International Journal of Legal Medicine

, Volume 123, Issue 4, pp 315–325 | Cite as

Pigment phenotype and biogeographical ancestry from ancient skeletal remains: inferences from multiplexed autosomal SNP analysis

  • Caroline Bouakaze
  • Christine Keyser
  • Eric Crubézy
  • Daniel Montagnon
  • Bertrand Ludes
Original Article

Abstract

In the present study, a multiplexed genotyping assay for ten single nucleotide polymorphisms (SNPs) located within six pigmentation candidate genes was developed on modern biological samples and applied to DNA retrieved from 25 archeological human remains from southern central Siberia dating from the Bronze and Iron Ages. SNP genotyping was successful for the majority of ancient samples and revealed that most probably had typical European pigment features, i.e., blue or green eye color, light hair color and skin type, and were likely of European individual ancestry. To our knowledge, this study reports for the first time the multiplexed typing of autosomal SNPs on aged and degraded DNA. By providing valuable information on pigment traits of an individual and allowing individual biogeographical ancestry estimation, autosomal SNP typing can improve ancient DNA studies and aid human identification in some forensic casework situations when used to complement conventional molecular markers.

Keywords

Autosomal SNPs Pigmentation Ancestry Ancient DNA SNaPshot 

References

  1. 1.
    Willerslev E, Cooper A (2005) Ancient DNA. Proc R Soc Lon 272:3–16CrossRefGoogle Scholar
  2. 2.
    Pakendorf B, Stoneking M (2005) Mitochondrial DNA and human evolution. Annu Rev Genomics Hum Genet 6:165–183PubMedCrossRefGoogle Scholar
  3. 3.
    Green RE, Krause J, Ptak SE et al (2006) Analysis of one million base pairs of Neanderthal DNA. Nature 444:330–336PubMedCrossRefGoogle Scholar
  4. 4.
    Krause J, Lalueza-Fox C, Orlando L et al (2007) The derived FOXP2 variant of modern humans was shared with Neandertals. Curr Biol 17:1908–1912PubMedCrossRefGoogle Scholar
  5. 5.
    Noonan JP, Hofreiter M, Smith D et al (2005) Genomic sequencing of Pleistocene cave bears. Science 309:597–599PubMedCrossRefGoogle Scholar
  6. 6.
    Noonan JP, Coop G, Kudaravalli S et al (2006) Sequencing and analysis of Neanderthal genomic DNA. Science 314:1113–1118PubMedCrossRefGoogle Scholar
  7. 7.
    Poinar HN, Schwarz C, Qi J, Shapiro B et al (2006) Metagenomics to paleogenomics: large-scale sequencing of mammoth DNA. Science 311:392–394PubMedCrossRefGoogle Scholar
  8. 8.
    Amory S, Keyser C, Crubézy E, Ludes B (2007) STR typing of ancient DNA extracted from hair shafts of Siberian mummies. Forensic Sci Int 166:218–229PubMedCrossRefGoogle Scholar
  9. 9.
    Haak W, Brandt G, Jong HN et al (2008) Ancient DNA, strontium isotopes, and osteological analyses shed light on social and kinship organization of the Later Stone Age. Proc Natl Acad Sci USA 105:18226–18231PubMedCrossRefGoogle Scholar
  10. 10.
    Keyser-Tracqui C, Crubézy E, Ludes B (2003) Nuclear and mitochondrial DNA analysis of a 2, 000-year-old necropolis in the Egyin Gol Valley of Mongolia. Am J Hum Genet 73:247–260PubMedCrossRefGoogle Scholar
  11. 11.
    Ricaut FX, Keyser-Tracqui C, Crubézy E, Ludes B (2005) STR-genotyping from human medieval tooth and bone samples. Forensic Sci Int 151:31–35PubMedCrossRefGoogle Scholar
  12. 12.
    Schultes T, Hummel S, Herrmann B (1999) Amplification of Y-chromosomal STRs from ancient skeletal material. Hum Genet 104:164–166PubMedCrossRefGoogle Scholar
  13. 13.
    Larcombe LA, Nickerson P, Hoppa RD, Matheson C (2005) Detection of a single nucleotide polymorphism in the IL-6 promoter region of ancient nuclear DNA. Infect Genet Evol 5:117–122PubMedCrossRefGoogle Scholar
  14. 14.
    Burger J, Kirchner M, Bramanti B, Haak W, Thomas MG (2007) Absence of the lactase-persistence-associated allele in early Neolithic Europeans. Proc Natl Acad Sci USA 104:3736–3741PubMedCrossRefGoogle Scholar
  15. 15.
    Lalueza-Fox C, Römpler H, Caramelli D et al (2007) A melanocortin 1 receptor allele suggests varying pigmentation among Neanderthals. Science 318:1453–1455PubMedCrossRefGoogle Scholar
  16. 16.
    Parra EJ (2007) Human pigmentation variation: evolution, genetic basis, and implications for public health. Am J Phys Anthropol Suppl 45:85–105CrossRefGoogle Scholar
  17. 17.
    Bennett DC, Lamoreux ML (2003) The color loci of mice—a genetic century. Pigment Cell Res 16:333–344PubMedCrossRefGoogle Scholar
  18. 18.
    Parra EJ, Kittles RA, Shriver MD (2004) Implications of correlations between skin color and genetic ancestry for biomedical research. Nat Genet 36:S54–S60PubMedCrossRefGoogle Scholar
  19. 19.
    Branicki W, Brudnik U, Wojas-Pelc A (2005) Genetic prediction of pigmentary traits in forensic studies. Prob Forensic Sci 64:343–357Google Scholar
  20. 20.
    Bouakaze C, Keyser C, Amory S, Crubézy E, Ludes B (2007) First successful assay of Y-SNP typing by SNaPshot minisequencing on ancient DNA. Int J Legal Med 121:493–499PubMedCrossRefGoogle Scholar
  21. 21.
    Keyser C, Romac S, Bouakaze C, Amory S, Crubézy E, Ludes B (2008) Tracing back ancient south Siberian population history using mitochondrial and Y-chromosome SNPs. Forensic Sci Int Genet Suppl Ser 1:343–345CrossRefGoogle Scholar
  22. 22.
    Keyser-Tracqui C, Ludes B (2005) Methods for the study of ancient DNA. Methods Mol Biol 297:253–264PubMedGoogle Scholar
  23. 23.
    Branicki W, Brudnik U, Kupiec T, Wolañska-Nowak P, Wojas-Pelc A (2007) Determination of phenotype associated SNPs in the MC1R gene. J Forensic Sci 52:349–354PubMedCrossRefGoogle Scholar
  24. 24.
    Duffy DL, Montgomery GW, Chen W et al (2007) A three-single-nucleotide polymorphism haplotype in intron 1 of OCA2 explains most human eye-color variation. Am J Hum Genet 80:241–252PubMedCrossRefGoogle Scholar
  25. 25.
    Eiberg H, Troelsen J, Nielsen M, Mikkelsen A, Mengel-From J, Kjaer KW, Hansen L (2008) Blue eye color in humans may be caused by a perfectly associated founder mutation in a regulatory element located within the HERC2 gene inhibiting OCA2 expression. Hum Genet 123:177–187PubMedCrossRefGoogle Scholar
  26. 26.
    Sturm RA, Duffy DL, Zhao ZZ et al (2008) A single SNP in an evolutionary conserved region within intron 86 of the HERC2 gene determines human blue-brown eye color. Am J Hum Genet 82:424–431PubMedCrossRefGoogle Scholar
  27. 27.
    Graf J, Hodgson R, van Daal A (2005) Single nucleotide polymorphisms in the MATP gene are associated with normal human pigmentation variation. Hum Mutat 25:278–284PubMedCrossRefGoogle Scholar
  28. 28.
    Lamason RL, Mohideen MA, Mest JR et al (2005) SLC24A5, a putative cation exchanger, affects pigmentation in zebra fish and humans. Science 310:1782–1786PubMedCrossRefGoogle Scholar
  29. 29.
    Soejima M, Koda Y (2007) Population differences of two coding SNPs in pigmentation-related genes SLC24A5 and SLC45A2. Int J Legal Med 121:36–39PubMedCrossRefGoogle Scholar
  30. 30.
    Myles S, Somel M, Tang K, Kelso J, Stoneking M (2007) Identifying genes underlying skin pigmentation differences among human populations. Hum Genet 120:613–621PubMedCrossRefGoogle Scholar
  31. 31.
    Yuasa I, Umetsu K, Harihara S et al (2007) Distribution of two Asian-related coding SNPs in the MC1R and OCA2 genes. Biochem Genet 45:535–542PubMedCrossRefGoogle Scholar
  32. 32.
    Römpler H, Dear PH, Krause J et al (2006) Multiplex amplification of ancient DNA. Nat Protoc 1:720–728PubMedCrossRefGoogle Scholar
  33. 33.
    Sanchez JJ, Endicott P (2006) Developing multiplexed SNP assays with special reference to degraded DNA templates. Nat Protoc 1:1370–1378PubMedCrossRefGoogle Scholar
  34. 34.
    Pritchard JK, Stephens M, Donnelly P (2000) Inference of population structure using multilocus genotype data. Genetics 155:945–959PubMedGoogle Scholar
  35. 35.
    The International HapMap Consortium (2003) The International HapMap Project. Nature 426:789–796CrossRefGoogle Scholar
  36. 36.
    Kozintsev AG, Gromov AV, Moiseyev VG (1999) Collateral relatives of American Indians among the Bronze Age populations of Siberia? Am J Phys Anthropol 108:193–204PubMedCrossRefGoogle Scholar
  37. 37.
    Moiseyev VG (2006) Nonmetric traits in early Iron Age cranial series from western and southern Siberia. Archaeol Ethnol Anthropol Eurasia 25:145–152CrossRefGoogle Scholar

Copyright information

© Springer-Verlag 2009

Authors and Affiliations

  • Caroline Bouakaze
    • 1
  • Christine Keyser
    • 1
    • 2
  • Eric Crubézy
    • 2
  • Daniel Montagnon
    • 1
  • Bertrand Ludes
    • 1
    • 2
  1. 1.Laboratoire d’Anthropologie MoléculaireInstitut de Médecine LégaleStrasbourg CedexFrance
  2. 2.Laboratoire d’Anthropobiologie, FRE 2960 CNRSUniversité Paul SabatierToulouseFrance

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