PNPLA3fatty liver allele was fixed in Neanderthals and segregates neutrally in humans

Abstract

ObjectiveFat deposition is modulated by environmental factors and genetic predisposition. Genome-wide association studies identifiedPNPLA3p.I148M (rs738409) as a common variant that increases risk of developing liver steatosis. When and how this variant evolved in humans has not been studied to date.DesignHere we analyse ancient DNA to track the history of this allele throughout human history. In total, 6444 published ancient (modern humans, Neanderthal, Denisovan) and 3943 published present day genomes were used for analysis after extracting genotype calls forPNPLA3p.I148M. To quantify changes through time, logistic and, by grouping individuals according to geography and age, linear regression analyses were performed.ResultsWe find that archaic human individuals (Neanderthal, Denisovan) exclusively carried a fixedPNPLA3risk allele, whereas allele frequencies in modern human populations range from very low in Africa to >50% in Mesoamerica. Over the last 15 000 years, distributions of ancestral and derived alleles roughly match the present day distribution. Logistic regression analyses did not yield signals of natural selection during the last 10 000 years.ConclusionArchaic human individuals exclusively carried a fixedPNPLA3allele associated with fatty liver, whereas allele frequencies in modern human populations are variable even in the oldest samples. Our observation might underscore the advantage of fat storage in cold climate and particularly for Neanderthal under ice age conditions. The absent signals of natural selection during modern human history does not support the thrifty gene hypothesis in case ofPNPLA3p.I148M.

Liver Diseases: Science, Fiction and the Foreseeable Future

“…Contrary to non-human primates, this risk allele was identified in all Neanderthals and Denisovans, which indicates that the risk allele emerged prior to the split between the Neanderthals and modern humans. Interestingly, however, present-day humans exhibit a wide range (i.e., 8% to 72%) of the presence of PNPLA3 p.I148M, depending on their ethnicity [40]. The authors may thus have identified the earliest evolutionarily known risk gene for developing certain severe liver diseases, but it is too early to assess whether and how this knowledge may be used in the future.…”