Fig 1.
Overview of the populations used and their allele frequencies for rs10166942, average temperature, and FST signatures.
(A) Geographic location of the 1KGP populations used, with the derived allele frequency of the rs10166942 allele in pie charts (T allele in color according to population), and their latitude. (B) In columns, annual mean temperature at the geographic location of each population, the level of FST-based population differentiation with YRI, the log10 empirical P-value of this FST value, and the proportion of SNPs in the 65 kb target region with an empirical P-value lower than 0.05.
Table 1.
Overview of populations and signatures of natural selection.
Geographic coordinates (in degrees), mean annual temperature (in degrees Celsius), and the frequency and signatures of selection for the rs10166942 T allele (empirical P-value), per population, ordered by latitude. DAF: derived allele frequency. Continents: (EUR) Europe, (EAS) East Asia, (SAS) South Asia, (AFR) Africa.
Fig 2.
Correlation between latitude and derived allele frequency.
Correlation of the frequency of the rs10166942 T allele with latitude. The fitted function (dashed line) results for the 1KGP data from (A) the PGLS and (B) GLMM analysis. (C) Results of the best model in the GLMM analysis of the SGDP dataset. The fitted response is shown as gridded surface, and the dots represent the average frequency of the rs10166942 T allele per cell of the gridded surface. Points above the surface are filled, points below are open. The volume of the points corresponds to the number of populations per cell.
Table 2.
All models considered, ordered by their fit (Model rank). Three measures of model support are shown: AIC, delta AIC, and Akaike weight. The cumulative probability are shown together with the resulting confidence set (models that together provide just over 0.95 cumulative probability; indicated by ‘yes’). Results are shown for the 1KGP in PGLS and GLMM analyses, the SGDP in a GLMM analysis, and the SGDP using only the Eurasian populations in a GLMM analysis.
Fig 3.
(A) Graphical representation of the three models (SSV, SDN, NTR) and their associated parameters. Birth of the allele and start time of selection are shown by black and red lines, respectively. The range of the prior distribution for time of selection start is depicted by a star and a blue line. A double headed arrow indicates population migration. (B) Posterior probabilities for each model and population. (C) Prior distribution of each parameter as a histogram. Posterior distribution of the SSV model parameters as a line for each population.
Table 3.
ABC results of the SSV model for each population.
Bayes factor (measure of confidence) and the resulting posterior probability (Post. Prob.) for the SSV model in each population, ordered by latitude. t0: time when selection starts; SNA: selection strength in non-African population; fsel: frequency of allele at selection start. The median of the posterior distribution of each inferred parameter is shown together with its 95% confidence interval (2.5%–97.5%).