Inferring genome-wide variation in mutation and selection from polymorphism and divergence data



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Despite half a century spent scrutinizing levels of naturally occuring polymorphism and, more recently, levels of between species divergence at the molecular level, we know embarrassingly little about which forces explain these patterns ( See a recent review (Leffler ) for an overview of the “old riddle”) although some recent analyses on large comprattive dataset suggest that some life history traits may have a pervasive effect on the amount of neutral nucleotide diversity at a very large phylogenetic scale. What do we know from previous studies is that :

  • . Mutation rate vary substantially throughout the genome and between species divergence for presumaly neutrally evolving regions/sites can reveal that variation;

  • The amount of drift experienced by a particular locus may also vary due to selection at linked sites. There is mounting evidence that this phenomenon is quite widespread although the quantitative effect of either positive and/or negative selection at linked sites h