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Reply to ‘No evidence for unknown archaic ancestry in South Asia’

Nature Genetics volume 50, pages 1637–1639 (2018)Cite this article

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Mondal et al. reply — In a 2016 paper1, we derived three main conclusions: (i) that all Asian and Pacific populations share a single origin and expansion out of Africa; (ii) that populations from South and Southeast Asia harbor a small proportion of ancestry from an unknown extinct hominin different from the Neanderthal and the Denisova; and (iii) that the distinctive characteristic of short stature in the Andamanese has resulted from strong positive selection on genes related to body size. The existence of admixture with an extinct hominin has been challenged by Skoglund et al.2, who have not been able to replicate our results in other datasets and have alleged that our statistical treatment of the data was improper, pointing out some possible sources of error.

Here, we (i) replicated our results in independent datasets; (ii) reexamined our data with a focus on possible sources of error, such as the number of individuals, differences in coverage and batch effects; and (iii) performed new statistical analysis to detect introgressed regions in the Andamanese and confirm their unknown origin. The new analyses both bolstered our confidence that our earlier inferences were correct and resulted in an improved model of introgression of modern humans with a hitherto-unknown archaic ancestry.

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Data availability

All sequences produced in this project have been deposited in the European Nucleotide Archive (ENA) under accession codes PRJEB11455 (Andamanese whole-genome sequences (FASTQ, BAM and VCF files)) and PRJEB16019 (all remaining continental Indian whole-genome sequences (FASTQ, BAM and a merged VCF file)).

References

  1. Mondal, M. et al. Nat. Genet. 48, 1066–1070 (2016).

    Article  CAS  Google Scholar 

  2. Skoglund, P., Mallick, S., Patterson, N. & Reich, D. Nat. Genet. 50, 632–633 (2018).

    Article  CAS  Google Scholar 

  3. Auton, A. et al. Nature 526, 68–74 (2015).

    Article  Google Scholar 

  4. Mallick, S. et al. Nature 538, 201–206 (2016).

    Article  CAS  Google Scholar 

  5. Green, R. E. et al. Science 328, 710–722 (2010).

    Article  CAS  Google Scholar 

  6. Meyer, M. et al. Science 338, 222–226 (2012).

    Article  CAS  Google Scholar 

  7. Prüfer, K. et al. Science 358, 655–658 (2017).

    Article  Google Scholar 

  8. Malaspinas, A. S. et al. Nature 538, 207–214 (2016).

    Article  CAS  Google Scholar 

  9. Lu, D. et al. Am. J. Hum. Genet. 99, 580–594 (2016).

    Article  CAS  Google Scholar 

  10. Vernot, B. & Akey, J. M. Science 343, 1017–1021 (2014).

    Article  CAS  Google Scholar 

Download references

Acknowledgements

Funding to J.B. was provided by the joint Spain–India bilateral grant PRI-PIBIN-2011-0942 from the Ministerio de Economía y Competitividad (Spain) and grant BFU2016-77961-P (AEI/FEDER, UE) awarded by the Agencia Estatal de Investigación (MINECO, Spain). This work was also supported by the Secretaria d’Universitats i Recerca del Departament d’Economia i Coneixement de la Generalitat de Catalunya (GRC 2017 SGR 702) and part of the ‘Unidad de Excelencia María de Maeztu’, funded by the MINECO (ref. MDM-2014-0370).

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Authors and Affiliations

  1. Institute of Genomics, University of Tartu, Tartu, Estonia

    Mayukh Mondal

  2. Servei de Genòmica, Universitat Pompeu Fabra, Barcelona, Catalonia, Spain

    Ferran Casals

  3. National Institute of BioMedical Genomics, Kalyani, West Bengal, India

    Partha P. Majumder

  4. Institut de Biologia Evolutiva (UPF-CSIC), Universitat Pompeu Fabra, Barcelona, Spain

    Jaume Bertranpetit

Authors
  1. Mayukh Mondal
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  2. Ferran Casals
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  3. Partha P. Majumder
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  4. Jaume Bertranpetit
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Correspondence to Mayukh Mondal.

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Mondal, M., Casals, F., Majumder, P.P. et al. Reply to ‘No evidence for unknown archaic ancestry in South Asia’. Nat Genet 50, 1637–1639 (2018). https://doi.org/10.1038/s41588-018-0280-z

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