genetic analysis of phenotypes and diseases has traditionally followed two approaches : family - based linkage analysis and population - based association studies . while in linkage analysis it is the co - segregation of alleles in families that is measured , population - based studies use non - random associations between phenotypes and alleles in populations to identify causative genes . linkage analysis has proven to be immensely successful as a means of identifying genes for a number of single gene diseases with simple mendelian inheritance ( eg see omim database ) . complex diseases are multifactorial , polygenic and often characterised by late age of onset , incomplete penetrance , locus heterogeneity and environmental exposures and , despite significant efforts , have not been amenable to family - based mapping . linkage disequilibrium ( ld ) is an important aspect of genetic association studies and is generated in a population through mutation , selection , drift , non - random mating and admixture . allelic associations due to ld are significant and are correlated with physical distance within small genomic regions but decay over time due to recombination [ 2 - 4 ] . ld - based association studies have been successful in both fine scale mapping   and initial disease gene mapping in homogeneous populations that have undergone recent bottlenecks ( eg hirschsprung disease in mennonites , bardet- beidle syndrome in bedouins ) . allelic associations can result either from direct functional effects of the alleles tested or indirectly through non - random associations between the allele measured and nearby functional alleles . since functional alleles in most genes are still unknown and are indeed an object of the research , ld is an important feature of how genes can be screened for alleles that alter disease risk . thus , there has been substantial focus on the extent of ld across the genome and the definition of statistical methods for disease gene mapping using ld [ 9 - 11 ] . in large cosmopolitan populations , however , ld may be difficult to detect when the mutation is old , since the amount of remaining ld may be small . additionally , false - positive associations due to population stratification are important confounders in ld - based association studies . the process of admixture itself creates ld between all loci , linked and unlinked , that have different allele frequencies in the parental populations . the magnitude of admixture linkage disequilibrium ( ald ) in an admixed population depends on the allele frequency differential between the parental populations , the level of admixture , the admixture dynamics , the time since admixture and the recombination rate between the loci . while ald between unlinked markers decays rapidly ( within two to four generations ) the exponential decrease in ald with genetic distance facilitates the differentiation of ald that is high between markers that are close together and genetically linked , from ald generated at unlinked loci . thus , if the parental populations differ in a trait or disease due to different frequencies of risk alleles , it should be possible to identify the loci containing these alleles using admixture mapping ( am ) [ 12 - 14 ] . the european colonial period that started in the late 1400s brought together in the new world populations that had been geographically isolated , namely , europeans , west africans and native americans . given the recent and common origin of all human populations , this admixture had only a small average effect on the gene pools of these new populations . in other words , for most genomic regions , the pre - colonial ( or parental ) populations had similar allele frequencies and , at these , admixture was of little consequence . at some other loci , however , there had been some change in allele frequency in the time since the separation of parental populations and it is at these loci where admixture has had an important effect . since populations like african americans , african caribbeans and mexican americans were formed in the recent past , allelic associations in these populations that were created by admixture extend over large distances . admixed populations represent a useful resource for mapping complex - disease genes by using this long - range ald , which requires fewer markers to screen the genome than other populations or approaches . understanding the genetic consequences of admixture is important because it can be both a confounding factor and a source of statistical power in gene identification studies . two models of admixture dynamics have been described to represent the extremes of the process by which an admixed population is formed : the continuous gene flow ( cgf ) model and the hybrid isolation ( hi ) model . in the hi model , admixture occurs immediately in a single generation without further contribution from either parental population , hence , ald is generated in a single generation and gradually decays in successive generations through independent assortment and recombination between loci . few false - positive results are thus expected in an association study under the hi model . alternatively , the cgf model represents a situation where admixture occurs at a steady rate in each generation , with contributions from one ( or all ) of the parental populations into the admixed population . ald under the cgf model increases in each generation , since new admixture is constantly occurring . a point will be reached , however ( when the admixture proportion = 0.5 ) , where continued admixture will actually decrease the ald , since added gene flow will result in the conversion of the admixed population into the introgressing parental population . figure 1 shows the amount of ald expected under these two models for linked and unlinked loci . for both models , association between markers simulation studies have shown that populations that have a demographic history more consistent with the cgf model of admixture retain ald over larger chromosomal regions and show significant associations between unlinked marker loci . while associations between unlinked markers could potentially lead to false - positives , conditioning upon parental admixture allows the distinction between associations arising due to true linkage and those due to cgf stratification to be made , thereby providing greater power for detecting ald over larger chromosomal distances . the amount of admixture linkage disequilibrium ( ald ) expected under the continuous gene flow ( cgf ) and hybrid isolation ( hi ) models of admixture for unlinked loci and loci linked at 5 cm . the results shown are for two loci with  = 0.54 and 0.49 , and with 50 per cent admixture in the first generation for the hi model and 1.9 per cent admixture for 36 generations under the cgf model ( equivalent to 50 per cent total ) . ald under the hi model decreases for both linked and unlinked loci , whereas ald under the cgf model for both linked and unlinked loci increases initially and then decreases ( adapted from pfaff et al . , 2001 ) there are several ways in which admixture can be an important resource in the elucidation of genetic factors that contribute to the risk of common disease . common diseases often have environmental components to their risk , and the clinical phenotype results from currently unknown interactions between environmental factors and underlying genotypes . decomposing the sources of variation it is possible to distinguish between the genetic and environmental explanations for ethnic differences in disease risk ( and investigating the mode of inheritance ) , by studying the relationship of disease risk to individual admixture [ 14,17 - 19 ] . for example , recent studies have demonstrated a strong relationship between proportional west african ancestry and the risk of systemic lupus erythematosus in admixed populations in trinidad . several common diseases ( eg hypertension , diabetes , obesity , prostate cancer and osteoporosis ) have differences in risk among population groups ( see table 1 ) . in situations where these differences have a genetic basis , genes underlying these differences can be identified by testing for locus ancestry by conditioning on parental admixture . as detailed by shriver et al . , this approach has a greater statistical power than family linkage studies for mapping polygenic traits . estimates of biogeographical ancestry ( bga ) , the proportional ancestry levels of an individual , can be used in conjunction with measured environmental effects for investigating the roles of environmental and inherited risks underlying complex traits [ 18 - 20 ] . it is important to recognise that associations between individual admixture and disease risk might reflect correlations between bga and socio - cultural variables and exposures . for example , hypothetically , if bga and years of education were to be correlated , hypertension might be correlated with bga , even though the causal risk factor was years of education or vice versa . diseases with possible genetic components based on ethnic differences in disease rates and hence amenable to admixture mapping admixture - based methods rely on using suitable markers and estimates of allele frequencies from appropriately identified parental populations . since ald is fairly new and extends over larger distances , fewer markers are required for am studies . markers informative for ancestry have been used in several contexts and have been referred to as ' ideal , '   ' private '   and ' unique ' . informativeness of such markers can be measured as the allele frequency differential (  ) , which is the absolute value of the difference of a particular allele between populations . microsatellites and insertion / deletion polymorphisms with  > 0.3 were recently called ' ethnic - difference markers ' ( edms )   suitable for mapping by admixture linkage disequilibrium ( mald ) . additionally , markers with high  and very high log likelihood allelic ratio ( llar ) between populations have been designated ' population specific alleles ' ( psas ) . this report followed from earlier work where markers with large allele frequency difference were identified to be appropriate for admixture studies , and most ( > 95 per cent ) of the arbitrarily identified biallelic markers had  < 50 per cent . thus , the authors proposed that ideal psas should have  > 50 per cent and also indicated that for multiallelic loci , a composite  could be estimated as one half the summation of the absolute value of allelic frequency differences for all alleles at that locus . it has also been shown that markers with lower  values , of approximately 30 per cent , can provide up to 80 per cent power for detecting associations at distances of 5 cm with a large enough sample size ( n = 1,000 ) . pfaff et al . , suggested referring to markers suitable for admixture studies as ' ancestry informative markers ' ( aims ) , given that the central feature of these markers is the ancestry information content ( f ) . the present authors agree that the term aim more accurately describes these markers and does so using language that is less likely to be misunderstood and misinterpreted . marker information content ' f ' denotes the locus - specific fst and is a value representative of the differentiation between two populations at a single locus . simulation studies for estimating the information content of markers with varying levels of f have shown that for 1,000 markers with average information content for ancestry at 40 per cent between two ancestral subpopulations , approximately 80 per cent of the information about ancestry can be extracted from an initial genome screen . after initial identification of regions showing admixture , more markers can be typed in these regions to increase extraction of information to nearly 100 per cent . it is well established , however , that only 5 - 15 per cent of the total genetic variation results from differences among human populations [ 30 - 32 ] . moreover , most alleles are shared between populations , and alleles common in one population are also common in other populations . thus , most genetic markers are unaffected by admixture and it is imperative to choose markers that show high levels of d ( and f ) between the parental populations . recent studies by several groups have focused on identifying panels of markers suitable for admixture studies . one notable study screened 744 microsatellite markers for composite d values and llar in four different populations and identified a genome spanning set of 315 markers ( average spacing 10 cm ,   0.3 ) for mapping in african americans and 214 markers ( average spacing of 16 cm ,   0.25 ) for mapping in hispanics . a dna pooling method was used to identify 151 aims ( microsatellites and short insertion / deletion polymorphisms ) , with  > 0.3 for mapping in mexican american populations to distinguish between european - american and native - american contributions . ninety - seven aims were identified for mapping in african - american populations   that show limited variation within africa . additional resources are available for obtaining marker frequency , and genotype and haplotype information , from the snp consortium ( tsc ; http://snp.cshl.org ) , the national center for biotechnology information 's ' dbsnp ' website ( http://www.ncbi.nlm.nih.gov/snp ) , the marshfield database ( http://research.marshfieldclinic.org/genetics/default.htm ) and the ongoing hapmap project . since the amount of ald created is proportional to the level of admixture in a population , it is important briefly to review studies on admixture levels across populations . those populations that are likely to be useful for admixture studies include african americans , mexican americans , cubans and puerto ricans in the usa , african caribbeans , various latin american populations , various groups in central and south america and the caribbean islands , anglo indians in india and ' coloured ' populations of south africa . various statistical approaches have been used to estimate admixture proportions in these populations and have been reviewed in detail elsewhere . these include a least squares method , a weighted least squares method   and likelihood methods . a recent review of admixture studies and admixture proportions of various latin american populations is provided by sans . african americans are a well - studied group with substantial european and west african contributions and a smaller native american contribution . a survey of current literature indicates that european admixture ranges from 3.5 per cent in the gullah sea islanders of south carolina , to 28 per cent in new orleans . admixture estimates in african - american populations can be highly variable across the usa , which is likely to reflect local variation in the demographic histories and social norms . us hispanics form a complex socio - political conglomerate including puerto ricans , cubans , spanish americans , mexican americans . the proportional contributions from parental europeans are estimated to be the largest , followed by a substantial native american ancestry and varying amounts of west african ancestry . in a sample of mexican americans from arizona , the admixture estimates obtained using a weighted least squares method showed 29  4 per cent native american , 68  5 per cent european and 3  2 per cent west african contribution . a recent study reports the following estimates for a hispanic population from the san luis valley , colorado : 62.7  2.1 per cent european , 34.1  1.9 per cent native american , 3.2  1.5 per cent west african . in puerto ricans from new york city , the estimates obtained were 53.3  2.8 per cent european , 29.1  2.3 per cent west african , 17.6  2.4 per cent native american . in a separate mexican - american population sample from california , european ancestry was estimated to be 60 per cent and native american contribution was estimated at 40 per cent . from these results , it is evident that , when studying any new admixed population sample , it is important to accurately determine the proportional contributions and not to rely on previously obtained estimates from a similar population . additionally , it is instructive to have information on the levels of stratification related to admixture that are present in the population under consideration . traits and diseases more prevalent in one population than in others are amenable to admixture analysis and some examples are listed in table 1 . most of the diseases shown in this table have a complex aetiology affected by multiple genes and environmental factors . earlier studies   focused on admixed populations as units of analysis in exploring relationships between ancestry and phenotypes . these authors showed that non - insulin - dependent ( type 2 ) diabetes mellitus prevalence is correlated with admixture proportions among a selection of populations with varying levels of native american ancestry . data like these provide compelling evidence for frequency differences in risk modifying alleles , but such data have not been collected for many diseases . another related approach is to test for individual admixture - phenotype correlations within an admixed population . correlations between ancestry and phenotypes have been detected and reported by various authors [ 14,17 - 19,44,45,47 ] . a prerequisite for testing ancestry / phenotype correlations is the presence of stratification related to admixture , which will be evident in variation in individual ancestry levels . figure 2 shows the distribution of bga estimates from three examples of hispanic population samples , puerto ricans from new york , mexicans from tlapa , mexico and hispanics from the san luis valley , colorado . substantial variation is observed in all three samples . with the san luis valley group , more variability is observed on the european - native american axis , while the new york group is more variable on the european - west african axis . following the argument of chakraborty and weiss , admixture proportions should be correlated with diseases / traits that differ in populations due to underlying genetic differences . in each of these population samples , strong positive correlation was observed between individual ancestry and skin pigmentation measured as melanin index ' m ' or lightness index ' l ' ( figures 3a , 3b and 3c ) . a significant negative correlation was also observed between the proportion of west african ancestry and bone mineral density ( bmd ) in the puerto rican sample . proportion west african ancestry and skin pigmentation ( measured as melanin index ) in individuals is also correlated in african americans from washington dc and african caribbeans from the uk , but not in european americans from state college , pennsylvania ( figure 4 ) . recently , correlations have been observed between proportion west african ancestry and lower insulin sensitivity , higher fasting insulin and acute insulin response to glucose in a combined sample of african - american and european - american children . in a separate sample of african - american females , west african admixture is associated with body mass index , fat mass , fat - free mass and bmd . it is important to keep in mind that ancestry - pheno - type correlations are dependent on both the existence of functional alleles at different frequencies in parental populations , and significant stratification related to admixture . although most admixed populations tested to date are structured , there is variation in the amount of stratification present , and this structure should be tested for explicitly when investigating a new population . each vertex represents a parental population , which for this plot are europeans , west africans and native americans . the three populations shown are hispanics from the san luis valley ( blank circles ) , puerto ricans from new york city ( grey diamonds ) and mexicans from tlapa , mexico ( grey triangles ) ( adapted from bonilla , 2003 ) the relationship between proportional ancestry and skin pigmentation in three hispanic populations . for all populations , proportional ancestry was estimated using the maximum likelihood ( ml ) method ( adapted from bonilla , 2003 ) . ( a ) percent native american ancestry versus lightness index ( l ) in hispanics from the san luis valley , colorado ( ancestry estimated using 22 aims ) . ( b ) percent native american ancestry versus melanin index in mexicans from tlapa , mexico ( ancestry estimates using 29 aims ) . ( c ) percent african ancestry versus melanin index ( m ) in puerto ricans from new york city ( ancestry estimated using 35 aims ) the relationship between percent african ancestry and skin pigmentation in three populations . percent african ancestry ( obtained using 34 aims and calculated by the maximum likelihood ( ml ) method ) and the melanin index ( m ) are shown for three populations , european americans from state college , pennsylvania ( diamonds ) , african americans from washington , dc and state college , pennsylvania ( squares ) and african caribbeans from britain ( triangles ) . 2003 ) theoretical and experimental studies have explored the parameters that characterise and affect admixture studies . the acronym mald was proposed   to designate the mapping method proposed originally by chakraborty and weiss , which exploited the long range allelic associations created through ald . parameters critical for mald include the genetic distance between markers and disease locus (  ) ; number of generations since admixture ( t ) ; proportion of admixture ( m ) from one parental population ; the allele frequency differential (  ) between parental populations ; and sample size ( n ) . simulation studies suggest that sample sizes of 200 - 300 patients , typed for 200 - 300 evenly spaced markers , each having allele frequency differentials > 0.3 , have a > 95 per cent chance of locating the causative gene , when there has been no new admixture from the parental population in the last four generations and no other sources of population structure or sample heterogeneity . other approaches proposed for using admixture include a method based on the transmission disequilibrium test ( tdt )   that assesses excess transmission of alleles derived from high - risk ancestors to affected offspring of parents who are heterozygous at the marker locus , containing one allele from each of two ancestral populations . a second tdt - based likelihood approach was developed that compared the transmission of haplotypes with non - transmission in affected offspring in an admixed population following a multipoint method . it obtained a likelihood statistic to determine the significance of various models under different scenarios . one fundamental limitation of mald as initially described and in its early extensions , is the effects of stratification on causing false - positive association . marker data at all loci are combined to estimate ancestry of alleles at each locus . when allelic ancestry at marker loci is known , this approach is analogous to a linkage analysis , hence the term am is more appropriate than mald for describing this method and to distinguish it from ld approaches . the underlying variation in ancestry of chromosomes of mixed descent is modelled to extract all of the information about linkage that is generated by admixture . for example , where a locus is assumed to account for variation in skin pigmentation between two parental groups , eg west africans and europeans , individuals can be classified according to whether they have 0 , 1 or 2 alleles of west african descent at this locus . by comparing these three groups for mean pigmentation level , holding all other factors constant , variation in pigmentation can be observed depending upon the number of alleles of west african ancestry in an individual . controlling for parental admixture eliminates association of the trait with ancestry at unlinked loci . by removing the background effects of ancestry , it is possible to observe the locus - specific effects on a trait / disease . allelic ancestry at a locus is inferred from the marker by using the conditional probability of each allelic state given the ancestry - specific allele frequencies . a complex hierarchical model with many nuisance parameters this is implemented using the admixmap program ( at http://www.lshtm.ac.uk/eph.eu/geneticepidemiologygroup/htm ) , which follows a bayesian approach with markov chain simulation , and incorporates the admixture of each individual 's parents and the random variation of ancestry on chromosomes inherited from each of the parents in the model . variation in individual admixture introduces population stratification , which in turn can inflate the number of significant associations that are observed   and is a potential confounder in association studies [ 29,57 - 59 ] . various statistical approaches have been developed to detect and control for stratification within a population sample [ 14,15,17,42,60 - 62 ] . for example , the dt / d0 test examines the relationship between the observed ld and the predicted ald between unlinked marker pairs for detecting structure within the sample . using individual ancestry as a conditioning variable in analysis of variance tests the bayesian approaches implemented by mckeigue et al . and pritchard et al . offer an advantage over classical maximum likelihood based methods   by allowing for missing genotype and ancestry data and modelling admixture hierarchically . methods have been developed to control for parental admixture   and to account for uncertain bga estimation . admixture - based methods rely on using suitable markers and estimates of allele frequencies from appropriately identified parental populations . since ald is fairly new and extends over larger distances , fewer markers are required for am studies . markers informative for ancestry have been used in several contexts and have been referred to as ' ideal , '   ' private '   and ' unique ' . informativeness of such markers can be measured as the allele frequency differential (  ) , which is the absolute value of the difference of a particular allele between populations . microsatellites and insertion / deletion polymorphisms with  > 0.3 were recently called ' ethnic - difference markers ' ( edms )   suitable for mapping by admixture linkage disequilibrium ( mald ) . additionally , markers with high  and very high log likelihood allelic ratio ( llar ) between populations have been designated ' population specific alleles ' ( psas ) . this report followed from earlier work where markers with large allele frequency difference were identified to be appropriate for admixture studies , and most ( > 95 per cent ) of the arbitrarily identified biallelic markers had  < 50 per cent . thus , the authors proposed that ideal psas should have  > 50 per cent and also indicated that for multiallelic loci , a composite  could be estimated as one half the summation of the absolute value of allelic frequency differences for all alleles at that locus . it has also been shown that markers with lower  values , of approximately 30 per cent , can provide up to 80 per cent power for detecting associations at distances of 5 cm with a large enough sample size ( n = 1,000 ) . pfaff et al . , suggested referring to markers suitable for admixture studies as ' ancestry informative markers ' ( aims ) , given that the central feature of these markers is the ancestry information content ( f ) . the present authors agree that the term aim more accurately describes these markers and does so using language that is less likely to be misunderstood and misinterpreted . marker information content ' f ' denotes the locus - specific fst and is a value representative of the differentiation between two populations at a single locus . simulation studies for estimating the information content of markers with varying levels of f have shown that for 1,000 markers with average information content for ancestry at 40 per cent between two ancestral subpopulations , approximately 80 per cent of the information about ancestry can be extracted from an initial genome screen . after initial identification of regions showing admixture , more markers can be typed in these regions to increase extraction of information to nearly 100 per cent . it is well established , however , that only 5 - 15 per cent of the total genetic variation results from differences among human populations [ 30 - 32 ] . moreover , most alleles are shared between populations , and alleles common in one population are also common in other populations . thus , most genetic markers are unaffected by admixture and it is imperative to choose markers that show high levels of d ( and f ) between the parental populations . recent studies by several groups have focused on identifying panels of markers suitable for admixture studies . one notable study screened 744 microsatellite markers for composite d values and llar in four different populations and identified a genome spanning set of 315 markers ( average spacing 10 cm ,   0.3 ) for mapping in african americans and 214 markers ( average spacing of 16 cm ,   0.25 ) for mapping in hispanics . a dna pooling method was used to identify 151 aims ( microsatellites and short insertion / deletion polymorphisms ) , with  > 0.3 for mapping in mexican american populations to distinguish between european - american and native - american contributions . ninety - seven aims were identified for mapping in african - american populations   that show limited variation within africa . additional resources are available for obtaining marker frequency , and genotype and haplotype information , from the snp consortium ( tsc ; http://snp.cshl.org ) , the national center for biotechnology information 's ' dbsnp ' website ( http://www.ncbi.nlm.nih.gov/snp ) , the marshfield database ( http://research.marshfieldclinic.org/genetics/default.htm ) and the ongoing hapmap project . since the amount of ald created is proportional to the level of admixture in a population , it is important briefly to review studies on admixture levels across populations . those populations that are likely to be useful for admixture studies include african americans , mexican americans , cubans and puerto ricans in the usa , african caribbeans , various latin american populations , various groups in central and south america and the caribbean islands , anglo indians in india and ' coloured ' populations of south africa . various statistical approaches have been used to estimate admixture proportions in these populations and have been reviewed in detail elsewhere . these include a least squares method , a weighted least squares method   and likelihood methods . a recent review of admixture studies and admixture proportions of various latin american populations is provided by sans . african americans are a well - studied group with substantial european and west african contributions and a smaller native american contribution . a survey of current literature indicates that european admixture ranges from 3.5 per cent in the gullah sea islanders of south carolina , to 28 per cent in new orleans . admixture estimates in african - american populations can be highly variable across the usa , which is likely to reflect local variation in the demographic histories and social norms . us hispanics form a complex socio - political conglomerate including puerto ricans , cubans , spanish americans , mexican americans . the proportional contributions from parental europeans are estimated to be the largest , followed by a substantial native american ancestry and varying amounts of west african ancestry . in a sample of mexican americans from arizona , the admixture estimates obtained using a weighted least squares method showed 29  4 per cent native american , 68  5 per cent european and 3  2 per cent west african contribution . a recent study reports the following estimates for a hispanic population from the san luis valley , colorado : 62.7  2.1 per cent european , 34.1  1.9 per cent native american , 3.2  1.5 per cent west african . in puerto ricans from new york city , the estimates obtained were 53.3  2.8 per cent european , 29.1  2.3 per cent west african , 17.6  2.4 per cent native american . in a separate mexican - american population sample from california , european ancestry was estimated to be 60 per cent and native american contribution was estimated at 40 per cent . as with african - american populations , there is substantial variation across populations . from these results , it is evident that , when studying any new admixed population sample , it is important to accurately determine the proportional contributions and not to rely on previously obtained estimates from a similar population . additionally , it is instructive to have information on the levels of stratification related to admixture that are present in the population under consideration . traits and diseases more prevalent in one population than in others are amenable to admixture analysis and some examples are listed in table 1 . most of the diseases shown in this table have a complex aetiology affected by multiple genes and environmental factors . earlier studies   focused on admixed populations as units of analysis in exploring relationships between ancestry and phenotypes . these authors showed that non - insulin - dependent ( type 2 ) diabetes mellitus prevalence is correlated with admixture proportions among a selection of populations with varying levels of native american ancestry . data like these provide compelling evidence for frequency differences in risk modifying alleles , but such data have not been collected for many diseases . another related approach is to test for individual admixture - phenotype correlations within an admixed population . correlations between ancestry and phenotypes have been detected and reported by various authors [ 14,17 - 19,44,45,47 ] . a prerequisite for testing ancestry / phenotype correlations is the presence of stratification related to admixture , which will be evident in variation in individual ancestry levels . figure 2 shows the distribution of bga estimates from three examples of hispanic population samples , puerto ricans from new york , mexicans from tlapa , mexico and hispanics from the san luis valley , colorado . substantial variation is observed in all three samples . with the san luis valley group , more variability is observed on the european - native american axis , while the new york group is more variable on the european - west african axis . following the argument of chakraborty and weiss , admixture proportions should be correlated with diseases / traits that differ in populations due to underlying genetic differences . in each of these population samples , strong positive correlation was observed between individual ancestry and skin pigmentation measured as melanin index ' m ' or lightness index ' l ' ( figures 3a , 3b and 3c ) . a significant negative correlation was also observed between the proportion of west african ancestry and bone mineral density ( bmd ) in the puerto rican sample . proportion west african ancestry and skin pigmentation ( measured as melanin index ) in individuals is also correlated in african americans from washington dc and african caribbeans from the uk , but not in european americans from state college , pennsylvania ( figure 4 ) . recently , correlations have been observed between proportion west african ancestry and lower insulin sensitivity , higher fasting insulin and acute insulin response to glucose in a combined sample of african - american and european - american children . in a separate sample of african - american females , west african admixture is associated with body mass index , fat mass , fat - free mass and bmd . it is important to keep in mind that ancestry - pheno - type correlations are dependent on both the existence of functional alleles at different frequencies in parental populations , and significant stratification related to admixture . although most admixed populations tested to date are structured , there is variation in the amount of stratification present , and this structure should be tested for explicitly when investigating a new population . each vertex represents a parental population , which for this plot are europeans , west africans and native americans . the three populations shown are hispanics from the san luis valley ( blank circles ) , puerto ricans from new york city ( grey diamonds ) and mexicans from tlapa , mexico ( grey triangles ) ( adapted from bonilla , 2003 ) the relationship between proportional ancestry and skin pigmentation in three hispanic populations . for all populations , proportional ancestry was estimated using the maximum likelihood ( ml ) method ( adapted from bonilla , 2003 ) . ( a ) percent native american ancestry versus lightness index ( l ) in hispanics from the san luis valley , colorado ( ancestry estimated using 22 aims ) . ( b ) percent native american ancestry versus melanin index in mexicans from tlapa , mexico ( ancestry estimates using 29 aims ) . ( c ) percent african ancestry versus melanin index ( m ) in puerto ricans from new york city ( ancestry estimated using 35 aims ) the relationship between percent african ancestry and skin pigmentation in three populations . percent african ancestry ( obtained using 34 aims and calculated by the maximum likelihood ( ml ) method ) and the melanin index ( m ) are shown for three populations , european americans from state college , pennsylvania ( diamonds ) , african americans from washington , dc and state college , pennsylvania ( squares ) and african caribbeans from britain ( triangles ) . theoretical and experimental studies have explored the parameters that characterise and affect admixture studies . the acronym mald was proposed   to designate the mapping method proposed originally by chakraborty and weiss , which exploited the long range allelic associations created through ald . parameters critical for mald include the genetic distance between markers and disease locus (  ) ; number of generations since admixture ( t ) ; proportion of admixture ( m ) from one parental population ; the allele frequency differential (  ) between parental populations ; and sample size ( n ) . simulation studies suggest that sample sizes of 200 - 300 patients , typed for 200 - 300 evenly spaced markers , each having allele frequency differentials > 0.3 , have a > 95 per cent chance of locating the causative gene , when there has been no new admixture from the parental population in the last four generations and no other sources of population structure or sample heterogeneity . other approaches proposed for using admixture include a method based on the transmission disequilibrium test ( tdt )   that assesses excess transmission of alleles derived from high - risk ancestors to affected offspring of parents who are heterozygous at the marker locus , containing one allele from each of two ancestral populations . a second tdt - based likelihood approach was developed that compared the transmission of haplotypes with non - transmission in affected offspring in an admixed population following a multipoint method . it obtained a likelihood statistic to determine the significance of various models under different scenarios . one fundamental limitation of mald as initially described and in its early extensions , is the effects of stratification on causing false - positive association . marker data at all loci are combined to estimate ancestry of alleles at each locus . when allelic ancestry at marker loci is known , this approach is analogous to a linkage analysis , hence the term am is more appropriate than mald for describing this method and to distinguish it from ld approaches . the underlying variation in ancestry of chromosomes of mixed descent is modelled to extract all of the information about linkage that is generated by admixture . for example , where a locus is assumed to account for variation in skin pigmentation between two parental groups , eg west africans and europeans , individuals can be classified according to whether they have 0 , 1 or 2 alleles of west african descent at this locus . by comparing these three groups for mean pigmentation level , holding all other factors constant , variation in pigmentation can be observed depending upon the number of alleles of west african ancestry in an individual . controlling for parental admixture eliminates association of the trait with ancestry at unlinked loci . by removing the background effects of ancestry , it is possible to observe the locus - specific effects on a trait / disease . allelic ancestry at a locus is inferred from the marker by using the conditional probability of each allelic state given the ancestry - specific allele frequencies . a complex hierarchical model with many nuisance parameters this is implemented using the admixmap program ( at http://www.lshtm.ac.uk/eph.eu/geneticepidemiologygroup/htm ) , which follows a bayesian approach with markov chain simulation , and incorporates the admixture of each individual 's parents and the random variation of ancestry on chromosomes inherited from each of the parents in the model . variation in individual admixture introduces population stratification , which in turn can inflate the number of significant associations that are observed   and is a potential confounder in association studies [ 29,57 - 59 ] . various statistical approaches have been developed to detect and control for stratification within a population sample [ 14,15,17,42,60 - 62 ] . for example , the dt / d0 test examines the relationship between the observed ld and the predicted ald between unlinked marker pairs for detecting structure within the sample . using individual ancestry as a conditioning variable in analysis of variance tests , it is possible to eliminate association of the trait with unlinked alleles . offer an advantage over classical maximum likelihood based methods   by allowing for missing genotype and ancestry data and modelling admixture hierarchically . methods have been developed to control for parental admixture   and to account for uncertain bga estimation . several theoretical and practical studies indicate that am approaches promise to be suitable for identifying genes causing complex diseases . methodological advancements have been made to offset the potential problems arising from association between unlinked loci by conditioning on parental admixture , and to detect and correct for population stratification . use of bayesian am   can take into consideration various uncertainties , including missing data values for estimating admixture proportions , and can overcome problems arising out of mis - specification of parental allele frequencies and promises to be an effective tool for admixture studies . this method , which is different from the classical disequilibrium - based approach that is more commonly used , is perhaps more suitable for disease gene mapping in admixed populations and has already been successfully used for mapping . table 2 summarises recent studies showing associations between ancestry and phenotypes / diseases and instances where am was used to identify genes . currently , the primary impediment to exhaustive am genome scans is the lack of verified aim panels . sufficient numbers of markers are available as candidate aims , but effort and resources are required to confirm these markers and to generate accurate parental allele frequencies . it seems inevitable that more such studies will be carried out in the near future to utilise the immense potential of this approach . diseases showing ancestry - phenotype correlation a = r ; b = risk ratio ; c = rank - order correlation . we thank dr paul mckeigue and dr esteban parra for helpful discussions on the subject . we also acknowledge helpful comments from an unknown reviewer . this work was supported in part by grants from nih