Taught Fall Semesters
The Evolution of Eukaryotes - Syllabus
Course number: 11:704:401
Instructors: Lena Struwe (Struwe@aesop.rutgers.edu), Debashish Bhattacharya
(bhattacharya@aesop.Rutgers.edu)
Taught: Monday and Wednesday: 12:35 – 1:55pm.
Summary of content:
The last decade has seen remarkable advances in our understanding of eukaryote origins
and the tree of life. Phylogenetic, molecular genetic, and in particular, genomic work
have allowed researchers to erect sophisticated hypotheses about the branching order of
eukaryotes, the role of gene transfer in shaping genomes, and the endosymbiotic origin of
the mitochondrion and the plastid. These research areas impinge directly on the ecology
and evolution of organisms, both uni- and multicellular and their phylogenetic
interrelationships. In the course, each of these broad areas will be looked at in detail
through lectures, paper-readings, and discussions.
Lecture content:
1. Origin of life (the first DNA/RNA, the first cell, when/where?) [DB]
2. Tree of life through history, what have scientists hypothesized? [LS]
3. Endosymbiosis and organelle origins [DB]
4. Role of horizontal gene transfer and endosymbiosis [DB]
5. Phylogenetic methods (maximum parsimony, maximum likelihood, alignments,
branch support); take-home assignment in phylogenetics [LS]
6. Formation of species, punctuated equilibrium, speciation basics [LS]
7. Extinction, surviving living fossils [LS]
8. Genomics as a tool for Tree of Life inference (phylogenomics) [DB]
9. Role of polyploidy in evolution [guest lecture: Stacy Bonos?]
10. Demo of PhyloSort software and introduction to take-home assignment in
phylogenomics [DB]
11. CLASS DEBATE: Is there a true tree of life?
12. Evolution of Life on Earth, a time-line (geological and temporal framework) [LS]
13. The Tree of Life (ToL), overview; major branches of eukaryotic ToL; key
evolutionary innovations; protist and algal diversity [DB]
14. The green ToL branch (plants, overview) [LS]
15. Evolution of life cycles and diploid/haploid stages in plants [LS]
16. The fungal ToL branch (fungi) [guest lecture: Ning Zhang?]
17. The insect ToL branch (insects) [guest lecture: Karl Kjer]
18. The ‘dinosaur’/bird/vertebrate branch [guest lecture: Kathleen Scott?]
19. The human ToL branch [guest lecture: TBA]
20. Origin of viruses [guest lecture: Siobain Duffy?]
21. Symbiosis and co-evolution, horizontal gene transfer (example: the
photosynthetic sea slug Elysia chlorotica) [DB]
22. Evolution of eukaryotic diseases and parasites (malaria, Ebola, etc) [guest lecture:
Siobain Duffy?]
23. CLASS DEBATE: Will climate change destroy the planet?
24. TBA
Student audience
Both advanced undergraduate and graduate students at SEBS or SAS will benefit from
training in approaches to understanding eukaryote phylogeny from their birth to the
interrelationships of extant clades.
Credits: 3 (2 lectures/week)
Prerequisites: Two semesters of general biology (01:119:101/102) or equivalent, AND
Fundamentals of Evolution 11:704:251 or equivalent. Contact instructors for special
permission if you do not have these prerequisites.
Course website and online content: A course website will be developed using the
ecollege course shell and include readings, gradebook, links to online resources such as
websites, articles, interactive materials, and videos, and also contain online selfassessment quizzes and forums for discussions of particular topics.
Course assessment:
2 exams, 2 take-home assignments (one each on phylogenetics & phylogenomics), and 1
larger essay on the evolution of a selected taxonomic group or evolutionary phenomena.
Evaluation and Grading:
Take-home assignment 1: 10%
Take-home assignment 2: 10%
Midterm: 30%
Final exam: 30%
Essay: 20%
Hands-on, practical content:
Take-home assignment of a phylogenetic analysis using datasets of DNA sequences from
about 20 species using freely available software programs. Covers DNA alignment,
sequence analysis, and phylogenetic analysis.
Take-home assignment of a phylogenomic analysis using datasets and freely available
software programs.
Lectures will incorporate hands-on examples of organismal groups whenever possible.
Readings: A variety of selected textbook chapters, scientific articles, and writings from
popular press.