Figures and data
The “chromosome community of rDNAs on five acrocentric chromosomes.
(A) The genomic locations of rDNA tandem repeats in human (Gibbons, et al. 2015) and mouse (Cazaux, et al. 2011). rDNAs are located on the short arms (human), or the proximal end of the long arms (mouse), of the chromosome. Either way, inter-chromosomal exchanges are permissible. (B) The organization of rDNA repeat unit. IGS (intergenic spacer) is not transcribed. Among the transcribed regions, 18S, 5.8S and 28S segments are in the mature rRNA while ETS (external transcribed spacer) and ITS (internal transcribed spacer) are excluded. (C) The pseudo-population of rRNA genes is shown by the “chromosomes community” map (Guarracino, et al. 2023), which indicates the divergence distance among chromosome segments. The large circle encompasses rDNAs from all 5 chromosomes. It shows the concerted evolution among rRNA genes from all chromosomes, which thus resemble members of a (pseudo-)population. The slightly smaller thin circle, from the analysis of this study, shows that the rDNA gene pool from each individual captures approximately 95% of the total diversity of human population. (D) A simple illustration that shows the transmissions of two new mutations (#1 and #2 in red letter). Mutation 1 experiences replication slippage, gene conversion and unequal crossover and grows to 9 copies (K = 9) after transmission. Mutation 2 emerges and disappears (K = 0). This shows how V(K) may be augmented by the homogenization process.
rRNA gene nucleotide diversity in the 10 M. m. domesticus strains of a global collection.
Fixation of mutations at two levels of species divergence, (Td1) and (Td2).
(Tf1) and (Tf2) are mutations with a shorter and longer fixation time, respectively for single-copy and multi-copy genes. Note that mutations with a longer Tf would show a lower fixation rate in short-term evolution.
Correlation of variant frequencies between human individuals.
The pairwise correlation of variant site frequency in the transcribed region of rDNAs among 6 individuals (2 Asians, 2 Europeans, and 2 Africans). The high correlations suggest that the diversity in each individual can well capture the population diversity. Each color represents a region of rDNA. The diagonal plots present the variant frequency distribution. The upper right section summarizes the Pearson correlation coefficients derived from the mirror symmetric plots in the bottom left. The analysis excluded the 18S, 3’ETS, and 5.8S regions due to the limited polymorphic sites. The result for IGS region is presented in Supplementary Figure S1.
rRNA gene nucleotide diversity in the 8 humans of a global collection.
Levels of polymorphism and divergence in mice.
(A) Phylogeny of Mus musculus and Mus spretus mice. The divergence times are obtained from http://timetree.org/. The line segment labeled 0.5 represents 0.5 Myrs. (B) FIS distribution within M. m. domesticus. The distribution of FIS for polymorphic sites in 3 outbred mouse strains or 10 mouse strains (including 7 inbred mice) in Table 1 (Inset) is shown. (C) FST distribution between M. m. domesticus and Mus spretus. Note that the F values rise above 0.8 only in (C).
Divergence in rRNA genes between M. m. domesticus and M. m. castaneus.
Divergence in rRNA genes between M. m. domesticus and Mus spretus.
Divergence in rRNA genes between Human and Chimpanzee.
The A/T to G/C and G/C to A/T changes in apes and mouse.
