"Even 50,000 years after the last human-Neanderthal mating, we can still see measurable impacts on gene expression," said Joshua Akey, of University of Washington in the US.
"Those variations in gene expression contribute to human phenotypic variation and disease susceptibility," Akey said.
Previous studies have found correlations between Neanderthal genes and traits such as fat metabolism, depression and lupus risk.
Researchers analysed ribonucleic acid (RNA) sequences in a dataset called the Genotype-Tissue Expression (GTEx) Project, looking for people who carried both Neanderthal and modern human versions of any given gene, one version from each parent.
"We find that for about 25 per cent of all those sites that we tested, we can detect a difference in expression between the Neanderthal allele and the modern human allele," said Rajiv McCoy, postdoctoral researcher at University of Washington.
Expression of Neanderthal alleles tended to be especially low in the brain and the testes, suggesting that those tissues may have experienced more rapid evolution since we diverged from Neanderthals about 700,000 years ago.
"We can infer that maybe the greatest differences in gene regulation exist in the brain and testes between modern humans and Neanderthals," Akey said.
"Previous work by others had already suggested that this allele affects alternative splicing. Our results support this molecular model, while also revealing that the causal mutation was inherited from Neanderthals," McCoy said.
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