Summary of the sequence data used in this study for the two autosomal (left, 41 and 870) and two X-linked (right, CAA and 380) loci. Each locus consisted of two sequenced segments of DNA separated by several kilobases (9.2 kb for locus 41, 11.4 kb for locus 870, 10.7 kb for locus CAA, and 9.2 kb for locus 380). A heavy black vertical line separates the two sequenced segments at each locus. Each locus is additionally broken up into the four different populations, indicated by four horizontal cells separated by heavy black lines. The California population is on top, then the New York, Europe alfalfa, and lastly Europe clover. There are 12 individuals per cell, each separated by a fine black horizontal line. Grey shading indicates that the sequence data were present; white indicates missing data (primarily due to heterozygous indels, see text). Above the boxes are asterisks that specify the approximate sequence position of SNPs. Fine black vertical lines indicate the direct observation of an indel at that position. A scale bar is given at the bottom of the diagram.