Science Advances—Only 1.5% to 7% of the modern human genome is uniquely human, according to an analysis of Neanderthal, Denisovan, and human genomes. The study* provides evidence for adaptive changes to the human genome within the past 600,000 years, most of which are connected to brain development. The findings also suggest that at least one wave of Neanderthals intermixed with the ancestors of all non-Africans and also point to Neanderthal and Denisovan genomic regions unique to South Asians. Scientists have found it difficult to determine which genes in the modern human genome were passed on from our hominin ancestors and which are uniquely our own. One particular roadblock is that humans harbor Neanderthal alleles, both from intermixing between human and Neanderthal populations and from incomplete lineage sorting, or alleles that predate the split between humans and Neanderthals but are not found in all humans. To circumvent these challenges, Nathan Schaefer and colleagues developed an improved ancestral recombination graph inference algorithm called Speedy Ancestral Recombination Graph Estimator (SARGE), which more effectively highlights alleles inherited from human intermixture with Neanderthals. The researchers ran SARGE on a panel of 279 modern human genomes, two Neanderthal genomes, and one Denisovan genome. They used the resulting ancestral recombination graph to map Neanderthal and Denisovan ancestry and the absence of both across modern human genomes. This enabled Schaefer et al. to identify mutations specific to humans and to determine that these mutations arose in 2 distinct bursts – one about 600,000 years ago and another about 200,000 years ago. Many of these mutations appear to affect genes involved in neural development and function, as well as RNA splicing.
Article Source: The open-access journal Science Advances news release
*“An ancestral recombination graph of human, Neanderthal, and Denisovan genomes,” by N.K. Schaefer; B. Shapiro; R.E. Green at University of California, Santa Cruz in Santa Cruz, CA; N.K. Schaefer at University of California, San Francisco in San Francisco, CA.