3.3.1 Inbreeding
Both individuals from Deme II showed considerably higher inbreeding
measured as length of runs of homozygosity (LnROHs; Figure 6a, Table S7)
and F ROH (Figure 6b) than those from Deme I.
Individual 1 from Deme II was the most homozygous; a total of 950,545 kb
involving 1,742 ROH segments were estimated as identically homozygous in
this individual. This translates into an F ROHfrom PLINK of 0.405 (95% CI: 0.405–0.405; Figure 6b). The second
individual from Deme II showed 1,520 ROH segments covering 782,973 kb
(Figure 6a) and F ROH=0.334 (95% CI:
0.334–0.334; Figure 6b). Much lower inbreeding levels were observed in
the individuals from Deme I. The first had 175 ROH segments expanded
over 75,092 kb with an F ROH=0.032 (95% CI:
0.032–0.032) and the second 276 ROH segments spanning 127,296 kb andF ROH=0.055 (95% CI: 0.055–0.055; Figure 6a, b).
Individuals from Deme II showed some ROH segments longer than 1,000 kb;
individual 1 had 114 such segments and individual 2 had 73.