Monday, December 19, 2011

Towards an unbiased study of parallel evolution
The investigation of parallel evolution is a powerful paradigm to study mechanisms of adaptation.  This review and opinion paper stresses the fact that although remarkable examples have been studied, molecular bases of adaptation are still poorly understood in the vast majority of cases.

In rare examples, a genetic variation has been linked to repeated and independent adaptation. In the examples of Mc1r , multiple mutations occurred in the same gene independently leading to different coat colours in mice.  In humans, lactose tolerance was acquired repeatedly due to mutations occurring independently in the same genes in different populations.  In the paper, authors describe mutations in Pitx1 which have occurred repeatedly in three spine stickleback fish leading to reduced pelvic armor plate which differentiates the sea water from the fresh water specie. These observations have been validated by transgenic animals demonstrating the fact that Pitx1 is the genetic basis of this recurrent phenotype and form of adaptation.

As a reader naïve to the field, I found that this paper describes well the obstacles that researchers are facing in the investigation of the molecular basis of adaptation.  Genetic data is sparse and the vast majority of species have not been sequenced. For those species who have been, only a small number of specimens were sequences.  Surprisingly, despite this lack of genetic (or genomic) data, the authors have categorized the different genetic bases to parallel adaptation into 3 groups : i) same mutation in the same gene, ii) different mutation in the same gene and  iii) mutations in different genes.  These very “formal” distinctions have stirred many questions and intrigued many of the students attending the tutorial including myself.  Maybe the fascination for species has drawn the authors to describe different “species” of mutations.  Others and myself thought that, given the scarcity of genetic or genomic data, these questions may be too premature.  Trained in medical genetics, I have repeatedly experienced the situation “iii)” where mutations at many different loci may give rise to the same phenotypic manifestation but  I was reminded, however,  that “disease” is not “adaptation” and although there may be many different ways of disrupting a mechanism only few may lead to specific advantages.  We also discussed the fact that these different “groups” may also be related to the complexity of the phenotype, e.g. : lactose tolerance, related to the function of one enzyme can only be related to the category “i) or ii)” as opposed to  much more composite and complexe phenotype such as “social cognition” for example  which would likely fall under the category “iii)”.

This is a perspective paper and there are no methods or results to critique.  Authors conclude that next generation sequencing will “come to the rescue” of the complex issue of genotype-phenotype correlations  and how they relate to adaptation.  I also share the optimism of the authors and believe that genomic technologies will provide a wealth of “unbiased” (as opposed to candidate gene approaches) data that will allow identifying the basis of many adaptive processes.  The following papers studied in the tutorial showed that this is the case and that many paradigms of evolution are being challenged now that data is available (cf. in other blogs the genomic  signatures of adaptation such as selective sweeps).  What I enjoyed the most in this tutorial were the discussions between students and senior researchers using the same tools and studying the same, phenomenon  (mutations, phenotypes) but driven by very different questions.

Best quote during the tutorial:  “The theory looked really sexy until the data was available”.

Elmer KR, & Meyer A (2011). Adaptation in the age of ecological genomics: insights from parallelism and convergence. Trends in ecology & evolution, 26 (6), 298-306 PMID: 21459472

(Posted by MRR for Sebastien Jacquemont)

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