1. Looking Back at Prerequisites Science: a methodical approach to the acquisition of knowledge Observation: Use the metric (SI) units to measure your world! Question: Be curious-the bad question is the one you fail to ask! Hypothesis: Make falsifiable educated guess to answer question Prediction: If the hypothesis is true… then the dependent variable will respond… when I manipulate the independent variable. Experiment: Manipulate the independent variable=treatment Compare the response to an unmanipulated control Analysis: Use statistical test and allow % for statistical error Type 1: rejecting a true H -- Type2: failing to reject false H Decision: Reject hypothesis or Cannot reject hypothesis

2. Looking Back at Prerequisites Biology: the Study of Life Cellular Structure (cell = unit of life) Metabolism = Homeostasis (PSN, Resp, N 2 fix, ferment, etc.) Growth = irreversible change in size Reproduction…failure = extinction Acclimatization-short term responses = behavior Adaptation-long term responses = evolution What are the fundamental properties of life?

3. Looking Back at Prerequisites Biology is multidimensional Cell Tissue Organ Organ System Organism Population Community Ecosystem This array is an example of what dimension? Levels of Organization What fields of biology are at each extreme? Biochemistry and Biophysics In this course our focus will be upon… These levels but only in reference to plants

4. Looking Back at Prerequisites Classification Domain BacteriaEukarya Kingdom Eubacteria Protista Or Plantae Plantae Phylum CyanophytaChlorophyta Anthophyta Magnoliophyta Class ProchlorophyceaeChlorophyceaeDicotyledonae Order ProchloralesUlvalesRosales Family ProchlorococcaceaeUlvaceaeRosaceae Genus ProchlorococcusUlvaRosa Species P. marinusU. lactucaR. multiflora Common MED4Sea lettuceWild Rose

5. The species name is a Latin binomial Dead Language Universally known The Genus name and a specific epithet Example: Brassica oleracea mustard of the garden Sometimes the binomial is not good enough! So we add a Latin variety name as well (also known as subspecies) Several examples of members of species Brassica oleracea

6. http://www.blueoniondesign.com/blog/cabbage.jpg Cabbage: Brassica oleracea capitata

7. http://www.hilltopfarms.org/images/kale.jpg Kale: Brassica oleracea acephala

8. http://www.vegetables.pe.kr/vegetablesgallery/leaf_vegetables/images/brussels%20sprouts_prince%20marvel.jpg Brussels sprouts: Brassica oleracea gemmifera

9. http://www.hrt.msu.edu/course/HRT204L/VEG_ID/kohlrabi.jpg Kohlrabi: Brassica oleracea caulorapa

10. http://www.cloverseed.com.hk/web_clover_c/broccoli/broccoli_monterey.jpg Broccoli: Brassica oleracea italica

11. http://green-acres.org/images/products/cauliflower.jpg Cauliflower: Brassica oleracea botrytis

12. http://www.burpee.com/jump.jsp?itemID=219&itemType=CATEGORY&iMainCat=13&iSubCat=219 Two Seasons Hybrid Brassica oleracea capitata Salad Delight Earliana King Slaw cultivar names in home language and in single quotes

13. How many species are there? What is a species? Animal species concept… if offspring are fertile then same species… does not apply among species of other kingdoms Prokaryotes (no sex) Algae (sex sometimes unknown) Allopolyploidy in plants

14. Shifting Kingdoms 23568 Bacteria Archaebacteria Archezoans Euglenoids Chrysophytes Green Algae Brown Algae Red algae Slime Molds True Fungi Bryophytes Tracheophytes Protozoans Myxozoans Multicellular Animals Lumpers Splitters

15. How Many Kingdoms? Multicellular Animals MyxozoansProtozoans Tracheophytes Bryophytes True Fungi Slime Molds Red algae Brown Algae Green Algae Chrysophytes EuglenoidsArchezoans Archaebacteria Bacteria Original Cell Extant Extinct Long Time with Prokaryotes only 8 5 3 2 1

16. How Long Ago? Multicellular Animals MyxozoansProtozoans Tracheophytes Bryophytes True Fungi Slime Molds Red algae Brown Algae Green Algae Chrysophytes EuglenoidsArchezoans Archaebacteria Bacteria Original Cell Extant Extinct Long Time with Prokaryotes only 0.5 1 2 3 4 BYBPOrigin of Life Cyanobacterial Oxygen First Eukaryotes Multicellular PlantsLand!

17. Evidence Categories History - clearer recently, more obscure anciently Fossils - stratigraphic depth, isotope decay, etc. Chemical - metabolic products such as O 2, S s Molecular - DNA sequence alterations, etc. Developmental sequences - onto- phylo- geny Biogeography - Pangea, Gondwana & Laurasia

18. How do we know the Evolution Pathway? Phylogenetic Systematics Inferences from comparison of extant organisms Characters-Attributes of the organism » Anatomy » Morphology » Development » Physiology » Macromolecule Sequences Polarizing Character States Plesiomorphies-Ancient, shared by descendants Apomorphies-More-recent derivatives » Synapomorphy-Shared among related organisms » Autapomorphy-Found only in one organism Use of outgroup to compare to ingroup

19. Typical Cladogram Common Ancestor Extant APresent Ancient Extinct Transitional Forms Time A A A This straight line of evolution is called anagenesis. Extant B This branching of evolution is called cladogenesis. A is the common ancestor of extant A and extant B

20. Typical Cladogram Common Ancestor Extant AExtant BPresent Ancient Time A A A Extant C A C are a grade (is paraphyletic) A C A A B are a clade A A B is the sister group of C A A B constitute a clade

21. Typical Cladogram Common Ancestor Extant AExtant CExtant BPresent Ancient Time A A A A Extinct! Extant DExtant E A D A E are a ? clade Common ancestor + A D E are a ? grade The ABC clade may be, say, a genus. The DE clade may be another genus… in the same family The ABCDE clade would be the family

22. Typical Cladogram Common Ancestor Extant AExtant CExtant DExtant EExtant BPresent Ancient Time A A A A Extinct! A On the other hand… AB are a genus C is a monotypic genus DE are a genus ABC might be one family DE are in another family ABCDE might constitute an order

23. Multicellular Animals MyxozoansProtozoans Tracheophytes Bryophytes True Fungi Slime Molds Red algaeBrown AlgaeGreen Algae Chrysophytes EuglenoidsArchezoans Archaebacteria Bacteria Original Cell Extant Extinct Living organisms are part of one clade Eukaryotic organisms are a clade Prokaryotic organisms are a grade (paraphyletic) Protists are polyphyletic (unnatural taxon) Plants are a clade (monophyletic) Animals and Fungi are a clade!

24. Character Number Taxon12345678910 OG0000000000 A0011100101 B1001001100 C0111010111 D0011010111 E1001000100 OG ABCDE 4 8

25. Character Number Taxon12345678910 OG0000000000 A0011100101 B1001001100 C0111010111 D0011010111 E1001000100 OG ABCDE 4 8 ACD BE 3 10

26. Character Number Taxon12345678910 OG0000000000 A0011100101 B1001001100 C0111010111 D0011010111 E1001000100 OG 4 8 BE ACD 3 10 1 CD A 6 9

27. Character Number Taxon12345678910 OG0000000000 A0011100101 B1001001100 C0111010111 D0011010111 E1001000100 OG 4 8 BE 3 10 1 CD A 6 9 autapomorphies DC 2 EB 7 5

28. How do you DO classification? 1.Get with a partner to form a team 2.Look over the cards you are given for your team 3.Every group gets the same set of 8 cards Bob Sue Deb Lou Jen Cal Hal Val 4.Sort the cards into what you believe may be natural groups Names do not count, use only shapes shown on card 5.Decide who will tell the class how you sorted your groups What theme unites/defines each group Warmup!

29. How do you DO classification? Sharing our Results

30. 1.This game is a cross-country race in a forest 2.All runners enter the forest by a single south entrance 3.The finish line is the northern boundary of the forest 4.Runners need not exit at any particular place at the finish 5.There are many trails through the woods Trails only bifurcate (form two branches) at forks Trails never join together or rejoin after forking 6.Along the trail straightaways are check-in stations 7.At each check-in station, a worker has a unique stamp 8.Each runner has a card that is stamped as s/he passes a station 9.Runners are not allowed to retrace a path 10.All runners must finish the race 11.Using the punch cards handed in at the finish line: Sketch the trail map Show all station locations (on the straightaways) Mark the exit used by each runner The Forest Meet!

31. BobSueDebLouJenCalHalVal xxxxxxxx xxxxx xx x xxxx xx x xx x xxx x x The Forest Meet Sharing our Results

32. BobSueDebLouJenCalHalValTotal xxxxxxxx8 xxxxx5 xx2 x1 xxxx4 xx2 x1 xx2 x1 xxx3 x1 x1 The Forest Meet Sharing our Results

33. The Forest Meet Sharing our Results Runners can finish anywhere along this northern edge Start All of the runners passed the circle station, so this station must be near the start

34. BobSueDebLouJenCalHalValTotal xxxxxxxx8 xxxxx5 xx2 x1 xxxx4 xx2 x1 xx2 x1 xxx3 x1 x1 The Forest Meet Sharing our Results

35. The Forest Meet Sharing our Results Runners can finish anywhere along this northern edge Start Five of the runners passed the teardrop station, but three did not, so our 8 runners must have divided into two groups Sue, Lou, Jen, Hal, ValBob, Deb, Cal

36. BobSueDebLouJenCalHalValTotal xxxxxxxx8 xxxxx5 xx2 x1 xxxx4 xx2 x1 xx2 x1 xxx3 x1 x1 The Forest Meet Sharing our Results

37. The Forest Meet Sharing our Results Runners can finish anywhere along this northern edge Start Four runners of the group of five passed the diamond station, but Hal did not, so he split away before this station Sue, Lou, Jen, Val Bob, Deb, Cal Hal Because paths do not rejoin, Hal is separated and thus we can draw him at the finish line Sue, Lou, Jen, Hal, Val

38. BobSueDebLouJenCalHalValTotal xxxxxxxx8 xxxxx5 xx2 x1 xxxx4 xx2 x1 xx2 x1 xxx3 x1 x1 The Forest Meet Sharing our Results

39. The Forest Meet Sharing our Results Finish Line Start Sue, Lou, Jen, Val Bob, Deb, Cal Hal Bob, Deb, and Cal all passed the triangle station so it was along the path they shared

40. BobSueDebLouJenCalHalValTotal xxxxxxxx8 xxxxx5 xx2 x1 xxxx4 xx2 x1 xx2 x1 xxx3 x1 x1 The Forest Meet Sharing our Results

41. The Forest Meet Sharing our Results Finish Line Start Sue, Val Deb, Cal Hal Deb, and Cal passed the star station, but Bob did not, so the group divided Jen, Lou Bob Jen and Lou passed the heart station, but Sue and Val passed the spade station, so the group of four divided Bob, Deb, Cal Sue, Lou, Jen, Val

42. The Forest Meet The rest are autapomorphies BobSueDebLouJenCalHalValTotal xxxxxxxx8 xxxxx5 xx2 x1 xxxx4 xx2 x1 xx2 x1 xxx3 x1 x1

43. The Forest Meet Autapomorphies! Start Hal Bob CalDebJenLouSueVal Deb, Cal Jen, LouSue, Val Notice the runners are in alphabetical order. But this is not the only solution All branches can be rotated: e.g.: Lou before Jen Sue-Val before Jen-Lou

44. But Wait! We have one really-slow runner just exiting! Here is his card…figure out his pathway The Forest Meet!

45. BobSueDebLouJenCalHalValRoss xxxxxxxxx xxxxxx xx x xxxx xx xx xx x xxx x xx The Forest Meet Sharing our Results

46. The Forest Meet Start Hal Bob CalDebJenLouSueVal What did Ross do? What is parsimonious? Are our ideas wrong? Maybe Ross followed Hal.. Then hit a rougue station? Ross

47. 1.This game is a cross-country race in a forest 2.All runners enter the forest by a single south entrance 3.The finish line is the northern boundary of the forest 4.Runners need not exit at any particular place at the finish 5.There are many trails through the woods Trails only bifurcate (form two branches) at forks Trails never join together or rejoin after forking 6.Along the trail straightaways are check-in stations 7.At each check-in station, a worker has a unique stamp 8.Each runner has a card that is stamped as s/he passes a station 9.Runners are not allowed to retrace a path 10.All runners must finish the race 11.Using the punch cards handed in at the finish line: Sketch the trail map Show all station locations (on the straightaways) Mark the exit used by each runner The Clade Race! 1. This game represents the evolution of some related organisms 2. The organisms are believed to be a clade (w/common ancestor) 3. The organisms we are using are all extant (none are fossils) 5. We make few assumptions about the evolution pathway Cladogenesis divides one species into two species We assume there is no convergent or parallel evolution 6. Anagenesis is expected to occur between generations 7. Evolution shows its record of changes in the genotype 8. The record of evolution in genotype is shown in the phenotype 9. Evolution is permanent; we assume no reversals of states 10. In this study, we are using no fossils of extinct clade members 11. Using the phenotypes observed in the extant organisms: 4. We make no assumptions about possible phenotypes observed Sketch the cladogram Show the location of character state transitions Show the relationships among the taxa

48. How do you DO cladistics? 1.Look at a group of organisms that you think are related 2.Find a not-too-distantly related (primitive?) out-group 3.Select characters that will help to distinguish the organisms 4.Polarize the character states by: Stratigraphic sequence (fossil sequence) Developmental sequence (ontogeny recaps phylogeny) Outgroup comparison 5.Build a data matrix 6.Group by number of synapomorphies (shared derived) 7.Sketch possible cladograms 8.Seek simplest (most parsimonious) cladogram