There is an very interesting paper in Nature (doi:10.1038/nature12961) about the Neanderthal genom part in modern men. It shows an a chromosome by chromosome demonstration how much of the Neanderthal ancestry is found in the autosomes and in the sex chromosome: about 1 % in autosome and considerable less in sex chromomes. In the Y-chromosome it is barely found.
When the two populations first encounterd some 50000 years ago (as a paper form PLOS suggested: DOI: 10.1371/journal.pgen.1002947) we can envisage how this was done: there was war and the Neanderthal female were raped after the man were killed. Whether this was a singular event or repeatingly done in the clash of general war betweem the two species is not documented, but when the progeny e.g. was selected for the “African” phenotyp then the Neatherthal would be not maintained in the Y chromosome.
Very suggestive! And much has not changed till modern times
A review in Science (DOI: 10.1126/science.1236828) deals with the human evolution 3 to 1.5 x 106 years ago. The aridity in Africa is supposed to drive expansion to other continents. Several parallel lineages were present. You may find this review at the local university or in an (English) bookshop.
A paper in Nature (Altitude adaptation in Tibetans caused by introgression of Denisovan-like DNA Emilia Huerta-Sánchez, Xin Jin, Asan et al.) says that DNA in Tibetans to adapt to the altitude can be attributed to an extinguished hominid precursor, the Denisovan: (cited from Nature)
Admixture with other hominin species helped humans to adapt to high-altitude environments; the EPAS1 gene in Tibetan individuals has an unusual haplotype structure that probably resulted from introgression of DNA from Denisovan or Denisovan-related individuals into humans, and this haplotype is only found in Denisovans and Tibetans, and at low frequency among Han Chinese.