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European Journal of Human Genetics logoLink to European Journal of Human Genetics
. 2011 Jul 27;20(1):102–110. doi: 10.1038/ejhg.2011.139

Natural positive selection and north–south genetic diversity in East Asia

Chen Suo 1,12, Haiyan Xu 1,12, Chiea-Chuen Khor 2, Rick TH Ong 1,2, Xueling Sim 1, Jieming Chen 2, Wan-Ting Tay 3, Kar-Seng Sim 2, Yi-Xin Zeng 4,5, Xuejun Zhang 6,7, Jianjun Liu 2, E-Shyong Tai 8,9, Tien-Yin Wong 3,9,10, Kee-Seng Chia 1,8, Yik-Ying Teo 2,8,11,*
PMCID: PMC3234507  PMID: 21792231

Abstract

Recent reports have identified a north–south cline in genetic variation in East and South-East Asia, but these studies have not formally explored the basis of these clinical differences. Understanding the origins of these variations may provide valuable insights in tracking down the functional variants in genomic regions identified by genetic association studies. Here we investigate the genetic basis of these differences with genome-wide data from the HapMap, the Human Genome Diversity Project and the Singapore Genome Variation Project. We implemented four bioinformatic measures to discover genomic regions that are considerably differentiated either between two Han Chinese populations in the north and south of China, or across 22 populations in East and South-East Asia. These measures prioritized genomic stretches with: (i) regional differences in the allelic spectrum for SNPs common to the two Han Chinese populations; (ii) differential evidence of positive selection between the two populations as quantified by integrated haplotype score (iHS) and cross-population extended haplotype homozygosity (XP-EHH); (iii) significant correlation between allele frequencies and geographical latitudes of the 22 populations. We also explored the extent of linkage disequilibrium variations in these regions, which is important in combining genetic association studies from North and South Chinese. Two of the regions that emerged are found in HLA class I and II, suggesting that the HLA imputation panel from the HapMap may not be directly applicable to every Chinese sample. This has important implications to autoimmune studies that plan to impute the classical HLA alleles to fine map the SNP association signals.

Keywords: positive selection, population genetics, clinal variation, linkage disequilibrium variation

Introduction

Several recent studies into the population genetics of Han Chinese have unveiled genetic evidence of population structure between northern and southern parts of China,1 as well as identifying latitudinal clines in genetic variation across China.2, 3 This is perhaps unsurprising, as numerous European and global studies4, 5 have previously observed similar correlations between geographical latitudes and variations in the frequencies of alleles that are linked to several human phenotypes, including skin pigmentation6, 7, 8 salt sensitivity,9, 10 lactose metabolism11, 12 and even morphology.13, 14, 15 A recent bioinformatics investigation into the association between signatures of evolutionary adaptation and candidate genes for common metabolic syndromes also yielded strong evidence of spatially varying patterns of positive natural selection in several metabolic genes, as well as in several SNPs that were previously implicated with the ability to tolerate cold climates.16, 17

One striking observation made from the Singapore Genome Variation Project (SGVP), when integrated with genome-wide data from East Asian populations in the Human Genome Variation Project (HGDP)18, 19 and in phase 2 of the International HapMap Project (HapMap),20 was that genomic variation in East and South-East Asia appears to follow a strong latitudinal cline (see Figure 1). The HGDP sampled from East and South-East Asian countries which included Cambodia, Japan and the Yakut tribe in East Siberia, as well as 15 distinct ethnic or population groups in China (see Figure 1a for the geographical distribution of the samples). Together with the South-East Asian Malay samples from SGVP (abbreviated MAS), Singapore Chinese with South China ancestries (CHS), Han Chinese from Beijing (CHB) and the Japanese from Tokyo (JPT), the latitudes of these 22 populations span between 3° and 63° north of the equator (Figure 1b). In a principal component analysis (PCA) of the genome-wide genotype data for these populations, the elements of the first axis of variation were found to reflect the latitude the samples originated from (Figure 1c). Although recent literature investigating the use of PCA in population genetics has highlighted the potential that clinical patterns may emerge in the absence of migration-linked gene flow and is instead a consequence of isolation-by-distance21, 22 (where gene flow happens between neighboring subgroups), this clinical pattern of genetic variation concurs with an independent finding from a recent pan-Asia study into the migration history across Asia, which revealed evidence of gene flow along a northern migratory route from South-East Asia into East Asia.23

Figure 1.

Figure 1

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Population structure in East and South-East Asian populations. (a) Geographical distribution of the 22 East and South-East Asian populations from the International HapMap Project, the Human Genome Diversity Project and the Singapore Genome Variation Project. The colors of the circles have been assigned according to the latitudes of the populations, following the blue–red spectrum with increasing latitude. (b) Names of the 22 population groups and their geographical coordinates, where the populations have been ranked according to their latitudes with the corresponding color codes that have been assigned. (c) Plot of the first two axes of variations from a principal components analysis of the genetic data from the 22 populations, the first axis of variation has been deliberately set as the vertical axis to reflect the correspondence between the scores of the first axis with latitude. Each circle represents an individual from one of the 22 populations, and the color of the circle defines the population membership according to the color scheme described in a and b).

As a country that spans a considerable latitudinal range, China is one of the few countries that provide a useful model for studying the impact of latitude or geography on genetic variation because of the relative similarity in genetic and cultural histories across the different ethnic and population groups in the country. This is particularly true if the focus is on the Han Chinese ethnic group, which forms the largest population group in China and is the dominant ethnic group in southern provinces, such as Guangdong and Fujian, where the Chinese population in Singapore mainly originated from; in northeastern provinces, such as Shandong and Jiangsu, where the trade and commerce center Shanghai is located in; and in northern provinces, such as Jilin, Liaoning and Hebei, where the capital, Beijing, is located in. Although genetic drift is likely to explain most of the subtle genetic variations in these populations, some of the larger differences between North and South Chinese may be the result of evolutionary adaptations as a consequence of environmental influences, including the effects of seasonality and climate, agricultural distribution across the country, or varying prevalence of infectious diseases.

The advent of inexpensive large-scale genotyping across the human genome offers unprecedented opportunities to survey interpopulation genetic variation, particularly when integrated with the suite of statistical and bioinformatics tools that are available for assessing population differences. At the SNP level, the Wright's24 FST offers a single metric for quantifying the variation in allele frequencies, whereas sophisticated methodologies, such as the iHS25 and XP-EHH26 statistics, for identifying the putative genomic signatures of positive natural selection allow interpopulation comparisons to be made at the haplotypic level. Here we leverage on these bioinformatic approaches to discover genomic regions that are most differentiated (i) between North and South Chinese; or (ii) across 22 populations in East and South-East Asia, subject to the condition that these regions exhibit consistent evidence across several bioinformatic metrics. In addition, we also investigate the extent of linkage disequilibrium (LD) variations in these regions, which have downstream implications on integrating data from genetic association studies from North and South Chinese.

Materials and methods

Datasets

Our analyses relied on genome-wide genotype data from three primary sources: (i) the East Asian panel of phase 2 of the International HapMap Project (abbreviated subsequently as HapMap);20 (ii) the HGDP;18, 19 (iii) the SGVP.1 The data from the HapMap consists of 3 821 888 autosomal SNPs that have been genotyped in 45 unrelated Han Chinese individuals from Beijing located in North-East China (abbreviated CHB) and 45 unrelated Japanese individuals from Tokyo (abbreviated JPT). Of the 1074 samples in the HGDP that are assayed on the Illumina HumanHap 650K BeadChip (Illumina, San Diego, CA, USA), we only considered the 228 unrelated samples from 18 population groups in East and South-East Asia. The SGVP database consists of 268 unrelated individuals from three population groups in Singapore that have been assayed on both the Affymetrix SNP6.0 (Affymetrix, Santa Clara, CA, USA) and Illumina 1M arrays. Our current analyses only consider the 96 Han Chinese individuals with ancestries originating from southern China (abbreviated CHS), and the 89 Malay individuals with ancestries from Peninsula Malaysia and Indonesia (abbreviated MAS, see reference 1 for a detailed description of the CHS and MAS samples), where 1 584 040 and 1 580 905 autosomal SNPs remained after quality checks, respectively. To validate the findings on the correlation between allele frequencies and latitudes, the genotype data of Chinese control samples from four independent genome-wide association studies conducted in Singapore (2434 Chinese population controls from the Singapore Prospective Study Program27, 28 and 2542 Malay population controls from the Singapore Malay Eye Study),29, 30 Guangzhou (980 control samples)2 and Shandong province (181 control samples)2 were used.

Analysis with 22 East and South-East Asian populations

Correlation between allele frequencies and latitude

To identify clinical variations in allele frequencies, we calculated the Pearson correlation coefficient R between the allele frequencies of each SNP and the geographical latitudes of the 22 populations at the 610 437 autosomal SNPs that are common across the HGDP, HapMap and SGVP databases. These populations consist of the 18 groups in East and South-East Asia from HGDP, the two East Asian populations from HapMap (CHB, JPT), and the Chinese (CHS) and Malay (MAS) samples from SGVP. The geographical locations (latitudes and longitudes) for the samples from HGDP are available online (http://www.cephb.fr/en/hgdp/table.php), whereas for the HapMap populations, we used the latitudes corresponding to Beijing and Tokyo. As the Chinese samples in Singapore are descended mainly from migrants originating from the Fujian and Guangdong provinces in China, we took the average of the latitudes for these provinces. The latitude for the Malay samples was obtained as the average latitude between Malaysia and Singapore. The P-value for the Pearson correlation coefficient R between the allele frequencies and latitudes for the 22 populations is calculated with the test statistic

graphic file with name ejhg2011139e1.jpg

which follows an approximate Student's t-distribution with 20° of freedom.

Population structure analysis with PCA

For the 22 populations (18 from HGDP, 2 from HapMap and 2 from SGVP), we selected a thinned set of 101 704 SNPs out of the 610 437 common autosomal SNPs by choosing every sixth SNP in order to minimize the use of correlated SNPs. We performed an eigenanalysis on this set of thinned SNPs with the pca option that is distributed as part of the eigenstrat software.31 To calculate the contribution of each SNP to the resultant principal components from the eigenanalysis, suppose the genotype of individual j at SNP i is defined as gij ∈ {0, 1, 2, NULL}. Let gij′ denote the normalized genotype, calculated as Inline graphic where ĝi denotes the average of gij across the individuals with non-NULL genotypes and pi denotes the allele frequency for SNP i. The loadings for SNP i for the kth principal component, γik, is subsequently calculated as Inline graphic where ajk is the corresponding element for individual j for the kth principal component. We do not use the SNP loadings for discovering regions of interest, but only as an additional source of evidence to corroborate the findings at interesting regions identified by the other metrics. We cross-reference every region that has been identified by the four approaches by checking whether there is at least one SNP in the region that lies in the top 0.1 or 0.5% of the distribution of the SNP loadings across the genome.

Comparisons between two populations in North and South China

Quantifying north–south population variation in China with FST

To assess whether there are considerable differences in the allelic architecture between populations with ancestries that are predominantly found in North China (CHB) and South China (CHS), we quantified the extent of the disparity in the allele frequencies at each SNP with the FST statistic.24 There are a total of 1 248 469 autosomal SNPs that are common between CHB and CHS, and the SNP level FST is calculated as

graphic file with name ejhg2011139e4.jpg

following Rosenberg et al32 for two populations, where p1 and p2 denote the allele frequencies of a chosen allele at a particular SNP in CHB and CHS, respectively.

North–south variation in signatures of positive natural selection

We used the iHS statistic25 and the XP-EHH metric26 to identify genomic signatures of positive natural selection in the CHB and CHS samples. The software used in the iHS and XP-EHH calculations are downloaded from http://hgdp.uchicago.edu/Software/.33

The iHS calculations are performed independently in each of the two populations, except that the iHS analysis of CHB is performed on a similar set of SNPs that the CHS database contains, to avoid differential signals that are attributed entirely to different SNP densities from the HapMap and SGVP databases. We used the recombination rates that are averaged across all the four HapMap phase 2 populations, and we normalized the raw iHS statistics in 20 derived allele frequency bins, each spanning 5%. The iHS signals are used to discover regions of interest if the iHS score in either one population is found in the top 0.1% but not in the top 1% of the other population.

The XP-EHH analysis was performed on the set of 1 102 122 SNPs common to CHB and CHS, and the resultant XP-EHH statistics were subsequently normalized to have a zero mean and unit variance. A clustering of SNPs displaying large positive values of the normalized XP-EHH statistic suggests that a selection event is likely to have occurred in the first population (CHB) relative to the second population (CHS), whereas a clustering of large negative values suggests a selection event is likely to have occurred in the second population relative to the first population. As such, we used the XP-EHH analysis between CHB and CHS to identify regions of interest, defined as regions with normalized XP-EHH signals in the top 0.01% of either tails of the genome-wide distribution of the XP-EHH scores, and noting the direction of these signals as this indicates whether the candidate selection event occurred in CHB or CHS.

Additional methods on quantifying interpopulation LD differences and further details of quantifying regional evidence of: (i) the correlation between allele frequencies and geographical latitude; and (ii) high FST can be found in the Supplementary Material.

Results

We used four mechanisms to discover genomic regions experiencing north–south clinical genetic variation in the East Asian populations from HapMap, HGDP and SGVP: (i) stretches of high FST SNPs between the 1 248 469 SNPs that are common to the HapMap Han Chinese from Beijing (CHB) and the Singapore Chinese samples with genetic ancestries from South China (CHS); (ii) regional evidence of SNPs found in the 22 East and South-East Asian populations where the allele frequencies are significantly correlated with the corresponding latitudes of the populations; (iii) genomic stretches where there are significant evidence of differential positive natural selection signals between CHB and CHS, when assessed using the XP-EHH metric; (iv) genomic regions where there are conflicting evidence of positive natural selection when assessed using the iHS metric in CHS and CHB. To avoid spurious findings from the use of a single discovery metric, we require each identified region to be supported by evidence from at least one of the other metrics, or to contain SNPs that are found to contribute significantly to the north–south cline as evident in the first axis of the principal component analysis in Figure 1 (see Table 1 for a summary of discovery and validation metrics, and Materials and Methods for the details of these metrics).

Table 1. A description of the bioinformatic metrics used to discover and validate genomic regions that are differentiated along a north–south cline.

Criteria Populations Discovery criterion Validation criterion
FST Overrepresentation of SNPs in a genomic region with high FST relative to genome-wide distribution of FST scores CHB vs CHS Top 0.1% of genome-wide distribution of regional evidence where: – Region defined by window sizes of 100 and 500 kb – Evidence defined by the P-value of the exact Binomial test for the proportion of SNPs with FST in the top 1st and 0.1st percentile, respectively, of the genome-wide distribution of FST scores Discovered region containing regional evidence found in the top 1% of the genome-wide distribution
Correlation between allele frequency and latitude In all, 22 East and South-East Asian population groups from HapMap, HGDP and SGVP Top 0.1 or 0.5% of genome-wide distribution of regional evidence where: – Region defined by window size of 500 kb – Evidence defined by the P-value of the exact Binomial test for the proportion of SNPs with Pearson correlation coefficient P-values <10−4 Existence of at least one SNP in discovered region with Bonferroni corrected P-value for the Pearson correlation coefficient test <0.05
XP-EHH CHB vs CHS Top 0.01% of the genome-wide distribution of the normalized XP-EHH scores Existence of at least one SNP in discovered region in the top 0.5% of genome-wide distribution of the normalized XP-EHH scores
Differential signals of iHS for CHB and CHS iHS calculated independently from CHB and CHS genotype data, with SNPs for CHB thinned to similar density as CHS CHB vs CHS SNP with iHS score in top 0.1% of the normalized genome-wide distribution in first population, but absent in the top 1% of normalized genome-wide distribution in second population Discovered region containing at least one SNP with iHS score in top 1% of normalized genome-wide distribution, but absent in the top 1% of normalized genome-wide distribution in second population
PCA SNP loadings for first axis of variation from Figure 1 In all, 22 East and South-East Asian population groups from HapMap, HGDP and SGVP No discovery mechanism from this Existence of at least one SNP in discovered region with PCA SNP loadings at least in the top 0.5% of the genome-wide distribution
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Abbreviations: CHB, Han Chinese from Beijing; CHS, Singapore Chinese with South China ancestries; HGDP, Human Genome Variation Project; iHS, integrated haplotype score; PCA, principal component analysis; SGVP, Singapore Genome Variation Project; XP-EHH, cross-population extended haplotype homozygosity.

The populations that each metric is applied on are also stated.

Clinical variation in allele frequencies with latitude

In the discovery phase, we identified five regions with an overrepresentation of SNPs exhibiting evidence of correlation (defined as a Pearson test of correlation P-value <10−4) between allele frequencies and the latitudes of 22 populations (see Table 2, Figure 2 and Supplementary Figures S1–S5). Each of these five regions displayed concordant evidence of population differentiation between northern and southern Chinese populations in at least one other validation metric, which perhaps unsurprisingly, almost always included SNPs with high loadings for the first axis of variation in the PCA from Figure 1 (Table 2).

Table 2. Regions identified across the genome which contains an overrepresentation of SNPs that exhibit strong correlations between allele frequencies and latitude in 22 East and South-East Asian populations in the HapMap, HGDP and SGVP.

Chr Start (Mb) End (Mb) MAF latitude correlation Pa (rsID) FST (CHB vs CHS) XP-EHHb (direction) iHS (CHB) iHS (CHS) SNP loadings (rsID) Genes
Top 0.1%
 6 32.610 33.110 2.1 × 10−5 (rs6901084) Top 0.5% Top 0.5% (positive) Top 0.01% Top 0.01% Top 0.1% (rs9268832) HLA-DRB1, HLA-DQA1-2, HLA-DOB, PSMB9, BRD2, TAP2, PSMB8, TAP1, HLA-DMB, HLA-DMA, HLA-DOA
 8 32.155 32.655 2.0 × 10−4 (rs4489283) No evidence Top 0.5% (positive) Top 0.5% Top 0.5% Top 0.1% (rs4489283) NRG1
                   
Top 0.5%
 3 39.038 39.538 6.6 × 10−5 (rs2370969) No evidence Top 0.1% (negative) Top 0.5% Top 0.1% Top 0.1% (rs1464047) WDR48, GORASP1, TTC21A, AXUD1, CMYA1, CX3CR1, CCR8, SLC25A38, LAMR1, MOBP
 3 136.038 136.538 9.3 × 10−4 (rs6762261) No evidence No evidence Top 0.1% Top 0.5% Top 0.5% (rs6788931) EPHB1
 6 18.610 19.110 9.5 × 10−4 (rs986148) No evidence Top 0.1% (positive) Top 0.1% No evidence No evidence NA
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Abbreviations: CHB, Han Chinese from Beijing; CHS, Singapore Chinese with South China ancestries; HGDP, Human Genome Variation Project; iHS, integrated haplotype score; SGVP, Singapore Genome Variation Project; XP-EHH, cross-population extended haplotype homozygosity.

a

Bonferroni corrected P-value for the test of correlation between allele frequencies and latitude of the 22 East and South-East Asian populations from HapMap, HGDP and SGVP. The Bonferroni correction is performed by multiplying the empirical P-value by the number of SNPs found in each region.

b

XP-EHH between CHB and CHS, with positive indicating evidence of positive selection in CHB, whereas negative indicating evidence of positive selection in CHS.

The table highlights the genomic stretches found in the top 0.1 and 0.5% of the genome-wide distribution for regional evidence of clinical variation in allele frequencies that are supported by concordant information from the SNP loadings of the first axis of variation in a principal component analysis of the 22 populations and from other bioinformatic evidences from the comparisons between CHB and CHS (FST, XP-EHH and differential signals of iHS). For each region, the SNP with the strongest evidence of MAF latitude correlation is reported.

Figure 2.

Figure 2

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Genomic regions identified with evidence of clinical genetic variation. Five regions emerged with regional evidence of significant correlations between the allele frequencies of SNPs and the geographical latitudes of 22 East and South-East Asian populations, according to the order as described in Table 2: (a) across the HLA gene cluster in class II of the MHC on chromosome 6; (b) the region on chromosome 4 encompassing the NRG1 gene; (c) between 39.04 and 39.54 Mb on chromosome 3 encompassing a cluster of genes; (d) the region on chromosome 3 encompassing the EPHB1 gene; (e) a gene desert between 18.61 and 19.11 Mb on chromosome 6. SNPs with correlation P-values less significant than 10−4 are represented by blue circles, while yellow diamonds represent SNPs with 10−5≤P-values<10−4; orange diamonds represent SNPs with 10−6≤P-values<10−5; red diamonds represent SNPs with P-values≤10−6. The SNPs exhibiting the strongest evidence of clinical variation in allele frequencies and SNP loadings of the first axis of variation in the PCA are also shown. Green bars at the top of each plot indicate the locations of genes in the region, and horizontal dotted lines linking to each bar indicate that the gene spans beyond the region shown in the figure.

One of the two regions in the top 0.1% of the genome-wide distribution spans a series of HLA genes between 32.61 and 33.11 Mb in class II of the major histocompatibility complex (MHC) region on chromosome 6, including -DRB1, -DQA1, -DQA2, -DOB, -DMB, -DMA and -DOA. Our analysis of this region reveals strong evidence of positive natural selection in both Han Chinese populations from Beijing (CHB) and Singapore (CHS), with iHS metrics in the top 0.01% of the genome-wide distributions for each of these two populations (Supplementary Figure S1), as well as concordant evidence from both XP-EHH and FST. The other region identified in the top 0.1% spans the NRG1 gene, and exhibited evidence of positive natural selection in both northern and southern Chinese with both iHS and XP-EHH (Supplementary Figure S2). The emergence of this region is perhaps unsurprising, as a detailed survey of the genetic variation at this gene in 39 populations has previously revealed significant differences in the frequency spectrum of alleles and haplotypes in intronic SNPs, which correlated with the geographical locations of the 39 populations.34 This region similarly emerged as one of the top regions in the human genome exhibiting evidence of regional variation in patterns of LD when assessed across all the HapMap phase 2 populations.35

One of the three regions found in the top 0.5% encompasses a cluster of genes between 39.04 and 39.54 Mb on chromosome 3 (Supplementary Figure S3) with associations to phenotypes and functions such as tumor suppression (TTC21A, AXUD1 and LAMR1), HIV progression with immunological tolerance and inflammation roles (CX3CR1), pyridoxine-refractory sideroblastic anemia in humans, while functionally responsible for anemic phenotype in an animal model with zebrafish embryos (SLC25A38), and a hereditary cardiomyopathy (arrhythmogenic right ventricular dysplasia) that causes sudden death in the young.36 Another region on chromosome 3 (136.04–136.54 Mb, see Supplementary Figure S4) encompasses the ephrin receptor EPHB1 where a strong correlation was established between EphB expression and degree of malignancy in colorectal cancer progression.37 The region identified on chromosome 6 was particularly intriguing given the absence of any genes in the vicinity (Supplementary Figure S5), as there were consistent evidence of positive selection occurring in North Chinese compared with South Chinese represented by a positive XP-EHH signal in the top 0.1% and an iHS signal in the top 0.1% in CHB, but absent even in the top 1% of the CHS signals.

Population differentiation between CHB and CHS

The availability of larger sample sizes from the Chinese populations in HapMap (45 CHB samples) and SGVP (96 CHS samples) allows the use of population genetics metrics to quantify the differences in the allelic spectrum and genomic signatures of positive natural selection between the two populations. By prioritizing genomic regions that emerged with consistent evidence of extreme differentiation between the two populations, we identified seven regions, of which the region on chromosome 6 between 18.61 and 19.11 Mb was previously seen with strong evidence of a latitudinal cline in allele frequency variation (see Table 3, Figure 3, and Supplementary Figures S7–S11).

Table 3. Regions identified across the genome by different discovery mechanisms using the three bioinformatic metrics calculated from the CHB and CHS genome-wide data from HapMap and SGVP.

Discovery mechanism Chr Start (Mb) End (Mb) FSTa (window size) XP-EHHb (direction) iHS (CHB) iHS (CHS) MAF latitude correlation Pc (rsID) SNP loadings (rsID) Genes
iHS 3 189.512 190.012 No evidence Top 0.5% (positive) Top 0.01% No evidence 2.5 × 10−3 (rs16863396) Top 0.5% (rs3817462) LPP
FST, iHS 4 100.552 101.052 Top 0.1% (100 kb, 500 kb) Top 0.5% (positive) Top 0.1% No evidence 7.7 × 10−3 (rs13150247) Top 0.1% (rs13150247) ADH gene cluster, RG9MTD2, MTTP, DAPP1, MAP2K1IP1, DNAJB14
iHS 6 18.610 19.110 No evidence Top 0.1% (positive) Top 0.1% No evidence 9.5 × 10−4 (rs986148) No evidence NA
FST, XP-EHH 6 29.795 29.895 Top 0.01% (100 kb, 500 kb) Top 0.01% (negative) No evidence No evidence 1.3 × 10−2 (rs1633021) Top 0.1% (rs3131020) HLA-F, HLA-G
FST 11 61.189 61.689 Top 0.1% (100 kb, 500 kb) Top 0.1% (positive) Top 0.5% No evidence No evidence Top 0.5% (rs1495941) FEN1, FADS1-3, RAB3IL1, BEST1, FTH1, INCENP
XP-EHH 12 71.358 73.069 Top 0.01% (100 kb) Top 0.01% (negative) No evidence Top 0.5% 8.6 × 10−3 (rs2102755) Top 0.5% (rs10879537) NA
FST, XP-EHH 13 97.957 98.957 Top 0.1% (100 kb, 500 kb) Top 0.01% (negative) No evidence Top 0.5% 9.1 × 10−2 (rs11069349) No evidence STK24, SLC15A1, DOCK9, PHGDHL1, GPR18, EBI2
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Abbreviations: CHB, Han Chinese from Beijing; CHS, Singapore Chinese with South China ancestries; HGDP, Human Genome Variation Project; iHS, integrated haplotype score; SGVP, Singapore Genome Variation Project; XP-EHH, cross-population extended haplotype homozygosity.

a

Regional evidence from the FST metric, where the size of the region containing evidence is defined in the parentheses.

b

XP-EHH between CHB and CHS, with positive indicating evidence of positive selection in CHB, whereas negative indicating evidence of positive selection in CHS.

c

Bonferroni corrected P-value for the test of correlation between allele frequencies and latitude of the 22 East and South-East Asian populations from HapMap, HGDP and SGVP. The Bonferroni correction is performed by multiplying the empirical P-value by the number of SNPs found in each region.

These metrics utilizing the discovery populations of CHB and CHS are described in Table 1.

Figure 3.

Figure 3

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Evidence of genetic differentiation between CHB and CHS around the LPP gene on chromosome 3. (a) Evidence of population differentiation between CHB and CHS from three discovery mechanisms looking at differential evidence of positive natural selection from iHS (top panel); regional clustering of SNPs with considerably different allelic spectrum between CHB and CHS (as quantified by the FST metric) relative to the genome, where the top 0.5% of the FST distribution corresponds to an empirical FST score of 2.7, top 0.1% corresponds to an empirical FST of 3.8% and the top 0.01% corresponds to an empirical FST of 17.0% (middle panel); XP-EHH signals comparing CHB and CHS that are found in either tails of the genome-wide distribution (bottom panel), with the diamonds representing signals in the top 0.5% (yellow), top 0.1% (orange) and top 0.01% (red) of the distribution. (b) Scatter plot of the frequencies of allele A for rs16863396, located at 189 715 374 bp on chromosome 3, across 22 populations in East and South-East Asia. The size of each circle represents the sample size of the population, and the color follows the assignment in Figure 1. The Pearson correlation and the corresponding P-value are calculated from the 22 populations. Four additional independent populations are shown in circles with decreasing shades of gray (with increasing latitude) for validating the clinical relationship between allele frequency and latitude.

Of the six additional regions, the region on chromosome 3 between 189.51 and 190.01 Mb encompassed the lipoma-preferred partner (LPP) gene that was recently implicated with celiac disease in numerous studies38, 39, 40 and was previously reported to have an important role in tumor metastasis,41, 42, 43 including in acute myeloid leukemia.44, 45 This region displayed consistent evidence of differential signals of positive natural selection that was only present in CHB and not in CHS (Figure 3a), an observation that was corroborated by the XP-EHH signals in the East Asian population groups from the HGDP Selection Browser (http://hgdp.uchicago.edu/cgi-bin/gbrowse/HGDP/),33 which displayed stronger evidence of positive selection in the populations from the north (Supplementary Figure S6). The discovered region also contained several SNPs, including rs16863396 (Figure 3b), that displayed significant evidence of a latitudinal cline in allele frequency variation (for rs16863396: empirical P-value=1.6 × 10−5, Bonferroni corrected P-value=2.5 × 10−3). The latter observation of the latitudinal cline in allele frequency variations was supported even after the inclusion of four additional populations with considerably larger sample sizes that are located at latitudes of between 3° north (Peninsula Malaysia) and 37° north (Shandong province; empirical P-value=9.2 × 10−6; Figure 3b).

Another region that emerged with strong evidence from two discovery mechanisms (FST, iHS), demonstrating signs of positive selection in CHB in the top 0.1% of the iHS signals across the genome but not even in the top 1% in CHS, encompassed the cluster of genes responsible for alcohol metabolism (alcohol dehydrogenase ADH gene cluster) on chromosome 4 (100.55–101.05 Mb). Strong corroborating evidence was observed from all other metrics (Table 3, Supplementary Figure S7), with the same SNP (rs13150247) observed to contribute significantly to the SNP loadings of the first PC in Figure 1 and also to display consistent evidence of a latitudinal cline in allele frequencies (empirical P-value=7.3 × 10−5, Bonferroni corrected P-value=7.7 × 10−3, Supplementary Figure S7).

The HLA-F and HLA-G region in class I of the MHC on chromosome 6 also emerged as a region with numerous high FST SNPs and with XP-EHH signals in the top 0.01% of the genome (Table 3, Supplementary Figure S8). Two other intronic regions on chromosomes 11 and 13 were similarly identified with consistent evidence of population differentiation between CHB and CHS by FST and XP-EHH (Supplementary Figures S9, S11). The former region is putatively selected in CHB and encompasses genes implicated in cancer pathogenesis (FEN1)46, 47 and iron metabolism (FTH1);48, 49 the latter region appears to be selected in CHS and contains the genes involved in pancreatic cancer inhibition (SLC15A1)50 and bipolar disorder (DOCK9).51

Discussion

The availability of at least 1.25 million SNPs, that is common to CHB and CHS, offered unprecedented opportunities to survey the genetic landscape between two Han Chinese population groups with genetic ancestries from North and South China. By including the 18 East Asian populations from HGDP, the HapMap Japanese samples and the South-East Asian Malays, we have a unique opportunity to survey the genetic variability in East and South-East Asia that is directly correlated to geography, an observation that has been reported in several similar studies performed in Europe,52, 53, 54 the Pacific islands,55 East Asia,1, 2, 56 South Asia57 and Africa.58 Regions that emerged in our survey include the alcohol dehydrogenase (ADH) gene cluster, the HLA regions in the MHC, and the regions on chromosomes 3 and 8 that encompass the genes LPP and NRG1, respectively (see Supplementary Material for additional discussion on these regions).

The observation of a north–south cline in genetic variation in China by us1 and others2, 3, 23 was made with the use of autosomal SNPs. This appears to be discordant with earlier findings from the use of mitochondrial DNA (mtDNA) and chromosome Y (chrY), which established a more complex migration pattern across China,59, 60 including a west–north passage,61 a east–west passage62 and a postglacial migration into East Asia from the north.63 The inference on migration and population demography with mtDNA and chrY is expected to be superior to the use of autosomal SNPs, as the lack of recombination allows the genealogy of individuals from different populations to be estimated more accurately. However, although there have been numerous reports on the complexity of the probable migration patterns, we noticed that even the literature from mtDNA and chrY is consistent in reporting the genetic diversity along a south–north migration cline.60, 62, 64, 65, 66, 67 In this article, we specifically focus on identifying the genomic regions that exhibited the strongest evidence of north–south diversity rather than to infer any migration and demographic patterns.

The analyses with the five bioinformatic metrics discovered 11 regions that were substantially differentiated between North and South Chinese populations. A natural extension is to evaluate the implications of these differences in medical genetics. We observed that all 11 regions displayed evidence of LD variation between CHB and CHS in the extreme 5% of the genome-wide distribution of LD differences, as quantified by the varLD statistic (see Supplementary Material and Table S1). The current strategy in genome-wide association studies aims to replicate the lead SNP exhibiting the strongest signal from each region in other populations. Regions containing strong evidence of LD variation between two populations have previously been found to exhibit larger differences in the statistical evidence at the index SNPs,35 which can confound meta-analyses of association studies from North and South Chinese populations. Conversely, fine mapping the unknown functional polymorphisms in these regions are likely to be more successful, as the different LD patterns are likely to imply the presence of different core haplotypes that are carrying the functional allele.68 Leveraging on these diverse haplotype patterns is expected to be an important feature when attempting to localize the possible candidates for the causal variants, as long-range LD that has benefited the discovery phase of GWAS is likely to confound the fine mapping phase by producing numerous perfect surrogates that are statistically indistinguishable from the true causal variant.

We have used three different bioinformatic metrics that are commonly used in population genetics to quantify population differences and identify signatures of positive natural selection. Two additional metrics looked at clinical patterns of genetic differentiation across 22 populations, as assessed by the correlation between allele frequencies and geographical latitudes, and by identifying SNPs that possess higher loadings in a PCA of genetic variation across these populations (Supplementary Table S2). Although the sample sizes in HGDP are particularly small for certain population groups for accurate inference of the allele frequencies, we have used four independent cohorts from large-scale genetic studies to validate the findings of geographical clines in the allele frequencies of the discovered SNPs.

One caveat with the use of these mechanisms for discovery and validation is that these metrics essentially prioritized regions in the tail of the genome-wide distributions, and the regions that emerged may not necessarily be functionally important or relevant. However, given that there is clear evidence of genetic variation between these populations from previous studies, we have sought to discover the genomic regions that may explain these interpopulation differences. In searching for regional evidence of population differences, we have searched for an overrepresentation of SNPs within each genomic region that either displayed high FST values or exhibited strong correlations between the allele frequencies and the latitudes. Although this avoids the problem of false positives introduced from isolated SNPs displaying strong evidence of population differentiation, the approach to search for a clustering of SNPs with strong evidence may inevitably be confounded by the presence of LD. However, as we require concordant evidence from multiple metrics, including iHS and XP-EHH, which use genetic distances for calculating the test statistics, and are thus more robust to effects of LD, we do not expect the regions that have emerged to be artifacts due to LD. A recent article describing a composite metric for identifying regions undergoing positive selection also showed that correlations between FST, iHS and XP-EHH are generally weak even in selected regions, particularly with increasing distance from the causal polymorphism.69 This further suggests it is unlikely our findings are due to chance occurrences of the same regions appearing in the tail of the distributions. However, it is important to recognize that these bioinformatic measures only provide an approach to prioritize genomic regions for downstream investigations, and our approach is not meant to provide conclusive evidence on the biological relevance and consequences.

This study has extended previous observations of geography-linked genetic variation to East and South-East Asia, and through a systematic survey of population genetics data from two Han Chinese populations, identified genomic regions that contribute to explain the observed north–south cline in genetic differences in China. Although most of the findings are association driven, this study highlights the potential of integrating genomic evidence at the level of population and evolutionary genetics for the science of anthropology, and in mapping the geographical variations in the incidences of diseases and complex human traits.70 With considerable variance in the incidences of major diseases across the different geographical regions,71 China presents a unique opportunity for exploring the effects of geography and climate on human genetics. The increasing availability of genome-wide data for multiple populations worldwide, including China, may finally herald the progression from anecdotal and observational evidence of population differences toward a more precise quantification of the genetic basis behind interpopulation variations.

Acknowledgments

We thank three anonymous reviewers for their constructive comments, which have greatly improved the article. This project acknowledges the support of the Yong Loo Lin School of Medicine from the National University of Singapore, National Medical Research Council, 0796/2003, Singapore and the Biomedical Research Council, 09/1/35/19/616, Singapore. The study used data generated by the International HapMap Consortium, the Singapore Genome Variation Project and the Human Genome Diversity Project. YYT acknowledges support from the National Research Foundation, NRF-RF-2010-05, Singapore.

The authors declare no conflict of interest.

Footnotes

Supplementary Information accompanies the paper on European Journal of Human Genetics website (http://www.nature.com/ejhg)

Author Contributions

YYT and KSC jointly conceived, designed and directed the experiment; YYT, CS and HX wrote the paper; YYT, CS, HX, XS, JC, RTHO and KSS analyzed the data; YXX, XZ, JL, EST and TYW contributed samples.

Supplementary Material

Supplementary Material
Click here for additional data file. (3.4MB, doc)

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