Population specific summary statistics
The nucleotide diversity (pi) of lice from each continent revealed
African lice had the highest diversity (0.318) compared to all other
non-African lice. Asian lice had the second highest diversity (0.175)
followed by South America (0.125), North America (0.110), Europe (0.099)
and Oceania (0.073). Hardy Weinberg Equilibrium (HWE) tests using SNP
heterozygosity revealed a pattern where most of the European and North
American countries had a higher percentage of loci that were
significantly out of HWE compared to Asian and African countries (Table
2). Each country had a different number of polymorphic sites.
Noticeably, African countries had the highest number of polymorphic
sites. Several countries had all polymorphic loci in HWE, which was
unexpected. Each of these were instances where the lice used are
suspected of coming either from a single human host or from a relatively
few. Based on the Hardy-Weinberg Equilibrium (HWE) calculations, whether
a specific locus was in/out of HWE seems to be a population-specific
phenomenon rather than a locus-specific event. The fraction of loci that
were out of HWE was different in each population. Summarized HWE results
can be found in Table 2.
Table 2: Population summary
statistics by country. Columns include major geographic regions,
country, number of individuals, total number of polymorphic SNPs in each
population, total SNPs that are significantly out of HWE, mean observed
SNP heterozygosity (Ho), mean expected SNP
heterozygosity (He) and percentage of SNPs that deviates
from HWE. SNP heterozygosity mean values were calculated per country.
Countries in each region are arranged by percentage out of HWE from high
to low where it was calculated as, number of loci withp <0.05/total polymorphic loci*100.