Figure 1.
Summary statistics for genomic variation.
The distributions of ROH statistics for Asian breeds (n = 7), Asian wild boars(n = 5), European breeds (n = 29), European wild boars (n = 6) and other species (n = 5). Groups are divided based on geography (Asians and Europeans), domestication (pigs and wild boars) and speciation (Other-species include the African Warthog Phacochoerus africanus and other representatives of the Sus genus being Sus barbatus, Sus celebensis, Sus verrucosus and Sus cebifrons). Values are averaged within individuals resulting in a single data point per ROH characteristic for each individual. 1A. nucleotide diversity including ROHs (*10−4 bp) 1B. nucleotide diversity excluding ROHs (*10−4 bp) 1C. Average ROH size (*104 bp) 1D. number of ROHs in the genomes of individuals.
Figure 2.
Total number of ROHs and proportion of the genome covered by ROHs.
2A. The average number of ROHs belonging to three size classes small (<100 Kbp) medium (0.1 to 5 Mbp) and large (>5 Mbp) for each of the different groups. 2B. The total size of the genome that is covered by the particular ROH size class in one individual, averaged per group. The Japanese wild boar is shown separately and is not included in the Asian group, as its demographic history from an island population and the associated ROH pattern is very distinct from all other sampled individuals. Asian wild boars (n = 4), Asian pigs (n = 7), European wild boars (n = 6), European pigs (n = 29), other species (n = 5).
Figure 3.
ROH size in pigs based on the 60K chip method and the re-sequencing method.
3A shows the correlation between both methods when the total sum of ROHs is taken from the re-sequencing method (‘Genomic ROHsum’) and the 60K chip method (‘60K ROHsum’). In 3B the correlation is shown when only the ROHs over 5 Mbp are taken into account for the re-sequencing method. The outlier for the Asian group (the Japanese wild boar) is not included in the R2 calculations.
Figure 4.
Number and cumulative ROH size (ROHs>5MB) for all genotyped individuals.
Number of ROHs and sum of ROHs detected by PLINK for all 241 individuals genotyped by the Illumina porcine 60k beadchip. Sum of ROHsize is *1000 bp. 4A. ROHs in domesticated individuals. Asian pigs are shown in red, orange and purple and the European pigs are in blue and green. 4B. ROHs in wild individuals. Asian wild boars are shown in red and orange and the European wild populations are displayed in green and blue. The dashed line represents the range of ROH number and ROH size for the domesticated individuals. The individuals marked with * are putative hybrids.
Figure 5.
Three-point ROH statistics for all 52 sequenced individuals.
On the x-axis, the number of ROHs in the genome per individual is plotted, the average ROH size (*104 bp) is displayed on the y-axis and the nucleotide diversity outside ROHs in a 10 kb window ‘nucleotide diversity (π-out *10−4)’ on the z-axis. Coloration is based on relatedness and geography, with individuals from the same populations having the same color.
Figure 6.
Characteristics of the porcine genome over relative chromosomal position.
Physical distribution of total nucleotide diversity (6A), nucleotide diversity outside ROHs (6B), GC content (6C), recombination rate (6D) over chromosomes. Relative chromosomal position is averaged for all chromosomes so that 0.0 represents the left telomeric region and 1.0 the far right telomere.
Figure 7.
Distribution of ROHs over relative chromosomal position.
ROHs were split into three size classes; big (x>5 Mbp), medium (0.1 to 5 Mbp) and small (x<0.1 Mbp). The distribution is relative only to the total number of ROH bins in that particular size class, and the distributions are averaged over all chromosomes. ROH distribution is given for four groups: European pigs (7A), European wild boars (7B), Asian pigs (7C) and Asian wild boars (including the Japanese, 7D).