Humans, Neanderthals, and the Y Chromosome

Scientists analyzing Y chromosomes of humans found that modern humans have no neanderthal DNA located on the Y chromosome. This is significant because there is neanderthal DNA found on the X chromosome. This has led scientists to try and determine why neanderthal DNA is found on the X chromosomes in modern humans, but not on the Y chromosome. It has been determined that between two and a half and four percent of modern human DNA is from the neanderthal genome. On the X chromosome of modern humans, we have genes such as MRC1 that code for things like hair color, and skin tone.  Others gave modern humans extra immune system defenses, and allergies. Tens of thousands of years ago, modern humans and neanderthals began to diverge and neanderthal Y chromosome DNA began to disappear in humans because it began to cause more and more miscarriages as the two species became less similar. 

Fernando Mendez at Stanford University compared the genes on the Y chromosome of two modern day males with the Y chromosome of a 49,000 year old neanderthal male. They found that three genes located on the Y chromosomes of neanderthals coded for immune response and when these are mis aligned with human DNA it caused a high rate of miscarriage because the mother rejected the hybrid baby. Since the neanderthal Y chromosome caused a high rate of miscarriages, neanderthal Y chromosome DNA was lost in the modern human population. Not only were immune system coding affected in modern humans, but protein coding was also affected.
 Scientist believe that sequencing the Y chromosome of neanderthals will give a more accurate picture as to when humans and neanderthals split. Previously, mitochondrial DNA which is passed on only from the mother to her offspring, has been used in order to determine the time since the two species diverged. Now scientist believe that humans and neanderthals split 580,000 years ago which is much more recent than previously though which was around 800,000 years ago. They also believe that the differences in the sperm of modern and neanderthal males may also give insights into the cause for the disappearance of neanderthal Y chromosome DNA.