Figure 1.
Stages of generation of a new individual in virtual genome evolution.
A. Two diploid parental genomes participate in the generation of a new offspring. Their chromosomes, represented here by 8 bit strings, consisted of 2048 bits in computer simulations. Defective alleles are indicated by 1, wild alleles by 0. B. During the genome replication, a new mutation, marked by an asterisk, is introduced with probability M into the replicated chromosomes. C. During the formation of gametes, the new copies of bitstrings recombine with probability C at the intergenic site randomly chosen from all allowed crossover sites. A given position is considered as “allowed” if both corresponding positions in two bitstrings are hotspots (marked by the red arrow). D. The chromosomes after mutation and recombination create gametes. E. The haploid gametes of two partners form the diploid zygote. During this process, one intergenic site in each haplotype is randomly chosen and a new hotspot is generated (indicated by the orange arrow) if this site has no hotspot otherwise the already existing hotspot is eliminated.
Figure 2.
Detrended cumulative plots based on data for the human chromosome 6.
A. Distribution of recombination hotspots along the chromosome. B. Distribution of the CCNCCNTNNCCNC (degenerate) motif and distribution of motif clusters along the chromosome. Data presented in this plot were obtained for clusters of eight or more motifs located on the same (Watson or Crick) DNA strand. C. Distribution of the specific CCACCTTGGCCTC motif along the chromosome for Watson and Crick strands separately. D. Comparison of the degenerate motif distribution along the human and chimpanzee chromosomes with the GC content for the human chromosome counted in 8 kb non-overlapping windows. The positions on the chromosome were normalized by division of real positions by the length of the human or chimpanzee chromosome 6, respectively. The increasing trends in the plots represent regions richer in hotspots or motifs than would be expected if they were evenly distributed in the chromosome, whereas the decreasing trends show the regions underrepresented in hotspots or motifs. The lack of points in the plot corresponds to the location of the centromere.
Figure 3.
Analyses of distances between neighbouring motifs.
To make a single plot, distances between motifs were presented as fractions of the whole chromosome, sorted ascending, and then the distances were cumulated from the shortest to the longest. Plots represent distributions of distances between degenerate 13-bp motifs for the human chromosome 6 in the genetic and physical scale. The same number of motifs distributed randomly or according to the uniform distribution are shown for comparison. In the case of random distribution, the minimum and maximum of distances between motifs locations are presented. Note that half of all distances analysed in this way (marked by the vertical dashed line) constitute 0.03, 0.11, 0.15, 0.5 of the chromosome length for the genetic and physical scales as well as for the random and uniform motif distributions, respectively. It means that motifs are the most clustered when analysed in the genetic scale.
Figure 4.
Detrended cumulative plots for real data and results from computer simulations.
A. Comparison of hotspot distribution in a virtual chromosome with motif distribution in the human chromosome 6. Positions “allowed” for recombination (double hotspots) are sites in the virtual chromosome where recombination can occur whereas single hotspots are sites where recombination is prohibited. Motifs were considered clustered when they were located in the chromosome closer to each other than at the average distance between all motifs. In contrast to that, the unclustered motifs were separated by larger than average distances. B. Distribution of heterozygous loci (defective alleles) and double hotspots (“allowed”) for the ancestral and two descendant populations, which evolved independently from the ancestral one for the next 100 000 MC steps of simulations. Note that in the regions of chromosomes with a lower recombination rate, a higher fraction of heterozygous positions of genes is observed.
Figure 5.
Genetic structure of the virtual chromosome after 3 million MC steps of simulations.
A. Distribution of defective alleles (heterozygous positions). B. Distribution of double hotspots which allowed for recombination. C. Distribution of single hotspots in which recombination was impossible. Data for all plots were decimated to show more clearly the distribution of hotspots or defective alleles.
Table 1.
Distribution of hotspots and defective alleles in different regions of the virtual chromosomes after 3 million MC steps.
Table 2.
Comparison of simulated data after 3 million MC steps with expected results for hotspots.
Table 3.
The common number of “allowed” (double) and single hotspot positions between the ancestral and descendant populations.
Table 4.
The common number of defective alleles at heterozygous positions between the ancestral and descendant populations.