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speciation_and_plasticity [2013/02/13 15:21] – [Modeling of speciation with gene flow in the presence of phenotypic plasticity] mkoppspeciation_and_plasticity [2019/03/21 10:21] (current) – external edit 127.0.0.1
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 ===== Background and general question ===== ===== Background and general question =====
-  * Speciation is a key topic in evolutionary biology (e.g. Coyne and Orr), and one in which mathematical modeling has for a long time played an important role (Gavrilets 2004). Following the biological species concept, speciation is evolution of RI.  +  * Speciation -- the splitting of an evolutionary lineage into two descendant lineages -- is a central topic in evolutionary biology (e.g. Coyne and Orr 2004), and one in which mathematical modeling has traditionally played a prominent role (Gavrilets 2004).  
-  * Traditionally, allopatric speciation; but mounting evidence for speciation with gene flow (parapatric or even sympatric). Speciation with gene flow is theoretically challenging because ... +  * The reason is that speciation  is a complex process that usually unfolds over long timescales, so that direct observations are difficult. Mathematical theory has been instrumental in determining the conditions for key components of speciation, such as adaptive divergence (e.g. Geritz et al. 1998), accumulation of genetic incompatibilities (e.g. Gavrilets ...) and species-specific mate choice (e.g. Dieckmann and Doebeli 1999).  
-  * Another recent development: allegedly important role for phenotypic plasticity+  * Here, we propose to develop mathematical models that will shed light on a topic of much recent interest: Whether speciation -- and, in particular, speciation with gene-flow, can be facilitated by phenotypic plasticity.
  
-  * Plasticity is the ability of ...  +  * A **species** is most commonly defined as a group inter-fertile individuals that cannot reproduce with members of other species (Mayr 1942). Thus, understanding speciation requires understanding the evolution of reproductive isolation.  
-  * Recently, plasticity has been advertised by some as a centerpiece of an "extended evolutionary synthesis", which is supposed to unify traditional population genetics with evolutionary developmental biology.  +  * According to the traditional view, speciation almost always requires a geographic barrier separating the range of an ancestral species (allopatric speciation). Two independently evolving subpopulations will then diverge between the nascent species (allopatric speciation) and become more and more incompatible, until they are recognized as separate species. 
-  * General thrust: Plasticity plays a leading role in phenotypic evolution, including "evolutionary novelties" and diversification ("genes follow development") +  * However, there is mounting evidence for the opposing view that speciation is also without a strict geographic barrier (parapatric or sympatric speciation). Such "speciation with gene-flow" (Smadja and Butlin 2011?) is theoretically challenging, because migration and hybridisation will counter-act genetic divergence, and because genetic recombination tends to destroy associations between sets of genes or characters. Most models of speciation with gene-flow assume a prominent role for divergent ecological selection pressures (Nosil 2012).   
-  * Wrt speciation, plasticity is thought to facilitate phenotypic/ecological divergence as well as evolution of RI. Suggested mechanisms include ... In particular, several of the proposed empirical examples (arctic charr etc.) imply speciation with gene flow. + 
 +  * **Phenotypic plasticity** is the ability of organisms with identical genotype to produce different phenotypes in response to different environments (e.g. West-Eberhard 2003). It is pervasive in nature, and often is crucial in helping organisms cope with variable environments.  
 +  * Recently, plasticity has been advertised by some as a centerpiece of an "extended evolutionary synthesis" (West-Eberhard 2003, Piggliucci and Müller 2009?), which aims to unify traditional population genetics with evolutionary developmental biology.  
 +  * The main argument is that plasticity plays a leading role evolution ("genes follow development"), including diversification and evolutionary novelties (West-Eberhard 2003). 
 +  * In the context speciation, plasticity is thought to facilitate phenotypic/ecological divergence as well as the evolution of reproductive isolation (West-Eberhard 2003, Pfennig et al. 2010, Pfenning and McGhee 2010, Fitzpatrick 2012). [Suggested mechanisms include ...] In particular, several of the proposed examples imply speciation with gene flow (e.g., ...). 
   * However, many proposed scenarios rely on verbal models, and many details remain unclear. This is particularly true for scenarios involving plasticity in an ecological adaptation trait (but see Thibert-Plante and Hendry 2011).    * However, many proposed scenarios rely on verbal models, and many details remain unclear. This is particularly true for scenarios involving plasticity in an ecological adaptation trait (but see Thibert-Plante and Hendry 2011). 
   * Open questions include:   * Open questions include:
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     * Under what conditions does plasticity facilitate or impede the evolution of reproductive isolation in the presence of gene flow?     * Under what conditions does plasticity facilitate or impede the evolution of reproductive isolation in the presence of gene flow?
     * If plastic traits themselves contribute to RI, what are the interactions between the evolution of environmentally and genetically induced reproductive barriers (see Fitzpatrick 2012)?     * If plastic traits themselves contribute to RI, what are the interactions between the evolution of environmentally and genetically induced reproductive barriers (see Fitzpatrick 2012)?
- 
 ===== Outline of project ===== ===== Outline of project =====
  
 ==== Literature Review ==== ==== Literature Review ====
   * As a first step, we will conduct a literature review with the aim of collecting and classifying the various mechanisms by which plasticity has been proposed to influence speciation/the evolution of reproductive isolation.    * As a first step, we will conduct a literature review with the aim of collecting and classifying the various mechanisms by which plasticity has been proposed to influence speciation/the evolution of reproductive isolation. 
-  * This will complement earlier reviews on the subject (West-Eberhard 2003, Pfennig et al. 2010,  +  * This will complement earlier reviews on the subject (West-Eberhard 2003, Pfennig et al. 2010, Fitzpatrick 2010).
-Fitzpatrick 2010).+
   * In particular, we will develop a classification along the following lines   * In particular, we will develop a classification along the following lines
     * Which traits are plastic (in particular, related to ecology, RI, or both)?     * Which traits are plastic (in particular, related to ecology, RI, or both)?
     * What type of plasticity?     * What type of plasticity?
     * What reproductive barriers are affected?     * What reproductive barriers are affected?
-    * How exactly does plasticity influence speciation?+    * What are the roles of plasticity in the various stages of the "speciation continuum"?
   * This work will clarify previous arguments and underlying assumptions, and will guide future theory and empirical work.    * This work will clarify previous arguments and underlying assumptions, and will guide future theory and empirical work. 
   * It will also provide the student (who has a background in mathematics) with an opportunity to get to know the biological literature.    * It will also provide the student (who has a background in mathematics) with an opportunity to get to know the biological literature. 
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   * Development of these models will be guided by insights gained during the literature review described above.   * Development of these models will be guided by insights gained during the literature review described above.
   * At the moment, it seems that the most pertinent scenario is the "developmental plasticity hypothesis of speciation" (WE 2003, Pfennig et al. 2010), which proposes the following sequence of events (after Fitzpatrick 2012):   * At the moment, it seems that the most pertinent scenario is the "developmental plasticity hypothesis of speciation" (WE 2003, Pfennig et al. 2010), which proposes the following sequence of events (after Fitzpatrick 2012):
-    * A population experiencing variable environments develops a polyphenism, i.e, the ability to express 2 discrete phenotypes as a function of an environmental cue+    * A population experiencing variable environments develops a polyphenism, i.e, the ability to express 2 discrete phenotypes as a function of an environmental cue; differential expression of this polyphenism will often induce some degree of reproductive isolation (e.g. if different morphs use different micro-habitats)
     * Two subpopulations experiencing primarily one or the other of the two environmental conditions will start accumulating genetic differences and, in some cases, may lose the ability to respond to the environmental cue (genetic assimilation).     * Two subpopulations experiencing primarily one or the other of the two environmental conditions will start accumulating genetic differences and, in some cases, may lose the ability to respond to the environmental cue (genetic assimilation).
-    * Reproductive isolation evolves as a by-product of genetic divergence or via reinforcement (selection to avoid mating with the "wrong" type)+    * Reproductive isolation evolves as a by-product of genetic divergence or via reinforcement (selection to avoid mating with the "wrong" type).  
 +  * Most verbal descriptions of the process are vague with respect to the geographic setting (and the exact mechanism leading to reproductive isolation). In particular, the second phase may be imagined to happen anywhere on a continuum between allopatry and sympatry. 
 + 
 +==== Secondary-contact scenario ==== 
 +  * First scenario: Divergence phase (step 2) happens in allopatry 
 +  * That is, plasticity evolves (or is already present), then two subpopulations continue to evolve in constant habitats, which should lead to a loss of plasticity and accumulation of genetic differences. Then, secondary contact is established, with selection for assortative mating.  
 +  * Verbal models predict evolution of assortative mating and maintenance of genetic differentiation. 
 +  * An alternative outcome might be a loss of genetic differentiation and a return to plasticity.  
 +  * We study this scenario under various assumptions: 
 +    * Model of plasticity:  
 +      * Continuous reaction norm 
 +      * Threshold trait 
 +      * Developmental network 
 +    * Mechanism of assortative mating: 
 +      * Magic-trait, self-referent phenotype matching (1-allele) 
 +      * Female preference for magic trait (2-allele) 
 +      * Female preference for independent signal trait? 
 +    * Spatial structure: complete sympatry or limited gene-flow after secondary contact 
 +  * Key questions include: 
 +    * What will happen to plasticity after secondary contact?
  
-=== Step 1: Genetic versus plastic divergence ===+==== Divergence with gene-flow ==== 
 +  * Here, we will study speciation without an allopatric phase 
 +  * Nevertheless, environmental induction implies some sort of spatial structure 
 +  * ... and expression of plasticity may itself lead to a reduction in gene flow (plastic magic trait) 
 +  * Previous models: Gavrilets and Vose 2007, Thibert-Plante and Hendry 2011 
 +  * We will follow these approaches by analyzing a model with the following ingredients: 
 +    * Two habitat types, connected by migration 
 +    * Plastic and genetic adaptation possible  
 +    * Ecological trait may influence mate choice 
 +    * Female preference and/or choosiness may evolve 
 +  * In contrast to Thibert-Plante and Hendry (2009), we will focus on scenarios that allow for the evolution of assortative mating  
 +  * Key questions: 
 +    * Interaction between plastic and genetic barriers to gene-flow 
 +    * Interaction between evolution of assortative mating and evolution of plasticity (e.g., AM might increase reliability of genetic cues, sensu Leimar et al. 2006) 
 +  * Methods: Population-genetics modeling, coupled with adaptive dynamics; stochastic individual-based simulations 
 +=== Old version: Genetic versus plastic divergence ===
   * The DPHS proposes that genetic divergence is preceded by the evolution of a purely plastic polyphenism.    * The DPHS proposes that genetic divergence is preceded by the evolution of a purely plastic polyphenism. 
   * This has a simple explanation if plasticity is the ancestral state of a lineage encountering a variable environment, but this then the question is why plasticity (and genetic polymorphism) evolved in the first place. Some advocates of the DPHS propose that novel phenotypes are generally more likely to arise by environmental induction (WE 2003, Uller and ???), but this is debated (Schwander and Leimar 2009, 2011).    * This has a simple explanation if plasticity is the ancestral state of a lineage encountering a variable environment, but this then the question is why plasticity (and genetic polymorphism) evolved in the first place. Some advocates of the DPHS propose that novel phenotypes are generally more likely to arise by environmental induction (WE 2003, Uller and ???), but this is debated (Schwander and Leimar 2009, 2011). 
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     * Are the results compatible with the predictions by Leimar et al. (2006)?     * Are the results compatible with the predictions by Leimar et al. (2006)?
  
-=== Step 2: Ecological plasticity and the evolution of reproductive isolation ===+=== Old version: Ecological plasticity and the evolution of reproductive isolation ===
   * The DPHS assumes plasticity in an ecological trait (an character conferring ecological adaptation). Our aim will be to study how such plasticity influences the evolution of prezygotic reproductive isolation.    * The DPHS assumes plasticity in an ecological trait (an character conferring ecological adaptation). Our aim will be to study how such plasticity influences the evolution of prezygotic reproductive isolation. 
   * To our knowledge, the only model on this subject is by Thibert-Plante and Hendry (2009). These authors assume ... Importantly, in one version of the model, the ecological trait also directly influences mate choice (i.e., it is a "magic trait"; Gavrilets 2004, Servedio et al. 2011).    * To our knowledge, the only model on this subject is by Thibert-Plante and Hendry (2009). These authors assume ... Importantly, in one version of the model, the ecological trait also directly influences mate choice (i.e., it is a "magic trait"; Gavrilets 2004, Servedio et al. 2011).