Modern alleles in archaic human Y chromosomes support origin of modern human paternal lineages in Asia rather than Africa

TL;DR

This study analyzes high-coverage archaic human Y chromosome data, providing evidence that supports the Asian origin of modern human paternal lineages over the African origin, based on observed allele reversion patterns.

Contribution

It introduces a coevolutionary model of archaic Y chromosomes and modern autosomes, challenging the traditional infinite site assumption and supporting the Asian origin hypothesis.

Findings

Archaic Y chromosomes carry modern alleles inconsistent with the Africa model.

Shared modern alleles differentiate Denisovans from Neanderthals.

Results support the coevolutionary Asia model over the Africa model.

Abstract

Recent studies have shown that hybridization between modern and archaic humans was commonplace in the history of our species. After admixture, some individuals with admixed autosomes carried the modern Homo Sapiens uniparental DNAs, while the rest carried the archaic versions. Coevolution of admixed autosomes and uniparental DNAs is expected to cause some of the sites in modern uniparental DNAs to revert back to archaic alleles, while the opposite process would occur (from archaic to modern) in some of the sites in archaic uniparental DNAs. This type of coevolution is one of the elements that differentiate the two different models of the Y phylogenetic tree of modern humans, rooting it either in Africa or East Asia. The expected reversion to archaic alleles is assumed to occur and is easily traceable in the Asia model, but is absent in the Africa model due to its infinite site assumption, which also precludes the independent or convergent mutation to modern alleles in archaic uniparental DNAs since mutations are assumed to occur randomly across a neutral genome, and convergent evolution is assumed not to occur. Here, we examined newly published high coverage Y chromosome sequencing data of two Denisovan and two Neanderthal samples to determine whether they carry modern-Homo Sapiens alleles in sites where they are not supposed to according to the Africa model. The results showed that a significant fraction of the sites that, according to the Asia model, should differentiate the original modern Y from the original archaic Y carried modern alleles in the archaic Y samples here. Some of these modern alleles were shared among all archaic humans while others could differentiate Denisovans from Neanderthals. The observation is best accounted for by coevolution of archaic Y and admixed modern autosomes, and hence supports the Asia model, since it takes such coevolution into account.