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Overview of the class! David A. Baum! N. Ivalú Cacho! •! 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%)! Logistics! Grading! Botany 563: Phylogenetic Analysis of Molecular Data! •! 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)! •! •! •! •! •! 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)! Readings! •! Readings by D. Baum (drafts)! •! Classic papers from the methodological literature! •! Accessible review papers! •! Case-studies to discuss! 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! 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! Jean-Baptiste Lamarck! •! French Naturalist (1744-1829)! •! Professor of “Worms and Insects” in Paris! •! The first scientific theory of evolution! Lamarck’s assumption! Charles Bonnet (Switzerland; 1720-1792)! •! Continuum between physical and biological world (followed Aristotle)! •! Scala Naturae (“Ladder of Life” or “Great Chain of Being”)! 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! Advanced forms started earlier! -.(1(&*, 0/)(, -%1*, -./)/*/$(, %#$%&'(# !"#$%&'()(&*+, 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..! Lyell, C. Principles of Geology, Vol. II, Chap. 1 ! Species 1! Species 2! Species 3! Common Ancestor! Common Ancestor! 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”! 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! The only figure in “On the Origin of Species”! 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! 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! 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! Argues for the centrality of phylogenetic trees in evolution and systematics and provided a framework for reconstructing phylogenies! 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..! 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! What a phylogenetic tree is:! !! A depiction of the descent relationships of a sample of “tips” (species, genes, etc.)! Terms used to describe a phylogenetic tree! Terminal node! Taxon! Tip! Leaf! Terminal branch/edge ! Clade! Internode! Internal branch! Edge! Node! Internal node! Root!