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Detecting adaptive changes at the molecular level: data from Drosophila and Arabidopsis

Evolutionary changes can be the result of different forces, while adaptive changes can only be explained by the action of natural selection. The comparative analysis of nucleotide sequences in different gene regions is a powerful tool to infer the locus-specific action of natural selection through the footprint that it leaves on linked variation. We are using both a gene-specific and a genome-wide approach to detect adaptive changes. In the gene-specific approach (or candidate gene approach), our work focuses in genes whose function might have been shaped by adaptive evolution. In Drosophila, we are studying genes that encode proteins involved in the olfactory response to chemical stimuli, while in Arabidopsis we are studying genes that encode enzymes of the phenylpropanoid pathway. The availability of the D. melanogaster genome sequence allows a genomics approach to detect the action of natural selection by studying variation in random genomic regions of this species (or of closely related species). We use D. simulans because, as compared to D. melanogaster, it has a higher effective population size and it lacks chromosomal polymorphism. 


Detecting the action of weak selection in Drosophila 

Different data sets from Drosophila indicate that codon usage bias is the result of weak selection. The effectiveness of this kind of selection increases with the effective population size and with the rate of recombination. The action of weak selection can be detected by the comparative intraspecific and interspecific analysis of DNA sequences from coding regions. With this aim we are analyzing:

  1. The level and pattern of polymorphism of preferred (slightly advantageous) mutations and unpreferred (slightly deleterious) mutations in different genomic regions in two species with marked differences in their effective size: D. subobscura and D. guanche.
  2. The synonymous divergence in genes with drastic interspecific differences in their recombination rate. As a first approach, we are cloning and sequencing in D. subobscura genes located in regions with normal recombination in this species but in regions with a strong reduction rate of recombination in D. melanogaster. 


Development of bioinformatic tools for the study of molecular evolution

The large volume of available DNA sequences requires new and powerful computational tools for their analysis. Indeed, the comparative analysis of genes and genomes can provide useful information on their origin and on the mechanisms involved in their evolution. With this goal we are developing bioinformatic tools for the analysis of DNA sequence variation in genes and genomes. We are currently developing algorithms and software for:

  1. The analysis of SNPs (Single Nucleotide Polymorphisms);
  2. The extensive analysis of nucleotide variation at small DNA coding and noncoding regions (level and pattern of variation, linkage disequilibria, recombination, codon bias, etc.);
  3. The analysis of the pattern of variation in whole genomes or chromosomes;
  4. Displaying the pattern of polymorphism (linkage disequilibria, nucleotide diversity, etc.) along large DNA regions of the genome. We are also developing statistical tests based on the coalescence theory for inferring the action of different demographic processes on DNA sequence variation.  
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