Analysis of Positive Selection at Single Nucleotide Polymorphisms Associated with Body Mass Index Does Not Support the “Thrifty Gene” Hypothesis  Guanlin Wang, John R. Speakman  Cell Metabolism  Volume 24, Issue 4, Pages 531-541 (October 2016) DOI: 10.1016/j.cmet.2016.08.014 Copyright © 2016 Elsevier Inc. Terms and Conditions

Cell Metabolism 2016 24, 531-541DOI: (10.1016/j.cmet.2016.08.014) Copyright © 2016 Elsevier Inc. Terms and Conditions

Figure 1 An Example of the LD Pattern in Three SNPs in the CEU Population We calculated the running average LOD score around the target SNP over a 500 kb range up and downstream. Here, we illustrate one SNP for the positive control set (rs4988235 adjacent to LCT), one BMI-associated SNP (rs9939609 in first intron of FTO), and one negative control SNP (rs2287652, intron in ADCK1), respectively, to show (from left to right) the hitchhiking pattern for a gene under positive selection. For rs4988235, which has been under strong positive selection, we can see there are many peaks around the target SNPs, which indicated possible hitchhiking events. For rs9939609 and rs2287652, there was only a single main peak around the SNP. Similar patterns for all other SNPs we studied are available on request. Cell Metabolism 2016 24, 531-541DOI: (10.1016/j.cmet.2016.08.014) Copyright © 2016 Elsevier Inc. Terms and Conditions

Figure 2 Results of the |DDAF| Test for 14 Populations of 1000 Genomes Project In the left panel, the x axis is a list of BMI-associated SNPs, while in the right panel, the x axis refers to the negative control SNPs. In both images, the y axis is the absolute value of DDAF. The bold x axis is the threshold for the positive selection. The identities of the BMI linked SNPs that were above the threshold are indicated. In total, there were 221 signals above the threshold among the BMI SNPs and 275 above the threshold in the negative controls. The SNPs showing positive selection signals were identified except for the AMR and EAS populations owing to space limitation (refer to Table S4 for identities). Positive controls can be found in Figure S3. Cell Metabolism 2016 24, 531-541DOI: (10.1016/j.cmet.2016.08.014) Copyright © 2016 Elsevier Inc. Terms and Conditions

Figure 3 XPCLR of BMI-Associated SNPs in the Left Panel and Negative Control SNPs in the Right Panel in 14 Populations from the 1000 Genomes Project XPCLR of BMI-associated SNPs (in the left panel) and negative control SNPs (in the right panel) in 14 populations in the 1000 Genomes Project. The bold x axis is the threshold for the positive selection. The identities of the BMI linked SNPs that were above the threshold are indicated. The SNPs showing positive selection signals were identified except for the EAS populations owing to space limitation (refer to Table S4 for identities). In total, there were 91 signals above the threshold among the BMI SNPs and 117 above the threshold in the negative controls. Cell Metabolism 2016 24, 531-541DOI: (10.1016/j.cmet.2016.08.014) Copyright © 2016 Elsevier Inc. Terms and Conditions

Figure 4 XPEHH of BMI-Associated SNPs in the Left Panel and the Negative Control SNPs in the Right Panel in 14 populations from the 1000 Genomes Project XPEHH of BMI-associated SNPs (in the left panel) and the negative control SNPs (in the right panel) in 14 populations of the 1000 Genomes Project. The bold x axis is the threshold for the positive selection. The identities of the BMI linked SNPs that were above the threshold are indicated. The SNPs showing positive selection signals were identified except for the EAS populations owing to space limitation (refer to Table S4 for identities). In total, there were 89 signals above the threshold among the BMI SNPs and 93 above the threshold in the negative controls. Almost all the positive control SNPs score were higher than 1, which indicated positive selection shown in Figure S3 in European populations (CEU, TSI, GBR, IBS, and FIN). Cell Metabolism 2016 24, 531-541DOI: (10.1016/j.cmet.2016.08.014) Copyright © 2016 Elsevier Inc. Terms and Conditions

Figure 5 Positive Selection Heatmap for BMI Associated SNPs The horizontal number (1 to 20) and vertical letter (a to f) encodes a specific alphanumeric combination which can be traced to identify each specific SNP in Table S2. Each single box with borders represents a single SNP. Within each box, the horizontal line is six selection tests and each vertical column shows a single test over 14 populations. Hence, each box represents 6 × 14 = 84 results. The blue blocks were used for non-significant alleles (<14/84 positive tests), yellow ones code for protective alleles (favoring leanness), while the red ones code for risky alleles (favoring obesity). Each block represents a single positive selection signal (A) Represents the selection heatmap of BMI-associated SNPs. Four of the BMI-associated SNPs were risky alleles (red colored). The intensity of color indicates the significance of the test. (B) One zoomed detailed SNP box (e5-rs3810291), which represents six representative selection tests to show the selection signals through the evolutionary history of the SNP. The numbers 250ky, 80ky, etc. represent the approximate time before the present over which the test can detect positive selection. Combining with Table S2, three SNPs rs3810291, rs12401738, and rs7904146 had positive selection signals during the past 30,000 years. (ky = 1,000 years.) Cell Metabolism 2016 24, 531-541DOI: (10.1016/j.cmet.2016.08.014) Copyright © 2016 Elsevier Inc. Terms and Conditions

Figure 6 Positive Selection Heatmap for Negative and Positive Control SNPs (A) The horizontal number (1–20) and vertical letter (a–f) encodes a specific alphanumeric combination that could be traced to each specific SNP in Table S3. Non-significant alleles (<14/84 significant tests) are coded blue, and significant alleles (≥14/84 significant tests) are coded green. (B) Shows the same pattern for the positive controls. (C) One zoomed SNP (g5-rs16891982). Details are as described in Figure 5. Cell Metabolism 2016 24, 531-541DOI: (10.1016/j.cmet.2016.08.014) Copyright © 2016 Elsevier Inc. Terms and Conditions