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Abstract
Tropical indigenous peoples in Asia (TIA) attract much attention for their unique appearance, whereas their genetic history and adaptive evolution remain mysteries. We conducted a comprehensive study to characterize the genetic distinction and connection of broad geographical TIAs. Despite the diverse genetic makeup and large interarea genetic differentiation between the TIA groups, we identified a basal Asian ancestry (bASN) specifically shared by these populations. The bASN ancestry was relatively enriched in ancient Asian human genomes dated as early as ∼50,000 years before the present and diminished in more recent history. Notably, the bASN ancestry is unlikely to be derived from archaic hominins. Instead, we suggest it may be better modeled as a survived lineage of the initial peopling of Asia. Shared adaptations inherited from the ancient Asian ancestry were detected among the TIA groups (e.g., LIMS1 for hair morphology, and COL24A1 for bone formation), and they are enriched in neurological functions either at an identical locus (e.g., NKAIN3), or different loci in an identical gene (e.g., TENM4). The bASN ancestry could also have formed the substrate of the genetic architecture of the dark pigmentation observed in the TIA peoples. We hypothesize that phenotypic convergence of the dark pigmentation in TIAs could have resulted from parallel (e.g., DDB1/DAK) or genetic convergence driven by admixture (e.g., MTHFD1 and RAD18), new mutations (e.g., STK11), or notably purifying selection (e.g., MC1R). Our results provide new insights into the initial peopling of Asia and an advanced understanding of the phenotypic convergence of the TIA peoples.
https://academic.oup.com/mbe/article/39/2/msab361/6481554?login=false
Tropical indigenous peoples in Asia (TIA) attract much attention for their unique appearance, whereas their genetic history and adaptive evolution remain mysteries. We conducted a comprehensive study to characterize the genetic distinction and connection of broad geographical TIAs. Despite the diverse genetic makeup and large interarea genetic differentiation between the TIA groups, we identified a basal Asian ancestry (bASN) specifically shared by these populations. The bASN ancestry was relatively enriched in ancient Asian human genomes dated as early as ∼50,000 years before the present and diminished in more recent history. Notably, the bASN ancestry is unlikely to be derived from archaic hominins. Instead, we suggest it may be better modeled as a survived lineage of the initial peopling of Asia. Shared adaptations inherited from the ancient Asian ancestry were detected among the TIA groups (e.g., LIMS1 for hair morphology, and COL24A1 for bone formation), and they are enriched in neurological functions either at an identical locus (e.g., NKAIN3), or different loci in an identical gene (e.g., TENM4). The bASN ancestry could also have formed the substrate of the genetic architecture of the dark pigmentation observed in the TIA peoples. We hypothesize that phenotypic convergence of the dark pigmentation in TIAs could have resulted from parallel (e.g., DDB1/DAK) or genetic convergence driven by admixture (e.g., MTHFD1 and RAD18), new mutations (e.g., STK11), or notably purifying selection (e.g., MC1R). Our results provide new insights into the initial peopling of Asia and an advanced understanding of the phenotypic convergence of the TIA peoples.
https://academic.oup.com/mbe/article/39/2/msab361/6481554?login=false
One question that has long been debated is whether the distinctive physical features (e.g., small body size, dark skin, curly hair, and broad nose, collectively known as “Negrito-like” phenotypes) shared by the tropical hunter-gatherers are ancestral or derived as a result of genetic convergence. Migliano et al. (2013) identified various signals of growth-related positive selection in different tropical indigenous populations, whereas Bergey et al. (2018) reported shared natural selections on height-related pathways in African and Asian rainforest hunter-gatherers. Relatively more analyses were carried out in single tropical indigenous populations or geographically related indigenous groups. Novel adaptive signals of height, hair, nasal morphology, and those in response to some extreme environmental stresses have been reported in each of these populations or groups (Liu et al. 2015; Lopez et al. 2019; Zhang et al. 2021). However, the current understanding of the genetic basis of the dark skin phenotype is rather limited. Over the past few decades, tremendous advances have been made in our understanding of the evolutionary history of light skin in Europeans and East Asians, whereas only a few recent studies revealed the skin color variations and related loci in populations of African ancestry (Bonilla et al. 2005; Beleza et al. 2013; Crawford et al. 2017; Hernandez-Pacheco et al. 2017; Lloyd-Jones et al. 2017; Martin et al. 2017). Interestingly, some of the dark pigmentation-associated variants could have been under parallel evolution in different continents (Crawford et al. 2017). An alternative argument is that dark skin, as well as other “Negrito-like” phenotypes, are probably products of convergent adaptations, as evidenced by extensive genetic differentiation among these populations (Endicott et al. 2003; GenomeAsia100K Consortium 2019). Although exposed to intensive ultraviolet (UV) radiation all year round at similar latitudes, the indigenous populations are more darkly pigmented than their counterparts. This was evidenced by visual impressions and reported melanin measures (demonstrated in supplementary note S1, Supplementary Material online). The long history and simple modes of subsistence (e.g., foraging, pastoralism, and horticulture) of these populations would give special insights into the genetic mechanism of human pigmentation evolution.