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

Daniela Contu; Laura Morelli; Federico Santoni; Jamie W. Foster; Paolo Francalacci; Francesco Cucca

doi:10.1371/journal.pone.0001430

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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 ,

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

Affiliation Laboratorio di Immunogenetica, Ospedale Microcitemico, Cagliari, Italy
⨯
Laura Morelli ,

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

Affiliation Dipartimento di Scienze Biomediche, Università di Sassari, Sassari, Italy
⨯
Federico Santoni,

Affiliation Center for Advanced Studies, Research and Development in Sardinia (CRS4), Pula, Italy
⨯
Jamie W. Foster,

Current address: Albert Park, Melbourne, Australia

Affiliation Dipartimento di Scienze Biomediche, Università di Sassari, Sassari, Italy
⨯
Paolo Francalacci,

Affiliation Dipartimento di Zoologia e Genetica Evoluzionistica, Università di Sassari, Sassari, Italy
⨯
Francesco Cucca

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

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

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

Daniela Contu,
Laura Morelli,
Federico Santoni,
Jamie W. Foster,
Paolo Francalacci,
Francesco Cucca

Published: January 9, 2008
https://doi.org/10.1371/journal.pone.0001430

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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.

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

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

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Probably Genotyping Error affects TMRCA calculation

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