Phylogeny and the Tree of Life

1. Phylogeny and the Tree of Life Chapter 26 BCOR 012 February 12, 2010

2. Outline for February 12, 2010 Systematics: Connecting Classification to Phylogeny Systematics, Taxonomy, and Phylogeny Constructing cladograms • Phylogenetic Classification • Molecular Systematics • Parsimony

3. Systematics is the study of biological diversity in an evolutionary context. It includes (among other aspects) taxonomy, classification, and phylogeny.

4. Taxonomy is the branch of systematics concerned with naming and classification. • Scientific names are binomials • Example: Acer saccharum - Acer is the genus name - it is a Latin noun - saccharum is the specific epithet - it is a Latin adjective Carolus Linnaeus 1707-1778

5. Classification What are systems of classification intended to do? (In other words, why do we bother with them?) 1. A system of classification is a helpful way to organize and retrieve information. Examples: the Library of Congress system for cataloging books; the alphabetical telephone directory

6. 2. A biological classification can allow you to make predictions about the organisms being classified, but only if the system is based on evolutionary relationship. Example: Predictions about the possible medicinal properties of plants are more likely to be accurate if those predictions are based on knowledge of the medicinal properties of that plant’s near relatives.

7. Taxus brevifolia Pacific yew

8. Biological classifications are hierarchical: each taxonomic group is nested within a more inclusive higher order group. (Note that only the genus name and specific epithet are italicized.)

9. From Two Kingdoms to Three Domains • Early taxonomists classified all species as either plants or animals • Later, five kingdoms were recognized: Monera (prokaryotes), Protista, Plantae, Fungi, and Animalia • More recently, the three domain system has been adopted: Bacteria, Archaea, and Eukarya

10. eukaryotes EUKARYA Dinoflagellates Land plants Forams Green algae Ciliates Diatoms Red algae Amoebas Cellular slime molds Euglena Trypanosomes Animals Leishmania Fungi Sulfolobus Green nonsulfur bacteria Thermophiles (Mitochondrion) Spirochetes Chlamydia Halophiles COMMON ANCESTOR OF ALL LIFE Green sulfur bacteria BACTERIA Methanobacterium Cyanobacteria both are prokaryotic (Plastids, including chloroplasts) ARCHAEA

11. Phylogeny and Classification “Our classifications will come to be, as far as they can be so made, genealogies.” - Charles Darwin, 1859

12. Phylogeny is the study of evolutionary relationships among organisms.

13. Willi Hennig, 1913 - 1976 Founder of Phylogenetic Systematics (also called cladistics) In phylogenetic analysis, taxa are associated on the basis of shared evolutionary innovations.

14. One of the evolutionary innovations shared by birds is the feather …

15. A cladogram is an evolutionary hypothesis: it summarizes information about ancestor- descendent relationships. Branch points represent an inferred common ancestor. On the diagram, the red star denotes the common ancestor of leopard and turtle, while the yellow star indicates the common ancestor of tuna, salamander, turtle, and leopard.

16. Clicker Question Q. Which of the following species pairs are most closely related? Species 1 and 2 Species 4 and 5 Species 3 and 4 A and C are equivalently correct E. No two species are more closely related to each other than they are to the other three 5 4 3 2 1 Phylogeny of five violet species

17. How to construct a cladogram: • Choose a study group • Choose an appropriate outgroup • Compile data matrix • Polarize characters • Use shared derived characters to associate study group taxa and construct the cladogram

18. The outgroup is the group used to polarize character states in the study group. It should be the group most closely related (on the basis of other lines of evidence) to the study group that is not actually part of the study group. lancelet

21. Kinds of Characters • Apomorphy - a derived character state • Synapomorphy - a shared derived character state • Autapomorphy - a derived character state unique to one study group member

22. Cladistic Analysis: Kinds of Groups

23. A monophyletic group includes a common ancestor and all of its descendents Example: Reptilia (defined to include birds)

24. A paraphyletic group includes a common ancestor and some but not all of its descendents Example: Reptilia (defined to exclude birds)

25. A polyphyletic group is a group whose members do not share a recent common ancestor Example: homeotherms (warm-blooded animals)

26. Phylogenetic Classification, Rules of the Game: In a phylogenetic classification, only monophyletic groups are named.If a paraphyletic group bears a name, it will be an informal one (e.g., ‘gymnosperms’)

27. The nested relationship of clades is reflected in the nested relationship of taxa in the resultant classification.

28. It it critical to distinguish homology from analogy in phylogeny reconstruction Incorrect interpretation of the four- chambered heart as a homology would lead to incorrect assessment of the relationship of birds and mammals. Convergent evolution of stem succulence in Euphorbiaceae and Cactaceae

29. The four-chambered heart evolved at least twice in vertebrate history.

30. Molecular Phylogenetics G In molecular phylogenetic studies, individual nucleotide positions are the characters, while the particular nucleotide occurring at that position is the character state.

31. Using parsimony analysis to choose among competing cladograms.

33. A B C Under the principle of parsimony, tree A would be preferred over B and C as it is one or two steps shorter.

34. A cladogram is an evolutionary hypothesis. It can be revised as new evidence becomes available.

35. It’s rather remarkable, wouldn’t you say? Molecular systematics is shedding new light on the evolution of life on earth.