General Information



by Bergstrom and Dugatkin

ISBN: 0393925927

The Beak of the Finch
by Jonathan Weiner

ISBN: 067973337X




RELEVANT READINGS (papers are linked below and can also be found on the Supplementary Materials page)

Monday, 8/4 The Great Naturalists and Deep Time.


Midway Trailer: This documentary trailer gives a glimpse of the devastating effects of the pacific garbage patch on albatrosses. An interview on the motivations behind the documentary can be found here and the accompanying photo series can be found here.

Joyce 2007: This paper gives an overview of some of the fascinating work that has been done on the in vitro replication and evolution of nucleic acids.

Dobzhansky 1973: This is a classic article that argues for the role of evolution in biology.

Nurse 2003: This article gives a perspective on the key overarching concepts of biology, including evolution.

Sleep 1989: This paper is a study of large impacts on the surface of the Earth and their implications for life.

Woese 1987: As we discussed in class, this paper covers Woese's discovery of the Archaea.

For some of Wallace's writings on biogeography and natural selection, see "A Wallace Line Reader" under "Naturalists with Genomes" in Supplementary Materials.

Tuesday, 8/5 Earth's timeline.
What the rocks say: the history of life in the fossil record.
(Lecture Slides)


This website can serve as a virtual museum for exploring some of the most important fossils in the world.

Saunders 2009: This paper describes the Siberian Traps and the surrounding hypothesis for the end Permian mass extinction.

Thewissen 2009: This excellent paper gives an overview of whale evolution and the fossil record that helps us understand it.

Richter 1986: This is the paper on Lord Kelvin's estimate of the age of the earth.

Wednesday, 8/6 Phylogeny.(Lecture Slides)


Arkive: A very cool archive of pictures and information about modern animal life.

Telford 2011: This paper discusses using genomic data to improve animal phylogenies.

Eren 2013: This very interesting paper describes a method known as oligotyping which uses information theory for comparing microbial rRNA sequences.

Hunt 1995: This paper describes modern efforts to understand the color blindness of the great John Dalton using the sequence of his DNA.

Chang et al 2002: This very interesting paper discusses work aimed at exploring dinosaur color vision.

Baum and Smith 2012: Tree Thinking: An Introduction to Phylogenetic Biology. This is the book on phylogeny that Rob mentioned in class.

Jeremy Nathans video: These are the video lectures on vision that Rob mentioned in class.

Thursday, 8/7 The Fact of Variation.(Lecture Slides)
The Fact of Heritability.(Lecture Slides)


Chou 2012: This is the paper we discussed during class about the robustness with which influenza viruses package eight RNAs.

Luria Delbruck 1943: This is the original paper on bacterial mutation that we referenced during our MATLAB coding session.

Jeremy Gunawardena's essay on patheticness: This paper is an excellent account of how we should think of models in biology.

Friday, 8/8 The forces of evolution: Natural selection in the wild.
(Natural Selection Lecture Slides)
(Coloration Lecture Slides)

Monday, 8/11 Population Genetics. (Lecture Slides)


Lectures on Population Genetics: This is one of the richest source of materials on population genetics that I am aware of. The 2006 lectures in Aarhus and the 2012 Uppsala lectures have been particularly helpful to me.

Tuesday, 8/12 The great transitions of eukaryotes and multicellularity. Species and speciation.
(Transitions Lecture Slides)
(Speciation Lecture Slides)


King 2004: This paper gives a discussion of the rise of multicellularity with particular attention paid to the choanoflagellates.

Ratcliff 2012: This is a recent experiment in yeast which shows the evolution of multicellularity in brewer's yeast.

Wednesday, 8/13 Species and speciation continued. The genome: one of modern biology's greatest ideas.
(Genome Lecture Slides)
(Human Evolution Lecture Slides)


Sarich 1967: This is Sarich and Wilson's radical paper suggesting that you can determine the relatedness of species using biochemical methods

Yunis 1982: This paper shows how examination of the macroscopic morphology of chromosomes was used to generate evolutionary hypotheses about humans and our closest primate relatives.

Babic 2008: This paper shows how examination of the macroscopic morphology of chromosomes was used to generate evolutionary hypotheses about humans and our closest primate relatives.


Thursday, 8/14 Naturalists with Genomes - Island Biogeography - Wallace and Indonesia.
(Lecture Slides)