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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%)
• Phylogenetic comparative methods (ca.
25%)
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)
Grading
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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
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
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
Jean-Baptiste Lamarck
• French Naturalist (17441829)
• Professor of “Worms and
Insects” in Paris
• The first scientific theory
of evolution
Lamarck’s assumption
• Continuum between physical
and biological world
(followed Aristotle)
• Scala Naturae (“Ladder of
Life” or “Great Chain of
Being”)
Charles Bonnet (Switzerland; 1720-1792)
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
present
Time
past
primitive
advanced
“Advancement”
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
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
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..
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
branch/edge
Terminal node
Taxon
Tip
Leaf
Clade
Internode
Internal branch
Edge
Node
Internal node
Root