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: Lab: 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 ( )
Professor of “Worms and Insects” in Paris
The first scientific theory of evolution
Lamarck was a French biologists who lived in the 18th century. He propounded the heretical idea that species were not created in their current form but have changed over time. His model was, however, at odds with current ideas. First he believed (as everybody did then) that life arises spontaneously all the time - that maggots could appear spontaneously on rotting meat without an adult laying eggs! His idea was that there is a ladder of life with superior forms (humans of course) near the top and lower forms on lower rungs (plants near the bottom). He imagined that all organisms had an internal drive to ascend the ladder during evolution. Those that started earlier (or had a stronger drive) would be higher than those that evolved later. He did not think of evolution in a tree-like form.
His model to explain adaptation was the popular idea of use-and-disuse or “the inheritance of acquired characters.” He imagined that when an organism tries to use an organ for some purpose repeatedly that organ will grow and, moreover, its offspring would start with an already enlarged organ. For example a giraffe would stretch for high leaves throughout its life and this would result in its offspring being borne with a longer neck. This mechanism was widely believe until the early 20th century. Now we know that it does not work - that there is no way that event going on during an organisms life can causes directed changes in its heritable material.

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

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

15. Charles Darwin ( )
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
Favored by Darwin. Quote. He recognize that this structure more accurately represents diversity.
Charles Darwin, On the Origin of Species; pages

17. The only figure in “On the Origin of Species”
The horizontal lines are arbitary time segments that we come an observe. The horizontal scale represents in this case some measure of degree of difference - but this is a convention that we will not usually follow.

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
t was left to two other Germans (Willi Hennig and Walter Zimmerman) to found the science of Phylogenetic Systematics. As a result of their contributions modern evolutionary biology depends heavily on reconstructing phylogenies and using them to gain knowledge about how evolutiob happened.

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
Taxon
Terminal node
Tip
Leaf
Clade
Internode
Internal branch
Edge
Node
Internal node
Root