Chronology of natural selection in Oceanian genomes

Brucato, Nicolas; André, Mathilde; Hudjashov, Georgi; Mondal, Mayukh; Cox, Murray P.; Leavesley, Matthew; Ricaut, François‐Xavier

doi:10.1016/j.isci.2022.104583

Cited by 5 publications

(4 citation statements)

References 81 publications

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“…Among these is the region encompassing the immunity-related GBP locus (Figure 3) which exhibits the highest selection peak in PNG lowlanders and shows haplotypes with sequence similarities to both Denisovan and Altai Neanderthal. Archaic introgression in this region has previously been reported in Melanesians 31,35 . But interestingly, the sequence of the introgressed haplotypes does not match with either Vindija 58 or Chagyrskaya 78 Neanderthals (data not shown).…”

Section: Archaic Introgressions In Loci Under Selectionmentioning

confidence: 52%

“…Denisovan introgressed variant might contribute to Tibetans adaptation to altitude 27 and affect the immune system of the PNG population 28 . Moreover, because some archaic variants show signals of selection among the overall Papuan population [29][30][31] , it is conceivable that archaic introgression has contributed to beneficial alleles in PNG populations. However, to date it remains elusive how to which extent archaic introgression contribution to local adaptation varies between PNG populations.…”

Section: Introductionmentioning

confidence: 99%

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

André

Brucato

Hudjasov

et al. 2022

Preprint

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Highlanders and lowlanders of Papua New Guinea (PNG) have faced distinct environmental conditions. These environmental differences lead to specific stress on PNG highlanders and lowlanders, such as hypoxia and environment-specific pathogen exposure, respectively. We hypothesise that these constraints induced specific selective pressures that shaped the genomes of both populations. In this study, we explored signatures of selection in newly sequenced whole genomes of 54 PNG highlanders and 74 PNG lowlanders. Based on multiple methods to detect selection, we investigated the 21 and 23 genomic top candidate regions for positive selection in PNG highlanders and PNG lowlanders, respectively. To identify the most likely candidate SNP driving selection in each of these regions, we computationally reconstructed allele frequency trajectories of variants in each of these regions and chose the SNP with the highest likelihood of being under selection with CLUES. We show that regions with signatures of positive selection in PNG highlanders genomes encompass genes associated with the hypoxia-inducible factors pathway, brain development, blood composition, and immunity, while selected genomic regions in PNG lowlanders contain genes related to immunity and blood composition. We found that several candidate driver SNPs are associated with haematological phenotypes in the UK biobank. Moreover, using phenotypes measured from the sequenced Papuans, we found that two candidate SNPs are significantly associated with altered heart rates in PNG highlanders and lowlanders. Furthermore, we found that 16 of the 44 selection candidate regions harboured archaic introgression. In four of these regions, the selection signal might be driven by the introgressed archaic haplotypes, suggesting a significant role of archaic admixture in local adaptation in PNG populations.

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Section: Archaic Introgressions In Loci Under Selectionmentioning

confidence: 52%

Section: Introductionmentioning

confidence: 99%

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

André

Brucato

Hudjasov

et al. 2022

Preprint

Self Cite

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“…However, unlike Neandertal DNA, which is present in populations with accessible GWAS data, Denisovan DNA lacks readily available association information from phenotype and expression cohorts, rendering such annotation approaches less practicable. Nonetheless, several studies have provided valuable insights into how Denisovan DNA has influenced phenotypic variation and facilitated adaptation in modern humans [24][25][26][27][28][29][30] . Notably, among them are well-documented instances where Denisovan DNA has been associated with adaptations related to high-altitude environments, metabolic processes, and immune responses.…”

Section: Introductionmentioning

confidence: 99%

Denisovan admixture facilitated environmental adaptation in Papua New Guinean populations

Yermakovich,

André,

Brucato

et al. 2024

Preprint

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Neandertals and Denisovans, having inhabited distinct regions in Eurasia and possibly Oceania for over 200,000 years, experienced ample time to adapt to diverse environmental challenges these regions presented. Among present-day human populations, Papua New Guineans (PNG) stand out as one of the few carrying substantial amounts of both Neandertal and Denisovan DNA, a result of past admixture events with these archaic human groups. This study investigates the distribution of introgressed Denisovan and Neandertal DNA within two distinct PNG populations, residing in the highlands of Mt Wilhelm and the lowlands of Daru Island. These locations exhibit unique environmental features, some of which may parallel the challenges that archaic humans once confronted and adapted to. Our results show that Denisovan-like haplotypes exhibit increased levels of population differentiation between PNG highlanders and lowlanders. The highly differentiated haplotypes, more common among highlanders, reside in genomic areas linked to brain development genes. Conversely, those more frequent in lowlanders overlap with genes enriched in immune response processes. Furthermore, Denisovan-like haplotypes displayed pronounced signatures of diversification within the major histocompatibility complex. Our findings suggest that Denisovan DNA has provided a valuable source of genetic variation to PNG genomes that facilitated adaptive responses to environmental challenges.

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“…However, unlike Neandertal DNA, which is present in populations with accessible GWAS data, Denisovan DNA lacks readily available association information from phenotype and expression cohorts, rendering such annotation approaches less practicable. Nonetheless, several studies have provided valuable insights into how Denisovan DNA has influenced phenotypic variation and facilitated adaptation in modern humans ( 24 – 30 ). Notably, among them are well-documented instances where Denisovan DNA has been associated with adaptations related to high-altitude environments, metabolic processes, and immune responses.…”

mentioning

confidence: 99%

Denisovan admixture facilitated environmental adaptation in Papua New Guinean populations

Yermakovich,

André,

Brucato

et al. 2024

Proc. Natl. Acad. Sci. U.S.A.

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Neandertals and Denisovans, having inhabited distinct regions in Eurasia and possibly Oceania for over 200,000 y, experienced ample time to adapt to diverse environmental challenges these regions presented. Among present-day human populations, Papua New Guineans (PNG) stand out as one of the few carrying substantial amounts of both Neandertal and Denisovan DNA, a result of past admixture events with these archaic human groups. This study investigates the distribution of introgressed Denisovan and Neandertal DNA within two distinct PNG populations, residing in the highlands of Mt Wilhelm and the lowlands of Daru Island. These locations exhibit unique environmental features, some of which may parallel the challenges that archaic humans once confronted and adapted to. Our results show that PNG highlanders carry higher levels of Denisovan DNA compared to PNG lowlanders. Among the Denisovan-like haplotypes with higher frequencies in highlander populations, those exhibiting the greatest frequency difference compared to lowlander populations also demonstrate more pronounced differences in population frequencies than frequency-matched nonarchaic variants. Two of the five most highly differentiated of those haplotypes reside in genomic areas linked to brain development genes. Conversely, Denisovan-like haplotypes more frequent in lowlanders overlap with genes associated with immune response processes. Our findings suggest that Denisovan DNA has provided genetic variation associated with brain biology and immune response to PNG genomes, some of which might have facilitated adaptive processes to environmental challenges.

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Chronology of natural selection in Oceanian genomes

Cited by 5 publications

References 81 publications

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

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

Denisovan admixture facilitated environmental adaptation in Papua New Guinean populations

Denisovan admixture facilitated environmental adaptation in Papua New Guinean populations

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