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Research Article

Y-Chromosome Based Evidence for Pre-Neolithic Origin of the Genetically Homogeneous but Diverse Sardinian Population: Inference for Association Scans

  • Daniela Contu equal contributor,

    equal contributor Contributed equally to this work with: Daniela Contu, Laura Morelli

    Affiliation: Laboratorio di Immunogenetica, Ospedale Microcitemico, Cagliari, Italy

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  • Laura Morelli equal contributor,

    equal contributor Contributed equally to this work with: Daniela Contu, Laura Morelli

    Affiliation: Dipartimento di Scienze Biomediche, Università di Sassari, Sassari, Italy

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  • Federico Santoni,

    Affiliation: Center for Advanced Studies, Research and Development in Sardinia (CRS4), Pula, Italy

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  • Jamie W. Foster,

    Affiliation: Dipartimento di Scienze Biomediche, Università di Sassari, Sassari, Italy

    Current address: Albert Park, Melbourne, Australia

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  • Paolo Francalacci,

    Affiliation: Dipartimento di Zoologia e Genetica Evoluzionistica, Università di Sassari, Sassari, Italy

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  • Francesco Cucca mail

    To whom correspondence should be addressed. E-mail: fcucca@uniss.it

    Affiliation: Dipartimento di Scienze Biomediche, Università di Sassari, Sassari, Italy

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  • Published: January 09, 2008
  • DOI: 10.1371/journal.pone.0001430

Reader Comments (3)

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Probably Genotyping Error affects TMRCA calculation

Posted by vineviz on 08 Feb 2008 at 00:53 GMT

We also assessed the TMRCA for the rare Sardinia-specific R-M18 haplogroup, and obtained a value of 8.1 (7.8–10.5) KYA.
http://plosone.org/article/info:doi/10.1371/journal.pone.0001430#article1.body1.sec2.p5

I did notice, however, what appears to be a genotyping error in haplogroup R-M18. One of the Cagliari haplotypes appears to have been classified as R-M18 when it should have been classified as R-M269.

This haplotype does not match any of the other seven haplotypes at five of the eight reported STRs, yet matches the majority allele for R-M269 at seven of the eight STRs. In a UPGMA phylogeny constructed using the haplotypes from this paper, it also clustered with R-M269 in all of the trees.

Including this R-M269 haplotype in the R-M18 TMRCA calculation dramatically increases the STR variance, thus producing an errantly large TMRCA calculation.