Shared Signature of Recent Positive Selection on theTSBP1–BTNL2–HLA-DRAGenes in Five Native Populations from North Borneo

Abstract

North Borneo is home to more than 40 native populations. These natives are believed to have undergone local adaptation in response to environmental challenges such as the mosquito-abundant tropical rainforest. We attempted to trace the footprints of natural selection from the genomic data of North Borneo (NB) native populations using a panel of ∼2.2 million genome-wide single nucleotide polymorphisms (SNPs). As a result, an ∼13 kb haplotype in the Major Histocompatibility (MHC) Class II region encompassing candidate genes TSBP1 – BTNL2 – HLA-DRA was identified to be undergoing natural selection. This putative signature of positive selection is shared among the five NB populations and is estimated to have arisen ∼5.5 thousand years (∼220 generations) ago, which coincides with the period of Austronesian expansion. Owing to the long history of endemic malaria in NB, the putative signature of positive selection is postulated to be driven by Plasmodium parasite infection. The findings of this study imply that despite high levels of genetic differentiation, the NB populations might have experienced similar local genetic adaptation resulting from stresses of the shared environment.

The Peopling and Migration History of the Natives in Peninsular Malaysia and Borneo: A Glimpse on the Studies Over the Past 100 years

“…This migration model is consistent with the alternative "Early Train" migration hypothesis proposed by Jinam et al (2012), which argues that there was a migration originating from Indochina or South China ~30-10 kya. Both hypotheses are supported at least in part, by several other lines of evidence: 1) close genetic affinity between the Sabahan natives and the Taiwanese aborigines and the Philippines aborigines but distantly related to the populations from mainland SEA (Yew et al, 2018a); 2) putative signals of positive selection driven by malaria infection found in the Sabahan natives occurred ~5 kya, which coincides with the period during Austronesian expansion (Hoh et al, 2020); 3) inference divergence time between the Negrito and Senoi coincides with the proposed period of "Early Train" hypothesis, posing the plausibility of the swiddening Austroasiatic agriculturist migration to Peninsular Malaysia, which resulted in declined effective population size of Negrito (Yew et al, 2018b); 4) inference using both uniparental and autosomal markers suggested primarily common ancestry for Taiwan or islands of SEA populations established before the Neolithic period (Soares et al, 2016); 5) the native from Sarawak (the Iban) showed a closer genetic affinity to Indonesia than the mainland SEA (Simonson et al, 2011).…”

“…Analysis of natural selection may be able to at least in part address this question ( Liu et al, 2015 ; Zhang et al, 2021 ). Several studies have been carried out in the SEA populations including the natives from Peninsular Malaysia and Borneo ( Liu et al, 2015 ; Liu et al, 2017 ; Hoh et al, 2020 ). However finer genotyping, phenotypic and environmental characteristics, along with a sample size on the indigenous populations are required to warrant a convincing conclusion.…”

Genetic Connections and Convergent Evolution of Tropical Indigenous Peoples in Asia

“…The arrival of Austroasiatic and Austronesian farmers from the north during the Late Paleolithic and Neolithic era forced the early inhabitants into separate areas, which added to the complex demographic history of these peoples ( Bellwood 2007 ; Jinam et al 2012 ; Lipson et al 2014 ). Many genetic studies have highlighted substantial distinction among geographically separated indigenous populations for their distinct genetic affinities and admixture patterns ( Endicott et al 2003 ; Reich et al 2010 , 2011 ; Jinam et al 2017 ; GenomeAsia100K Consortium 2019 ), but only a few have characterized the genomic footprints of their possibly shared evolution ( Hoh et al 2020 ).…”