1. BIOL 471 – Methods in Systematics: Topic -- Phylogenetics I.Phylogenetic terms and concepts A.Phylogeny 1. Defined 2. Phylogeny vs. tokogeny 3. Clade and monophyletic group 4. Sister group

2. BIOL 471 – Methods in Systematics: Topic -- Phylogenetics I.Phylogenetic terms and concepts A.Phylogeny 1. Defined 2. Phylogeny vs. tokogeny 3. Clade and monophyletic group 4. Sister group Willi Hennig (German; 1913-1976) Grundzüge einer Theorie der Phylogenetischen Systematik (Hennig, 1950).

3. BIOL 471 – Methods in Systematics: Topic -- Phylogenetics I.Phylogenetic terms and concepts B. Cladogram 1. Defined 2. Styles 2. Branches and nodes; internal vs. external branches

4. BIOL 471 – Methods in Systematics: Topic -- Phylogenetics I.Phylogenetic terms and concepts C.Characters and homology 1. Cladogram as a framework for studying the origin of variation among species. 2. Characters and character states 3. Apomorphies vs. plesiomorphies Autapomorphy vs. synapomorphy Synapomorphy vs. symplesiomorphy Hashmarks 4. Homology, analogy, and homoplasy

5. BIOL 471 – Methods in Systematics: Topic -- Phylogenetics I.Phylogenetic terms and concepts C.Characters and homology 1. Cladogram as a framework for studying the origin of variation among species. 2. Characters and character states 3. Apomorphies vs. plesiomorphies Autapomorphy vs. synapomorphy Synapomorphy vs. symplesiomorphy Hashmarks 4. Homology, analogy, and homoplasy e.g., useful characters for tetrapod phylogenetics Skeletal Limbs (legs): zero, four Fur: no, yes Tail: yes, no Bipedality: no, yes

6. BIOL 471 – Methods in Systematics: Topic -- Phylogenetics I.Phylogenetic terms and concepts C.Characters and homology 1. Cladogram as a framework for studying the origin of variation among species. 2. Characters and character states 3. Apomorphies vs. plesiomorphies Autapomorphy vs. synapomorphy Synapomorphy vs. symplesiomorphy Hashmarks 4. Homology, analogy, and homoplasy e.g., useful characters for tetrapod phylogenetics Skeletal Limbs (legs): zero, four Fur: no, yes Tail: yes, no Bipedality: no, yes Outgroup: fish (also some invertebrate) Ingroup: (amphibians, reptiles, monkeys, non- human apes, humans)

7. BIOL 471 – Methods in Systematics: Topic -- Phylogenetics I.Phylogenetic terms and concepts C.Characters and homology 1. Cladogram as a framework for studying the origin of variation among species. 2. Characters and character states 3. Apomorphies vs. plesiomorphies Autapomorphy vs. synapomorphy Synapomorphy vs. symplesiomorphy Hashmarks 4. Homology, analogy, and homoplasy Bats Birds Insects

8. BIOL 471 – Methods in Systematics: Topic -- Phylogenetics I.Phylogenetic terms and concepts C.Characters and homology 1. Cladogram as a framework for studying the origin of variation among species. 2. Characters and character states 3. Apomorphies vs. plesiomorphies Autapomorphy vs. synapomorphy Synapomorphy vs. symplesiomorphy Hashmarks 4. Homology, analogy, and homoplasy Modern cetaceans: vesitigial pelvis &, occassionally hind “limbs”

9. BIOL 471 – Methods in Systematics: Topic -- Phylogenetics I.Phylogenetic terms and concepts C.Characters and homology 1. Cladogram as a framework for studying the origin of variation among species. 2. Characters and character states 3. Apomorphies vs. plesiomorphies Autapomorphy vs. synapomorphy Synapomorphy vs. symplesiomorphy Hashmarks 4. Homology, analogy, and homoplasy Basilosaurus had 2 tiny legs, probably used as claspers when mating. basilosaurids and dorudontids (ca. 40-30 Ma)

10. BIOL 471 – Methods in Systematics: Topic -- Phylogenetics II. Cladistics A. The taxon-by-character matrix

11. BIOL 471 – Methods in Systematics: Topic -- Phylogenetics II. Cladistics B.Synapomorphies as evidence of recency of common ancestry 1. Ingroup vs. outgroup 2. Parsimony and Ockham’s Razor 3. Parsimony the optimality criterion as a means of dealing with incongruence

12. BIOL 471 – Methods in Systematics: Topic -- Phylogenetics

13. II.Cladistics C. Minmizing “steps” is the practical application of parsimony

14. BIOL 471 – Methods in Systematics: Topic -- Phylogenetics Snail Hagfish Perch Salamander Lizard Mouse Chimp Human

15. BIOL 471 – Methods in Systematics: Topic -- Phylogenetics Notochord; hollow dorsal nerve chord

16. BIOL 471 – Methods in Systematics: Topic -- Phylogenetics Notochord; hollow dorsal nerve chord

17. BIOL 471 – Methods in Systematics: Topic -- Phylogenetics Notochord; hollow dorsal nerve chord vertebrae; jaws

18. BIOL 471 – Methods in Systematics: Topic -- Phylogenetics vertebrae; jaws Lungs, 4-legs Notochord; hollow dorsal nerve chord

19. BIOL 471 – Methods in Systematics: Topic -- Phylogenetics vertebrae; jaws Claws or nails Lungs, 4-legs Notochord; hollow dorsal nerve chord

20. BIOL 471 – Methods in Systematics: Topic -- Phylogenetics vertebrae; jaws Claws or nails Fur; mammary glands Notochord; hollow dorsal nerve chord Lungs, 4-legs

21. BIOL 471 – Methods in Systematics: Topic -- Phylogenetics vertebrae; jaws Claws or nails Fur; mammary glands Loss of tail Notochord; hollow dorsal nerve chord Lungs, 4-legs

22. BIOL 471 – Methods in Systematics: Topic -- Phylogenetics vertebrae; jaws Claws or nails Fur; mammary glands Loss of tail Notochord; hollow dorsal nerve chord Lungs, 4-legs 10 “steps”

23. BIOL 471 – Methods in Systematics: Topic -- Phylogenetics How to evaluate an alternative cladogram?

24. BIOL 471 – Methods in Systematics: Topic -- Phylogenetics Notochord; hollow dorsal nerve chord How to evaluate an alternative cladogram?

25. BIOL 471 – Methods in Systematics: Topic -- Phylogenetics vertebrae; jaws Notochord; hollow dorsal nerve chord How to evaluate an alternative cladogram?

26. BIOL 471 – Methods in Systematics: Topic -- Phylogenetics vertebrae; jaws Notochord; hollow dorsal nerve chord Lungs, 4-legs How to evaluate an alternative cladogram?

27. BIOL 471 – Methods in Systematics: Topic -- Phylogenetics vertebrae; jaws Notochord; hollow dorsal nerve chord Lungs, 4-legs Claws or nails How to evaluate an alternative cladogram?

28. BIOL 471 – Methods in Systematics: Topic -- Phylogenetics vertebrae; jaws Notochord; hollow dorsal nerve chord Lungs, 4-legs Claws or nails Fur; mammary glands How to evaluate an alternative cladogram?

29. BIOL 471 – Methods in Systematics: Topic -- Phylogenetics vertebrae; jaws Notochord; hollow dorsal nerve chord Lungs, 4-legs Claws or nails Fur; mammary glands tail How to evaluate an alternative cladogram?

30. BIOL 471 – Methods in Systematics: Topic -- Phylogenetics vertebrae; jaws Notochord; hollow dorsal nerve chord Lungs, 4-legs Claws or nails Fur; mammary glands tail 17 “steps” How to evaluate an alternative cladogram?

31. BIOL 471 – Methods in Systematics: Topic -- Phylogenetics II.Cladistics C. Minmizing “steps” is the practical application of parsimony

32. BIOL 471 – Methods in Systematics: Topic -- Phylogenetics III. Sources of variation for characters A.Morphological and anatomical variation

33. BIOL 471 – Methods in Systematics: Topic -- Phylogenetics III. Sources of variation for characters B. Genetic (e.g., DNA sequence) variation 1. Source of genetic data 2. Alignment of DNA sequences.

34. BIOL 471 – Methods in Systematics: Topic -- Phylogenetics III. Sources of variation for characters B. Genetic (e.g., DNA sequence) variation 1. Source of genetic data 2. Alignment of DNA sequences.

35. BIOL 471 – Methods in Systematics: Topic -- Phylogenetics III. Sources of variation for characters B. Genetic (e.g., DNA sequence) variation 1. Source of genetic data. 2. Alignment of DNA sequences.

36. BIOL 471 – Methods in Systematics: Topic -- Phylogenetics I.Phylogenetic terms and concepts A.Phylogeny 1. Defined 2. Phylogeny vs. tokogeny 3. Clade and monophyletic group 4. Sister group