Selection pressure
We used a Bayesian approach, as incorporated in BayeScan (Foll
& Gaggiotti 2008) to estimate candidate loci (island of
differentiation) under natural selection between the Japanese and
European populations. The approach estimates a posterior probability for
each locus being under selection based on the allele frequencies of the
two populations being significantly more or less divergent than the
total shared allele frequencies of all loci in the dataset. The method
incorporates uncertainties of small population sizes and varying
effective population size, thus appropriate for our study. We analyzed
the combined SNP set of Japanese and European isolates where the two
populations were compared, using default settings. The resulting files
were analyzed in R, after formatting with PGDSpider (Lischer &
Excoffier 2011).
Signatures of selective sweeps can be investigated both within
population using the integrated haplotype homozygosity (IHH) or between
populations applying the population extended haplotype homozygosity
(XP-EHH) (Voight et al. 2006). Considering that IHH is dependent
on knowledge of the ancestral state, we focused on the XP-EHH approach
to detect selective sweeps in which the selected allele has approached
fixation within one population. The analysis was done using the R
program rehh (Gautier & Vitalis 2012). Since
calculation of XP-EHH is dependent on knowledge of haplotypes, the data
was first phased using fastPHASE v.1.4 with default settings
(Scheet & Stephens 2006).
All significant loci in predicted genes were further analyzed for
function by InterProScan, using version InterPro 83.0
(www.ebi.ac.uk/interpro/). InterPro and PFAM domains were used for
evaluation of gene function.