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

• 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 (1744-1829)

• 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

“Advancement”

primitive advanced

Time

past

present

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

Common Ancestor

Species 2Species 1 Species 3

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

• 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

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

InternodeInternal branchEdge

NodeInternal node

Root

Terminal branch/edge

TaxonTerminal node

TipLeaf

Clade