Figure 1

Illustrating the effect of the distance threshold, G , on cluster formation. Suppose genome A has marker order 1,2,3,4,5,6; genome B has 1,2,3,6,5,4; and genome C has 3,1,2,4,5,6. The strips are [1, 2], [3], [4–6]. The clusters at G = 4 (a) are [1, 2] and [4–6] (the singleton [3] is deleted). At G = 5 (not shown), some of these are combined together. Specifically, d(2, 3) = 1 + 1 + 2 = 4 < 5, so an edge is added between markers 2 and 3, joining their clusters together. The clusters at G = 5 are [1–3] and [4–6] and the order within the clusters varies by genome, giving micro-rearrangements. At G = 6 and 7 (b), edges are added within clusters, but not between clusters, so clusters do not change. At G = 8 (not shown), two edges are added that would join the clusters into [1–6] Specifically, d(2, 4) = 2 + 4 + 1 = 7 < 8 and d(3, 4) = 1 + 3 + 3 = 7 < 8.