Journal Club

Spring 2017: Recombination in Evolution

Week 1: A bit of introductory reading
Lewis-Rogers, N., K. A. Crandall and D. Posada, 2004 Evolutionary analyses of genetic recombination. Dynamical genetics 408. [pdf]

Week 3: QTL Mapping
Weber, J. N., B. K. Peterson, and H. E. Hoekstra. 2013. Discrete genetic modules are responsible for complex burrow evolution in Peromyscus mice. Nature 493:402-405. [pdf] [supplemental info]

Week 5: Intragenomic recombination variation

Roesti, Marius, Dario Moser, and Daniel Berner. “Recombination in the Threespine Stickleback Genome—Patterns and Consequences.” Molecular Ecology 22, no. 11 (2013): 3014-27. [pdf]

 

Spring 2016: Readings in Adaptation

Week 12: More Stickleback Genetic Architecture

COLOSIMO, P. F., K. E. HOSEMANN, S. BALABHADRA, G. VILLARREAL, M. DICKSON, J. GRIMWOOD, J. SCHMUTZ, et al. 2005. Widespread parallel evolution in sticklebacks by repeated fixation of ectodysplasin alleles. Science 307: 1928-1933.

  • Link to the paper

Week 11 (5 April 2016) Genetic architecture of armor in Stickleback

Colosimo PF, Peichel CL, Nereng K, Blackman BK, Shapiro MD, et al. (2004) The Genetic Architecture of Parallel Armor Plate Reduction in Threespine Sticklebacks. PLoS Biol 2(5): e109. doi: 10.1371/journal.pbio.0020109

Week 10 21 Marchl 2016) Evolution of armor in Stickleback

BELL, M. A., W. E. AGUIRRE, AND  N. J. BUCK. 2004. Twelve years of contemporary armor evolution in a threespine stickleback population. Evolution 58: 814-824.

Week 6 (7 Mar 2016): Parallelism in adaptation

This week we will continue with experimental evolution in E. coli.

SAXER, G., AND  M. TRAVISANO. 2016. Parallelism in adaptive radiations of experimental Escherichia coli populations. Evolution 70: 98-110.

Week 5(1 Mar 2016): Evolution of Cit+ in E. coli

This week we will think more about the LTEE that we discussed last week.  We will focus on a molecular analysis of the evolution of the ability to metabolize citrate – a trait that is non-characteristic for E. coli.  This happened around generation 31,000 of the experiment in one replicate. This was probably not the result of a single mutation event that led to the new phenotype, but likely the combination of many mutational events that happened over the course of the experiment (detailed in the supplemental reading). This week’s reading is on a genomic analysis of the Cit+ line of E. coli to try to dissect the genetic changes that allowed for the evolution of this novel phenotype.

  • Link to the paper from Nature
  • Link to a paper  in PNAS that discusses the complex evolution of the novel phenotype

Week 4 (23 Feb 2016): Experimental Evolution in E. coli 

This week we will dive back to the first of many papers from Rich Lenski’s experimental evolution experiments.  It is a long and dense paper, but do your best to pull out the important points.  We will read more papers on this system so this will serve as a nice foundation for the next couple of weeks.

LENSKI, R. E., M. R. ROSE, S. C. SIMPSON, AND  S. C. TADLER. 1991. Long-Term Experimental Evolution in Escherichia coli. I. Adaptation and Divergence During 2,000 Generations. The American Naturalist 138: 1315-1341.

  • Link to the paper at Harvard

Week 3 (16 Feb 2016): (un)predictability of evolution

This week we will start to think about time scales of adaptation, especially in reference to how we define adaptation.  We will consider a long-term study by Peter and Rosemary Grant on evolution of beak size in Darwin’s finches – an adaptation to food source (different beaks are advantageous when considering different types of seeds in the bird’s diet).  When reading the article, think about how we have discussed definitions of adaptations and how those definitions are affected by results such as those presented here.

GRANT, P. R., AND  B. R. GRANT. 2002. Unpredictable Evolution in a 30-Year Study of Darwin’s Finches. Science 296: 707-711.

  • Link to the paper at Science

Week 2 (2 Feb 2016): Strong Inference in the study of adaptation

Strong Infernece (Platt 1964) is a means of doing science that requires the application of the four following steps to problems in science: (1) Devising alternate hypotheses, (2) Devising a crucial experiment with alternative possible outcomes, each of which will exclude one or more of the hypotheses, (3) Carrying out the experiments, and (4) Recycling the procedure, making subhypotheses to refine the possibilities that remain after the initial crucial experiments.As is true of all scientific discouse, there are obviously some people out there questioning the appropriateness of the focus on strong inference (for example O’Donohue and Buchanan 2001).This week we will look at a paper that uses a strong inference approach to test hypotheses about the adaptive value of acclimation – the ability of organisms to show an increase in fitness in environments with which they are ‘familiar’. Note that acclimation is not an evolutionary force as it all happens within an individual – it is a form of phenotypic plasticity. The paper shows the development of a strong inference approach to test a variety of evolutionary scenarios of acclimation to temperature.HUEY, R. B., D. BERRIGAN, G. W. GILCHRIST, AND J. C. HERRON. 1999. Testing the adaptive significance of acclimation: A strong inference approach. American Zoologist 39: 323-336.

  • Link to the paper at American Zoologist
  • Link to a book chapter by the same authors outlining the strong inference approach.

Week 1 (26 Jan 2016): Spandrels

This week we dive in to a classic in evolutionary biology – Gould and Lewontin’s Spandrels of San Marco. This paper has been controversial from the day it was published – with arguments over the merits of their arguments occurring even today. There are also a wealth of discussions of the paper, a few of which are also linked here for further reading.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 B: Biological Sciences 205: 581-598.

  • Link to the paper at the Proceedings website.
  • Link to the wikipedia article on the article.
  • Link to one of the many rants about the article from the Oikos Blog
  • Link to an interview with Lewontin by E. O. Wilson – an interesting read.

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