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Next: Individual vs population-based diversity

TODO List
 * REF: Fitch classification homologs
 * REF: Diekman sympatric speciation
 * REF: drosophila rover and sitter
 * REF: mutational priming (e.g. yeast REF Ferea et al?).

=Coping with variable environments=

So far we have looked at the effects of spatial pattern formation on what evolves, and the effect of coding structure on how things evolve, and how that leads to evolutionary signatures in coding structure. We have therewith seen the importance of eco-evolutionary processes and evolutionary genomics. At this stage we make more explicit a core aspect of evolutionary processes, i.e. a changing environment, and ask: //How to cope with a variable environment?//

From the perspective of constructive evolution, we can say that evolution makes wonderful things, something that population genetics cannot take into account. Moreover, evolution leaves its signatures, e.g. in coding structure. However in most of the model studies we have discussed an artificial trick is used: **artificial fitness criterion**, which:
 * is harder for evolution, i.e. a constraint
 * is easier for us (we can evaluate and consider what evolutionary process does relative to the fitness criterion)
 * **we focus on how evolution solves a predefined problem**
 * we do something artificial to focus on something that is certainly there, i.e. evolution
 * however, we still allow the problem to be solved in many different ways

Instead, let us now consider evolutionary systems that must cope with //variable environments// (Note that in [|game theory] one considers different strategies and determines which survive, i.e. there is no differentiation within one individual, only different individuals). For this we consider **individual-based diversity** versus **population-based diversity**. In other words, do individuals have particular alleles? Or does each individual have duplicated genes and different alleles?

In this light it is interesting to consider different types of [|homologs] as classified by Fitch (REF):
 * **orthologs**: homologs that diversified due to evolution in different species, i.e. population-based diversity
 * **paralogs**: duplication and diversification within a genome, i.e. individual-based diversity

Such differences could have implications for how speciation occurs. Generally sympatric speciation is considered in terms of competition avoidance (cf Diekman REF). Alternatively however one could envisage paralogs evolving in two environments, whereby individuals living in either environment could loose either paralog and become reproductively incompatible (Note that this leads to false orthologs!). This alternative mechanism can solve two problems:
 * how to invade a new environment if one is not adapted to it?
 * how to adapt to a new environment if one hasn't invaded it?

This reasoning illustrates that in order to adapt to a changing environment the following processes can be important:
 * [|polymorphism]: population-based diversity, cf drosophila rover and sitter phenotypes (REF)
 * **behavioural or [|physiological plasiticity] (versatility)**: e.g. [|polyethism in social insects], metabolic adaptation (e.g. yeast)
 * **evolutionary versatility**: changing the genome, regulation and mutational priming (e.g. yeast REF).

Given such a diverse array of adaptive potential we therefore pose the following question: //How, when and where to adapt in which way?//

Next: Individual vs population-based diversity