Positive selection in the genomes of two Papua New Guinean populations at distinct altitude levels

Mathilde André, Nicolas Brucato, Georgi Hudjasov, Vasili Pankratov, Danat Yermakovich, Francesco Montinaro, Rita Kreevan, Jason Kariwiga, John Muke, Anne Boland, Jean-François Deleuze, Vincent Meyer, Nicholas Evans, Murray P. Cox, Matthew Leavesley, Michael Dannemann, Tõnis Org, Mait Metspalu, Mayukh Mondal () and François-Xavier Ricaut ()
Additional contact information
Mathilde André: University of Tartu
Nicolas Brucato: Université Toulouse 3 – Paul Sabatier (UT3)
Georgi Hudjasov: University of Tartu
Vasili Pankratov: University of Tartu
Danat Yermakovich: University of Tartu
Francesco Montinaro: University of Tartu
Rita Kreevan: University of Tartu
Jason Kariwiga: University 134
John Muke: Social Research Institute Ltd
Anne Boland: Centre National de Recherche en Génomique Humaine (CNRGH)
Jean-François Deleuze: Centre National de Recherche en Génomique Humaine (CNRGH)
Vincent Meyer: Centre National de Recherche en Génomique Humaine (CNRGH)
Nicholas Evans: Australian National University
Murray P. Cox: Massey University
Matthew Leavesley: University 134
Michael Dannemann: University of Tartu
Tõnis Org: University of Tartu
Mait Metspalu: University of Tartu
Mayukh Mondal: University of Tartu
François-Xavier Ricaut: Université Toulouse 3 – Paul Sabatier (UT3)

Nature Communications, 2024, vol. 15, issue 1, 1-15

Abstract: Abstract Highlanders and lowlanders of Papua New Guinea have faced distinct environmental stress, such as hypoxia and environment-specific pathogen exposure, respectively. In this study, we explored the top genomics regions and the candidate driver SNPs for selection in these two populations using newly sequenced whole-genomes of 54 highlanders and 74 lowlanders. We identified two candidate SNPs under selection - one in highlanders, associated with red blood cell traits and another in lowlanders, which is associated with white blood cell count – both potentially influencing the heart rate of Papua New Guineans in opposite directions. We also observed four candidate driver SNPs that exhibit linkage disequilibrium with an introgressed haplotype, highlighting the need to explore the possibility of adaptive introgression within these populations. This study reveals that the signatures of positive selection in highlanders and lowlanders of Papua New Guinea align closely with the challenges they face, which are specific to their environments.

Date: 2024
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DOI: 10.1038/s41467-024-47735-1

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