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Why is it so surprising that convergent evolution may use the same genes in different species?

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Hey, so I'm writing a piece on the convergent and parallel evolution of genes involved in domestication but I'm a little confused. 

A lot of the literature talks about certain genes that are involved in domestication appearing 'more often than by chance' in orthologous (the same) genetic loci of multiple crops (i.e. trait A is controlled by gene A in crop 1. The same trait A has evolved convergently by a gene in crop 2 that is on the same part of the chromosome of crop 2 as gene A was on crop 1). Essentially, phenotypic convergence is controlled through genotypic convergence.

However, I feel like I'm missing the significance of this point. Surely, it shouldn't be surprising that there has been parallel evolution occurring on the same genetic loci when these two species are related (e.g. cereal crops Sorghum and Maize share similar genes involved in domestication trait of 'seed size increase' and as a result the genes involved in this process are on similar loci for both crops)? This would make sense - one gene controls one trait in one crop why is it SO SURPRISING the same gene controls the same trait in another crop??

Also another question: if this was true then why are other phenotypic traits in related species NOT controlled by the same genes (e.g. seed-shattering trait in cereal crops is controlled by different genes in different species of crop)? 

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