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A time-calibrated coalescent tree from the distal non-duplicated region flanking the SVR (leftmost grey arrow in panel a ) across 94 assembled haplotypes (the tree from the proximal region in Extended Data Fig. 4 ). The number next to each tip corresponds to the structural haplotype that the sequence is physically linked to, and the colour of the circle at each tip corresponds to its consensus haplotype structure (see the inset structural tree). The copy numbers of each amylase gene and pseudogene are also shown next to the tips of the tree. The asterisk indicates the single, recent origin of the premature stop codon in AMY1 .

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