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--- projects [2013/02/10 19:32] – [Potential PhD project on speciation] mkopp
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-====== Projects ======
-===== Manuscript Sebastian =====
-__List of Figures:__
-  * Fig. 1: selection coefficient
-  * Fig. 2: first step, no correlation, alpha_1 bar as function of gamma
-  * Fig. 3: first step, no correlation, alpha_1 bar as function of n (complexity)
-  * Fig. 4: first step, no correlation, histograms
-  * Fig. 6: first step, no correlation, heat plot
-  * Fig. 7: selectional correlation, all steps, alpha_1 bar
-  * Fig. 8: selectional correlation, all steps, rho_alpha
-  * Fig. 9: selectional correlation, first step, heat plot and histograms
-  * Fig. 10: selectional correlation, fitness gradient
-  * Fig. 11: selectional correlation, diving kite
-  * Fig. 11a: selectional correlation, time series, flying kite
-  * Fig. 12: mutational correlation, all steps, various measures, n = 2
-  * Fig. 12: mutational correlation, all steps, various measures, n = 3
-  * Fig. 14: mutational correlation, first step, heat plots
-  * Fig. 15: mutational correlation, time series, flying kite
-  * Fig. 16: mutational and selective correlation, rho_alpha
-===== Project extinction risk =====
-__Ideas (25 Jan 2013):__
-  * Deadline is April 2!
-  * Main topic is climate change, adaptation, and plasticity, not necessarily evolutionary rescue
-  * Unclear to what degree the article will be a review or a modeling paper
-  * Need to read up recent reviews, especially Chevin
-  * One idea: explain assumptions behind and consequences of Bürger & Lynch model
-__Moving optimum model__
-  * Key idea: Calculate evolutionary rates in haldanes;
-    * choose reasonable set of genetic parameters
-    * focus on varying ecological parameters (N, B, v, omega, theta)
-  * Preliminary observations in small populations
-    * Rates of evolution generally increase as the optimum pulls away
-    * Genetic variances stay high until just before extinction; may even reach a big shortly before extinction
-    * Initial rate of evolution low even with strong selection? Requires analysis of allele frequencies (-> standing variation project)
-  * To do: find way to compactly visualize evolutionary rates
-    * over which time window?
-    * haldanes calculates over which interval?
-__Potential topics__
-  * Focus on evolutionary rates might be justified, since models tend to be dynamic
-  * Phenotypic adaptation by genetic evolution: all of quantitative genetics:-), starting with breeders/Lande equation
-  * Evolution of plasticity: been reviewed several times
-  * Evolutionary rates: Andrew should know all about those
-  * Maybe here our simulations fit in
-  * Evolutionary rescue: note exactly the topic
-  * Evolutionary rescue and plasticity: Good review in Chevin et al. 2012
-  * Plasticity facilitates genetic adaptation: West-Eberhard etc., some more concrete models showing this to be the case
-  * Something about the expected contribution from genetics and plasticity? Is this possible? (Ghalambor 2007)
-  * Different kinds of environmental change (sudden, moving, fluctuating; kinds of noise)
-  * Plasticity vs. tolerance
-  * Constraints and limits to adaptive evolution
-  * Costs and limits of plasticity
-  * Evolvability <-> environmental variability
-===== Potential PhD project on speciation =====
-Interesting topics:
-  * parapatric speciation
-  * female preferences
-  * genomic islands
-  * mixed geographic modes
-  * interaction between magic and non-magic traits (see van Doorn and Weissing 2004)
-  * plasticity
-Sources of inspiration:
-  * List of questions in Nosil book
-  * Butlin et al review
-  * To some degree Smadja and Butlin review
-Potential topic: Phenotypic plasticity and speciation
-  * Reviews: Pfennig et al. 2010, Fitzpatrick 2012, Minelli & Fusco 2012
-  * Start with more specific review about classification of scenarios and links to theory (complementary to Pfennig et al. 2010)? -- Focus on evolution of RI; classify according to types of plasticity, type of plastic traits, ...
-  * Make a list of proposed theoretical scenarios
-    * The clearest concepts seem to the **developmental plasticity hypothesis of speciation** and the **flexible stem hypothesis** for adaptive radiations
-  * Make a list of proposed empirical examples
-    * arctic charr
-    * cichlids
-    * flowering time
-    * sticklebacks?
-    * tiger salamanders?
-    * examples from WE book
-  * Use Thibert-Plante and Hendry (2011) as starting point (see my review on it), but focus more on evolution of female preferences? (Or use assortative mating instead?)
-  * Some potential model ingredients/variants:
-    * female preference vs. assortative mating
-    * automatic vs. classic plastic magic trait
-    * linear reaction norm vs. threshold characters
-    * geographic setting (but two-island model seems the most natural choice)
-    * counter-gradient variation (non-adaptive plasticity)?
-  * Try to model the arctic charr scenario?
-  * See list of questions in Fitzpatrick 2012
-  * Use Draghi and Whitlock approach to model plasticity?
-  * Plastic magic traits...
-  * **Key question: Interaction between evolution of non-random mating and genetic assimilation**
-  * Interaction between evolution of plastic and non-plastic barriers?
-===== Comments on Adrianna's manuscript =====
-  * Is this a critique of W-E's theory of speciation, or rather of her theory phenotypic evolution per se?
-  * Describe the DPHS in more details (as in Pfennig et al. 2010, Fitzpatrick 2012)?