Fig. 3

Divergence distribution of L1 families. L1 families were shared and had similar copy numbers in O. palustris and S. hispidus until just prior to the extinction of L1. L1 experienced a slow-down (middle left panel) in S. hispidus until it recovers (bottom panels - note that the copy number axis is 10x that of the top and middle panels). L1 families in each row are arranged in chronological order with the youngest families on the left. The species analyzed in each row is indicated at the right. Names of families are noted on the top of each panel. L1 copy number is plotted by percent divergence from the corresponding subfamily consensus in 1% bins. The divergence of each family is approximated by the peak of the distribution. L1 copy numbers are normalized as copies per three Gbp of MiSeq sequence which approximates the copy number per haploid genome. Panel a shows the shared families and panel b shows the Sigmodon-specific families. L1 and B1 families (in all figures) that correspond to similar divergence are given the same color and this color coding is consistent in all figures showing L1 and B1 divergence: L1-OS2, red; L1-OSP1, green; and, L1-OSP2, blue