Human populations evolved throughout the Old World for over 1 million years. However, anatomical characteristics of modern humans are thought to have evolved only in Africa in the last 200 thousand years. To this day, the extent to which archaic human populations contributed to the modern human gene pool is largely unknown. This work explores the evidence of genetic contribution from archaic populations at two loci in chromosome 12. Two different archaic humans, Neandertal and Denisova, living respectively in West Eurasia and in East Asia, have been indicated as potential contributors to anatomically modern human populations outside of Africa. This research shows the presence in non-Africans of two distinct introgressive alleles from archaic populations at the immune genes OAS1 and STAT2. In addition to the detection of patterns of genetic variation previously proposed as indicators of genetic introgression from archaic populations, it was possible to use the sequence of archaic individuals to infer a recent common ancestry between the introgressive modern allele and the archaic sequences. The analysis of genetic variation at the genomic region containing the gene STAT2 shows the presence of introgressive Neandertal-like and Denisova-like haplotypes. The elevated frequency in Melanesian populations of the haplotype introgressive from Neandertals suggests that this haplotype has been adaptive in Melanesians (APPENDIX B). A haplotype of the gene OAS1, nearly restricted to Melanesian populations, provides evidence of introgression from a population with genetic affinities to Denisova. The introgressive haplotype carries non-synonymous variants predicted to have functional significance and a block of very deep divergence with the remaining modern sequences (APPENDIX A). A second haplotype, observed mostly in Eurasian populations, shows evidence of having introgressed recently from Neandertals. The Neandertal-like haplotype also contains a block with very deep divergence with the remaining modern sequences (APPENDIX C). Blocks of very deep divergence within introgressive haplotypes suggest an important role of ancient population structure in the evolution of humans.

In the present body of work two primary subjects have been addressed, both individually and in their correspondence, namely 1) the potential for Neanderthals to have contributed to the Modern Human population, and 2) the genetic diversity of one of the most prehistorically impactful human popuations, the Armenians. The first subject is addressed by assessing 1000 mutations in 384 current humans, particularly for those mutations which appear to derive from the Neanderthal lineage. Additionally, the validity of the Neanderthal sequences themselves is evaluated through alignment analysis of fragementary DNA derived from the Vindija Cave sample. Armenian genetic diversity is analyzed through the autosomal short tandem repeats, y-chromsome single nucleotide polymorphisms, and y-chromosome short tandem repeats. The diversity found indicates that Armenians are a diverse group which has been genetically influenced by the various migrations and invasions which have entered their historic lands. Further, we find evidence that Armenians may be closely associated with the peopling of Europe.