phylogeny, trees, & cladistics

chapter27+

misconceptions• bad evolutionary terms

• higher, lower• more evolved, less

evolved• evolution does not

make things better!• evolution results in

differences• evolution is not over!

• basic terminology - orienting yourself• root (basal)• sister taxa• node• internode• terminal branch

CBA D EO

trees

root

nodes

BCA D EO CB

trees• nodes can pivot. same tree

• nodes can pivot. same tree

CBA D EO C B ADE

trees so…• why not?

phylogeny• recapitulation -- “ontogeny

recapitulates phylogeny” • systematics --

• phenetics • cladistics (primitive vs. derived)

• synapomorphies -• autapomorphies -• synplesiomorphies -

embryo developmentturtle chicken horse human

• adaptations? • directional?• vestigial structures

• convergence... • analogy -- homoplasy• homology (homologous)--

• shared by descent

human cat whale bat

• cladogram or phenogram or tree (dendrogram)• outgroup - some more distantly related organism • ingroup - the groups we are looking at

Tetrapods

Amniotes

diapsids

Living “fish” (outgroup) Living

amphibians Mammals Birds Living reptiles

hair, warm blood

feathers, warm blood

double eyelid

diapsid skull

amniotic egg

two arms, two legs

example tree:

cladistics • phylogenetic trees are used to create taxonomic units... (taxa, taxon, genus, pl. genera)• monophyletic--

• clades / lineages• polyphyletic -- • paraphyletic --

• Basic Cladistic methods • Hennig argumentation • Wagner method

• when adding taxa, you can join the taxa to any node or terminal branch.

1 2 3 4 5 steps

outgroup 0 0 0 0 0

A 1 1 0 0 0

B 1 0 0 1 1

C 1 0 1 1 1

234

o ABCo CA B

1

45

23

o A o AB o AB C

4

3

1AB 10000

parsimony • wagner method cladistic analysis• count the number of steps between each group and the

outgroup• start with the group that has the smallest number of steps from

the outgroup. continue in ascending order.• when adding a taxon to the tree, you add it to the place that

requires the fewest evolutionary steps (or changes).• you need to evaluate all nodes (not counting the outgroup)

and all terminal branches (not the outgroup).• after you attach a taxon to the tree, you should evaluate the

character states for the node you just created.• when you are done, if there are any polytomies, map the

characters onto the tree to see if you can resolve them.

1 2 3 4 5 6 7 8 9 10 steps

outgroup 0 0 0 0 0 0 0 0 0 0

A 1 0 0 0 1 1 0 0 0 1 4

B 1 0 0 0 1 0 0 0 0 1 3

C 0 0 0 0 0 0 0 0 1 1 2

D 0 1 1 0 0 0 1 1 0 1 5

E 0 1 1 1 0 0 0 1 0 1 5

1 2 3 4 5 6 7 8 9 10 steps

outgroup

0 0 0 0 0 0 0 0 0 0

A 1 0 0 0 1 1 0 0 0 1 4

B 1 0 0 0 1 0 0 0 0 1 3

C 0 0 0 0 0 0 0 0 1 1 2

D 0 1 1 0 0 0 1 1 0 1 5

E 0 1 1 1 0 0 0 1 0 1 5

o C o BC o BC A

13

4 675

6

4

625

4

o BC D A

BC 0 0 0 0 0 0 0 0 0 1

AB 1 0 0 0 1 0 0 0 0 1

76

o BC D AE

o BC D AE

o BCD AE

o BC D AE

o BCD AE

18

3

4

5

67

2

9

10

183

4

5

67

2

9

10

18

3

4

5

67

2

9

10

10 steps

10 steps

10 stepsUNRESOLVED

POLYTOMIES? taxa 1 2 3 4 5 steps

outgroup (Poecilia) 0 0 0 0 0

Hyla 1 0 1 0 0 2

Eurycea 1 0 0 0 1 2

Anolis 1 1 1 1 0 4

Parus 1 1 1 1 1 5

Homo 1 1 1 0 0 3

taxa 1 2 3 4 5 steps

outgroup (Poecilia)

0 0 0 0 0

Hyla 1 0 1 0 0 2

Eurycea 1 0 0 0 1 2

Anolis 1 1 1 1 0 4

Parus 1 1 1 1 1 5

Homo 1 1 1 0 0 3

o hyla o hylaeurycea o hylaeurycea homo

12

3

HyEu 1 0 0 0 0

HyHo 1 0 1 0 0

214

2

3

323

4

3

o hylaeurycea homo anolis

12

AnHo 1 1 1 0 0

o hylaeurycea homo anolisparus

example trees• lots of different ways to draw a

tree

• plate tectonics• continental drift

• inner earth• core• mantle• crust

• plates drift on liquid mantle• area cladograms

evolutionary history

australian lungfish

south american lungfishafrican lungfish

evolutionary history• mass extinctions

• “the big 5”• permian• cretaceous

• 6th?

big changes• exaptations

• selection is constrained by what exists• gradual change?

• series of changes.