The study analyzes the distribution and genetic coverage of alleles of archaic origin (mainly Neanderthal and Denisovan) in modern humans, based on population data and simulations. It was confirmed that archaic variants map well to population structure (e.g., East Asians, South Asians, Europeans), and their distribution is not random. Most common archaic alleles occur between populations, but South Asians are distinguished by having the highest number of unique Denisovan variants, often at low frequencies, which may be due to admixture from distinct Denisovan populations. A statistical East Asian has more Neanderthal alleles than a European. East Asians have more homogeneous and frequent alleles, while Europeans have retained more unique variants. Simulations showed that the empirical data was best represented by a two-pulse model of Neanderthal admixture in East Asians (3% and 0.5%), which better explained the observed variation than a single admixture model. Papuans, having the highest proportion of Denisovans, show minimal sharing of Denisovan variants with other populations, supporting the thesis of multiple, independent admixture events with different Denisovan groups. The study highlights the complexity of population histories and the importance of analyzing the frequency and distribution of archaic alleles in understanding the evolution of modern humans.
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