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Detecting adaptive
changes at the molecular level: data from Drosophila
and Arabidopsis
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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. |
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Detecting
the action of weak selection in Drosophila
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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. |
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Development
of bioinformatic tools for the study of molecular evolution
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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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 Last
updated: October 11, 2006
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