Botany 563: Phylogenetic Analysis of Molecular Data David A. Baum N. Ivalú Cacho.
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Transcript of Botany 563: Phylogenetic Analysis of Molecular Data David A. Baum N. Ivalú Cacho.
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Botany 563: Phylogenetic Analysis of Molecular Data
David A. Baum
N. Ivalú Cacho
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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%)
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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)
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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)
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Readings
• Readings by D. Baum (drafts)
• Classic papers from the methodological literature
• Accessible review papers
• Case-studies to discuss
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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
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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
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Jean-Baptiste Lamarck
• French Naturalist (1744-1829)
• Professor of “Worms and Insects” in Paris
• The first scientific theory of evolution
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Lamarck’s assumption
• Continuum between physical and biological world (followed Aristotle)
• Scala Naturae (“Ladder of Life” or “Great Chain of Being”)
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Charles Bonnet (Switzerland; 1720-1792)
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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
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Advanced forms started earlier
“Advancement”
primitive advanced
Time
past
present
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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..
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Lyell, C. Principles of Geology, Vol. II, Chap. 1
Common Ancestor
Species 2Species 1 Species 3
Common Ancestor
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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”
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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
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The only figure in “On the Origin of Species”
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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
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• 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
An example: Bessey
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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
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Argues for the centrality of phylogenetic trees in evolution and systematics and provided a framework for reconstructing phylogenies
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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
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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..
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What a phylogenetic tree is:
A depiction of the descent relationships of a sample of “tips” (species, genes, etc.)
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Terms used to describe a phylogenetic tree
InternodeInternal branchEdge
NodeInternal node
Root
Terminal branch/edge
TaxonTerminal node
TipLeaf
Clade