After the genomes of multiple Homo neanderthalensis individuals were sequenced, it became clear that this species diverged from the Homo sapiens lineage about 540,000 years ago. The two species evolved separately until about 40,000 years ago when they encountered one another again in the region that would become Europe. The Neantherthals became extinct around 30,000 years ago.
Please answer the following questions about genomes and genes for these species.
2A. The single nucleotide mutation rate in both species is about 1 per 109 base pair per year. With a genome size of 3 billion base pairs, how many fixed single nucleotide differences would you expect to see between the two genomes when the two species
first encountered each other? Explain your calculations.
2B. In the genomes of modern Europeans, remnants of the Neanderthal genome now can be identified (i.e. many Neanderthal- specific mutations can be seen in the human genomes). How can we be sure this is "Neanderthal DNA" in the human genome and
not just a bunch of mutations that occurred independently at different times in the human lineage?
2C. Why are there no remnants of the Neandertal Y-chromosome in the modern human population?