(A) Neanderthals didn't live in Africa, which is why sub-Saharan African populations have no trace of Neanderthal DNA, but other populations share DNA with Neanderthals, as discovered by a paleogeneticist at the Max Planck Institute in Germany that sequenced the Neanderthal genome.
which wrongly modify Africa
(B) Having sequenced the Neanderthal genome, a paleogeneticist at the Max Planck Institute in Germany has concluded that any human whose ancestral group developed outside Africa has inherited DNA from Neanderthals; since Neanderthals didn't live in Africa, sub-Saharan African populations have no trace of Neanderthal DNA.
I think this is correct and convey meaning clearly
(C) Neanderthals didn't live in Africa, which is why sub-Saharan African populations have no trace of Neanderthal DNA, but a paleogeneticist at the Max Planck Institute in Germany who sequenced the Neanderthal genome has concluded that other humans share DNA with Neanderthals.
which wrongly modify Africa
(D) After sequencing the Neanderthal genome, the Max Planck Institute in Germany where a paleogeneticist researched the Neanderthal-human link, has concluded that any human whose ancestral group developed outside Africa has inherited DNA from Neanderthals; since Neanderthals didn't live in Africa, sub-Saharan African populations have no trace of Neanderthal DNA.
the paleogeneticist sequenced the genome, not the institute
(E) The sequencing of the Neanderthal genome by a paleogeneticist at the Max Planck Institute in Germany has led to the conclusion that humans whose ancestral group developed outside Africa has inherited DNA from Neanderthals and sub-Saharan Africans have no trace of Neanderthal DNA due to Neanderthals not living in Africa.
this is a little bit confusing