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Botany 563: Phylogenetic Analysis of Molecular Data

Botany 563: Phylogenetic Analysis of Molecular Data. David A. Baum N. Ivalú Cacho. Overview of the class. Graduate students (systematics; molecular evolution) and advanced undergraduates who are engaged in evolutionary research Methods of phylogenetic analysis (ca. 75%)

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Botany 563: Phylogenetic Analysis of Molecular Data

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  1. Botany 563: Phylogenetic Analysis of Molecular Data David A. Baum N. Ivalú Cacho

  2. Overview of the class • Graduate students (systematics; molecular evolution) and advanced undergraduates who are engaged in evolutionary research • Methods of phylogenetic analysis (ca. 75%) • Phylogenetic comparative methods (ca. 25%)

  3. Logistics • Lecture: • Tue & Thu 1:00-2:15pm • Including discussions and activities • Lab: • Wed 1:20p-3:20p or Thu 10:00a-12:00p (Genetics/Biotechnology Rm.1240) • Hands-on experience with phylogenetic analysis (including: PAUP*, GARLI, RaxML, MrBayes, r8s, Mesquite, BUCKy)

  4. Grading • In lab assignments: 30% • 2 midterm exams (take-home): 30% • Participation: 10% • Either: Cumulative final exam: 30% • Or: Paper and poster presentation: 30% (strongly recommended for graduate students)

  5. Readings • Readings by D. Baum (drafts) • Classic papers from the methodological literature • Accessible review papers • Case-studies to discuss

  6. Introduction to Phylogenetic Systematics • The study of the evolutionary history of species, genes, and other biological entities • The use of phylogenies to obtain information about evolutionary phenomena

  7. History of “tree-thinking” • Evolutionary (transmutationist) views were original tied to ideas of progress up a “ladder of life” • Charles Darwin was the first to see clearly that evolutionary biology implies a tree like form

  8. Jean-Baptiste Lamarck • French Naturalist (1744-1829) • Professor of “Worms and Insects” in Paris • The first scientific theory of evolution

  9. Lamarck’s assumption • Continuum between physical and biological world (followed Aristotle) • Scala Naturae (“Ladder of Life” or “Great Chain of Being”)

  10. Charles Bonnet (Switzerland; 1720-1792)

  11. Lamarck’s evolution • Life progresses upward due to an internal drive towards perfection • Why are primitive organisms still around? • Spontaneous generation of new life constantly • Mechanisms of change? Inheritance of acquired characters

  12. present Time past primitive advanced “Advancement” Advanced forms started earlier

  13. Charles Lyell (1797–1875) • English Geologist, mentor to Charles Darwin • Summarized (and attacked) Lamarck’s views • Anti-evolutionist • Noted that evolution implies a tree-like form..

  14. Species 1 Species 2 Common Ancestor Common Ancestor Lyell, C. Principles of Geology, Vol. II, Chap. 1 Species 3

  15. Charles Darwin (1809 -1882) • Best known for On the Origin of Species (1859) • Abundant evidence for evolution • Proposed a mechanism: natural selection • Accepted Lyell’s view that evolution implies a “tree of life”

  16. The affinities of all the beings of the same class have sometimes be represented by a great tree. I believe this simile largely speaks the truth…… …The green and budding twigs may represent existing species; and those produced during former years may represent the long succession of extinct species….. ….the great Tree of Life….covers the earth with ever-branching and beautiful ramifications Charles Darwin, On the Origin of Species; pages 131-132

  17. The only figure in “On the Origin of Species”

  18. The next 100 years • Systematics continued to follow a ladder-of-life model while using the tree of life metaphor • Systematists looked for (and saw) continuity and directional trends among living species and used these to develop classifications

  19. An example: Bessey • Some of Bessey’s “dicta” • Homogenous structures “higher” than heterogeneous • Woody stems more “primitive” than herbaceous stems • Opposite leaves “preceded” alternative leaves • “Primitive” flowers have many stamens

  20. The Beginning of Phylogenetics • Willi Hennig (entomologist) and Walter Zimmerman (botanist) developed formal methods for reconstructing phylogenies • Hennig’s book “Phylogenetic Systematics” was translated into English and ultimately stimulated great changes in systematic practice

  21. Argues for the centrality of phylogenetic trees in evolution and systematics and provided a framework for reconstructing phylogenies

  22. Their principles • Phylogenies are objectively real • Relationship is evolutionary kinship (closely related organisms share a recent common ancestor) • Phylogenetic relatedness should be the sole basis of classifications • Characters that vary among organisms contain information on the phylogeny

  23. Ever since Hennig.. • Claims about classification were controversial but ultimately accepted • Computational and molecular methods became available • Phylogenetics reformulated as a series of statistical estimation problems • It has become important for many biological problems..

  24. What a phylogenetic tree is: • A depiction of the descent relationships of a sample of “tips” (species, genes, etc.)

  25. Terms used to describe a phylogenetic tree Terminal branch/edge Terminal node Taxon Clade Tip Leaf Internode Internal branch Edge Node Internal node Root

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