1. Phylogeny [phylo = tribe, family; gen = creation, birth] taxonomy: classifying and naming organisms taxon, taxa (pl.): classification unit (e.g. genus, order) systematics: taxonomy based on phylogeny cladistics: modern approach to systematics clade: group of spp. with common ancestor Biological diversity and classification Biol 121, Fall 2010, Tom Buckley 01 Sep 10

2. Biological diversity and classification Reminders: 1. print out the lab handout from WebCT and bring it to lab 2. bring your textbook to lab

3. Hierarchy of classification Species: Panthera pardus Genus: Panthera Family: Felidae Order: Carnivora Class: Mammalia Phylum: Chordata Kingdom: Animalia ArchaeaDomain: Eukarya Bacteria Domain Kingdom Phylum/Division Class Order Family Genus Species Kids Prefer Cheese Over Fried Green Spinach King Phillip came over for great spaghetti. Keeping Precious Creatures Organized For Grumpy Scientists

4. Phylogenetic trees concepts: common ancestors sister taxa trees show sequence, not time what is sister taxon of Panthera pardus?

5. monophyletic group: last common ancestor and all of its descendants (a.k.a. clade) polyphyletic group: does not include last common ancestor paraphyletic group: includes last common ancestor, but not all descendants Phylogenetic trees

6. Classification Carolus Linnaeus (1707-1778) binomial nomenclature Homo sapiens L. genus (always capitalised) (abbreviated after first use) specific epithet (never capitalised) authority species name (italics or underlined) {

7. Nomenclature... which is valid? Humans are members of the species sapiens. Humans are members of the species Homo sapiens. Humans are members of the species H. sapiens. Humans are members of the species Homo Sapiens.     

8. Bison bison

9. Marmota marmota http://en.wikipedia.org/wiki/List_of_tautonyms

10. How phylogenies are inferred homology: similarity due to shared ancestry cf. analogy: similarity due to something else either coincidence or convergent evolution e.g. opposable thumbs in orangutans and humans e.g. wings in bats and birds

11. Convergence: cacti vs euphorbs

13. Convergence: Equisetum vs Casuarina (diverged 400 MYA)

14. examples: http://evolution.berkeley.edu/evolibrary/search/topicbrowse2.php?topic_id=55 How phylogenies are inferred homology: similarity due to shared ancestry cf. analogy: similarity due to something else analogies are also called homoplasies

15. How phylogenies are inferred homology: similarity due to shared ancestry phenotypic: based on anatomy, morphology, physiology molecular: based on DNA sequences

16. How phylogenies are inferred shared ancestral characters shared derived characters = homologies conifers flowering plants vascular seedless plant Q: is vascular tissue homologous or analogous in conifers & flowering plants? vascular seed plant = analogies

17. How phylogenies are inferred outgroup vs ingroup (e.g. ferns are an outgroup of seed plants) conifers flowering plants seed plants vascular seedless plant vascular seed plant seeds evolved here ferns

18. Deducing phylogenies by parsimony some gene Ancestor "ancestral sequence" = A outgroup? ingroup?

19. fewest assumptions, simplest story A A C C A C A C A C C A ACA # of mutations:1 22 some gene Ancestor "ancestral sequence" = A Deducing phylogenies by parsimony

20. tree based on genetic data: Induction or deduction? birds & crocs share traits: e.g., 4-chamber heart shared trait: more likely ancestral than derived Q: where is common ancestor of birds and crocs? 1 2 3 4 Q: when did 4-chambered heart likely evolve? did dinosaurs have 4-chambered hearts? YES, PROBABLY

21. element number of protons (atomic #) electronic structure chemical behaviour Fossil dating

22. Isotopes: different # of neutrons Carbon-12 ( 12 C)Carbon-14 ( 14 C) 6 protons 6 neutrons 6 protons 8 neutrons element chemical behaviour

23. Radiometric cosmic rays (neutrons) 14 N 14 CO 2 12 CO 2 12 C 14 N 14 C 12 C 14 N 14 C 12 C 14 N 14 C 12 C isotopes Dating fossils

24. 2 Kingdoms: animals plants (incl. protists, prokaryotes, fungi) Phylogenies keep changing 5 Kingdoms: prokaryotes protists fungi animals plants 3 Domains: Archaea Bacteria Eukarya Many Kingdoms...

25. Domains Q: are multicellular organisms monophyletic? red boxes: non-colonial, multicellular organisms monophyletic group: last common ancestor and all of its descendants

26. Mastering Biology http://www.masteringbiology.com/