Figure 3.

Analysis of L1 source-offspring relationships using 3′ transductions. (A) Pie chart depicting the proportion of offspring attributable to each of the 38 FL-L1 source elements identified in this study. One hundred twenty-one out of 4118 (2.9%) of the L1s identified had 3′ transductions that could be used to identify the FL-L1 source elements that produced these offspring insertions (Supplemental Table S9). Note that this method can only be used to track source/offspring relationships for L1′s that produce 3′ transductions. The LRE3, Chr 6: 13191033, and Chr 1: 119394974 FL-L1 source elements are indicated in red, blue, and green, respectively. (B) Circos plot (Krzywinski et al. 2009) depicting the genomic landscape of source-offspring relationships summarized in A. Red, blue, and green arrows indicate the three FL-L1 source elements highlighted in A. (C–E) Individual Circos plots tracking offspring for the three most active FL-L1 source elements from A. Each source-offspring relationship is colored based on the population in which the offspring element is found (gray if found in multiple populations). (F) LRE3 was sequenced from an individual of European descent (top), along with eight FL-L1 LRE3 offspring. Sequence changes compared to the L1.3 FL-L1 element (Dombroski et al. 1993) are shown as blue, green, yellow, red, or black vertical lines representing C, A, G, T, or deletion mutations, respectively. All eight sequenced FL-L1 offspring of LRE3 have two intact ORFs (dark gray bars). The first poly(A) tail is shown in bright green, with transduced sequence shown in light gray. Offspring elements that have a 3′ transduction also have a second poly(A) tail (bright green). The five population-specific FL-L1 elements are indicated by the 1000 Genomes Project population colors next to the elements. (G) LRE3 transduction family, displayed in a similar manner to Figure 2 (American [AMR]-specific offspring not shown; n = 3). Each pie chart represents either LRE3 (labeled) or one LRE3 offspring locus from C. Borders of each pie are colored red if the element is a FL-L1 (n = 20), or purple if it has a 5′ inversion (n = 2). (H) Source and offspring element population distributions. Shown for each source element is the total number of offspring (top), the population distribution of the source element (middle), and the aggregate population distribution of all offspring (bottom). Highlighted with colored arrows are source elements from A. Red bars indicate where offspring were only found in the American continental population. Vertical black dotted lines separate source elements into one of three classes: found in all populations (left), found predominantly in OOA populations (middle), and found in a subset of other populations (right).