1	PHYLOGENY Connecting organisms into branching patterns showing origins and relationships
2	Reading Chapter 26 P. 556-561 The Molecular Clock, Box 26.1, p.566 Study Figure 26.3 and be prepared to vote for your choice in class.
3	CLASSIFICATION is HIERARCHICAL OR NESTED Linnaeus set up a hierarchical system to organize animal and plant taxa Kingdom, phylum, class, order, family, genus Classification system arose before the concept of evolution was understood. A hierarchical system seemed a good way to organize the data. Our current ideas of the continuity of life lead naturally to a hierarchical organization.
4	Names of categories in plants
5	Cladogenesis, Anagenesis, & Extinction
6	Anagenesis Anagenesis, not mentioned in your text, refers to speciation (origin of new species) within a lineage. Anagenesis acknowledges that the species of today, say coyotes, may be sufficiently different from the coyotes of some earlier time, say 90,000 ya, that they should be recognized as a separate species even though there is continuity of descent.
7	Phenetic classification The Linnaean system based groups on overall similarity. Though it is hierarchical, it did not claim to show the evolutionary origins of groups. Birds and Whales are two groups that come out quite differently in the cladistic approach to classification.
8	CLADISTICS Cladistics attempts to generate phylogenies (branching patterns showing the origin and history of taxa). http://www.ucmp.berkeley.edu/clad/clad1.html Cladistics believes the best phylogenies are based on identifying shared derived characteristics shared derived characteristics are called synapomorphies
9	CLADISTICS What assumptions do cladists make? 1. Groups of organisms are related by descent from a common ancestor. 2. There is a bifurcating pattern of cladogenesis. (no splits into more than two lines) 3. Change accumulates thru time and is irreversible (or reversed the fewest times possible =parsimony).
10	Reading a Phylogeny
11	Linnaean versus cladistic Using cladistic principles and the rule that all named groups must be monophyletic 1) Birds would not be a CLASS of vertebrates because they are within the reptile clade. Birds would be within the CLASS that included reptiles as well. 2) The hoofed mammals, artiodactyls, would have to include the whales, as whales and hippos have synapomorphies.
12	Generating a PHYLOGENY
13	DNA Sequence of some enzyme for Species A, B & C A ATTCCCCTAACCTACACATAAGCGA B ATTGCCGTAGCTTACAAATAGCCGA C ATCGCCGTAACTTACAAATAGACGA
14	The Difference Matrix
15	For these sequences B & C are most closely related, so the correct phylogeny is:
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17	Which pattern is not [[[[[6,5]4]3]2]1]?
18	DNA Sequences A ATTCCTGTAG CTTACACATA GCCGA B ATTGCTCTAG CTTACACATA ACCGA C ATCGCCGTAA CTTACGGATA GACGA D ATCGCCGTAA CCTACAGATA GACGA
19	Differences among the four sequences
20	Shared derived characters
21	Phylogeny of Four Sequences with synapomorphies shown
22	Concepts of Phylogeny All current species on the same row. Time order on Y axis –either up or down Collapse branches to a single trunk (called the root). Monophyletic group = clade = A group that includes the ancestral taxa, all of its descendants, and only its descendants.
23	Vocabulary Hierarchical Cladistic Clade Monophyletic Synapomorphy Shared derived Phylogeny Anagenesis Phenetic Parsimony Node Rotation about node