HARS ( Human Accelerated Regions ) Humans Have Disproportionate Amount of Genomic Changes

Many animals have regions where their genomes are different from other animals even in regions which are "conserved" in other branches of the "tree of life". But none to the degree of humans. We have regions which are different in us that are conserved in everything else, including chimps.

This paper is a good starting point for understanding them. There is much more to learn as we first learned about them in 2006.

Here is a description from the paper ...

HARs are short, ∼260 bp on an average, stretches of DNA, to 97% noncoding. They are conserved in vertebrates, including Pan troglodytes, but not in Homo sapiens, in whom the conserved sequences were subjected to significantly, in many cases dramatically, higher rates of single nucleotide substitutions (Hubisz and Pollard 2014).

If something is conserved in all vertebrates then it is very strong evidence that it is vital to keep as-is, yet humans and humans alone have dramatically higher rates of coding differences. Not just in single-nucleotide substitutions either.  

As became clear starting in 2003 (Locke et al. 2003), the human genome is also subject to an important number of complex genomic rearrangements, including segmental duplications, that can also, because of their large size, affect coding genes (Fortna et al. 2004), in particular, create new functional paralogs (Charrier et al. 2012; Dennis et al. 2012, 2017). An example is given on figure 1b. Human-specific deletions may also remove regulatory sequences (McLean et al. 2011). An example is shown on figure 1c. The study of the patterns of human-specific large structural variants is currently in its infancy (Dennis and Eichler 2016), but it has already become clear that the impact of these variants in the context of human evolution is paramount.

Did Neanderthals have these changes? Not all of them. They did not measure the deletions and re-arragnements, but in terms of single nucleotide substitutions they were missing 8.3% of them- the full suite is literally only present in our species. The tests for other things such as hCondels showed a bigger gap- Neanderthals lacking 12% of them. And the tests were not sophisticated enough to spot what may be the biggest difference of all- large scale re-arrangement of sections of the genome.   

Humans are a distinct, unique, and relatively recent species.