Fig. 1
Phylogenetic relationship and promoter length distribution of young mouse L1 subfamilies. A A partial mouse L1 phylogenetic tree that consists of the youngest subfamilies. Adapted from Fig. 1 of Sookdeo et al. [34] under Creative Commons Attribution 4.0 International License (https://creativecommons.org/licenses/by/4.0/). The tree was built with the longest non-recombining region of ORF2 sequences using the maximum-likelihood method. The numbers indicate the percentage of time the labeled note was present in 1000 bootstrap replicates of the data. Downward arrows indicate the acquisition of a new 5’UTR. The age of each subfamily, in million years (Myr), was estimated by calculating the average pairwise divergence of the 3’UTR and converting the divergence to time assuming a neutral rodent genomic substitution rate of 1.1% per million year (see Table 1 of the original publication). We applied styling changes to highlight the Tf, Gf, and A subfamilies. Note, historically, the nomenclature of Tf and Gf subfamilies features a subscripted F (e.g., TF and GF) [35, 38] but here we follow the conventions established in Sookdeo et al. [34], which accommodate multiple Tf and Gf subfamilies (e.g., Tf_I/II/III and Gf_I/II). B Distribution of the 5’UTR start position in different L1 subfamilies. For each subfamily, the number of L1 loci is tallied according to their starting nucleotide position relative to the tether (T), the first ten individual monomers (M1 to M10), M11 and beyond (M11 +). C Inverse relationship between the average number of monomers and subfamily age. A simple linear regression line and the corresponding equation were shown along with individual data points