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--- projects [2013/02/10 18:26] – [Potential PhD project on speciation] mkopp
+++ projects [2019/03/21 10:21] – external edit 127.0.0.1
@@ Line 5: / Line 5: @@
 ====== Projects ======
+  * [[Speciation and plasticity]]
+  * [[Adaptation to climate change]]
+  * [[Standing genetic variation]]
 ===== Manuscript Sebastian =====
@@ Line 71: / Line 75: @@
   * interaction between magic and non-magic traits (see van Doorn and Weissing 2004)
   * plasticity
+  * sensory drive
+  * species recognition
 Sources of inspiration:
@@ Line 77: / Line 83: @@
   * To some degree Smadja and Butlin review
-Potential topic: Phenotypic plasticity and speciation
+Potential topic: Phenotypic plasticity and speciation with gene flow
   * 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)?
+  * 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, types of reproductive barriers... The Pfennig et al. 2010 paper is pretty vague in parts; Fitzpatrick 2012 is clearer and already discusses adaptive vs. maladaptive plasticity, and plasticity in divergence vs. RI;
   * 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
-    * sticklebacks
+    * flowering time
+    * sticklebacks?
+    * tiger salamanders?
     * examples from WE book
+    * a considerable number of examples seem to include speciation with gene flow
   * 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)?
+    * secondary contact after genetic assimilation: reinforcement or return to plasticity?
   * Try to model the arctic charr scenario?
   * See list of questions in Fitzpatrick 2012
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   * Interaction between evolution of plastic and non-plastic barriers?
-===== Comments on Adrianna's manuscript =====
+===== Possible continuations for Elma =====
-  * Is this a critique of W-E's theory of speciation, or rather of her theory phenotypic evolution per se?
+  * Stationary probability (time spent in certain intervals)
-  * Describe the DPHS in more details (as in Pfennig et al. 2010, Fitzpatrick 2012)?
+  * Etienne will try to solve the limiting case m = v
+  * Time before a certain level of maladaptation is reached
+  * Stochastic movement of optimum
+  * Make theta a function of distance to optimum (this would imply that the carrying capacity decreases with increasing maladaptation); alternatively, add a probability of extinction (Poisson) that increases with maladaptation
+  * Add explicit population dynamics (logistic growth or exponential growth with cut-off; the latter would allow to study evolutionary rescue during exponential decline)
+  * Etienne: Model is easier to analyze if fluctuations around deterministic trend are treated as Brownian motion -> is this a justifiable approximation or potentially a way to model adaptation involving standing variation? - Check literature on Brownian motion models for quantitative traits