Admixture estimation using skin reflectance data

Several different methods are suggested for the estimation of admixture proportions in hybrid populations based on skin reflectance data. These methods are applied to hybrid populations of known ancestry and yield results generally quite similar to those expected based on a simple genetic model. Results indicate the usefulness of these methods in hybridization studies and in the development and refinement of models of the genetics of skin color.     

Admixture and skin color in the transplanted Tlaxcaltecan population of Saltillo,Mexico

Ethnohistoric accounts and serological analyses have documented the genetic effects of transplantation and admixture of several subpopulations of Tlaxcaltecans in Saltillo, Mexico. Interpopulational affinities are assessed using skin reflectance readings taken at the upper inner arm site with a Photovolt Model 670 reflectance spectrophotometer for these groups, focusing on the barrios of La Minita and Chamizal. Genetic distance analyses based on blood groups and skin reflectance data are in close agreement and reflect differential rates of admixture for these groups. Admixture estimates for a dihybrid model (Indian-Spanish) were derived from skin reflectances and show a slight tendency for underestimation of Spanish admixture when compared to blood group estimates. Application of a trihybrid model incorporating West African admixture shows similar estimates based on blood groups, immunoglobulins, and skin color.     

Skin color variation in eastern Nepal

The purpose of this paper is to provide skin color data on several endogamous groups of eastern Nepal and to demonstrate genetic microdifferentiation in skin color. Skin reflectance measures were taken at the upper inner arm and forehead sites, using the British DSL Model 99 Reflectance Spectrophotometer fitted with blue, green, and red filters. Measurements on 484 males representing six endogamous groups (Jirel, Sunwar, Sherpa, Tamang, Brahman, Chetri) were utilized. After adjusting for group-specific age effects, multivariate likelihood ratio permutation tests were used to assess ethnic differences in skin reflectance means and covariance matrices. Ethnic group membership had a highly significant effect on skin color at the upper inner arm site and at the forehead site. Differential tanning responses among groups were also detected and may represent the influence of genotype-environment interaction on reflectance traits. Mahalanobis distance analysis revealed patterns of microdifferentiation that are inconsistent with oral historical accounts. Little support was found for the ethnohistorical belief that Jirels are a hybrid group descended from Sunwars and Sherpas, even though this scenario is supported by linguistic, anthropometric, and dermatoglyphic data. We suggest that while reflectometric studies of skin pigmentation may be useful in assessing the macrodifferentiation of human populations, the use of skin color in differentiation studies at the local population level needs to be carefully evaluated.     

Development of two multiplex mini-sequencing panels of ancestry informative SNPs for studies in Latin Americans: an application to populations of the State of Minas Gerais (Brazil)

Admixture occurs when individuals from parental populations that have been isolated for hundreds of generations form a new hybrid population. Currently, interest in measuring biogeographic ancestry has spread from anthropology to forensic sciences, direct-to-consumers personal genomics, and civil rights issues of minorities, and it is critical for genetic epidemiology studies of admixed populations. Markers with highly differentiated frequencies among human populations are informative of ancestry and are called ancestry informative markers (AIMs). For tri-hybrid Latin American populations, ancestry information is required for Africans, Europeans and Native Americans. We developed two multiplex panels of AIMs (for 14 SNPs) to be genotyped by two mini-sequencing reactions, suitable for investigators of medium-small laboratories to estimate admixture of Latin American populations. We tested the performance of these AIMs by comparing results obtained with our 14 AIMs with those obtained using 108 AIMs genotyped in the same individuals, for which DNA samples is available for other investigators. We emphasize that this type of comparison should be made when new admixture/population structure panels are developed. At the population level, our 14 AIMs were useful to estimate European admixture, though they overestimated African admixture and underestimated Native American admixture. Combined with more AIMs, our panel could be used to infer individual admixture. We used our panel to infer the pattern of admixture in two urban populations (Montes Claros and Manhua?u) of the State of Minas Gerais (southeastern Brazil), obtaining a snapshot of their genetic structure in the context of their demographic history.     

汉族和藏族的皮肤反射系数分析

人类的肤色是在遗传和环境因素的共同作用下形成的。最近在人类复杂性状基因定位中,统计学和遗传学研究方法的发展,使得肤色相关基因有可能利用这些方法来甄别。而且,有了Photovolt ColorWalk色度计等便携的新式光谱反射系数测量工具,研究者可以方便准确地测量大量人群的皮肤反射系数作为遗传学研究用的人类表型性状。我们衣物Photovolt ColorWark测试了372人的一个汉族群体和274人的一个藏族群体的上臂内侧不受阳光照射的皮肤反射系数,以建立反射系数测量的基准数据。我们调查了年龄、性别、居住地纬度、种族等不同因素对皮肤反射系数的影响,也调查了皮肤反射系数的正态分布。在这些研究结果的基础上我们设计了皮肤反射系数遗传学研究的策略。     

Skin reflectance relationships with temperature and skinfolds

Skin reflectance measurements were taken with six filters at a site on the medial aspect of the upper arm (underarm) prior to and following topical application of a cold compress. Skinfolds were measured at the underarm and triceps sites. The experiment was designed to test for effects of skin surface temperature and subcutaneous fat variations on skin color as determined by reflectometry. Topical cold-induced erythema of the skin produced marked declines in % reflectance at the shorter visible wavelengths over the range of violet, blue, and green, and only slight declines in % reflectance at the longer visible wavelengths (red range). This is consistent with the observation from past work that there is little hemoglobin absorptance at the red end of the visible spectrum. A positive relationship between the change in % reflectance following topical cold application and underarm skinfold was recorded. Hence, the thickness of fat deposits may contribute to variation in skin reflectance. Since only large temperature differences influenced skin reflectance measurements, the need is not great for fieldworkers to control for surface temperature at the underarm site during skin reflectance survey.     

The influence of hypoxia on the thermal sensitivity of skin colouration in the bearded dragon, Pogona vitticeps

One physiological mechanism used by reptiles to remain within thermal optima is their ability to reversibly alter skin colour, imparting changes in overall reflectance, and influencing the rate of heat gain from incident radiation. The ability to lighten or darken their skin is caused by the movement of pigment within the dermal chromatophore cells. Additionally, lizards, as ectotherms, significantly lower their preferred body temperatures when experiencing stressors such as hypoxia. This decrease in preferred temperature has been proposed to be the result of a downward adjustment of the thermal set-point, the temperature around which the body temperature is typically defended. We tested the hypothesis that lightening of the skin in lizards would be modified by hypoxia in a manner consistent with the known reduction in preferred temperatures. Skin colouration values of the dorsal skin of bearded dragons were analysed at three different levels of oxygen (20.8, 9.9 and 4.9 kPa) and at temperatures spanning the preferred temperature range (30, 32, 34, 36, 38 and 40 C). Hypoxic lizards lightened their skin at lower ambient temperatures more than normoxic ones, and in an oxygen-dependent fashion. The orchestrated adjustment of skin reflectance suggests that this physiological trait is being regulated at a new and lower set-point. Evidence from this study demonstrates that skin colouration plays a role in body temperature regulation and that the reduction in temperature set-point so prevalent in hypoxia is also manifested in this physiological trait.     

Skin colorimetry in Belize. II. Inter- and intra-population variation

Skin colorimetry readings taken in Belize, Central America (formerly British Honduras) with the two most commonly used portable reflectometers reveal significant differences in mean reflectance between Garifuna (Black Caribs) and Creoles, and between Garifuna in two settlements. These differences are related to variation in African, Indian, and European admixture, as estimated from serological markers. Sex differences are not evident in univariate comparisons, but females are significantly lighter than males in multivariate analyses of variance. Polynomial age trends exist in some groups for certain variables, but account for a very small amount of the variation in skin color within these groups.     

Cytonuclear Theory for Haplodiploid Species and X-Linked Genes. I. Hardy-Weinberg Dynamics and Continent-Island, Hybrid Zone Models

We develop models that describe the cytonuclear structure for either a cytoplasmic and nuclear marker in a haplodiploid species or a cytoplasmic and X-linked marker in a diploid species. Sex-specific disequilibrium statistics that summarize nonrandom cytonuclear associations in such systems are defined, and their basic Hardy-Weinberg dynamics and admixture formulae are delimited. We focus on the context of hybrid zones and develop continent-island models whereby individuals from two genetically differentiated source populations migrate into and mate within a single zone of admixture. We examine the effects of differential migration of the sexes, assortative mating by pure type females, and census time (relative to mating and migration), as well as special cases of random mating and migration subsumed under the general models. We show that pure type individuals and nonzero cytonuclear disequilibria can be maintained within a hybrid zone if there is continued migration from both source populations, and that females generally have a greater influence over these cytonuclear variables than males. The resulting theoretical framework can be used to estimate the rates of assortative mating and sex-specific gene flow in hybrid zones and other zones of admixture involving haplodiploid or sex-linked cytonuclear data.     

A coalescent-based estimator of admixture from DNA sequences

A variety of estimators have been developed to use genetic marker information in inferring the admixture proportions (parental contributions) of a hybrid population. The majority of these estimators used allele frequency data, ignored molecular information that is available in markers such as microsatellites and DNA sequences, and assumed that mutations are absent since the admixture event. As a result, these estimators may fail to deliver an estimate or give rather poor estimates when admixture is ancient and thus mutations are not negligible. A previous molecular estimator based its inference of admixture proportions on the average coalescent times between pairs of genes taken from within and between populations. In this article I propose an estimator that considers the entire genealogy of all of the sampled genes and infers admixture proportions from the numbers of segregating sites in DNA sequence samples. By considering the genealogy of all sequences rather than pairs of sequences, this new estimator also allows the joint estimation of other interesting parameters in the admixture model, such as admixture time, divergence time, population size, and mutation rate. Comparative analyses of simulated data indicate that the new coalescent estimator generally yields better estimates of admixture proportions than the previous molecular estimator, especially when the parental populations are not highly differentiated. It also gives reasonably accurate estimates of other admixture parameters. A human mtDNA sequence data set was analyzed to demonstrate the method, and the analysis results are discussed and compared with those from previous studies.     

Social class,admixture, and skin color variation in Mexican-Americans and Anglo-Americans living in San Antonio,Texas

Social class may act in different ways as a barrier to gene flow in urban populations, depending on ethnicity. We test the hypothesis that biological variation is affected by social class subdivision using skin reflectance data collected for 393 Anglo-American and 930 Mexican-American adults in the major urban population of San Antonio, Texas. Two socioeconomic groups were sampled for the Anglo-American population: a middle-income transitional group and a high-income suburban group. In addition, we sampled a third socioeconomic group for Mexican-Americans: a low income barrio. Sex and age effects on skin color are minimal. Social class has no effect on skin color variation for Anglo-Americans, whereas there is a highly significant effect on social class subdivision for Mexican-Americans. Admixture estimates were derived from skin reflectance data and show that the proportion of native American ancestry decreases as social class increases.     

Heritability and components of phenotypic expression in skin reflectance of Mestizos from the Peruvian Lowlands

Skin reflectance was measured on the inner upper arm and forehead of a sample of 209 Mestizos ranging in age from 2 to 64 years living in the town of Lamas in the Eastern Peruvian Lowlands. The sample consisted of 43 father-son, 42 father-daughter, 62 mother-son, and 70 mother-daughter pairs. The sample also consisted of 57 brother-brother, 60 sister-sister and 139 brother-sister pairs. The reflectance measurements were made with a Photovolt Reflection Meter, model 670. Stepwise polynomial regression techniques were used to derive standardized residual values. Then using these residual values parent-offspring, sibling intraclass correlations and components of the phenotypic expression of skin reflectance were calculated. The study indicates that 1) the parent-offspring and sibling correlation coefficients conformed with the theoretical correlations expected assuming polygenic inheritance; 2) the husband-wife correlations indicate a high degree of assortative mating for skin color, but despite this effect the parent-offspring and sibling correlation coefficients are lower than the values expected under the influence of autosomal genes; 3) estimates of heritability and components of phenotypic expression indicate that about 55% of the total variability in skin reflectance could be attributed to the influence of additive genetic factors; and 4) there is no evidence of X-linkage in the inheritance of skin color.     

New conversion formulae for light-skinned populations using photovolt and E.E.L. reflectometers

Recent research in Belize revealed that published conversion coefficients for use between the two most commonly used reflectance spectro-photometers were inadequate when applied to dark-skinned populations. New research in Ireland shows that the published conversion coefficients for light-skinned populations are also inadequate. A total of 320 school children from Longford, Ireland were measured for skin reflectances at the upper inner arm site with the Photovolt Model 670 and the E.E.L. Reflectance Spectrophotometers. Six and nine filters respectively were used to sample the visible spectrum. Multiple regression techniques were then used to estimate new conversion coefficients which accurately predict readings for one instrument by using some or all of the measurements from the other. Double cross-validation techniques showed the inadequacy of the old (1967) formulae and the very high accuracy of the new ones. Some problems encountered in this study, but not in the one which produced new formulae for dark-skinned populations, suggest further work may be necessary. Additional independently sampled light-skinned populations have not been measured on both machines, so conclusive cross-validation of the new coefficients must remain tentative. Despite this drawback, the new formulae presented here are almost certainly an improvement over the old ones. These new conversion formulae may allow previously impossible comparisons of worldwide data on similar populations.     

Gm 3;5,13,14 and stated-admixture: independent estimates of admixture in American Indians.

Bernstein's formula for the estimation of the amount of admixture (m) in a hybrid population has been used frequently since its publication in 1931. While mathematically correct, it has not been shown to be correct in practice, because an independent estimate from a large sample has not been available. We have compared the estimate of m for Caucasian admixture derived by using Bernstein's formula with that estimated from stated-admixture (Sa) within a sample of 5,759 Native Americans. There was a linear relationship between the two variables (m = -.000275 + .714Sa; r = .976 for the grouped data, P = .0001).     

Unexpected ancestry of Populus seedlings from a hybrid zone implies a large role for postzygotic selection in the maintenance of species

In the context of potential interspecific gene flow, the integrity of species will be maintained by reproductive barriers that reduce genetic exchange, including traits associated with prezygotic isolation or poor performance of hybrids. Hybrid zones can be used to study the importance of different reproductive barriers, particularly when both parental species and hybrids occur in close spatial proximity. We investigated the importance of barriers to gene flow that act early vs. late in the life cycle of European Populus by quantifying the prevalence of homospecific and hybrid matings within a mosaic hybrid zone. We obtained genotypic data for 11 976 loci from progeny and their maternal parents and constructed a Bayesian model to estimate individual admixture proportions and hybrid classes for sampled trees and for the unsampled pollen parent. Matings that included one or two hybrid parents were common, resulting in admixture proportions of progeny that spanned the whole range of potential ancestries between the two parental species. This result contrasts strongly with the distribution of admixture proportions in adult trees, where intermediate hybrids and each of the parental species are separated into three discrete ancestry clusters. The existence of the full range of hybrids in seedlings is consistent with weak reproductive isolation early in the life cycle of Populus. Instead, a considerable amount of selection must take place between the seedling stage and maturity to remove many hybrid seedlings. Our results highlight that high hybridization rates and appreciable hybrid fitness do not necessarily conflict with the maintenance of species integrity.     

Maximum-likelihood estimation of admixture proportions from genetic data

For an admixed population, an important question is how much genetic contribution comes from each parental population. Several methods have been developed to estimate such admixture proportions, using data on genetic markers sampled from parental and admixed populations. In this study, I propose a likelihood method to estimate jointly the admixture proportions, the genetic drift that occurred to the admixed population and each parental population during the period between the hybridization and sampling events, and the genetic drift in each ancestral population within the interval between their split and hybridization. The results from extensive simulations using various combinations of relevant parameter values show that in general much more accurate and precise estimates of admixture proportions are obtained from the likelihood method than from previous methods. The likelihood method also yields reasonable estimates of genetic drift that occurred to each population, which translate into relative effective sizes (N(e)) or absolute average N(e)'s if the times when the relevant events (such as population split, admixture, and sampling) occurred are known. The proposed likelihood method also has features such as relatively low computational requirement compared with previous ones, flexibility for admixture models, and marker types. In particular, it allows for missing data from a contributing parental population. The method is applied to a human data set and a wolflike canids data set, and the results obtained are discussed in comparison with those from other estimators and from previous studies.     

Evaluating the ability of Bayesian clustering methods to detect hybridization and introgression using an empirical red wolf data set

Bayesian clustering methods have emerged as a popular tool for assessing hybridization using genetic markers. Simulation studies have shown these methods perform well under certain conditions; however, these methods have not been evaluated using empirical data sets with individuals of known ancestry. We evaluated the performance of two clustering programs, baps and structure , with genetic data from a reintroduced red wolf (Canis rufus) population in North Carolina, USA. Red wolves hybridize with coyotes (C. latrans), and a single hybridization event resulted in introgression of coyote genes into the red wolf population. A detailed pedigree has been reconstructed for the wild red wolf population that includes individuals of 50–100% red wolf ancestry, providing an ideal case study for evaluating the ability of these methods to estimate admixture. Using 17 microsatellite loci, we tested the programs using different training set compositions and varying numbers of loci. structure was more likely than baps to detect an admixed genotype and correctly estimate an individual's true ancestry composition. However, structure was more likely to misclassify a pure individual as a hybrid. Both programs were outperformed by a maximum‐likelihood‐based test designed specifically for this system, which never misclassified a hybrid (50–75% red wolf) as a red wolf or vice versa. Training set composition and the number of loci both had an impact on accuracy but their relative importance varied depending on the program. Our findings demonstrate the importance of evaluating methods used for detecting admixture in the context of endangered species management.     

The Admixture Structure and Genetic Variation of the Archipelago of Cape Verde and Its Implications for Admixture Mapping Studies

Recently admixed populations offer unique opportunities for studying human history and for elucidating the genetic basis of complex traits that differ in prevalence between human populations. Historical records, classical protein markers, and preliminary genetic data indicate that the Cape Verde islands in West Africa are highly admixed and primarily descended from European males and African females. However, little is known about the variation in admixture levels, admixture dynamics and genetic diversity across the islands, or about the potential of Cape Verde for admixture mapping studies. We have performed a detailed analysis of phenotypic and genetic variation in Cape Verde based on objective skin color measurements, socio-economic status (SES) evaluations and data for 50 autosomal, 34 X-chromosome, and 21 non-recombinant Y-chromosome (NRY) markers in 845 individuals from six islands of the archipelago. We find extensive genetic admixture between European and African ancestral populations (mean West African ancestry = 0.57, sd = 0.08), with individual African ancestry proportions varying considerably among the islands. African ancestry proportions calculated with X and Y-chromosome markers confirm that the pattern of admixture has been sex-biased. The high-resolution NRY-STRs reveal additional patterns of variation among the islands that are most consistent with differentiation after admixture. The differences in the autosomal admixture proportions are clearly evident in the skin color distribution across the islands (Pearson r = 0.54, P-value<2e–16). Despite this strong correlation, there are significant interactions between SES and skin color that are independent of the relationship between skin color and genetic ancestry. The observed distributions of admixture, genetic variation and skin color and the relationship of skin color with SES relate to historical and social events taking place during the settlement history of Cape Verde, and have implications for the design of association studies using this population.     

The magnitude and origin of European-American admixture in the Gila River Indian Community of Arizona: a union of genetics and demography.

Complementary genetic and demographic analyses estimate the total proportion of European-American admixture in the Gila River Indian Community and trace its mode of entry. Among the 9,616 residents in the sample, 2,015 persons claim only partial Native American heritage. A procedure employing 23 alleles or haplotypes at eight loci was used to estimate the proportion of European-American admixture, m(a), for the entire sample and within six categories of Caucasian admixture calculated from demographic data, md. The genetic analysis gave an estimate of total European-American admixture in the community of 0.054 (95% confidence interval [CI] .044-.063), while an estimate from demographic records was similar, .059. Regression of m(a) on md yielded a fitted line m(a) = .922md, r = .959 (P = .0001). When total European-American admixture is partitioned between the contributing populations, Mexican-Americans have provided .671, European-Americans .305, and African-Americans .023. These results are discussed within the context of the ethnic composition of the Gila River Indian Community, the assumptions underlying the methods, and the potential that demographic data have for enriching genetic measurements of human admixture. It is concluded that, despite the severe assumptions of the mathematical methods, accurate, reliable estimates of genetic admixture are possible from allele and haplotype frequencies, even when there is little demographic information for the population.     

Ecological factors in skin color variation among Papua New Guineans

An EEL reflectance spectrophotometer was used to measure the skin color of the inner upper arm and the forearm of 913 Karkar Islanders (Madang District) and 684 Lufa villagers (Eastern Highlands District). The samples were subdivided to study sex, age, and population variation against a background of ecological observations, including sunlight exposure, clothing, and erythemally effective wavelengths of ultraviolet light (Robertson, unpublished Ph.D. thesis, 1974). Population differences in sex and age variation in upper arm skin color may largely be attributable to the effects of culturally associated clothing differences. Not only do the Lufa villagers wear substantially less clothing than the Karkars, but also their arms are exposed more frequently to ultraviolet light during heavy manual work in unshaded gardens. For the melanin content of the forearm skin there are similar patterns of age variation in both populations; however, the populations differ in mean percentage of reflectance throughout most of the age span. These between-population differences are interpreted as a consequence of greater average daily exposure to sunlight and the higher intensity of ultraviolet light in the highland environment. On the forearm the percentage of reflectance at 685 nm decreases more rapidly with age in the prepubertal and adult age groups, a result attributed to endocrine changes superimposed on cumulative changes in the melanin pigmentary mechanism.