networkProblem: These are equally

parsimonious

A C DB




A. Scope



D A BC


A C DB


Problem: These are equallyparsimonious

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1 step on this

A. Scope



OG A BCD

2 steps on this rooted tree, either way…


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

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How to infer a phylogenyOrHow to build a cladogram:Synapomorphies

Snail

Hagfish

Perch

Salamander

Lizard

Mouse

Chimp

Human

http://research.amnh.org/~siddall/methods/day2.html

Snail

Hagfish

Perch

Salamander

Lizard

Mouse

Chimp

Human

Evidences for relationships? Shared derived character states.

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Notochord; hollow dorsal nerve chord





vertebrae; jaws

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vertebrae; jaws

Lungs, 4-legs



vertebrae; jaws

Claws or nails

Lungs, 4-legs



vertebrae; jaws

Claws or nails

Fur; mammary glands


Lungs, 4-legs

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vertebrae; jaws

Claws or nails

Fur; mammary glands

Loss of tail


Lungs, 4-legs

II. Cladogram ConstructionC. Parsimony


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

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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


2. For multiple characters at a time (e.g., Tutorial 2, but below is different)

a. Start with all possible ingroup topologies

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2. For multiple characters at a time (e.g., Tutorial 2)

b. Use parsimony to map characters



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


Lungs, 4-legs

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How to evaluate an alternative cladogram? Parsimony (number of steps)




vertebrae; jaws

vertebrae; jaws


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vertebrae; jaws

vertebrae; jaws


Lungs, 4-legs

Lungs, 4-legs


vertebrae; jaws

vertebrae; jaws


Lungs, 4-legs

Lungs, 4-legs

Claws or nails

Claws or nails


vertebrae; jaws

vertebrae; jaws


Lungs, 4-legs

Lungs, 4-legs

Claws or nails

Claws or nails

Fur; mamm

Fur; mammary glands

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vertebrae; jaws

vertebrae; jaws


Lungs, 4-legs

Lungs, 4-legs

Claws or nails

Claws or nails

Fur; mamm

Fur; mammary glands

tail


17 “steps”

vertebrae; jaws

vertebrae; jaws


Lungs, 4-legs

Lungs, 4-legs

Claws or nails

Claws or nails

Fur; mamm

Fur; mammary glands

tail


18 “steps”

karate

http://www.youtube.com/watch?v=_kRb06w_XPo

vertebrae; jaws

vertebrae; jaws


Lungs, 4-legs

Lungs, 4-legs

Claws or nails

Claws or nails

Fur; mamm

Fur; mammary glands

tail

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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


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)?

Magnoliophyta (angiosperms)Magnoliopsida (dicots)Liliopsida (monocots)


rosids


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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)?

Magnoliophyta (angiosperms)Magnoliopsida (dicots)Liliopsida (monocots)

magnoliids



rosids


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.

magnoliids

nymphaeids(water-lilies & friends)nymphaeids(water-lilies & friends)


rosids


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Dr. Hardy’s classifications of angiosperms:

Magnoliopsida (angiosperms)Various monophyletic subclasses.

Magnoliidae

Nymphaeidae

Asteridae

Rosidae

Caryophyllidae

Proteidae

Ranunculidae

Liliidae


2. Construction of new classification schemes

(e.g., cycads)

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1. Most parsimonious cladogram from Stevenson (1992).

2. Classification based on cladogram.


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...

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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

unfused filament hairs.8. Anthers strongly curved,

but not spirally coiled.3. 5-8.4-8.

A

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

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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

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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?

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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.

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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?

NS (mesic)

S (xeric)

S (xeric)NS (mesic)

NS (mesic)

NS (mesic)

S (xeric)

S (xeric)

NS (mesic)

NS (mesic)

NS (mesic)S (xeric)

Documents

I. Terms & Concepts