1. Reconstructing the History of Lineages
Chapter 11
Tereza Jezkova
School of Life Sciences, University of Nevada, Las Vegas
March 2011

2. PHYLOGENETICS
study of evolutionary relatedness among organisms (through molecular data and morphological data)

3. Cladograms
Sister taxa
taxon O E D C
Common
Ancestor B A

4. O E D C B A THE basic logic of phylogenetics:
a natural taxon is a monophyletic group
(all descendant taxa and their common ancestor)
monophyletic
Common
Ancestor
monophyletic O
Common Ancestor E D C B A
Fig. 11.4A

5. O E D C B A THE basic logic of phylogenetic systematics:
a natural taxon is a monophyletic group
(all descendant taxa and their common ancestor) O E D C B A
Fig. 11.4A

6. O E D C B A Other kinds of groups are not natural:
paraphyletic groups (some, but not all descendant taxa and their common ancestor) O E D C B A
Fig. 11.4B

7. Example of a paraphyletic group:
Reptiles are paraphyletic if birds are removed

8. O E D C B A Other kinds of groups are not natural:
polyphyletic groups (descendant taxa trace back through two or more ancestors before reaching a common ancestor) O E D C B A
Fig. 11.4C

9. Example of a polyphyletic group: warm-blooded animals (Mammals+Birds)

10. character state change
Characters (morphological, ecological, behavioral, molecular):
traits that vary across taxa and clades
character state change
primitive
character state
derived
character state

11. homologous characters (homology):
characters whose traits are shared between two or more taxa or clades because of inheritance from a common ancestor

12. homologous characters (homology):
characters whose traits are shared between two or more taxa or clades because of inheritance from a common ancestor
pouch
KOALA
pouch
POSSUM
pouch

13. homoplasious characters (homoplasy):
characters whose traits are shared between two or more taxa but evolved independently

14. NOT USEFUL homoplasious characters (homoplasy):
characters whose traits are shared between two or more taxa but evolved independently
NOT USEFUL
FINS
FINS
FINS
FINS

15. character state change
character state evolution
character state change
primitive
character state
derived
character state

16. characters: dinosaurs birds crocodiles feathers
Feathers are derived character state for birds
Primitive character state is not to have feathers

17. characters: dinosaurs snakes lizards crocodiles leglessness
Leglessness is a derived character state for snakes
Primitive character state is to have legs

18. primitive vs. derived characters:
unique derived (one clade)
shared derived (two or more clades)

19. primitive vs. derived characters:
shared primitive
shared-primitive
for this clade

20. primitive vs. derived characters:
shared-derived
for this clade
shared-primitive
for this clade

21. primitive vs. derived characters:
shared primitive characters are not useful in diagnosing a monophyletic group

22. primitive vs. derived characters:
Unique derived characters are not useful in diagnosing a monophyletic group

23. primitive vs. derived characters:
Only shared derived characters can be used to diagnose a monophyletic group.

24. Correct Incorrect primitive vs. derived characters:
Only shared derived characters can be used to diagnose a monophyletic group.
Correct
Incorrect

25. Outgroups used to polarize primitive  derived direction of character state changes in the ingroupB A
Fig. 11.5

26. Reconstructing trees
Choose the taxa
ex: Vertebrates

27. Reconstructing trees
2. Determine the characters

28. Reconstructing trees
3. Determine polarity of characters

29. Reconstructing trees
4. Group taxa by shared derived characters

30. Reconstructing trees 5. Repeat with all characters
work out conflicts (none in this example)

31. Reconstructing trees
6. Complete the tree

32. Reconstructing trees
6. Use parsimony principle to choose the best tree
one change better (shorter tree) than two

33. EXCERCISE
Outgroup
Species A
Species B
Species C
Species D
Species E

34. Data Matrix Character OG Sp A Sp B Sp C Sp D Sp E Claws 1 Chin Hair1
Chin Hair
Horn
Tail
Spikes
Digits
Spots
Tympanum
Lateral Fold
Nostril

35. Data Matrix ABCE CE ABCDE C D AB ABDE B Character OG Sp A Sp B Sp C
Sp D
Sp E
Claws 1
Chin Hair
Horn
Tail
Spikes
Digits
Spots
Tympanum
Lateral Fold
Nostril
ABCE CE
ABCDE C D AB
ABDE B

36. Molecular phylogenetics

37. EXCERCISE #Elephas_maximus_(Asian_elephant)
AG-G--CT--TGA-AG--GA-AT-TC--T-TGAG-A-A-CAACAAAGCA--A-TCATTTGA-T-TTA---A-GT--AT-AGATGC-T-CAGTATA-AGA-AA-A-A-CA-AA-G-AGAGAC-ATTC-CATCC-C-A--A---TTCCT-T-TGA-ATGT--GTTTTATG-AG-TT-TAT-CAGTCAG-A-ACA--T—CA-T-AT--C-CTT--C-AACA--AGC-AT-TTTGA---GAAA-GGC-A-GAGACAA-T-G-CAT--TAGATT--TTCTT-A-C---CAAA-TCCTATG-A-T

38. EXCERCISE