The mutations humans acquired from Neanderthals are slowly being purged from the genome overtime.
Modern humans with non-African ancestry get between one and four percent of their DNA from Neanderthals. This species of hominid lived in Europe, the Middle East and central Asia until roughly 30,000 years ago, but their DNA has endured through the years—passed on to many populations of Homo Sapiens during a period of interbreeding between the species that began roughly 50,000 years ago.
So what happened to the rest of that Neanderthal DNA? Why don’t contemporary non-African humans have more than just a few percent of Neanderthal genes?
http://www.smithsonianmag.com/smart-news/study-reveals-why-humans-dont-have-more-neanderthal-dna-180961047/
IM Human and Neanderthal skulls (Wikimedia Commons/DrMikeBaxter) https://commons.wikimedia.org/wiki/File:Sapiens_neanderthal_comparison_en_blackbackground.png