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Research Article| Volume 9, P33-41, March 2014

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Autosomal and Y-STR analysis of degraded DNA from the 120-year-old skeletal remains of Ezekiel Harper

  • Angie Ambers
    Correspondence
    Corresponding author at: Institute of Applied Genetics, Department of Forensic and Investigative Genetics, University of North Texas Health Science Center, 3500 Camp Bowie Boulevard, Fort Worth, TX, USA. Tel.: +1 469 667 9407.
    Affiliations
    Institute of Applied Genetics, Department of Forensic and Investigative Genetics, University of North Texas Health Science Center, 3500 Camp Bowie Boulevard, Fort Worth, TX, USA

    Department of Biological Sciences, University of North Texas, 1511 West Sycamore, Denton, TX, USA
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  • Harrell Gill-King
    Affiliations
    Department of Biological Sciences, University of North Texas, 1511 West Sycamore, Denton, TX, USA

    Laboratory of Forensic Anthropology, Center for Human Identification, University of North Texas, Department of Biological Sciences, 1511 West Sycamore, Denton, TX, USA
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  • Dennis Dirkmaat
    Affiliations
    Mercyhurst Archaeological Institute, Hirtzel Forensic Anthropology Laboratory, Department of Applied Forensic Sciences, Mercyhurst College, 501 East 38th Street, Erie, PA, USA
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  • Robert Benjamin
    Affiliations
    Department of Biological Sciences, University of North Texas, 1511 West Sycamore, Denton, TX, USA
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  • Jonathan King
    Affiliations
    Institute of Applied Genetics, Department of Forensic and Investigative Genetics, University of North Texas Health Science Center, 3500 Camp Bowie Boulevard, Fort Worth, TX, USA
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  • Bruce Budowle
    Affiliations
    Institute of Applied Genetics, Department of Forensic and Investigative Genetics, University of North Texas Health Science Center, 3500 Camp Bowie Boulevard, Fort Worth, TX, USA

    Center of Excellence in Genomic Medicine Research (CEGMR), King Abdulaziz University, Jeddah, Saudi Arabia
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      Abstract

      The 120-year-old skeletal remains of Confederate Civil War soldier Captain Ezekiel “Zeke” Harper were exhumed by court order in January 2011 for DNA analysis. The goal of the DNA testing was to support or refute whether Captain Harper had fathered a son (Earl J. Maxwell) with his Native American maid prior to his murder in 1892. Bones with adequate structural integrity (left tibia, right tibia, right femur, mandible, four teeth) were retrieved from the burial site and sent to the Institute of Applied Genetics in Fort Worth, Texas for analysis. Given the age and condition of the remains, three different extraction methods were used to maximize the probability of DNA recovery. The majority of the DNA isolates from over fifty separate bone sections yielded partial autosomal STR genotypes and partial Y-STR haplotypes. After comparing the partial results for concordance, consensus profiles were generated for comparison to reference samples from alleged family members. Considering the genetic recombination that occurs in autosomal DNA over the generations within a family, Y-STR analysis was determined to be the most appropriate and informative approach for determining potential kinship. Two of Earl J. Maxwell's grandsons submitted buccal samples for comparison. The Y-STR haplotypes obtained from both of these reference samples were identical to each other and to the alleles in Ezekiel Harper's consensus profile at all 17 loci examined. This Y-STR haplotype was not found in either of two major Y-STR population databases (U.S. Y-STR database and YHRD). The fact that the Y-STR haplotype obtained from Ezekiel's skeletal remains and Earl's grandsons is not found in either population database demonstrates its rarity and further supports a paternal lineage relationship among them. Results of the genetic analyses are consistent with the hypothesis that Earl J. Maxwell is the son of Ezekiel Harper.

      Keywords

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      References

        • Maxwell H.
        History of Tucker County, West Virginia: From the Earliest Explorations and Settlements to the Present Time.
        Preston Publishing Company, Kingwood, West Virginia1884
      1. S. French, The Harper Brothers: Rebel Guides of the Alleghenies, in: The Morgan Messenger, December 7, 2005, p. 8.

      2. S. French, Two Brothers Lead Rebel Guerrilla Raids, in: The Washington Times, October 28, 2005.

      3. Confederate Irregular Warfare 1861–1865: Partisan Ranger Units and Guerrilla Commands. http://www.frontiernet.net/∼lws/Partisan%20Rangers%20Info.html.

        • Loreille O.M.
        • Parr R.L.
        • McGregor K.A.
        • Fitzpatrick C.M.
        • Lyon C.
        • Yang D.Y.
        • Speller C.F.
        • Grimm M.R.
        • Grimm M.J.
        • Irwin J.A.
        • Robinson E.M.
        Integrated DNA fingerprint analyses in the identification of 60-year-old mummified human remains discovered in an Alaskan glacier.
        J. Forensic Sci. 2010; 55: 813-818
        • Cooper A.
        • Poinar H.N.
        • Ancient D.N.A.
        Do it right or not at all.
        Science. 2000; 18: 1139-1141
        • Yang D.Y.
        • Watt K.
        Contamination controls when preparing archaeological remains for ancient DNA analysis.
        J. Archaeol. Sci. 2005; 32: 331-336
        • Wang D.Y.
        • Chang C.W.
        • Lagacé R.E.
        • Calandro L.M.
        • Hennessy L.K.
        Developmental validation of the AmpFℓSTR® Identifiler® Plus PCR Amplification kit: an established multiplex assay with improved performance.
        J. Forensic Sci. 2012; 57: 453-465
        • Ferreira I.
        Use of the PrepFiler BTA™ Forensic DNA Extraction Kit and the AmpFℓSTR® Identifiler® Plus Kit in real case samples.
        Forensic News. 2011;
        • Kemp B.M.
        • Smith D.G.
        Use of bleach to eliminate contaminating DNA from the surface of bones and teeth.
        Forensic Sci. Int. 2005; 154: 53-61
        • Poinar H.N.
        Criteria of authenticity for DNA from ancient and forensic samples.
        Int. Congr. Ser. 2003; 1239: 575-579
        • Gilbert M.T.P.
        • Hansen A.J.
        • Willerslev E.
        • Turner-Walker G.
        • Collins M.
        Insights into the processes behind the contamination of degraded human teeth and bone samples with exogenous sources of DNA.
        Int. J. Osteoarchaeol. 2006; 16: 156-164
        • Taberlet P.
        • Griffin S.
        • Goossens B.
        • Questiau S.
        • Manceau V.
        • Escaravage N.
        • Waits L.P.
        • Bouvet J.
        Reliable genotyping of samples with very low DNA quantities using PCR.
        Nucleic Acids Res. 1996; 24: 3189-3194
        • Cowen S.
        • Debenham P.
        • Dixon A.
        • Kutranov S.
        • Thomson J.
        • Way K.
        An investigation into the robustness of the consensus method of interpreting low-template DNA profiles.
        Forensic Sci. Int. Genet. 2011; 5: 400-406
      4. Generon Hi-Flow® DNA Purification Spin Columns, User manual and information booklet, www.generon.co.uk/Literature/Generon_DNA_Purification_Spin_Col.pdf.

      5. Applied Biosystems, AmpFlSTR® Yfiler® PCR Amplification Kit User Manual, Publication Number 4358101 (Revised September 2012).

        • Willuweit S.
        • Roewer L.
        Y chromosome haplotype reference database (YHRD): update.
        Forensic Sci. Int. Genet. 2007; 1: 83-87
        • Sparkes R.
        • Kimpton C.P.
        • Watson S.
        • Oldroyd N.J.
        • Clayton T.M.
        • Barnett L.
        • Arnold J.
        • Thompson C.
        • Hale R.
        • Chapman J.
        • Urquhart A.
        • Gill P.
        The validation of a 7-locus multiplex STR test for use in forensic casework: (I). Mixtures, aging, degradation and species studies.
        Int. J. Legal Med. 1996; 109: 186-194
        • Takahashi M.
        • Kato Y.
        • Mukoyama H.
        • Kanaya H.
        • Kamiyama S.
        Evaluation of five polymorphic microsatellite markers for typing DNA from decomposed human tissues – correlation between the size of the alleles and that of the template DNA.
        Forensic Sci. Int. 1997; 90: 1-9
        • Schneider P.M.
        • Bender K.
        • Mayr W.R.
        • Parson W.
        • Hoste B.
        • Decorte R.
        • Cordonnier J.
        • Vanek D.
        • Morling N.
        • Karjalainen M.
        • Marie-Paule C.C.
        • et al.
        STR analysis of artificially degraded DNA – results of a collaborative European exercise.
        Forensic Sci. Int. 2004; 139: 123-134
        • Whitaker J.P.
        • Clayton T.M.
        • Urquhart A.J.
        • Millican E.S.
        • Downes T.J.
        • Kimpton C.P.
        • Gill P.
        Short tandem repeat typing of bodies from a mass disaster: high success rate and characteristic amplification patterns in highly degraded samples.
        Biotechniques. 1995; 18: 670-677
        • Noren L.
        • Hedell R.
        • Ansell R.
        • Hedman J.
        Purification of crime scene DNA extracts using centrifugal filter devices.
        Investig. Genet. 2013; 4: 1-8