quals

Reading materials for qualifying exams.
Contact [[email protected]] link2 with questions.

** see [this link] link100 for a great short but broad list of readings too **

reading list

Initial list generated by Matt MacManes [here] link1. Readings organized below are grouped by when we will read them, but numbers are to indicate their position in the original list by MacManes. Links provided when available. A possibly useful addition of papers can be found from an old seminar with Vaughn Cooper [here] link23.

Week 1 - Dipping your beak into the gene pool

([paper1] link3) Boag, P. T., and P. R. Grant. 1981. Intense natural selection in a population of Darwin’s finches in the Galapagos. Science 214: 82-85
([paper3] link4) Grant, P. R. and B. R. Grant. 2002. Unpredictable evolution in a 30-year study of Darwin’s Finches. Science 296:707-711.
([paper 16] link5) Losos 2009 Adaptation and diversification on islands

Week 2 - How fit are theories of evolution?

([paper 2] link6) Gould, S. J. and R. C. Lewontin. 1979. The spandrels of San Marco and the Panglossian paradigm: a critique of the adaptationist programme. Proceedings of the Royal Society of London. Series B. 205:581-598.
([paper 5] link7) Orr, H. A., and J. A. Coyne. 1992. The genetics of adaptation: a reassessment. American Naturalist 140:725-742
([paper 13] link8) Lewontin 1970 The Units of Selection.

Week 3 - The birds and the bees: the nature of sexual selection

([paper 4] link9) Hamilton W. D. and M. Zuk. 1982. Heritable true fitness and bright birds: a role for parasites? Science 218:384-387.
([paper 15] link10) Trivers R. L. and Willard D. E. 1973. Natural selection of parental ability to vary the sex ratio of offspring. Science 179(4068):90-2. See also [here] link11 for additional links describing the work.
([paper 17] link12) Emlen 2012 A Mechanism of Extreme Growth and Reliable Signaling in Sexually Selected Ornaments and Weapons.
([paper 14] link13) Bateman (1948) “Intra-sexual selection in Drosophila. See [here] link14 for some contemporary commentary.

Week x - Drift vs. selection, round 1:

([unlisted paper] link24) King J. L. and T. H. Jukes. 1969. Non Darwinian evolution. Science 164:788-798. ([unlisted paper] link25) Levy S. F. et al. 2015. Quantitative evolutionary dynamics using high-resolution lineage tracking. Nature 519(7542):181-6.

Week 4 - Selection modes

([paper 6] link22) M. Z. Ludwig, et al., "Evidence for stabilizing selection in a eukaryotic enhancer element," Nature 403 (2000), 564-567
no paper available ([paper 7] link15) A. L. Hughes and M. Nei, "Patter of nucleotide substitutions at major histocompatibility complex class I loci reveals overdominant selection," Nature 335 (1988), 167-170. See [here] link21 for second paper published the following year.
no paper available ([paper 9] link16) J. H. McDonald and M. Kreitman, "Adaptive protein evolution at the AHD locus in Drosophila," Nature 351 (1991), 652-654
no paper available ([paper 11] link17) Tomoko Ohta, "Slightly Deleterious Mutant Substitutions in Evolution," Nature 246 (1973), 96-98

Week 5 - Selection rates and STDs

([paper 8] link18) N. A. Moran, "Accelerated evolution and Muller's Ratchet in Endosymbiotic bacteria," PNAS 93 (1996), 2873-2878.
([paper 10] link19) T. Miyata and T. Yasunaga, "Rapidly evolving mouse alpha globin related pseudogene and its evolutionary history," PNAS 78 (1981), 450-453.
([paper14] link20) Hickey 1982 SELFISH DNA: A SEXUALLY-TRANSMITTED NUCLEAR PARASITE