Analysis
In the 2016 Science interview Pääbo indeed said that there has been a “cleansing” of archaic genes, referring to natural selection removing many Neanderthal-derived alleles from modern genomes. Subsequent studies have shown that functional Neanderthal DNA has been disproportionately lost over tens of thousands of years, indicating ongoing purifying selection. The overall proportion of Neanderthal ancestry has remained around 1–2%, but the composition has shifted to retain less deleterious segments.
Background
Modern non‑African humans carry about 1–2% Neanderthal DNA, a legacy of interbreeding that occurred roughly 50,000–60,000 years ago. Genomic analyses have revealed that many introgressed alleles, especially those in protein‑coding or regulatory regions, have been selected against, leading to a gradual reduction in Neanderthal genetic contribution over the subsequent 40,000 years. This process is often described as a “purifying” or “cleansing” of archaic DNA.
Verdict summary
Pääbo’s claim that Neanderthal ancestry has been gradually purged from modern humans over the past ~40,000 years is supported by genetic evidence and matches his statements in the 2016 Science interview.