Download Lecture 01: Intro

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)!
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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!
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!
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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..!
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!