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I am currently investigating 2 genes in Arabidopsis taliana that are a product of a recent duplication even (observable from synteny and phylogenetic analysis). In addition to the molecular and biochemical functions of these genes, I was wondering how evolution is acting on them at the population level. There the genome sequence of 1300 ecotypes of Arabidopsis from all around the globe available. So, I was wondering if I could use all these sequences to quantify nucleotide diversity and/or Tajima´s D? However, I am not sure if this is conceptually right, since I am not using an actual population, but I am just aligning 1300 sequences as "global population". what do you think? is this a good approach to see the level of variation for each gene "globally"? is this "global" view scientifically and statistically relevant?

Regards

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