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It doesn't really surprise me, even with small % differences of genetic sequences, you would expect most genes to vary (in this case 83%) because these small differences should be spread evenly. According to the paper, there's 2-3% genes that have changed enough to say they have 'adaptively radiated', and so stating that the 1.2% sequence difference has a big effect in terms of protein structure it doesn't really seem backed up if only 2-3% of genes show significant adaptive radiation.

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