Abstract
The indigenous populations from Peninsular Malaysia, locally known as Orang Asli, continue to adopt an agro-subsistence nomadic lifestyle, residing primarily within natural jungle habitats. Leading a hunter-gatherer lifestyle in a tropical jungle environment, the Orang Asli are routinely exposed to malaria. Here we surveyed the genetic architecture of individuals from four Orang Asli tribes with high-density genotyping across more than 2.5 million polymorphisms. These tribes reside in different geographical locations in Peninsular Malaysia and belong to three main ethno-linguistic groups, where there is minimal interaction between the tribes. We first dissect the genetic diversity and admixture between the tribes and with neighboring urban populations. Later, by implementing five metrics, we investigated the genome-wide signatures for positive natural selection of these Orang Asli, respectively. Finally, we searched for evidence of genomic adaptation to the pressure of malaria infection. We observed that different evolutionary responses might have emerged in the different Orang Asli communities to mitigate malaria infection.
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Acknowledgments
This study is supported by Ministry of Science, Technology and Innovation (MOSTI) grant erBiotek Grant # 100-RM/BIOTEK 16/6/2 B (1/2011) and [100-RMI/GOV 16/6/2 (19/2011)] awarded to BP Hoh and ME Phipps; and the Ministry of Education Long-term Research Grant Scheme (LRGS) funded RM34,000 for genotyping the Che Wong samples. We thank the JAKOA for their full cooperation and assistance throughout the study, the medical team from Faculty of Medicine Universiti Teknologi MARA, the Cardio-Metabolic research team at Monash University Sunway Campus, Juli Edo and Mahmood Ameen from Universiti Malaya for their involvement during sample collection, and all subjects who voluntarily participated in this study. L. P. W., R. T. H. O. and Y. Y. T. acknowledge support by the National Research Foundation, Prime Minister’s Office, Singapore under its Research Fellowship (NRF-RF-2010-05) and administered by the National University of Singapore. S. X. is Max Planck Independent Research Group Leader and member of CAS Youth Innovation Promotion Association. S. X. gratefully acknowledges support by the National Science Foundation of China (NSFC) grants (91331204 and 31171218) and the support of K. C.Wong Education Foundation, Hong Kong.
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X. Liu and Y. Yunus contributed equally.
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All genomic positions in the supporting information are reported in GRCh37 coordinates.
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Liu, X., Yunus, Y., Lu, D. et al. Differential positive selection of malaria resistance genes in three indigenous populations of Peninsular Malaysia. Hum Genet 134, 375–392 (2015). https://doi.org/10.1007/s00439-014-1525-2
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DOI: https://doi.org/10.1007/s00439-014-1525-2