Phylogeny and the Tree of Life

1. Phylogeny and the Tree of Life Chapter 26 BCOR 012 February 4,7, 2011

2. Outline for February 4,7 2011 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 • speciation • taxonomy • 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. 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.)

6. Fig. 26-4 Species Order Family Genus Pantherapardus Panthera Felidae Taxidea taxus Taxidea Carnivora Mustelidae Lutra lutra Lutra Canis latrans Canidae Canis Canis lupus

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

8. Phylogeny is the study of the pattern of divergence history. (as opposed to speciation, which addresses process.) Willi Hennig, 1913 - 1976 Founder of Phylogenetic Systematics (also called cladistics) Assembling a phylogeny using cladistics, taxa are associated on the basis of shared evolutionary innovations.

9. One of the evolutionary innovations shared by birds is the feather … Homology, the sharing of an innovation (derived character) because of its invention in a common ancestor.

10. Serial Homology of the Lobster

11. Figure 34.4b-c  Chordate segmentation

12. CRUSTACEANS COMPARED - EVOLUTIONARY HOMOLOGY

13. CRUSTACEANS COMPARED: EVOLUTIONARY TRANSFORMATION ROCK CRAB LOBSTER

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

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

16. Fig. 26-8b 3 4

17. DNA Evolution: stable and labile characters relate to function. Example: Homeobox genes, which govern variation in serial homologs.

18. The homeobox (in the gene) codes for a homeodomain (in the protein synthesized from the gene). The homeodomain has a precise three-dimensional structure related to its function. In evolution, the homeodomain is relatively stable because it has a precise job.

19. Amino acid sequences compared for the homeotic gene Ubx insects arthropods Dm - Fruitfly Tc - Beetle Jc - Butterfly Ak - Onycho- phoran Decides six legs or more

21. Parsimony

22. Under the principle of parsimony, tree A would be preferred over B and C as it is one step shorter. Ockham's razor.: when trying to choose between multiple competing theories the simplest theory is probably the best.

23. 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

24. 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

25. 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

26. The primitive character is the one shared by the outgroup and some, but not all, of the study group.

27. 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

29. 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 • Symplesiomorphy – a shared primitive character state

30. Cladistic Analysis and Classification: Kinds of Groups

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

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

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

34. For Phylogenetic Classification, taxa (taxonomic groups) should be natural groups, that is groups reflecting phylogeny. 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’)

35. The nested relationship of clades is reflected in the nested relationship of taxa in the resultant classification. All are monophyletic groups.

36. 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