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Africa
Modern humans arose in Africa approximately 200 kya (thousand years ago). Examination of mitochondrial DNA (mtDNA), Y-chromosome DNA, and X-chromosome DNA indicate that the earliest population to leave Africa consisted of approximately 1500 males and females. It has been suggested by various studies that populations were geographically “structured” to some degree prior to the expansion out of Africa; this is suggested by the antiquity of shared mtDNA lineages. One study of 121 populations from various places throughout the continent found 14 genetic and linguistic “clusters,” suggesting an ancient geographic structure to African populations. In general, genotypic and phenotypic analysis have shown  “large and subdivided throughout much of their evolutionary history.”

Genetic analysis has supported archaeological hypotheses of a large-scale migrations of Bantu speakers into Southern Africa approximately 5 kya. Microsatellite DNA, single nucleotide polymorphisms (SNPs), and insertion/deletion polymorphisms (INDELS) have shown that Nilo-Saharan speaking populations originate from Sudan. Furthermore, there is genetic evidence that Chad-speaking descendents of Nilo-Saharan speakers migrated from Sudan to Lake Chad about 8 kya. Genetic evidence has also indicated that non-African populations made significant contributions to the African gene pool. For example, the Saharan African Beja people have high levels of Middle-Eastern as well as East African Cushitic DNA.

Europe
Analysis of mtDNA shows that Eurasia was occupied in a single migratory event between 60 and 70 kya. Genetic evidence shows that occupation of the Near East and Europe happened no earlier than 50 kya. Studying haplogroup U has shown separate dispersals from the Near East both into Europe and into North Africa.

Much of the work done in archaeogenetics focuses on the Neolithic transition in Europe. Cavalli-Svorza’s analysis of genetic-geographic patterns led him to conclude that there was a massive influx of Near Eastern populations into Europe at the start of the Neolithic. This view led him  “to strongly emphasize the expanding early farmers at the expense of the indigenous Mesolithic foraging populations.” mtDNA analysis in the 1990’s, however, contradicted this view. M.B. Richards estimated that merely 10-22% of extant European mtDNA’s had come from Near Eastern populations during the Neolithic. Most mtDNA’s were “already established” among existing Mesolithic and Paleolithic groups. Most “control-region lineages” of modern European mtDNA are traced to a founder event of reoccupying northern Europe towards the end of the Last Glacial Maximum (LGM). One study of extant European mtDNA’s suggest this reoccupation occurred after the end of the LGM, although another suggests it occurred before. Analysis of haplogroups V, H, and U5 support a “pioneer colonization” model of European occupation, with incorporation of foraging populations into arriving Neolithic populations. Furthermore, analysis of ancient DNA, not just extant DNA, is shedding light on some issues. For instance, comparison of neolithic and mesolithic DNA has indicated that the development of dairying preceded widespread lactose tolerance.

South Asia
Studies of mtDNA line M suggest that the first occupants of India were Austro-Asiatic speakers who entered about 45-60 kya. The Indian gene pool has contributions from an African source population, as well as West Asian and Central Asian populations from migrations no earlier than 8 kya. The lack of variation in mtDNA lineages compared to the Y-chromosome lineages indicate that primarily males partook in these migrations. The discovery of two subbranches U2i and U2e of the U mtDNA lineage, which arose in Central Asia has “modulated” views of a large migration from Central Asia into India, as the two branches diverged 50 kya. Furthermore, U2e is found in large percentages in Europe but not india, and vice versa for U2i, implying U2i is native to India.

East Asia
Analysis of mtDNA and NRY (non-recombining region of Y chromosome) sequences have indicated that the first major dispersal out of Africa went through Saudi Arabia and the Indian coast 50-100 kya, and  a second major dispersal occurred 15-50 kya north of the Himalayas.

Much work has been done to discover the extent of north-to-south and south-to-north migrations within Eastern Asia. Comparing the genetic diversity of northeastern groups with southeastern groups has allowed archaeologists to conclude many of the northeast Asian groups came from the southeast. The Pan-Asian SNP (single nucleotide polymorphism) study found “a strong and highly significant correlation between haplotype diversity and latitude,” which, when coupled with demographic analysis, supports the case for a primarily south-to-north occupation of East Asia. Archaeogenetics has also been used to study hunter-gatherer populations in the region, such as the Ainu from Japan and Negrito groups in the Philippines. For example, the Pan-Asian SNP study found that Negrito populations in the Philippines and the Negrito populations in the Phillipines were more closely related to non-Negrito local populations than to each other, suggesting Negrito and non-Negrito populations are linked by one entry event into East Asia.

Americas
Archaeogenetics has been used to better understand the populating of the Americas from Asia. Native American mtDNA haplogroups have been estimated to be between 15 and 20 kya, although there is some variation in these estimates. Genetic data has been used to propose various theories regarding how the Americas were colonized. Although the most widely held theory suggests “three waves” of migration after the LGM through the Bering Strait, genetic data have given rise to alternative hypotheses. For example, one hypothesis proposes a migration from Siberia to South America 20-15 kya and a second migration that occurred after glacial recession. Y-chromosome data has led some to hold that there was a single migration starting from the Aldai Mountains of Siberia between 17.2- 10.1 kya, after the LGM. Analysis of both mtDNA and Y-chromosome DNA reveals evidence of “small, founding populations.” Studying haplogroups has led some scientists to conclude that a southern migration into the Americas from one small population was impossible, although separate analysis has found that such a model is feasible if such a migration happened along the coasts.

Australia and New Guinea
Finally, archaeogenetics has been used to study the occupation of Australia and New Guinea. The aborigines of Australia and New Guinea are phenotypically very similar, but mtDNA has shown that this is due to convergence from living in similar conditions. Non-coding regions of mt-DNA have shown “no similarities” between the aboriginal populations of Australia and New Guinea. Furthermore, no major NRY lineages are shared between the two populations. The high frequency of a single NRY lineage unique to Australia coupled with “low diversity of lineage-associated Y-chromosomal short tandem repeat (Y-STR) haplotypes” provide evidence for a “recent founder or bottleneck” event in Australia. But there is relatively large variation in mtDNA, which would imply that the bottleneck effect impacted males primarily. Together, NRY and mtDNA studies show that the splitting event between the two groups was over 50kya, casting doubt on recent common ancestry between the two.