Human Genetics

, Volume 115, Issue 1, pp 57–68 | Cite as

Ancestral proportions and their association with skin pigmentation and bone mineral density in Puerto Rican women from New York city

  • Carolina BonillaEmail author
  • Mark D. Shriver
  • Esteban J. Parra
  • Alfredo Jones
  • José R. Fernández
Original Investigation


Hispanic and African American populations exhibit an increased risk of obesity compared with populations of European origin, a feature that may be related to inherited risk alleles from Native American and West African parental populations. However, a relationship between West African ancestry and obesity-related traits, such as body mass index (BMI), fat mass (FM), and fat-free mass (FFM), and with bone mineral density (BMD) in African American women has only recently been reported. In order to evaluate further the influence of ancestry on body composition phenotypes, we studied a Hispanic population with substantial European, West African, and Native American admixture. We ascertained a sample of Puerto Rican women living in New York (n=64), for whom we measured BMI and body composition variables, such as FM, FFM, percent body fat, and BMD. Additionally, skin pigmentation was measured as the melanin index by reflectance spectroscopy. We genotyped 35 autosomal ancestry informative markers and estimated population and individual ancestral proportions in terms of European, West African, and Native American contributions to this population. The ancestry proportions corresponding to the three parental populations are: 53.3±2.8% European, 29.1±2.3% West African, and 17.6±2.4% Native American. We detected significant genetic structure in this population with a number of different tests. A highly significant correlation was found between skin pigmentation and individual ancestry (R 2=0.597, P<0.001) that was not attributable to differences in socioeconomic status. A significant association was also found between BMD and European admixture (R 2=0.065, P=0.042), but no such correlation was evident with BMI or the remaining body composition measurements. We discuss the implications of our findings for the potential use of this Hispanic population for admixture mapping.


Bone Mineral Density Skin Pigmentation Admixture Mapping Individual Admixture Puerto Rican Woman 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.



We are grateful to all participants in this research study. We also thank Dr. Rick Kittles for helpful comments on the manuscript and Lane Destro for helping with the genotyping. This work was supported in part by grants from NIH/NIDDK (DK53958) and NIH/NHGRI (HG002154) to M.D.S., NIH grant 1P30AG/NR15294 to J.R.F., and a Wenner-Gren Foundation Developing Countries Training Fellowship to C.B.


  1. Akey JM, Sosnoski D, Parra E, Dios S, Heister K, Su B, Bonilla C, Jin L, Shriver MD (2001) Melting curve analysis of SNPs (McSNP): a simple gel-free low-cost approach to SNP genotyping and DNA fragment analysis. BioTechniques 30:358–367PubMedGoogle Scholar
  2. Alaluf S, Atkins D, Barrett K, Blount M, Carter N, Heath A (2002) Ethnic variation in melanin content and composition in photoexposed and photoprotected human skin. Pigment Cell Res 15:112–118CrossRefPubMedGoogle Scholar
  3. Bean FD, Tienda M (1987) The Hispanic population of the United States. Russel Sage Foundation, New YorkGoogle Scholar
  4. Bonilla C, Parra EJ, Pfaff CL, Dios S, Marshall JA, Hamman RF, Ferrell RE, Hoggart CL, McKeigue PM, Shriver MD (2004) Admixture in the Hispanics of the San Luis Valley, Colorado, and its implications for complex trait gene mapping. Ann Hum Genet 68:139–153CrossRefPubMedGoogle Scholar
  5. Chakraborty R, Weiss KM (1988) Admixture as a tool for finding linked genes and detecting that difference from allelic associations between loci. Proc Natl Acad Sci USA 85:9119–9123PubMedGoogle Scholar
  6. Chakraborty R, Ferrell RE, Stern MP, Haffner SM, Hazuda HP, Rosenthal M (1986) Relationship of prevalence of non-insulin dependent diabetes mellitus to Amerindian admixture in the Mexican Americans of San Antonio, Texas. Genet Epidemiol 3:435–454PubMedGoogle Scholar
  7. Crawford PB, Story M, Wang MC, Ritchie LD, Sabry ZI (2001) Ethnic issues in the epidemiology of childhood obesity. Pediatr Clin North Am 48:855–878PubMedGoogle Scholar
  8. Díaz Soler LM (1953) Historia de la esclavitud negra en Puerto Rico (1493–1890). Ediciones de la Universidad de Puerto Rico, Puerto RicoGoogle Scholar
  9. Duffy DL, Box NF, Chen W, Palmer JS, Montgomery GW, James MR, Hayward NK, Martin NG, Sturm RA (2004) Interactive effects of MC1R and OCA2 on melanoma risk phenotypes. Hum Mol Genet 13:447–461CrossRefPubMedGoogle Scholar
  10. Fernández JR, Shriver MD, Beasley TM, Rafla-Demetrious N, Parra E, Albu J, Nicklas B, Ryan AS, McKeigue PM, Hoggart CJ, Weinsier RL, Allison DB (2003) Association of African genetic admixture with resting metabolic rate and obesity among women. Obes Res 11:904–911PubMedGoogle Scholar
  11. Fernández-Cobo M, Jobes DV, Yanagihara R, Nerurkar VR, Yamamura Y, Ryschkewitsch CF, Stoner GL (2001) Reconstructing population history using JC virus: Amerinds, Spanish, and Africans in the ancestry of modern Puerto Ricans. Hum Biol 73:385–402PubMedGoogle Scholar
  12. Fox C, Esparza J, Nicolson M, Bennett PH, Schulz LO, Valencia ME, Ravussin E (1999) Plasma leptin concentrations in Pima Indians living in drastically different environments. Diabetes Care 22:413–417PubMedGoogle Scholar
  13. Gardner LI Jr, Stern MP, Haffner SM, Gaskill SP, Hazuda HP, Relethford JH, Eifler CW (1984) Prevalence of diabetes in Mexican Americans. Relationship to percent of gene pool derived from Native American sources. Diabetes 33:86–92PubMedGoogle Scholar
  14. Gower BA (1999) Syndrome X in children: influence of ethnicity and visceral fat. Am J Hum Biol 11:249–257CrossRefGoogle Scholar
  15. Hanis CL, Chakraborty R, Ferrell RE, Schull WJ (1986) Individual admixture estimates: disease associations and individual risk of diabetes and gallbladder disease among Mexican-Americans in Starr County, Texas. Am J Phys Anthropol 70:433–441Google Scholar
  16. Hanis CL, Hewett-Emmett D, Bertin TK, Schull WJ (1991) Origins of US Hispanics. Implications for diabetes. Diabetes Care 14:618–627PubMedGoogle Scholar
  17. Hazuda HP, Haffner SM, Stern MP, Eifler CW (1988) Effects of acculturation and socioeconomic status on obesity and diabetes in Mexican Americans. The San Antonio heart study. Am J Epidemiol 128:1289–1301PubMedGoogle Scholar
  18. Hoggart CJ, Parra EJ, Shriver MD, Bonilla C, Kittles RA, Clayton DG, McKeigue PM (2003) Control of confounding of genetic associations in stratified populations. Am J Hum Genet 72:1492–1504CrossRefPubMedGoogle Scholar
  19. King RA, Willaert RK, Schmidt RM, Pietsch J, Savage S, Brott MJ, Fryer JP, Summers CG, Oetting WS (2003) MC1R mutations modify the classic phenotype of oculocutaneous albinism type 2 (OCA2). Am J Hum Genet 73:638–645CrossRefPubMedGoogle Scholar
  20. Kittles RA, Chen W, Panguluri RK, Ahaghotu C, Jackson A, Adebamowo CA, Griffin R, Williams T, Ukoli F, Adams-Campbell L, Kwagyan J, Isaacs W, Freeman V, Dunston GM (2002) CYP3A4-V and prostate cancer in African Americans: causal or confounding association because of population stratification? Hum Genet 110:553–560CrossRefPubMedGoogle Scholar
  21. Lautenberger JA, Stephens JC, O’Brien SJ, Smith MW (2000) Significant admixture linkage disequilibrium across 30 cM around the FY locus in African Americans. Am J Hum Genet 66:969–978PubMedGoogle Scholar
  22. Long JC (1991) The genetic structure of admixed populations. Genetics 127:417–428PubMedGoogle Scholar
  23. Long JC, Williams RC, Urbanek M (1995) An E-M algorithm and testing strategy for multiple-locus haplotypes. Am J Hum Genet 56:799–810PubMedGoogle Scholar
  24. Martínez-Cruzado JC, Toro-Labrador G, Ho-Fung V, Estevez-Montero MA, Lobaina-Manzanet A, Padovani-Claudio DA, Sanchez-Cruz H, Ortiz-Bermudez P, Sanchez-Crespo A (2001) Mitochondrial DNA analysis reveals substantial Native American ancestry in Puerto Rico. Hum Biol 73:491–511PubMedGoogle Scholar
  25. McKeigue PM, Carpenter JR, Parra EJ, Shriver MD (2000) Estimation of admixture and detection of linkage in admixed populations by a Bayesian approach: application to African-American populations. Ann Hum Genet 64:171–186Google Scholar
  26. Melton LJ III, Marquez MA, Achenbach SJ, Tefferi A, O’Connor MK, O’Fallon WM, Riggs BL (2002) Variations in bone density among persons of African heritage. Osteoporos Int 13:551–559CrossRefGoogle Scholar
  27. Okosun IS (2000) Ethnic differences in the risk of type 2 diabetes attributable to differences in abdominal adiposity in American women. J Cardiovasc Risk 7:425–430PubMedGoogle Scholar
  28. Parra EJ, Marcini A, Akey J, Martinson J, Batzer MA, Cooper R, Forrester T, Allison DB, Deka R, Ferrell RE, Shriver MD (1998) Estimating African American admixture proportions by use of population-specific alleles. Am J Hum Genet 63:1839–1851PubMedGoogle Scholar
  29. Pfaff CL, Parra EJ, Bonilla C, Heister K, McKeigue PM, Kamboh MI, Hutchinson RG, Ferrell RE, Boerwinkle E, Shriver MD (2001) Population structure in admixed populations: effect of admixture dynamics on the pattern of linkage disequilibrium. Am J Hum Genet 68:198–207PubMedGoogle Scholar
  30. Pritchard JK, Stephens M, Rosenberg NA, Donnelly P (2000) Association mapping in structured populations. Am J Hum Genet 67:170–181Google Scholar
  31. Raymond M, Rousset F (1995) Genepop, version 2.0,
  32. Rouse I (1992) The Tainos: rise and decline of the people who greeted Columbus. Yale University Press, New HavenGoogle Scholar
  33. Samet JM, Coultas DB, Howard CA, Skipper BJ, Hanis CL (1988) Diabetes, gallbladder disease, obesity, and hypertension among Hispanics in New Mexico. Am J Epidemiol 128:1302–1311PubMedGoogle Scholar
  34. Sánchez Korrol V (1994) From colonia to community: the history of Puerto Ricans in New York city. University of California Press, BerkeleyGoogle Scholar
  35. Shriver MD, Parra EJ (2000) Comparison of narrow-band reflectance spectroscopy and tristimulus colorimetry for measurements of skin and hair color in persons of different biological ancestry. Am J Phys Anthropol 112:17–27CrossRefPubMedGoogle Scholar
  36. Shriver MD, Parra EJ, Dios S, Bonilla C, Norton H, Jovel C, Pfaff C, Jones C, Massac A, Cameron N, Baron A, Jackson T, Argyropoulos G, Jin L, Hoggart CJ, McKeigue PM, Kittles RA (2003) Skin pigmentation, biogeographical ancestry and admixture mapping. Hum Genet 112:387–399PubMedGoogle Scholar
  37. Stern MP, Knapp JA, Hazuda HP, Haffner SM, Patterson JK, Mitchell BD (1991) Genetic and environmental determinants of type II diabetes in Mexican Americans. Is there a “descending limb” to the modernization/diabetes relationship? Diabetes Care 14:649–654PubMedGoogle Scholar
  38. Sturm RA, Teasdale RD, Box NF (2001) Human pigmentation genes: identification, structure and consequences of polymorphic variation. Gene 277:49–62CrossRefPubMedGoogle Scholar
  39. Sundquist J, Winkleby MA, Pudaric S (2001) Cardiovascular disease risk factors among older black, Mexican-American, and white women and men: an analysis of NHANES III, 1988–1994. Third National Health and Nutrition Examination Survey. J Am Geriatr Soc 49:109–116CrossRefPubMedGoogle Scholar
  40. Wagner DR, Heyward VH (2000) Measures of body composition in blacks and whites: a comparative review. Am J Clin Nutr 71:1392–1402PubMedGoogle Scholar
  41. Wagner JK, Parra EJ, Norton HL, Jovel C, Shriver MD (2002) Skin responses to ultraviolet radiation: effects of constitutive pigmentation, sex, and ancestry. Pigment Cell Res 15:385–390CrossRefPubMedGoogle Scholar
  42. Wang J, Thornton JC, Burastero S, Shen J, Tanenbaum S, Heymsfield SB, Pierson RN Jr (1996) Comparisons for body mass index and body fat percent among Puerto Ricans, blacks, whites and Asians living in the New York City area. Obes Res 4:377–384PubMedGoogle Scholar
  43. Weiss KM, Ferrell RE, Hanis CL (1984) A New World syndrome of metabolic diseases with a genetic and evolutionary basis. Yearbook Phys Anthropol 27:153–178Google Scholar
  44. Williams RC, Long JC, Hanson RL, Sievers ML, Knowler WC (2000) Individual estimates of European genetic admixture associated with lower body-mass index, plasma glucose, and prevalence of type 2 diabetes in Pima Indians. Am J Hum Genet 66:527–538PubMedGoogle Scholar
  45. Ye J, Parra EJ, Sosnoski DM, Hiester K, Underhill PA, Shriver MD (2002) Melting curve SNP (McSNP) genotyping: a useful approach for diallelic genotyping in forensic science. J Forensic Sci 47:593–600PubMedGoogle Scholar

Copyright information

© Springer-Verlag 2004

Authors and Affiliations

  • Carolina Bonilla
    • 1
    Email author
  • Mark D. Shriver
    • 2
  • Esteban J. Parra
    • 3
  • Alfredo Jones
    • 4
  • José R. Fernández
    • 5
  1. 1.National Human Genome CenterHoward UniversityWashingtonUSA
  2. 2.Department of AnthropologyThe Pennsylvania State UniversityUniversity ParkUSA
  3. 3.Department of AnthropologyUniversity of Toronto at MississaugaMississaugaCanada
  4. 4.New York Obesity Research CenterSt. Luke’s/Roosevelt Hospital CenterNew YorkUSA
  5. 5.Department of Nutrition Sciences and the Clinical Nutrition Research CenterThe University of Alabama at BirminghamBirminghamUSA

Personalised recommendations