BACKGROUND
high throughput sequencing technologies have prompted sequencing of human genomes at the population level.
for instance, the  <dig> genomes project has reported genome resequencing data from  <dig> populations and aims to analyze the genomes of a total of  <dig> populations  <cit> .
these projects provide us with immense amounts of information regarding human genomic variation and the functional properties of such variation.
still, the coverage of world-wide variation remains limited, and virtually no whole genome resequencing data is available involving populations in western asia, a region encompassing the eastern mediterranean basin and the middle east  <cit> .
western asia has been the main corridor through which initial out-of-africa migrations have populated eurasia  <cit> .
moreover, the region experienced a massive demographic expansion during the early holocene with the establishment of large, agricultural societies in the region  <cit> , which subsequently shaped the genetic structure of europe through migrations  <cit> .
the demography of the region was later influenced by the movement of turkic speaking populations beginning from 11th century a.d., which occurred with disputed intensity and frequency, but with undoubtedly profound linguistic impact  <cit> .
in addition to early population movements, there were subsequent population events that had a major influence on the genetic variation in the region, including demographic shrinkage and early 20th century migration, followed by major population expansion and local migrations in the late 20th and early 21st century  <cit> .
locus specific population genetic studies have addressed some of these issues, demarcating y chromosome  <cit> , mtdna  <cit> , alu
<cit>  and snp genotypes  <cit>  in the general turkish population.
however, an integrative, genome-wide assessment of genomic variation is still missing.
in addition to providing insights into the demographic history of the population, resequencing studies are gaining prominence for identifying variants that are associated with complex, sometimes population specific diseases  <cit> .
such assessments are not possible using array technologies, as array probes are designed based on common variation and hence suffer from ascertainment bias  <cit> .
it is expected that most common genomic variation is shared among populations and only a small percentage of overall genomic variation is confined to geographic regions.
however, rare or private  variants have stirred recent attention and may explain heritable diseases and local adaptation .
such variants may explain the genetic components of diseases that occur at unusual frequencies in turkey, including behçet’s  <cit> , familial mediterranean fever  <cit> , and beta thalassemia  <cit> .
in this paper, we present, for the first time, high coverage  whole genome re-sequencing data from  <dig> individuals from turkey, covering at least  <dig> % of the genome at 1x, and at least  <dig> % at 5x .
we sampled the genomes from diverse geographical regions in turkey, leading to the identification of  <dig>  novel snvs,  <dig>  novel indels, and a non-redundant total of  <dig>  deletion polymorphisms.
it has been shown previously in comparable population genomics studies that even extremely high accuracy snp calling pipelines cannot avoid a small fraction of false-positive snps.
these have been shown to be significantly enriched among population specific and rare variants.
for instance, a recent study has predicted to have approximately  <dig>  false-positive snps per genome, even if the overall snp calling accuracy is  <dig> % and the majority of these snps were found to be population specific  <cit> .
to assess the extend to which the population specific variants we detected are false-positives, we used pcr followed by sanger sequencing.
indeed, of the  <dig> variable snv and indel sites that are population specific  <dig> of them  were falsely called as variable sites.
this is in contrast with our overall validation results and indicates much higher false-positive rate among the novel variants.
however, these results do not change our observation that there are hundreds of thousands of novel variants found in the turkish population.table  <dig>
summary of the turkish genome project
1
2
3
1indels between 1–50 bp.
2deletions >50 bp.
3deletions that are not previously reported in the  <dig> genomes project .
our results showed that genetic variation within turkey clusters with european populations, while showing signatures of admixture from african and east asian populations, consistent with influence of potential north african interactions and altaic admixture.
based on our analysis of snps reported in gwas studies that show the highest frequency differences between turkey and european populations, we find snps associated with pigmentation and cholesterol level.
RESULTS
whole genome analysis and variant discovery
we recruited  <dig> healthy volunteers from across turkey .
the individuals were included in the study irrespective of their mother-tongue/ethnicity; we refer to them collectively as “turkish”.figure  <dig>
brief summary of the turkish genome project.
a map of turkey showing provinces where volunteers were recruited in color.
allele frequencies of the snps found in turkish samples and annotated as novel vs. known .
functional annotation of the novel snps.
we isolated dna from blood samples obtained from each individual, and generated whole genome shotgun  sequence data at high coverage ranging between  <dig> to 48x, using the illumina platform .
using bwa  <cit>  and gatk  <cit> , we identified an average of  <dig> , <dig> snps per individual, and a non-redundant total of  <dig> , <dig> snps, of which  <dig>   were found to be novel when compared to dbsnp v <dig> and the  <dig> genomes project .
we observed that  <dig>  of the novel snps found were identified as non-synonymous mutations in protein coding sequence .
we also indentified a total of  <dig> , <dig> short  indels.
additionally, using variationhunter  <cit>  we identified  <dig>  large  deletions per individual on average .
to estimate the false discovery and false negative rates  of our snp calls, we analyzed the same samples using affymetrix  <dig>  snp arrays  to genotype for common snps.
we then compared the microarray results with the snp calls we generated from wgs.
assuming the snp arrays as the gold standard, we estimated the fdr to be at  <dig> % and fnr as  <dig> %.
common genetic variation in contemporary turkey
next we studied the  <dig> genomes with respect to major patterns of population diversity, structure, and migration, comparing these profiles with those in the  <dig> genomes project  <cit> .
we found that genome-wide nucleotide diversity  in turkey is comparable to that observed in europeans, while lower than in africans or admixed native american populations, and higher than in east asians .
even though we expect lower values of π in turkish populations as compared to african populations, it was surprising to find π in european populations equal to or slightly higher than that observed in turkey.
we expected that turkish genomes might exhibit significantly higher nucleotide diversity, given turkey’s location at the crossroads of out-of-africa migrations, as well as more recent population movements  <cit> .
still, this result should be taken with caution given differences in snp calling procedures and power between the turkish and  <dig> genomes project datasets, which could potentially affect estimated diversity levels.
to obtain an overview of population relationships, we conducted principal component analyses using  <dig> individuals randomly selected from each one of the  <dig> populations within the  <dig> genomes project, combined with the profiles from turkey .
the first two principal components of the combined dataset replicated the global genetic structure identified in earlier studies .
within this picture, the genetic variation observed among turkish population clusters with variation observed in european populations .
the genome profiles from turkey also overlapped with those of native american populations.
this is interesting, because the genetic affinity of native american populations to both east asia and europe has traditionally been attributed to their asian origins and subsequent admixture with europeans  <cit> .
however, this picture has recently been reinterpreted as evidence of shared ancient north eurasian ancestry in native americans and europeans  <cit> .
this result implies that significant ancient north eurasian ancestry might also be found in turkish genetic profiles; this requires further study.figure  <dig>
population genetic relationships between turkey and world-wide populations.
the first two principal components of the turkish genome dataset combined with  <dig> individual population subsets from the  <dig> genomes project dataset.
the first and second components explain 6% and 5% of the total variance, respectively.
a population tree based on “treemix” analysis.
the populations included are as follows: turkey ; toscani in italia ; iberian populations in spain ; british from england and scotland ; finnish from finland ; utah residents with northern and western european ancestry ; han chinese in beijing, china ; japanese in tokyo, japan ; han chinese south ; yoruba in ibadan, nigeria ; luhya in webuye, kenya .
populations with high degree of admixture  were not included to simplify the analysis.
the yoruban population was used to root the tree.
in total four migration events were estimated.
the weights for the migration events predicted to originate from the east asian branch into current-day turkey was  <dig> , from the ancestral eurasian branch into the turkey-tuscan clade was  <dig> , from the african branch into iberia was  <dig> , from the japanese branch into finland was  <dig> .
the first three principal components of the turkish genome dataset  and neighbor-joining trees of the  <dig> subjects .
the upper and lower panels show the same data, except for being colored according to latitude and longitude of subject locations, respectively.
the first, second and third principal components each explain ~7% of the total variance.
names of the provinces where each sample are recruited from are listed in additional file 1: table s <dig>
we then estimated the maximum likelihood population tree with migration using the treemix software  <cit>  .
the treemix program models populations as having ancestry from multiple parental populations, it can then calculate migration weights  <cit> .
these weights are correlated with the fraction of alleles contributed by a parental population; however, they are not an unbiased predictor of this fraction.
in the treemix analysis, turkish samples clustered together with south europe/mediterranean populations: iberians from spain and tuscans from italy .
within the worldwide population tree, two of the four predicted migration events involved turkey.
the strongest predicted migration event represents admixture from the root of the east asian branch into turkey, which could be reflecting central/south asian population migration  <cit> .
the second migration pattern represents admixture from the root of the eurasian branch  to the common node between turkey and italy.
the algorithm predicts a parallel branch from africa into spain.
these patterns plausibly reflect south mediterranean admixture into north mediterranean, as observed for other populations in the mediterranean basin  <cit> .
the weight for the migration event predicted to originate from the branch ancestral to all eurasians , to the turkey-tuscan clade, was only  <dig> .
in comparison, the weight for the migration event predicted to originate from the branch ancestral to east asia  into current-day turkey was  <dig> .
although this implies a major population event from the east to west asia, we note that these weights are not direct estimates of the migration rates.
first, the original contributing populations to the ancestral population in turkey are not known.
for instance, we do not know the exact genetic relationship between current-day east asian populations and the turkic speakers from central asia who migrated into anatolia about  <dig>  years before present.
in fact, hodoglugil and mahley, using hgdp genotyping data, predict that south asian contribution to turkey's population was significantly higher than east/central asian contributions  <cit> , suggesting that the genetic variation of medieval central asian populations may be more closely related to south asian populations, or that there was continued low level migration from south asia into anatolia.
another possibility is ancient north eurasian genetic contribution to both the historical anatolian and east asian populations  <cit> , which might have been interpreted as migration in this dataset.
second, pickrell and pritchard  <cit>  also note that in their simulations, the weights underestimate relatively high admixture proportions.
data from more closely related populations coupled with extensive population genetic simulation may eventually allow determining the relative contributions of migration events that shaped population variation in turkey.
finally, we investigated possible population structure within turkey.
principal component analyses did not reveal any subclustering among the  <dig> individuals, and we found no evidence for longitudinal or latitudinal divergence .
supporting this lack of structure, we found no correlation between genetic distances among subjects and geographic distances among subject locations .
one explanation for this observed pattern is the well-documented high-levels of recent population mobility within this geographic region  <cit> .
however, this pattern might not be exclusive to turkey; for example, a neighbor joining tree of  <dig> tuscan individuals in the  <dig> genomes project similarly displays a star-like phylogeny , i.e., we observe long terminal branches coalescing at about the same time, indicating lack of structure within the population.
genetic variants exhibiting unusual frequency in the turkish samples
the assessment of whole genome and exome sequencing data at the population level has shown that due to recent population growth, human populations carry an excess of rare genetic variants  <cit> , many of which can be functional  <cit> .
indeed, we identified  <dig>  synonymous or non-synonymous rare –i.e., variants that were found in a single turkish chromosome but not in any other population - and  <dig> synonymous or non-synonymous private –found in more than  <dig> turkish chromosomes, but not in any other population- single nucleotide variants  in the turkish population .
as expected, rare snvs are significantly more likely to be non-synonymous than snps observed in multiple populations .
we further scrutinized  <dig> non-synonymous private alleles.
interestingly, one of these genes, ccdc <dig>  was shown to evolve under positive selection in humans, and diverged from neandertals  <cit> .
indeed, the non-synonymous private snp in the turkish population observed at chr19: <dig>  is a t- > c mutation and homologous to denisovan haplotype at the orthologous site.figure  <dig>
the proportion of synonymous and non-synonymous snps.
snps that are found in a single chromosome among the  <dig> turkish genomes  show a significant increase in the proportion of non-synonymous snps  to synonymous snps , as compared to all snps observed in the same population .
this increase is even more visible among snps that are seen in a single chromosome and are novel  .
we then explored potentially functional variants at higher or lower frequency in the turkish population relative to the closely related european populations .
for this, we compiled the frequencies of published gwas snps among samples resequenced by the  <dig> genomes project  <cit> .
we then compared the frequencies of these snps in continental populations with what we observed in the turkish population .
as expected, the frequency distribution of snps in the turkish population is, by and large, similar to that observed among european populations.
to identify potential outliers to this expectation, we compared the frequency distributions of the european and turkish populations and identified  <dig> snps displaying the highest frequency differences between these populations .figure  <dig>
the allele frequency of gwas snps.
the density distribution of allele frequency of gwas snps among world populations.
the distribution of gwas snps in turkey  is more similar to that of the european population  as compared to east asian  and african  populations, indicating a greater proportion of ancestry sharing between tur and eur.
meanwhile, there is a higher proportion of common snps in both tur and eur than asn and afr, which is likely due to ascertainment bias in the gwas studies as described in  <cit> .
the allele frequency of gwas snps between turkish  and european  populations.
the red dots indicate snps in the  <dig>  percentile  of the absolute allele frequency distributions between turkish and european populations.
rs <dig> and rs <dig>  both affecting herc <dig> gene, are in strong linkage disequilibrium and, as such, have identical allele frequencies in european and turkish populations.
they are represented as two overlapping dots with  <dig>  allele frequency in turkish population  and  <dig>  allele frequencies in european population .
the frequency distribution of derived and ancestral alleles for rs <dig> in africa  europe , asia  and americas  and turkey .
note the increased frequency of the derived allele in the turkish population.
among these  <dig> snps,  <dig> exist at lower frequencies in turkey compared to europe.
we found that both are related to pigmentation  <cit> , and hair color  <cit> .
pigmentation is a genetic and variable trait in humans  <cit> , with lighter skin color being associated with better vitamin d absorption, but higher incidence of skin cancer  <cit> .
as such, human pigmentation correlates with latitude and the low frequency of this snp in turkish population as compared to europe may reflect positive selection for these alleles in northern europe and/or selection against the alleles in southern europe and turkey.
to our surprise,  <dig> of the  <dig> snps that show higher frequency in turkish population as compared to europeans are associated with lower total cholesterol counts.
this is particularly interesting, given that the turkish population has indeed been shown to have lower cholesterol than western european populations, including total cholesterol, and high and low density lipoprotein cholesterol measures, while carrying relatively high triglyceride levels  <cit> .
although cholesterol levels are strongly shaped by diet and lifestyle, they are also under the influence of genetic factors  <cit> .
the frequency distribution of one of these snps , associated with total cholesterol counts  <cit> , is fixed in asian continent and almost fixed among african populations, decreased to slightly above 90% in turkish populations, further decreasing to 49% among europeans.
therefore, similar to what is observed for pigmentation related snps, rs <dig> is best explained by clinal adaptation or drift patterns.
more striking is the frequency distribution of rs <dig>  another snp associated with total cholesterol count  <cit> , which reaches almost 70% in turkish populations, but is at lower than 10% frequency in africa and remains a minor allele in other eurasian populations  .
intriguingly, however, for both cholesterol level related snps, the variant at high frequency in turkey  is reported to elevate total cholesterol levels  <cit> .
hence, the contribution of these variants to phenotypic differences between populations needs further study.
deletion polymorphisms
we used the mrfast aligner  <cit>  together with the variationhunter  <cit>  algorithm to discover deletions in the genomes of the samples resequenced in this study.
we merged individual sample-based callsets, then used the genome strip tool  <cit>  to both genotype and in silico validate our discovery callset .
in summary, we identified  <dig>  deletions per individual, with a non-redundant total of  <dig>  deletions.
to assess novelty, we compared against the  <dig> genomes project datasets , and found  <dig> novel deletions per sample on average .
we did not find any whole-gene deletions, but 21/ <dig> deletions were predicted to delete coding exons where 10/ <dig> were predicted in more than one chromosome .
we also analyzed the genomic structure at the 17q <dig> locus, a region with increased plasticity , where eight different haplotypes are characterized  <cit> .
previous studies have shown that all eight haplotypes show themselves as an inversion polymorphism that exist as two main variants: a direction-orientation haplotype, h <dig>  prevalent in most human populations and an inverted haplotype, h <dig> which predominantly occurs in european populations  and presents itself as an 970-kbp inversion  <cit> .
this complex region has been shown to be associated with increased fecundity and an increase in global recombination and it was shown that the h <dig> haplotype is enriched in europeans  <cit> .
we have found an allele frequency of  <dig> % for 17q <dig>  h1/h <dig> inversion polymorphism in the samples we analyzed, which shows an increase when compared to european populations at 25% allele frequency  <cit> .
one of the samples, sequenced at 34x coverage, was also homozygous for h <dig> inversion allele .
CONCLUSIONS
although the  <dig> genomes project published in  <dig>  <cit>  had aimed to provide a comprehensive map of human genetic variation, it was not complete: populations in the eastern mediterranean and the middle east were missing from that study.
in this paper, we present data from high depth whole genome sequencing of  <dig> individuals from modern day turkey to complement the  <dig> genomes project in an effort to extend our understanding of normal human genetic variation.
we provide the first preliminary genome-wide map of single nucleotide variation, as well as deletion polymorphisms in this population and in western asia.
our analyses show that genetic variation of the contemporary turkish population is best described within the context of the southern european/mediterranean gene pool.
however, we predict notable genetic sharing between turkey’s population and east asian and african populations.
as expected from recent studies, rare and private genetic variation in turkey has presumably more functional impact than variation shared among populations.
we further identified snps that were previously associated with diseases that show allele frequency differentiation between turkey and other western european populations.
among these, those associated with pigmentation were at lower frequencies in turkey than in europe; meanwhile variants associated with total cholesterol levels were at higher levels in the former.
overall, our study improves the framework for population genomics studies in the region, and should incite novel genome-wide association studies in turkey.
future studies using larger sample sizes will be able to elucidate population structure and history in more detail.

 high throughput sequencing technologies have prompted sequencing of human genomes at the population level. for instance, the genomes project has reported genome resequencing data from populations and aims to analyze the genomes of a total of populations. these projects provide us with immense amounts of information regarding human genomic variation and the functional properties of such variation. still, the coverage of world-wide variation remains limited, and virtually no whole genome resequencing data is available involving populations in western asia, a region encompassing the eastern mediterranean basin and the middle east. western asia has been the main corridor through which initial out-of-africa migrations have populated eurasia. moreover, the region experienced a massive demographic expansion during the early holocene with the establishment of large, agricultural societies in the region, which subsequently shaped the genetic structure of europe through migrations. the demography of the region was later influenced by the movement of turkic speaking populations beginning from 11th century a.d., which occurred with disputed intensity and frequency, but with undoubtedly profound linguistic impact. in addition to early population movements, there were subsequent population events that had a major influence on the genetic variation in the region, including demographic shrinkage and early 20th century migration, followed by major population expansion and local migrations in the late 20th and early 21st century. locus specific population genetic studies have addressed some of these issues, demarcating y chromosome, mtdna, alu and snp genotypes in the general turkish population. however, an integrative, genome-wide assessment of genomic variation is still missing. in addition to providing insights into the demographic history of the population, resequencing studies are gaining prominence for identifying variants that are associated with complex, sometimes population specific diseases. such assessments are not possible using array technologies, as array probes are designed based on common variation and hence suffer from ascertainment bias. it is expected that most common genomic variation is shared among populations and only a small percentage of overall genomic variation is confined to geographic regions. however, rare or private variants have stirred recent attention and may explain heritable diseases and local adaptation. such variants may explain the genetic components of diseases that occur at unusual frequencies in turkey, including behçet’s, familial mediterranean fever, and beta thalassemia. in this paper, we present, for the first time, high coverage whole genome re-sequencing data from individuals from turkey, covering at least % of the genome at 1x, and at least % at 5x. we sampled the genomes from diverse geographical regions in turkey, leading to the identification of novel snvs, novel indels, and a non-redundant total of deletion polymorphisms. it has been shown previously in comparable population genomics studies that even extremely high accuracy snp calling pipelines cannot avoid a small fraction of false-positive snps. these have been shown to be significantly enriched among population specific and rare variants. for instance, a recent study has predicted to have approximately false-positive snps per genome, even if the overall snp calling accuracy is % and the majority of these snps were found to be population specific. to assess the extend to which the population specific variants we detected are false-positives, we used pcr followed by sanger sequencing. indeed, of the variable snv and indel sites that are population specific of them were falsely called as variable sites. this is in contrast with our overall validation results and indicates much higher false-positive rate among the novel variants. however, these results do not change our observation that there are hundreds of thousands of novel variants found in the turkish population.table summary of the turkish genome project 1 2 3 1indels between 1–50 bp. 2deletions >50 bp. 3deletions that are not previously reported in the genomes project. our results showed that genetic variation within turkey clusters with european populations, while showing signatures of admixture from african and east asian populations, consistent with influence of potential north african interactions and altaic admixture. based on our analysis of snps reported in gwas studies that show the highest frequency differences between turkey and european populations, we find snps associated with pigmentation and cholesterol level.  whole genome analysis and variant discovery we recruited healthy volunteers from across turkey. the individuals were included in the study irrespective of their mother-tongue/ethnicity; we refer to them collectively as “turkish”.figure brief summary of the turkish genome project. a map of turkey showing provinces where volunteers were recruited in color. allele frequencies of the snps found in turkish samples and annotated as novel vs. known. functional annotation of the novel snps. we isolated dna from blood samples obtained from each individual, and generated whole genome shotgun sequence data at high coverage ranging between to 48x, using the illumina platform. using bwa and gatk, we identified an average of, snps per individual, and a non-redundant total of, snps, of which were found to be novel when compared to dbsnp v and the genomes project. we observed that of the novel snps found were identified as non-synonymous mutations in protein coding sequence. we also indentified a total of, short indels. additionally, using variationhunter we identified large deletions per individual on average. to estimate the false discovery and false negative rates of our snp calls, we analyzed the same samples using affymetrix snp arrays to genotype for common snps. we then compared the microarray results with the snp calls we generated from wgs. assuming the snp arrays as the gold standard, we estimated the fdr to be at % and fnr as %. common genetic variation in contemporary turkey next we studied the genomes with respect to major patterns of population diversity, structure, and migration, comparing these profiles with those in the genomes project. we found that genome-wide nucleotide diversity in turkey is comparable to that observed in europeans, while lower than in africans or admixed native american populations, and higher than in east asians. even though we expect lower values of π in turkish populations as compared to african populations, it was surprising to find π in european populations equal to or slightly higher than that observed in turkey. we expected that turkish genomes might exhibit significantly higher nucleotide diversity, given turkey’s location at the crossroads of out-of-africa migrations, as well as more recent population movements. still, this result should be taken with caution given differences in snp calling procedures and power between the turkish and genomes project datasets, which could potentially affect estimated diversity levels. to obtain an overview of population relationships, we conducted principal component analyses using individuals randomly selected from each one of the populations within the genomes project, combined with the profiles from turkey. the first two principal components of the combined dataset replicated the global genetic structure identified in earlier studies. within this picture, the genetic variation observed among turkish population clusters with variation observed in european populations. the genome profiles from turkey also overlapped with those of native american populations. this is interesting, because the genetic affinity of native american populations to both east asia and europe has traditionally been attributed to their asian origins and subsequent admixture with europeans. however, this picture has recently been reinterpreted as evidence of shared ancient north eurasian ancestry in native americans and europeans. this result implies that significant ancient north eurasian ancestry might also be found in turkish genetic profiles; this requires further study.figure population genetic relationships between turkey and world-wide populations. the first two principal components of the turkish genome dataset combined with individual population subsets from the genomes project dataset. the first and second components explain 6% and 5% of the total variance, respectively. a population tree based on “treemix” analysis. the populations included are as follows: turkey; toscani in italia; iberian populations in spain; british from england and scotland; finnish from finland; utah residents with northern and western european ancestry; han chinese in beijing, china; japanese in tokyo, japan; han chinese south; yoruba in ibadan, nigeria; luhya in webuye, kenya. populations with high degree of admixture were not included to simplify the analysis. the yoruban population was used to root the tree. in total four migration events were estimated. the weights for the migration events predicted to originate from the east asian branch into current-day turkey was, from the ancestral eurasian branch into the turkey-tuscan clade was, from the african branch into iberia was, from the japanese branch into finland was. the first three principal components of the turkish genome dataset and neighbor-joining trees of the subjects. the upper and lower panels show the same data, except for being colored according to latitude and longitude of subject locations, respectively. the first, second and third principal components each explain ~7% of the total variance. names of the provinces where each sample are recruited from are listed in additional file 1: table s we then estimated the maximum likelihood population tree with migration using the treemix software. the treemix program models populations as having ancestry from multiple parental populations, it can then calculate migration weights. these weights are correlated with the fraction of alleles contributed by a parental population; however, they are not an unbiased predictor of this fraction. in the treemix analysis, turkish samples clustered together with south europe/mediterranean populations: iberians from spain and tuscans from italy. within the worldwide population tree, two of the four predicted migration events involved turkey. the strongest predicted migration event represents admixture from the root of the east asian branch into turkey, which could be reflecting central/south asian population migration. the second migration pattern represents admixture from the root of the eurasian branch to the common node between turkey and italy. the algorithm predicts a parallel branch from africa into spain. these patterns plausibly reflect south mediterranean admixture into north mediterranean, as observed for other populations in the mediterranean basin. the weight for the migration event predicted to originate from the branch ancestral to all eurasians, to the turkey-tuscan clade, was only. in comparison, the weight for the migration event predicted to originate from the branch ancestral to east asia into current-day turkey was. although this implies a major population event from the east to west asia, we note that these weights are not direct estimates of the migration rates. first, the original contributing populations to the ancestral population in turkey are not known. for instance, we do not know the exact genetic relationship between current-day east asian populations and the turkic speakers from central asia who migrated into anatolia about years before present. in fact, hodoglugil and mahley, using hgdp genotyping data, predict that south asian contribution to turkey's population was significantly higher than east/central asian contributions, suggesting that the genetic variation of medieval central asian populations may be more closely related to south asian populations, or that there was continued low level migration from south asia into anatolia. another possibility is ancient north eurasian genetic contribution to both the historical anatolian and east asian populations, which might have been interpreted as migration in this dataset. second, pickrell and pritchard also note that in their simulations, the weights underestimate relatively high admixture proportions. data from more closely related populations coupled with extensive population genetic simulation may eventually allow determining the relative contributions of migration events that shaped population variation in turkey. finally, we investigated possible population structure within turkey. principal component analyses did not reveal any subclustering among the individuals, and we found no evidence for longitudinal or latitudinal divergence. supporting this lack of structure, we found no correlation between genetic distances among subjects and geographic distances among subject locations. one explanation for this observed pattern is the well-documented high-levels of recent population mobility within this geographic region. however, this pattern might not be exclusive to turkey; for example, a neighbor joining tree of tuscan individuals in the genomes project similarly displays a star-like phylogeny, i.e., we observe long terminal branches coalescing at about the same time, indicating lack of structure within the population. genetic variants exhibiting unusual frequency in the turkish samples the assessment of whole genome and exome sequencing data at the population level has shown that due to recent population growth, human populations carry an excess of rare genetic variants, many of which can be functional. indeed, we identified synonymous or non-synonymous rare –i.e., variants that were found in a single turkish chromosome but not in any other population - and synonymous or non-synonymous private –found in more than turkish chromosomes, but not in any other population- single nucleotide variants in the turkish population. as expected, rare snvs are significantly more likely to be non-synonymous than snps observed in multiple populations. we further scrutinized non-synonymous private alleles. interestingly, one of these genes, ccdc was shown to evolve under positive selection in humans, and diverged from neandertals. indeed, the non-synonymous private snp in the turkish population observed at chr19: is a t- > c mutation and homologous to denisovan haplotype at the orthologous site.figure the proportion of synonymous and non-synonymous snps. snps that are found in a single chromosome among the turkish genomes show a significant increase in the proportion of non-synonymous snps to synonymous snps, as compared to all snps observed in the same population. this increase is even more visible among snps that are seen in a single chromosome and are novel. we then explored potentially functional variants at higher or lower frequency in the turkish population relative to the closely related european populations. for this, we compiled the frequencies of published gwas snps among samples resequenced by the genomes project. we then compared the frequencies of these snps in continental populations with what we observed in the turkish population. as expected, the frequency distribution of snps in the turkish population is, by and large, similar to that observed among european populations. to identify potential outliers to this expectation, we compared the frequency distributions of the european and turkish populations and identified snps displaying the highest frequency differences between these populations.figure the allele frequency of gwas snps. the density distribution of allele frequency of gwas snps among world populations. the distribution of gwas snps in turkey is more similar to that of the european population as compared to east asian and african populations, indicating a greater proportion of ancestry sharing between tur and eur. meanwhile, there is a higher proportion of common snps in both tur and eur than asn and afr, which is likely due to ascertainment bias in the gwas studies as described in. the allele frequency of gwas snps between turkish and european populations. the red dots indicate snps in the percentile of the absolute allele frequency distributions between turkish and european populations. rs and rs both affecting herc gene, are in strong linkage disequilibrium and, as such, have identical allele frequencies in european and turkish populations. they are represented as two overlapping dots with allele frequency in turkish population and allele frequencies in european population. the frequency distribution of derived and ancestral alleles for rs in africa europe, asia and americas and turkey. note the increased frequency of the derived allele in the turkish population. among these snps, exist at lower frequencies in turkey compared to europe. we found that both are related to pigmentation, and hair color. pigmentation is a genetic and variable trait in humans, with lighter skin color being associated with better vitamin d absorption, but higher incidence of skin cancer. as such, human pigmentation correlates with latitude and the low frequency of this snp in turkish population as compared to europe may reflect positive selection for these alleles in northern europe and/or selection against the alleles in southern europe and turkey. to our surprise, of the snps that show higher frequency in turkish population as compared to europeans are associated with lower total cholesterol counts. this is particularly interesting, given that the turkish population has indeed been shown to have lower cholesterol than western european populations, including total cholesterol, and high and low density lipoprotein cholesterol measures, while carrying relatively high triglyceride levels. although cholesterol levels are strongly shaped by diet and lifestyle, they are also under the influence of genetic factors. the frequency distribution of one of these snps, associated with total cholesterol counts, is fixed in asian continent and almost fixed among african populations, decreased to slightly above 90% in turkish populations, further decreasing to 49% among europeans. therefore, similar to what is observed for pigmentation related snps, rs is best explained by clinal adaptation or drift patterns. more striking is the frequency distribution of rs another snp associated with total cholesterol count, which reaches almost 70% in turkish populations, but is at lower than 10% frequency in africa and remains a minor allele in other eurasian populations. intriguingly, however, for both cholesterol level related snps, the variant at high frequency in turkey is reported to elevate total cholesterol levels. hence, the contribution of these variants to phenotypic differences between populations needs further study. deletion polymorphisms we used the mrfast aligner together with the variationhunter algorithm to discover deletions in the genomes of the samples resequenced in this study. we merged individual sample-based callsets, then used the genome strip tool to both genotype and in silico validate our discovery callset. in summary, we identified deletions per individual, with a non-redundant total of deletions. to assess novelty, we compared against the genomes project datasets, and found novel deletions per sample on average. we did not find any whole-gene deletions, but 21/ deletions were predicted to delete coding exons where 10/ were predicted in more than one chromosome. we also analyzed the genomic structure at the 17q locus, a region with increased plasticity, where eight different haplotypes are characterized. previous studies have shown that all eight haplotypes show themselves as an inversion polymorphism that exist as two main variants: a direction-orientation haplotype, h prevalent in most human populations and an inverted haplotype, h which predominantly occurs in european populations and presents itself as an 970-kbp inversion. this complex region has been shown to be associated with increased fecundity and an increase in global recombination and it was shown that the h haplotype is enriched in europeans. we have found an allele frequency of % for 17q  h1/h inversion polymorphism in the samples we analyzed, which shows an increase when compared to european populations at 25% allele frequency. one of the samples, sequenced at 34x coverage, was also homozygous for h inversion allele.  although the genomes project published in had aimed to provide a comprehensive map of human genetic variation, it was not complete: populations in the eastern mediterranean and the middle east were missing from that study. in this paper, we present data from high depth whole genome sequencing of individuals from modern day turkey to complement the genomes project in an effort to extend our understanding of normal human genetic variation. we provide the first preliminary genome-wide map of single nucleotide variation, as well as deletion polymorphisms in this population and in western asia. our analyses show that genetic variation of the contemporary turkish population is best described within the context of the southern european/mediterranean gene pool. however, we predict notable genetic sharing between turkey’s population and east asian and african populations. as expected from recent studies, rare and private genetic variation in turkey has presumably more functional impact than variation shared among populations. we further identified snps that were previously associated with diseases that show allele frequency differentiation between turkey and other western european populations. among these, those associated with pigmentation were at lower frequencies in turkey than in europe; meanwhile variants associated with total cholesterol levels were at higher levels in the former. overall, our study improves the framework for population genomics studies in the region, and should incite novel genome-wide association studies in turkey. future studies using larger sample sizes will be able to elucidate population structure and history in more detail. 
a number of variants associated with skin color and total cholesterol levels show frequency differentiation between the turkish populations and european populations. here, we present whole genome sequences of turkish individuals resequenced at high coverage. in addition, we document a significant enrichment of non-synonymous private alleles, consistent with recent observations in european populations. we show that the genetic variation of the contemporary turkish population clusters with south european populations, as expected, but also shows signatures of relatively recent contribution from ancestral east asian populations. however, to date, there have been no studies to assess the genetic variation at the whole genome level using whole genome sequencing. this study provides the first map of common genetic variation from western asian individuals and thus helps fill an important geographical gap in analyzing natural human variation and human migration. furthermore, we have analyzed the 17q inversion polymorphism region and found increased allele frequency of % for h1/h inversion polymorphism when compared to european populations that show about 25% of allele frequency. our data will help develop population-specific experimental designs for studies investigating disease associations and demographic history in turkey.
 turkey is a crossroads of major population movements throughout history and has been a hotspot of cultural interactions. several studies have investigated the complex population history of turkey through a limited set of genetic markers. however, to date, there have been no studies to assess the genetic variation at the whole genome level using whole genome sequencing. here, we present whole genome sequences of turkish individuals resequenced at high coverage.  we show that the genetic variation of the contemporary turkish population clusters with south european populations, as expected, but also shows signatures of relatively recent contribution from ancestral east asian populations. in addition, we document a significant enrichment of non-synonymous private alleles, consistent with recent observations in european populations. a number of variants associated with skin color and total cholesterol levels show frequency differentiation between the turkish populations and european populations. furthermore, we have analyzed the 17q inversion polymorphism region and found increased allele frequency of % for h1/h inversion polymorphism when compared to european populations that show about 25% of allele frequency.  this study provides the first map of common genetic variation from western asian individuals and thus helps fill an important geographical gap in analyzing natural human variation and human migration. our data will help develop population-specific experimental designs for studies investigating disease associations and demographic history in turkey. electronic supplementary material the online version of this article contains supplementary material, which is available to authorized users. issue-copyright-statement© the author 2014 