1. Lecture 6- Phylogeny & Systematics- part I Chapter 26 in Campbell Biology text S2014

2. Fig. 26-1

3. Not a snake: A legless lizard How do we know? *Lacks features common to most or all snakes: No fused eyelid No mobile jaw Post-anal tail length too long How would we know those are important characters?

4. Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings Overview: Investigating the Tree of Life Phylogeny is the evolutionary history of a species or group of related species (branching pattern, the historical pattern of speciation) The discipline of systematics determines the evolutionary relationships of organisms and contributes to taxonomy- the giving of names Systematists use fossil, molecular, physiand genetic data to infer evolutionary relationships

5. Fig. 26-2

6. Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings Concept 26.1: Phylogenies show evolutionary relationships Phylogenies represent the branching pattern of relationships (the history) of life. Taxonomy is the ordered division and naming of organisms

7. Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings Binomial Nomenclature In the 18th century, Carolus Linnaeus published a system of taxonomy based on similarities between animals and plants Two key features of his system remain useful today: two-part names for species and hierarchical classification (the “ranks”)

8. Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings The two-part scientific name of a species is called a binomial The first part of the name is the genus The second part, called the specific epithet, is unique for each species within the genus The first letter of the genus is capitalized, and the entire species name is italicized Both parts together name the species (not the specific epithet alone)

9. Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings Hierarchical Classification Linnaeus introduced a system for grouping species in increasingly broad categories The taxonomic groups from broad to narrow are domain, kingdom, phylum, class, order, family, genus, and species A taxonomic unit at any level of hierarchy is called a taxon (plural= taxa)

10. Fig. 26-3 Species: Panthera pardus Genus: Panthera Family: Felidae Order: Carnivora Class: Mammalia Phylum: Chordata Kingdom: Animalia ArchaeaDomain: Eukarya Bacteria

11. Fig. 26-3a Class: Mammalia Phylum: Chordata Kingdom: Animalia Archaea Domain: EukaryaBacteria

12. Fig. 26-3b Species: Panthera pardus Genus: Panthera Family: Felidae Order: Carnivora

13. Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings Linking Classification and Phylogeny Systematists depict evolutionary relationships in branching phylogenetic trees

14. Fig. 26-4 Species Canis lupus Panthera pardus Taxidea taxus Lutra lutra Canis latrans OrderFamilyGenus Carnivora Felidae Mustelidae Canidae Canis Lutra Taxidea Panthera Other groups worth studying in here, perhaps without names?

15. If species was hard to define, what’s a Genus, or a Family or a “Class”? Some commonly used taxon ranks: Domain Phylum Subphylum Class Subclass Superorder Order Suborder Infraorder Superfamily Epifamily Family Infrafamily Tribe Subtribe Infratribe Supergenus Genus Subgenus Species group Species Subspecies Race/variety/ cultivar Similarity? Not really measurable Number of included groups? Not even close!

16. Number of taxa? Formicidae = a family of insects (ants) >20,000 species Felidae = a family of mammals (cats) 41 species Homo = a genus of mammals: 1 species Tegenaria = a genus of spiders: 100 species

17. Taxonomy’s naughty secret: Ranks above species have NO consistent scientific or biological meaning! So why use them? For practical reasons: sometimes a species name doesn’t tell you enough, sometimes it tells you too much!

18. Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings Linnaean classification and phylogeny can (and often do) differ from each other They can (and often do) ‘fit’ because, the way evolutionary history works, it can be split into a “hierarchy of groups” (smaller groups group together into larger groups). This is not a coincidence, it is because close relatives look more similar than distant ones.

19. Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings A phylogenetic tree represents a hypothesis about evolutionary relationships Each NODE or branching point, represents the divergence of two species Sister taxa are pairs of groups that share an immediate common ancestor

20. Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings A rooted tree includes a branch to represent the last common ancestor of all taxa in the tree A polytomy is a branch from which more than two groups emerge

21. Fig. 26-5 Sister taxa ANCESTRAL LINEAGE Taxon A Polytomy Common ancestor of taxa A–F Branch point (node) Taxon B Taxon C Taxon D Taxon E Taxon F

22. Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings What does this tree show? A C B D F E G H J I K L M N O P Not much… this is the “dreaded comb!” (really, a giant POLYTOMY)

23. Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings This is more like it: a fully dichotomous tree!

24. Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings What We Can and Cannot Learn from Phylogenetic Trees Phylogenetic trees do show patterns of descent Phylogenetic trees do not always indicate when species evolved or how much genetic change occurred in a lineage (that’s extra information which can be included, after developing the tree) It should never be assumed that a taxon “evolved” from the taxon next to it… they evolved from a common ancestor. (e.g. humans didn’t ‘evolve’ from chimps- chimps and humans share a recent common ancestor).

25. Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings Applying Phylogenies Phylogeny provides important information about similar characteristics in closely related species Phylogenies can have practical applications: A phylogeny was used to identify the species of whale from which “whale meat” originated

26. Fig. 26-6 Fin (Mediterranean) Fin (Iceland) RESULTS Unknown #10, 11, 12 Unknown #13 Blue (North Pacific) Blue (North Atlantic) Gray Unknown #1b Humpback (North Atlantic) Humpback (North Pacific) Unknown #9 Minke (North Atlantic) Minke (Antarctica) Minke (Australia) Unknown #1a, 2, 3, 4, 5, 6, 7, 8

27. Fig. 26-6a Unknown #9 Minke (North Atlantic) Minke (Antarctica) Minke (Australia) Unknown #1a, 2, 3, 4, 5, 6, 7, 8 RESULTS 2 logical conclusions here?

28. Fig. 26-6b Blue (North Pacific) Blue (North Atlantic) Gray Unknown #1b Humpback (North Atlantic) Humpback (North Pacific) 1 logical conclusion here?

29. Fig. 26-6c Fin (Mediterranean) Fin (Iceland) Unknown #13 Unknown #10, 11, 12 Any logical conclusions here?

30. Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings Phylogenies of anthrax bacteria helped researchers identify the source of a particular strain of anthrax Phylogenies of HIV viruses have helped us trace the virus back to SIV’s – Simian Immunodeficiency Viruses- and we know that there have been at least 4 cross-infections from monkeys/apes to humans.

31. Fig. 26-UN1 A B A A B B C CC D D D (a) (b) (c) Why can trees be rearranged in some ways, and still mean the same thing?

32. How are phylogenies ‘made?’ “Classic Phylogeny” – Ernst Haeckel, ‘argument from authority’ Phylogeny/Systematics/ Taxonomy were considered ‘more art than science’ for a long time.

33. Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings Concept 26.2: Phylogenies are inferred from morphological and molecular data To infer phylogenies, systematists gather information about morphologies, genes, behavior, and biochemistry of living organisms Any trait (called a “character”) that can be inherited, can be used for making a data matrix -good characters should vary between groups -should come in different forms that can be told apart rather easily (4 eyes vs. 6, or A,C,G, and T)

34. Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings Morphological and Molecular Homologies Organisms with similar morphologies or DNA sequences are likely to be more closely related than organisms with different structures or sequences

35. Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings Sorting Homology from Analogy Only after constructing a complete phylogeny, can systematists really distinguish whether a similarity is the result of homology or analogy Homology is similarity due to shared ancestry Analogy is similarity due to convergent evolution

36. Fig. 26-7 Classic ANALOGIES

37. Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings Convergent evolution occurs when similar environmental pressures and natural selection produce similar (analogous) adaptations in organisms from different evolutionary lineages

38. Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings Classic HOMOLOGIES

39. Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings Bat and bird wings are homologous as forelimbs, but analogous as functional wings Analogous structures or molecular sequences that evolved independently are also called homoplasies (=“false homologies”) Homology can be distinguished from analogy by comparing fossil evidence and the degree of complexity, and FROM THE PHYLOGENY

40. Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings Evaluating Molecular Homologies Systematists use computer programs and mathematical tools when analyzing comparable DNA segments from different organisms

41. Fig. 26-8 Deletion Insertion 1 2 3 4

42. Fig. 26-8a Deletion Insertion 1 2

43. Fig. 26-8b 3 4

44. Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings It is also important to distinguish homology from analogy in molecular similarities -first we make a hypothesis of “primary homology”- this is the alignment step (computer programs are a big help) -then when we calculate the tree, we can look at the branching patterns and see if any similarities between the species are due to homology (ancestral similarity) or analogy (also called homoplasy or convergent evolution)

45. Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings Cladistics Cladistics groups organisms by common descent A clade is a group of species that includes an ancestral species and all its descendants Clades can be nested in larger clades, but not all groupings of organisms qualify as clades

46. Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings A valid clade is monophyletic, signifying that it consists of the ancestor species and all its descendants

47. Fig. 26-10 A A A BBB CCC D D D EEE FF F G GG Group III Group II Group I (a) Monophyletic group (clade) (b) Paraphyletic group (c) Polyphyletic group

48. Fig. 26-10a A B C D E F G Group I (a) Monophyletic group (clade)

49. Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings A paraphyletic grouping consists of an ancestral species and some, but not all, of the descendants

50. Fig. 26-10b A B C D E F G Group II (b) Paraphyletic group

51. Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings A polyphyletic grouping consists of various species that lack a recent common ancestor

52. Fig. 26-10c A B C D E F G Group III (c) Polyphyletic group

53. Paraphyly and polyphyly are both bad- neither makes good groups Another small point: never group things by what they “aren’t” only what they ARE: Birds = subgroup of dinosaurs with feathers & wings = good! Invertebrates = animals without backbones = bad! (Insects and starfish are NOT closely related!)

54. Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings Shared Ancestral and Shared Derived Characters In comparison with its ancestor, an organism has both shared and different characteristics

55. Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings A shared ancestral character is a character that originated in an ancestor of the taxon A shared derived character is an evolutionary novelty unique to a particular clade A character can be both ancestral and derived, depending on the context

56. Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings Inferring Phylogenies Using Derived Characters When inferring evolutionary relationships, it is useful to know in which clade a shared derived character first appeared

57. Fig. 26-11 TAXA Lancelet (outgroup) Lamprey Salamander Leopard Turtle Tuna Vertebral column (backbone) Hinged jaws Four walking legs Amniotic (shelled) egg CHARACTERS Hair (a) Character table Hair Hinged jaws Vertebral column Four walking legs Amniotic egg (b) Phylogenetic tree Salamander Leopard Turtle Lamprey Tuna Lancelet (outgroup) 0 00 0 0 0 00 0 0 00 000 1 11 1 1 1 1 11 1 1 11 11

58. Fig. 26-11a TAXA Lancelet (outgroup) Lamprey Salamander Leopard Turtle Tuna Vertebral column (backbone) Hinged jaws Four walking legs Amniotic (shelled) egg CHARACTERS Hair (a) Character table 0 00 0 0 0 0 0 0 0 00 0 00 1 1 1 1 11 1 11 1 1 11 1 1

59. Fig. 26-11b Hair Hinged jaws Vertebral column Four walking legs Amniotic egg (b) Phylogenetic tree Salamander Leopard Turtle Lamprey Tuna Lancelet (outgroup)

60. Fig. 26-11b Hair Hinged jaws Vertebral column Four walking legs Amniotic egg (b) Phylogenetic tree Salamander Leopard Turtle Lamprey Tuna Lancelet (outgroup) This is a ‘cartoon’ – not how phylogenies really work, from a ‘process’ point of view. Phylogenetics is NOT a ‘hunt’ for special characters. We collect large amounts of data, subject to rigorous analysis, so there will be multiple characters supporting each branch. Changing one ‘character’ does not change the tree!