While the debate remains unsettled , evidence from mitochondrial DNA and Y-chromosomal DNA sequencing indicates that little or no gene flow occurred between H. neanderthalensis and H. sapiens , and , therefore , the two were separate species . Evidence from sequencing mitochondrial DNA indicated that no significant gene flow occurred between H. neanderthalensis and H. sapiens , and , therefore , the two were separate species that shared a common ancestor about 660,000 years ago .